http://2013.igem.org/wiki/index.php?title=Special:Contributions/B00401107&feed=atom&limit=50&target=B00401107&year=&month=2013.igem.org - User contributions [en]2024-03-28T12:56:27ZFrom 2013.igem.orgMediaWiki 1.16.5http://2013.igem.org/Team:NTU-Taida/Human_practice/PlatformTeam:NTU-Taida/Human practice/Platform2013-09-28T03:59:20Z<p>B00401107: /* Platform */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Platform}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Platform==<br />
<br />
We have helped establish the bio-science society to communicate with scientists. Some interview to scientists and social activity about bio-science are held on this platform.<br />
[[File:NTU-Taida-platform-1.jpg|700px|thumb|center|]]<br />
[[File:NTU-Taida-platform-2.jpg|700px|thumb|center|]]<br />
The platform is currently available in Chinese: <br />
http://investigatortw.wordpress.com/ <br />
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{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Human Practice}}</div>B00401107http://2013.igem.org/File:NTU-Taida-NCTU-2.jpgFile:NTU-Taida-NCTU-2.jpg2013-09-28T03:54:17Z<p>B00401107: </p>
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<div></div>B00401107http://2013.igem.org/File:NTU-Taida-NCTU-3.jpgFile:NTU-Taida-NCTU-3.jpg2013-09-28T03:53:37Z<p>B00401107: </p>
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<div></div>B00401107http://2013.igem.org/File:NTU-Taida-NCTU-1.jpgFile:NTU-Taida-NCTU-1.jpg2013-09-28T03:52:35Z<p>B00401107: </p>
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<div></div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practiceTeam:NTU-Taida/Human practice2013-09-28T03:46:57Z<p>B00401107: /* Human practice overview */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Human Practice}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
=Human practice overview=<br />
To stimulate de novo ideas and promote synthetic biology and igem, we have held many activities.<br />
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In design thinking workshop, we constructed prototypes of solution to environmental problems and asked visitors in NTU hospital. Through these process, we hope to collect more opinions from public and make our thinking more creative and practical.<br />
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In the winter vacation, our team were separated into three groups. Each group should come up with a complete project and attainable experiment design and were arranged to throw a presentation. Via presentation, we obtained many valuable advises.<br />
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At July, to fit our projects, we actively contacted the department of laboratory medicine and have an opportunity to visit the laboratory about bacterial identification in NTU hospital. In this short visit, not only did we acquire many information of routine bacterial identification nowadays, but we redesigned part of our experiments.<br />
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In summer vacation, we promote synthetic biology and igem competition to many research clubs in high school. Also, we cooperated with other teams including NYMU and NTU-Taiwan and interacted with other teams including teams in Taiwan and in mainland China through two conferences—one of which was held by NCTU team, the other of which was held by our teams.<br />
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Finally, we decided to establish a student club in our university NTU as a platform for students interested in biology. This platform will continuously hold activities promoting igem and synthetic biology. <br />
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<html><br />
<span style="align:center";><img src="/wiki/images/e/e0/NTU-Taida-HP.png" width="700px"></span></html><br />
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{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Human Practice}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Notebook/ProtocolTeam:NTU-Taida/Notebook/Protocol2013-09-28T03:40:12Z<p>B00401107: /* Protocol */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Protocol}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
== Protocol ==<br />
===Here are all the protocols we have used in our experiments.===<br />
<br />
== Transformation ==<br />
<br />
# Add dd water 20 ul into biobrick kit, pipette and extract.<br />
# Prepare competent cells on ice.<br />
# Mix 100 ul of competent cells with 15 ul plasmids (1 ul for biobrick kit extract) in eppendorfs and put on ice for 30 mins. <br />
# Heat shock 42<sup>o</sup>C 90 secs and put them on ice for 3 mins. <br />
# Add LB broth 1000 ul to the eppendorfs.<br />
# Put on ice for 2 mins.<br />
# Incubate at 37<sup>o</sup>C for 20 mins. <br />
# Centrifuge for 2 mins. Drop the supernatant, and resuspend the cells with remaining medium.<br />
# Spread the cells on LB agar plates with appropriate antibiotics and incubate at 37 <sup>o</sup>C for 18 hrs.<br />
<br />
== E coli culture ==<br />
# Add 3mL LB/Amp (50 μl/mL) in each tube<br />
# Pick up plate and use tip to scrape a single colony<br />
# Soak the colony inside the incubation tube<br />
# Put the tubes on the shaker of 37℃ and incubate overnight(16hr)<br />
<br />
== Conventional assembly==<br />
<br />
<br />
===Digestion=== <br />
# Calculate the amount of each reagent { total 15 ul (vector 20ul): two RE 0.7ul/10Xbuffer 1.5ul or 1.5 ug <br />
(vector 2ul)/DNA=1000ng/ddH2O=remaining}<br />
# Adding each reagent ddH2O10XbufferDNARE<br />
(37℃ incubator) After 2 hr digestion, put all the samples to go electrophoresis.<br />
===Electrophoresis preparation===<br />
# Agarose gel synthesis:<br />
1% Agarose: 0.8g agarose +80 ml TAE buffer<br />
# Mix and heat in microwave oven until boiling for about 2 minutes. (If EtBr is necessary, it is added after this step)<br />
# The mixture is added into the gel plate to create one 40ml well and two 20ml well.<br />
# 20 minutes is required to form the gel.<br />
<br />
===Electrophoresis===<br />
# DNA mixture is loaded add loading dye (1.5 ) is added into the eppendorf.<br />
# Load the dye mixture into the well, as well as the marker (general ruler, preserved in 4∘C fridge, upper right) and start to electrophoresis for 30 minutes.<br />
===Results===<br />
# Add SYBR dye (must be protected from light, packed in an aluminum foil)<br />
# Add 5 of 10000X SYBR Safe to TAE solution and swirl the container gently to mix. (SYBR safe stock is on 4∘C refrigerator)<br />
# Sock the gel in the container; ensure the gel is fully immersed during staining.<br />
# Incubate for 15~20 minutes (continuously agitate the gel on an orbital shaker at 50rpm)<br />
# ※If the signal is not strong enough, the gel can be stained longer or the staining solution has to be replaced.<br />
===Gel extraction===<br />
# Cut the insert and vector from the gel with blade<br />
# Put into gel extraction column and centrifuge 13,000 rpm for 30 sec<br />
# Use the elution samples for DNA ligation<br />
===Ligation=== <br />
# vector 0.5 μl<br />
#insert 1 μl<br />
#ligase buffer 1.5 μl<br />
#ligase 0.5 μl<br />
#ddH2O 11.5 μl<br />
# Place under room temperature for about 3 hr <br />
(Place under 16℃ and react for 16 hours)<br />
(Stock at -20℃ refrigerator, if it would not be dealt right away) <br />
===Transformation===<br />
# Competent cells (100ul) were mixed with plasmids (15ul)(1ul for biobrick kit extract) in eppendorfs and put on ice for 30 mins.<br />
# They were under 42oC heat shock for 90 seconds and put on ice for 3 mins. <br />
# Luria-Bertani (LB) broth (1000ul) was added to the eppendorfs.<br />
# Cells were incubated at 37oC for 20 mins.<br />
# They were centrifuged for 2 mins. The supernatant was dropped, and the remaining medium was pipetted to resuspend the cells.<br />
# Cells were spread on LB agar plates with ampicillin, incubated for 18 hours. (37<sup>o</sup>C)<br />
<br />
===E.coli culture===<br />
# Add 3mL LB/Amp (50 μl/mL) in each tube<br />
# Pick up plates and use tip to scrape a single colony<br />
# Soak the colony inside the incubation tube (each plasmids 5 tube)<br />
# Put the tubes on the shaker of 37℃ incubate, overnight(16hr)<br />
===Selection===<br />
# Spin down 1.0ml of E. coli overnight cells in a microcentrifuge. (13,000 rpm, room temp., 30~45 sec) and remove medium.<br />
# Add 50μl of TEN (10 mM Tris-HCl, pH8.0, 1 mM EDTA, 100mM NaCl)<br />
# Vortex for 2 min. Turn upside down for 5 times. (VWR multivirtexer)<br />
# Add 70μl phenol/chloroform/isoamyl alcohol (25/24/1, with 1% β-ME)<br />
# Vortex for 2~3 seconds, microcentrifuge for 10 min.<br />
# Transfer upper solution 70 μl (without touching the interface) to new microcentrifuge tube.<br />
# Add 20μl of NH4OAc (7.5M) and 100μl of isopropanol (room temp.)<br />
# Vortex for 5 sec, microcentrifuge for 1 min (room temp.)<br />
# Wash the pellet with 70% EtOH(1ml) and dry it completely.<br />
# Use a paper towel to help dry the alcohol.<br />
# Re-suspend the pellet in 15μl of ddH2O and 1/50 RNase.<br />
# Add the ddH2O an d RNase together before adding into the eppendorf.<br />
===Digestion (check)=== <br />
# samples for each of 7 kinds DNA <br />
# Enzyme: EcoR I, Pst I, add 0.2 microliter to each reaction(15 microliter)<br />
# DNA: 5 microliter (3 if already done minipreparation)<br />
# Add 10X buffer, ddH2O, enzymes, DNA together<br />
# Digest in 37 degree incubator for 1.5 hrs<br />
==3A Assembly==<br />
===Restriction Digest===<br />
====Materials====<br />
#Your two part samples: Miniprepped DNA (in BioBrick RFC[10] plasmid backbones)<br />
#Linearized plasmid backbone (with a different resistance to the plasmid backbones containing your part samples)<br />
#EcoRI, XbaI, SpeI, PstI<br />
#NEB Buffer 2<br />
#BSA<br />
#dH20<br />
===Procedure===<br />
====Digest Reaction====<br />
#dH20<br />
#NEB Buffer 2<br />
#BSA<br />
#DNA and Enzymes<br />
#Digest Part A with EcoRI and SpeI<br />
#Digest Part B with XbaI and PstI<br />
#Digest linearized plasmid backbone with EcoRI and PstI<br />
#Combine 1 ul of each restriction digest reaction with 1 ul of ligase in a 25 ul reaction.<br />
#Transform the ligation product.<br />
#If the input parts are good, almost all colonies will be correct.<br />
#If desired analyze the transformation with single colony PCR followed by agarose gel electrophoresis.<br />
#Miniprep clones that generated a band of the appropriate size.<br />
#Sequence the clone.<br />
#Record the sequence information in the Registry.<br />
<br />
==DNA Minpreparation==<br />
Tips for 10 min plasmid DNA minipreparation <br />
#Grow 2.0 ml overnight culture<br />
#Spin down 1.0 ml if E. coli overnight cells in a microcentrifuge (13,000 rppm, room temp., 30-45 sec) and remove medium. <br />
#Add 50 ul of TEN (10 mM Tris-HCl, pH8.0, 1 mM EDTA, 100mM NaCl)<br />
#Vortex for 2 min. (VWR multivortexer)<br />
#Add 70 ul phenol/chloroform/isoamyl alcohol (25/24/1, with 1% &beta;-ME)<br />
#Vortex for 2-3 sec, microcentrifuge for 10 min (room temp.)<br />
#Transfer upper solution 70 ul (without touching the interface) to new microcentrifuge tube<br />
#Add 20 ul of NH<sub>4</sub>OAc (7.5M) and 100 ul of isopropanol (room temp.)<br />
#Vortex for 5 sec, microcentrifuge for 1 min (room temp.)<br />
#Wash the pellet with 70 % EtOH (1 ml) and dry it completely.<br />
#Resuspend the pellet in 15 ul of dd H2O or TE. and 1 / 50 RNase. Store at -20oC<br />
<br />
Note. Use 4 ul of DNA for digestion (30-60 min in 15 ul with RNase or “express” digestion 3 X 10 sec in a microwave oven), use 18 ul for sequencing. <br />
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<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Team, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/TargetTeam:NTU-Taida/Project/Target2013-09-28T03:28:09Z<p>B00401107: /* Long Term Project: Quorum Sensing array */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Target}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Project Target Molecules==<br />
<br />
Quorum sensing (QS) signals can be transmitted through several types of molecules. In our project, we used Rhl, Las and PQS quorum sensing signals as our target. Both Rhl and Las systems use acyl homoserine lactones (AHLs) as quorum sensing targets, while PQS uses 2-heptyl-3-hydroxy-4-quinolone as its QS target. <br />
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[[File:NTU-Taida-target-1.jpg|600px|thumb|center|Figure.1]]<br />
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==Acyl-homoserine lactone and quorum sensing transcriptional regulator==<br />
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For gram negative bacteria, Acyl-homoserine lactones (AHLs) are used as quorum sensing signals. AHL consists of a five-member homoserine lactone ring and an acyl side chain. The length and the substitution group of the side chain determine the specificity of AHL-receptor binding. On the other hand, the transcriptional regulator consists of an N-terminal ligand-binding domain (to bind AHL) and a C-terminal DNA binding domain.<br />
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[[File:NTU-Taida-target-2.jpg|700px|thumb|center|Figure.2]]<br />
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==Long Term Project: Quorum Sensing array==<br />
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Since the structure of the ligand-binding domain enables it to have certain interaction with AHLs that have different side chain length, and the interaction is still obvious when the length difference is in 2 carbons, a multi-QS system with their AHL of 4, 8, 12-C side chain could detect and identify AHL from 2~14 carbons; applying the idea of linear combination.<br />
<br />
What we have used, Rhl, Las and PQS are all original from ''Pseudomonas aeruginosa''. According to the fact that strains with different drug-resistance also have different combination of QS expression level, our system may not only distinguish bacteria between species but also within species. <br />
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[[File:NTU-Taida-target-3.jpg|700px|thumb|center|Figure.3]]<br />
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==Reference==<br />
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{{:Team:NTU-Taida/Templates/Reference|Author=Ling EA, ''et al''|Essay=A novel plasmid for detection of N-acyl homoserine lactones|Journal=Elsevier}}<br />
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{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/OverviewTeam:NTU-Taida/Project/Overview2013-09-28T03:24:19Z<p>B00401107: /* Overview */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Overview}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
=Overview=<br />
Our IGEM project aims to tailor an '''instant bacteria identification array'''. We chose '''Quorum sensing molecules (QS molecules)''' instead of traditional biochemical reactions as our main targets to achieve our goals. As a cell-cell communication pathway, Quorum sensing phenomenon regulates '''virulence gene expression''' and has recently been considered as a new target for therapeutic application. We proposed a novel method to identify bacteria by '''the expression pattern''' of many QS receptors from the intensity of fluorescent signals.<br />
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For the sakes of sensitivity and the consideration of time, we underwent process of cloning and designed both '''positive feedback''' and '''negative regulation circuits''' insides plasmids containing quorum sensing receptors (or transcriptional regulator) conjugated with florescent proteins. These plasmids were transformed into ''E. Coli'' DH5α. They would act as '''biosensors''' when meeting quorum sensing molecules.<br />
<br />
We would like to identify bacterial strains both '''between species''' and '''within species'''. For Gram negative species, AHL is a common quorum sensing molecule. Different receptors, however, target different kinds of '''AHL (Acylhomoserine Lactone)''' depending on its carbon number of the acyl group. We targeted to construct an array of QS sensors, consisting of sensor for 4-carbon, 8-carbon, 12-carbon and 14-carbon AHL. Because QS sensors are also able to sense AHL molecules with '''a closer number of carbons''', this biosensor array can detects 2~14 carbon AHLs. In addition to AHL, we also developed '''novel biosensor—PQS''' for new type of quorum sensing molecule in iGem—'''Quinolones'''.<br />
<br />
To achieve a complete array, a lot of '''measurements''' are indispensable. We manipulated simple qualitative experiments for its property and the fluorescent protein expression via polyacrylamide gel electrophoresis stained by coomassie blue. Next, we bought molecules including AHL and Quinolones and utilized '''ELISA plate reader''' and '''flow cytometer''' to calibrate the '''standard diagram''' (intensity of florescent protein—time) of different biosensors added with series dilution of AHL in 96-well plate. At the third stage, the '''supernatant of bacteria''' (between species and within species) were taken into experiments. By replacement of AHL or Quinolones with the supernatant of bacteria, we depicted new curves, and compared it with each other and also standard diagram. With the efforts of the teams, we proved our idea. The responses of different strains of bacteria to our array varied greatly.<br />
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To put it into practice, we aligned circuits of different quorum sensing receptors to form an array to test '''clinical samples''' like septum, blood, urine, etc. After collecting enough data of different clinical bacterial strains and build up a database, we hope to build up a new system for bacteria identification.<br />
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[[File:NTU-Taida-overview-1.jpg|700px|thumb|center|Figure.3]]<br />
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{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/BackgroundTeam:NTU-Taida/Project/Background2013-09-28T03:11:44Z<p>B00401107: /* Routine Identification */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Background}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Bacterial infection==<br />
<br />
Bacterial infection is the invasion of bacteria into one’s body. They reproduce and multiply themselves, causing disease by local cellular injury, secretion of toxins, or antigen-antibody reaction in the host. The spectrum of bacteria changes with time and the introduction of antibacterial agents. Nowadays, the emerging issue in this field is the appearance of '''multiple drug-resistant (MDR) bacteria''' and '''extensive drug-resistant (XDR) bacteria'''. Yet the development of resistant strains of bacteria could be limited by the judicious use of antibiotics. In order to use the appropriate drug, knowing the antibiotic pattern of the invading bacteria is of importance. The routine process to identify causative organism in hospital, culturing and sensitivity testing for a specific antibiotic, is found to be sensitive.<br />
<br />
Bacterial infection may be further classified by where the infection occurs, into '''community-acquired infection''' and '''nosocomial infection'''. The strains of bacteria, infection site, and epidemiological transmission pathway all differ between them. Nosocomial infection is of increased importance. MDR or XDR are present in hospital environments such as MRSA (Methicillin-resistant ''Staphylococcus aureus'') and ''Acinetobacter''. Urinary tract infections, pneumopathy, and infections of surgery site are most common because of the formation of biofilm on the surface of catheters, endo-tubes, etc. What’s worse, due to the drug-resistance, diagnosis and treatment of bacterial nosocomial infection become a serious problem. It's urgent to develop new system of bacterial identification and drugs.<br />
<br />
==Quorum Sensing System in Gram Positive Bacteria==<br />
<br />
Gram-positive bacteria, characterized with a relatively thick layer of peptidylglycan, generally use peptides as quorum sensing molecules. These peptides are called '''autoinducing peptides (AIPs)'''; when produced by specialized AI synthase, they can be either transported from the cells through a specific membrane-bound transporter, or processed and secreted directly from the membrane. A high concentration of extracellular AIPs indicates high cell density. By binding to its cognate membrane-bound sensor kinase or intracellular receptor, the quorum sensing signal is transmitted back and spread to other bacterial cells, creating an '''inter-cellular communication network'''. The cytoplasmic response regulator, which controls the downstream virulence factors and AIP synthase, is phosphorylated by the histidine kinase receptor upon extracellular binding of AIPs, or is activated by the intracellular receptor-AIP complex itself (Figure 1).<br />
<br />
<br />
Together from a module-based point of view, the whole process of quorum sensing includes production, detection and response. Collectively, these modules are termed a two-component system.<br />
<br />
<br />
Clinically important Gram-positive bacteria include ''Staphylococcus aureus'' and ''Streptococcus pneumoniae'', responsible for skin and respiratory infections respectively. ''S. aureus'' uses the agr as its quorum sensing system.<br />
<br />
[[File:NTU-Taida-background-5.jpg|700px|thumb|center|Figure.1]]<br />
<br />
==Quorum Sensing System in Gram negative Bacteria==<br />
<br />
The cell wall of Gram-negative bacteria is composed of a relatively thin layer of peptidoglycan and an outer membrane which contains lipopolysaccharide (LPS). Due to its structure, quorum sensing molecules '''diffuse''' through the cell membrane and bind with '''intracellular receptors'''. <br />
[[File:NTU-Taida-background-3.jpg|||center|Figure.2]]<br />
<br />
Generally speaking, quorum sensing system in gram negative bacteria functions as follows (Take LasI/LasR system for example):<br />
<br />
The LasI gene encodes an '''autoinducer synthase(LasI)''', and this autoinducer synthase produces quorum sensing molecules(autoinducers) called '''acyl-homoserine lactone(AHLs)'''. Another gene LasR encodes for the '''response regulator of the autoinducers'''. Regulators bind with autoinducers and form complexes. They bind on target promoters, and then either activate or inhibit relevant down-stream genes.<br />
[[File:NTU-Taida-background-4.jpg|700px||center|Figure.3]]<br />
<br />
<br />
Under low bacterial concentration, target genes are under minimum expression (Figure a above), but as bacterial concentration elevates, AHL molecules begin to bind with the intracellular response regulators and promote the expression of target genes, many of them related to '''bacterial virulence''' or biofilm formation. Therefore, there is a close relationship between bacterial resistance and quorum sensing. Besides having species-specific quorum sensing system, many species of gram-negative bacteria share a type of quorum sensing molecule, the AI-2(autoinducer-2) molecule.<br />
<br />
==Routine Identification==<br />
Laboratory medicine (see also Visit[https://2013.igem.org/Team:NTU-Taida/Human_practice/Visit]) plays a crucial role in hospital and the identification of infecting bacteria are big part of it. According to the visit to professor Po-Ren Hsueh, a visiting staff in the department of laboratory medicine in NTU hospital, the routine identification of bacteria and sensitivity tests are mainly through the incubation in the plate. The method through mass spectrometry, having substantial advancement nowadays, can quickly identify bacteria in minutes, while methods via bio-chemical reactions require machines and chips (see figure below) including types for Gram positive, Gram negative, anaerobic bacteria, etc. However, these two methods detect mainly in protein levels, require expensive machines and cannot provide the antibiotic-sensitivity information making us back to the process of incubation.<br />
{|align='center'<br />
|[[File:NTU-Taida-project-background11.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background12.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background13.jpg|250px|center|thumb]]<br />
|}<br />
<br />
==PQS system in ''Pseudomonas aeruginosa''==<br />
<br />
To date, it has been found that ''Pseudomonas aeruginosa'' has at least four quorum sensing systems: '''Las system''' (Las from e”las”tase), '''Rhl system''' (Rhl from “rh”amno”l”ipids), '''Qsc system''' (Qsc from “Q”uorum “s”ensing “c”ontroller ), and '''PQS system''' (PQS from “P”seudomonas “q”uinolone “s”ignal). In general, Las system is responsible for toxin expression; Rhl system is responsible for secretion system; Qsc system is as a negative regulator of Las system and Rhl system; PQS system is responsible for the virulence. The four systems also have interactions with each other.<br />
<br />
Among these four systems, Las, Rhl and Qsc system all contain an AHL (acyl -homoserine lactone) activated receptor. Las system and Qsc system use 12-C AHL as QS (Quorum Sensing) molecules; on the other hand, Rhl system prefers to use 4-C AHL as QS molecules.<br />
<br />
However, interestingly, PQS system is not activated through AHL, but a '''quinoline derivative''': 2-heptyl-3,4-dihydroxyquinoline (also called “PQS”). Once PQS binds to pqsR, pqsR ─ as a transcriptional factor ─ can further activates two operons: pqsABCDE and phnAB (phn from "ph"e"n"azine). These two operons encode the enzymes that can synthesize PQS, and pqsE can catalyze PQS to become phenazine. Importantly, these phenazine products have been demonstrated to be involved in '''virulence of the organisms'''. For example, the phenazine pyocyanin production can enhance the ability of Pseudomonas aeruginosa to colonize the lungs of cystic fibrosis patients.<br />
[[File:NTU-Taida-project-background14.jpg|200px|center|thumb|quinolone]]<br />
<br />
==Reference==<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Arul Jayaraman and Thomas K.Wood|Essay=Bacterial Quorum Sensing:Signals, Circuits, and Implications for Biofilms and Disease|Journal=Annu. Rev. Biomed. Eng. 2008. 10:145–67}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Rutherford,''et al''|Essay=Bacterial quorum sensing: its role in virulence and possibilities for its control|Journal=Cold Spring Harb Perspect Med. 2012 Nov 1;2(11)}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Antunes LCM, ''et al''|Essay=Quorum sensing in bacterial virulence|Journal=Microbiology(2010), 156, 2271–2282}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Lo´ pez D, ''et al''|Essay=Biofilms|Journal=Cold Spring Harb Perspect Biol 2010 ; 2:a000398}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jimenez PN, ''et al''|Essay=The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa|Journal=Microbiol. Mol. Biol. Rev. 2012, 76(1):46}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Kendra P. Rumbaugh|Essay=Quorum Sensing: Methods and Protocols|Journal=Methods in Molecular Biology, vol. 692}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jitesh A Soares and Brian MM Ahmer|Essay=Detection of acyl-homoserine lactones by Escherichia and Salmonella|Journal=Microbiology 2011, 14:188–193}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Hsueh PR, ''et al''|Essay=Consensus review of the epidemiology and appropriate antimicrobial therapy of complicated urinary tract infections in Asia-Pacific region|Journal=The British Infection Association 2011}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Vanessa Sperandio|Essay=SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen|Journal=Gut Microbes 1:6, 432-435; November/December 2010}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Dubern, ''et al''|Essay=Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species|Journal=Mol Biosyst (2008) vol. 4 (9) pp. 882}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Diggle, ''et al''|Essay=4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives|Journal=Int J Med Microbiol (2006) vol. 296 (2-3) pp. 83-91}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Steindler, ''et al''|Essay=Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors|Journal=FEMS Microbiol Lett (2007) vol. 266 (1) pp. 1-9}}<br />
<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/BackgroundTeam:NTU-Taida/Project/Background2013-09-28T03:05:43Z<p>B00401107: </p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Background}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Bacterial infection==<br />
<br />
Bacterial infection is the invasion of bacteria into one’s body. They reproduce and multiply themselves, causing disease by local cellular injury, secretion of toxins, or antigen-antibody reaction in the host. The spectrum of bacteria changes with time and the introduction of antibacterial agents. Nowadays, the emerging issue in this field is the appearance of '''multiple drug-resistant (MDR) bacteria''' and '''extensive drug-resistant (XDR) bacteria'''. Yet the development of resistant strains of bacteria could be limited by the judicious use of antibiotics. In order to use the appropriate drug, knowing the antibiotic pattern of the invading bacteria is of importance. The routine process to identify causative organism in hospital, culturing and sensitivity testing for a specific antibiotic, is found to be sensitive.<br />
<br />
Bacterial infection may be further classified by where the infection occurs, into '''community-acquired infection''' and '''nosocomial infection'''. The strains of bacteria, infection site, and epidemiological transmission pathway all differ between them. Nosocomial infection is of increased importance. MDR or XDR are present in hospital environments such as MRSA (Methicillin-resistant ''Staphylococcus aureus'') and ''Acinetobacter''. Urinary tract infections, pneumopathy, and infections of surgery site are most common because of the formation of biofilm on the surface of catheters, endo-tubes, etc. What’s worse, due to the drug-resistance, diagnosis and treatment of bacterial nosocomial infection become a serious problem. It's urgent to develop new system of bacterial identification and drugs.<br />
<br />
==Quorum Sensing System in Gram Positive Bacteria==<br />
<br />
Gram-positive bacteria, characterized with a relatively thick layer of peptidylglycan, generally use peptides as quorum sensing molecules. These peptides are called '''autoinducing peptides (AIPs)'''; when produced by specialized AI synthase, they can be either transported from the cells through a specific membrane-bound transporter, or processed and secreted directly from the membrane. A high concentration of extracellular AIPs indicates high cell density. By binding to its cognate membrane-bound sensor kinase or intracellular receptor, the quorum sensing signal is transmitted back and spread to other bacterial cells, creating an '''inter-cellular communication network'''. The cytoplasmic response regulator, which controls the downstream virulence factors and AIP synthase, is phosphorylated by the histidine kinase receptor upon extracellular binding of AIPs, or is activated by the intracellular receptor-AIP complex itself (Figure 1).<br />
<br />
<br />
Together from a module-based point of view, the whole process of quorum sensing includes production, detection and response. Collectively, these modules are termed a two-component system.<br />
<br />
<br />
Clinically important Gram-positive bacteria include ''Staphylococcus aureus'' and ''Streptococcus pneumoniae'', responsible for skin and respiratory infections respectively. ''S. aureus'' uses the agr as its quorum sensing system.<br />
<br />
[[File:NTU-Taida-background-5.jpg|700px|thumb|center|Figure.1]]<br />
<br />
==Quorum Sensing System in Gram negative Bacteria==<br />
<br />
The cell wall of Gram-negative bacteria is composed of a relatively thin layer of peptidoglycan and an outer membrane which contains lipopolysaccharide (LPS). Due to its structure, quorum sensing molecules '''diffuse''' through the cell membrane and bind with '''intracellular receptors'''. <br />
[[File:NTU-Taida-background-3.jpg|||center|Figure.2]]<br />
<br />
Generally speaking, quorum sensing system in gram negative bacteria functions as follows (Take LasI/LasR system for example):<br />
<br />
The LasI gene encodes an '''autoinducer synthase(LasI)''', and this autoinducer synthase produces quorum sensing molecules(autoinducers) called '''acyl-homoserine lactone(AHLs)'''. Another gene LasR encodes for the '''response regulator of the autoinducers'''. Regulators bind with autoinducers and form complexes. They bind on target promoters, and then either activate or inhibit relevant down-stream genes.<br />
[[File:NTU-Taida-background-4.jpg|700px||center|Figure.3]]<br />
<br />
<br />
Under low bacterial concentration, target genes are under minimum expression (Figure a above), but as bacterial concentration elevates, AHL molecules begin to bind with the intracellular response regulators and promote the expression of target genes, many of them related to '''bacterial virulence''' or biofilm formation. Therefore, there is a close relationship between bacterial resistance and quorum sensing. Besides having species-specific quorum sensing system, many species of gram-negative bacteria share a type of quorum sensing molecule, the AI-2(autoinducer-2) molecule.<br />
<br />
==Routine Identification==<br />
Laboratory medicine (see also Visit[https://2013.igem.org/Team:NTU-Taida/Human_practice/Visit]) plays a crucial role in hospital and the identification of infecting bacteria are big part of it. According to the visit to professor Po-Ren Hsueh, a visiting staff in the department of laboratory medicine in NTU hospital, the routine identification of bacteria and sensitivity tests are mainly through the incubation in the plate. The method through mass spectrometry, having substantial advancement nowadays, can quickly excite proteins in bacteria, match in database and identify bacteria in 5 min, while methods via bio-chemical reactions require machines and chips (see figure below) including types for Gram positive, Gram negative, anaerobic bacteria, etc, and identify bacteria. However, these two methods detect mainly in protein levels, require expensive machines and cannot provide the antibiotic-sensitivity information making us back to the process of incubation.<br />
{|align='center'<br />
|[[File:NTU-Taida-project-background11.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background12.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background13.jpg|250px|center|thumb]]<br />
|}<br />
<br />
==PQS system in ''Pseudomonas aeruginosa''==<br />
<br />
To date, it has been found that ''Pseudomonas aeruginosa'' has at least four quorum sensing systems: '''Las system''' (Las from e”las”tase), '''Rhl system''' (Rhl from “rh”amno”l”ipids), '''Qsc system''' (Qsc from “Q”uorum “s”ensing “c”ontroller ), and '''PQS system''' (PQS from “P”seudomonas “q”uinolone “s”ignal). In general, Las system is responsible for toxin expression; Rhl system is responsible for secretion system; Qsc system is as a negative regulator of Las system and Rhl system; PQS system is responsible for the virulence. The four systems also have interactions with each other.<br />
<br />
Among these four systems, Las, Rhl and Qsc system all contain an AHL (acyl -homoserine lactone) activated receptor. Las system and Qsc system use 12-C AHL as QS (Quorum Sensing) molecules; on the other hand, Rhl system prefers to use 4-C AHL as QS molecules.<br />
<br />
However, interestingly, PQS system is not activated through AHL, but a '''quinoline derivative''': 2-heptyl-3,4-dihydroxyquinoline (also called “PQS”). Once PQS binds to pqsR, pqsR ─ as a transcriptional factor ─ can further activates two operons: pqsABCDE and phnAB (phn from "ph"e"n"azine). These two operons encode the enzymes that can synthesize PQS, and pqsE can catalyze PQS to become phenazine. Importantly, these phenazine products have been demonstrated to be involved in '''virulence of the organisms'''. For example, the phenazine pyocyanin production can enhance the ability of Pseudomonas aeruginosa to colonize the lungs of cystic fibrosis patients.<br />
[[File:NTU-Taida-project-background14.jpg|200px|center|thumb|quinolone]]<br />
<br />
==Reference==<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Arul Jayaraman and Thomas K.Wood|Essay=Bacterial Quorum Sensing:Signals, Circuits, and Implications for Biofilms and Disease|Journal=Annu. Rev. Biomed. Eng. 2008. 10:145–67}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Rutherford,''et al''|Essay=Bacterial quorum sensing: its role in virulence and possibilities for its control|Journal=Cold Spring Harb Perspect Med. 2012 Nov 1;2(11)}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Antunes LCM, ''et al''|Essay=Quorum sensing in bacterial virulence|Journal=Microbiology(2010), 156, 2271–2282}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Lo´ pez D, ''et al''|Essay=Biofilms|Journal=Cold Spring Harb Perspect Biol 2010 ; 2:a000398}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jimenez PN, ''et al''|Essay=The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa|Journal=Microbiol. Mol. Biol. Rev. 2012, 76(1):46}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Kendra P. Rumbaugh|Essay=Quorum Sensing: Methods and Protocols|Journal=Methods in Molecular Biology, vol. 692}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jitesh A Soares and Brian MM Ahmer|Essay=Detection of acyl-homoserine lactones by Escherichia and Salmonella|Journal=Microbiology 2011, 14:188–193}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Hsueh PR, ''et al''|Essay=Consensus review of the epidemiology and appropriate antimicrobial therapy of complicated urinary tract infections in Asia-Pacific region|Journal=The British Infection Association 2011}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Vanessa Sperandio|Essay=SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen|Journal=Gut Microbes 1:6, 432-435; November/December 2010}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Dubern, ''et al''|Essay=Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species|Journal=Mol Biosyst (2008) vol. 4 (9) pp. 882}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Diggle, ''et al''|Essay=4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives|Journal=Int J Med Microbiol (2006) vol. 296 (2-3) pp. 83-91}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Steindler, ''et al''|Essay=Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors|Journal=FEMS Microbiol Lett (2007) vol. 266 (1) pp. 1-9}}<br />
<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/BackgroundTeam:NTU-Taida/Project/Background2013-09-28T03:04:16Z<p>B00401107: /* Quorum Sensing System in Gram Positive Bacteria */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Background}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Bacterial infection==<br />
<br />
Bacterial infection is the invasion of bacteria into one’s body. They reproduce and multiply themselves, causing disease by local cellular injury, secretion of toxins, or antigen-antibody reaction in the host. The spectrum of bacteria changes with time and the introduction of antibacterial agents. Nowadays, the emerging issue in this field is the appearance of '''multiple drug-resistant (MDR) bacteria''' and '''extensive drug-resistant (XDR) bacteria'''. Yet the development of resistant strains of bacteria could be limited by the judicious use of antibiotics. In order to use the appropriate drug, knowing the antibiotic pattern of the invading bacteria is of importance. The routine process to identify causative organism in hospital, culturing and sensitivity testing for a specific antibiotic, is found to be sensitive.<br />
<br />
Bacterial infection may be further classified by where the infection occurs, into '''community-acquired infection''' and '''nosocomial infection'''. The strains of bacteria, infection site, and epidemiological transmission pathway all differ between them. Nosocomial infection is of increased importance. MDR or XDR are present in hospital environments such as MRSA (Methicillin-resistant ''Staphylococcus aureus'') and ''Acinetobacter''. Urinary tract infections, pneumopathy, and infections of surgery site are most common because of the formation of biofilm on the surface of catheters, endo-tubes, etc. What’s worse, due to the drug-resistance, diagnosis and treatment of bacterial nosocomial infection become a serious problem. It's urgent to develop new system of bacterial identification and drugs.<br />
<br />
==Quorum Sensing System in Gram Positive Bacteria==<br />
<br />
Gram-positive bacteria, characterized with a relatively thick layer of peptidylglycan, generally use peptides as quorum sensing molecules. These peptides are called '''autoinducing peptides (AIPs)'''; when produced by specialized AI synthase, they can be either transported from the cells through a specific membrane-bound transporter, or processed and secreted directly from the membrane. A high concentration of extracellular AIPs indicates high cell density. By binding to its cognate membrane-bound sensor kinase or intracellular receptor, the quorum sensing signal is transmitted back and spread to other bacterial cells, creating an '''inter-cellular communication network'''. The cytoplasmic response regulator, which controls the downstream virulence factors and AIP synthase, is phosphorylated by the histidine kinase receptor upon extracellular binding of AIPs, or is activated by the intracellular receptor-AIP complex itself (Figure 1).<br />
<br />
<br />
Together from a module-based point of view, the whole process of quorum sensing includes production, detection and response. Collectively, these modules are termed a two-component system.<br />
<br />
<br />
Clinically important Gram-positive bacteria include ''Staphylococcus aureus'' and ''Streptococcus pneumoniae'', responsible for skin and respiratory infections respectively. ''S. aureus'' uses the agr as its quorum sensing system.<br />
<br />
[[File:NTU-Taida-background-5.jpg|700px|thumb|center|Figure.1]]<br />
<br />
==Routine Identification==<br />
Laboratory medicine (see also Visit[https://2013.igem.org/Team:NTU-Taida/Human_practice/Visit]) plays a crucial role in hospital and the identification of infecting bacteria are big part of it. According to the visit to professor Po-Ren Hsueh, a visiting staff in the department of laboratory medicine in NTU hospital, the routine identification of bacteria and sensitivity tests are mainly through the incubation in the plate. The method through mass spectrometry, having substantial advancement nowadays, can quickly excite proteins in bacteria, match in database and identify bacteria in 5 min, while methods via bio-chemical reactions require machines and chips (see figure below) including types for Gram positive, Gram negative, anaerobic bacteria, etc, and identify bacteria. However, these two methods detect mainly in protein levels, require expensive machines and cannot provide the antibiotic-sensitivity information making us back to the process of incubation.<br />
{|align='center'<br />
|[[File:NTU-Taida-project-background11.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background12.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background13.jpg|250px|center|thumb]]<br />
|}<br />
<br />
==Quorum Sensing System in Gram negative Bacteria==<br />
<br />
The cell wall of Gram-negative bacteria is composed of a relatively thin layer of peptidoglycan and an outer membrane which contains lipopolysaccharide (LPS). Due to its structure, quorum sensing molecules '''diffuse''' through the cell membrane and bind with '''intracellular receptors'''. <br />
[[File:NTU-Taida-background-3.jpg|||center|Figure.2]]<br />
<br />
Generally speaking, quorum sensing system in gram negative bacteria functions as follows (Take LasI/LasR system for example):<br />
<br />
The LasI gene encodes an '''autoinducer synthase(LasI)''', and this autoinducer synthase produces quorum sensing molecules(autoinducers) called '''acyl-homoserine lactone(AHLs)'''. Another gene LasR encodes for the '''response regulator of the autoinducers'''. Regulators bind with autoinducers and form complexes. They bind on target promoters, and then either activate or inhibit relevant down-stream genes.<br />
[[File:NTU-Taida-background-4.jpg|700px||center|Figure.3]]<br />
<br />
<br />
Under low bacterial concentration, target genes are under minimum expression (Figure a above), but as bacterial concentration elevates, AHL molecules begin to bind with the intracellular response regulators and promote the expression of target genes, many of them related to '''bacterial virulence''' or biofilm formation. Therefore, there is a close relationship between bacterial resistance and quorum sensing. Besides having species-specific quorum sensing system, many species of gram-negative bacteria share a type of quorum sensing molecule, the AI-2(autoinducer-2) molecule.<br />
<br />
==PQS system in ''Pseudomonas aeruginosa''==<br />
<br />
To date, it has been found that ''Pseudomonas aeruginosa'' has at least four quorum sensing systems: '''Las system''' (Las from e”las”tase), '''Rhl system''' (Rhl from “rh”amno”l”ipids), '''Qsc system''' (Qsc from “Q”uorum “s”ensing “c”ontroller ), and '''PQS system''' (PQS from “P”seudomonas “q”uinolone “s”ignal). In general, Las system is responsible for toxin expression; Rhl system is responsible for secretion system; Qsc system is as a negative regulator of Las system and Rhl system; PQS system is responsible for the virulence. The four systems also have interactions with each other.<br />
<br />
Among these four systems, Las, Rhl and Qsc system all contain an AHL (acyl -homoserine lactone) activated receptor. Las system and Qsc system use 12-C AHL as QS (Quorum Sensing) molecules; on the other hand, Rhl system prefers to use 4-C AHL as QS molecules.<br />
<br />
However, interestingly, PQS system is not activated through AHL, but a '''quinoline derivative''': 2-heptyl-3,4-dihydroxyquinoline (also called “PQS”). Once PQS binds to pqsR, pqsR ─ as a transcriptional factor ─ can further activates two operons: pqsABCDE and phnAB (phn from "ph"e"n"azine). These two operons encode the enzymes that can synthesize PQS, and pqsE can catalyze PQS to become phenazine. Importantly, these phenazine products have been demonstrated to be involved in '''virulence of the organisms'''. For example, the phenazine pyocyanin production can enhance the ability of Pseudomonas aeruginosa to colonize the lungs of cystic fibrosis patients.<br />
[[File:NTU-Taida-project-background14.jpg|200px|center|thumb|quinolone]]<br />
<br />
==Reference==<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Arul Jayaraman and Thomas K.Wood|Essay=Bacterial Quorum Sensing:Signals, Circuits, and Implications for Biofilms and Disease|Journal=Annu. Rev. Biomed. Eng. 2008. 10:145–67}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Rutherford,''et al''|Essay=Bacterial quorum sensing: its role in virulence and possibilities for its control|Journal=Cold Spring Harb Perspect Med. 2012 Nov 1;2(11)}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Antunes LCM, ''et al''|Essay=Quorum sensing in bacterial virulence|Journal=Microbiology(2010), 156, 2271–2282}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Lo´ pez D, ''et al''|Essay=Biofilms|Journal=Cold Spring Harb Perspect Biol 2010 ; 2:a000398}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jimenez PN, ''et al''|Essay=The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa|Journal=Microbiol. Mol. Biol. Rev. 2012, 76(1):46}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Kendra P. Rumbaugh|Essay=Quorum Sensing: Methods and Protocols|Journal=Methods in Molecular Biology, vol. 692}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jitesh A Soares and Brian MM Ahmer|Essay=Detection of acyl-homoserine lactones by Escherichia and Salmonella|Journal=Microbiology 2011, 14:188–193}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Hsueh PR, ''et al''|Essay=Consensus review of the epidemiology and appropriate antimicrobial therapy of complicated urinary tract infections in Asia-Pacific region|Journal=The British Infection Association 2011}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Vanessa Sperandio|Essay=SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen|Journal=Gut Microbes 1:6, 432-435; November/December 2010}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Dubern, ''et al''|Essay=Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species|Journal=Mol Biosyst (2008) vol. 4 (9) pp. 882}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Diggle, ''et al''|Essay=4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives|Journal=Int J Med Microbiol (2006) vol. 296 (2-3) pp. 83-91}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Steindler, ''et al''|Essay=Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors|Journal=FEMS Microbiol Lett (2007) vol. 266 (1) pp. 1-9}}<br />
<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/BackgroundTeam:NTU-Taida/Project/Background2013-09-28T02:59:54Z<p>B00401107: /* Bacterial infection */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Background}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Bacterial infection==<br />
<br />
Bacterial infection is the invasion of bacteria into one’s body. They reproduce and multiply themselves, causing disease by local cellular injury, secretion of toxins, or antigen-antibody reaction in the host. The spectrum of bacteria changes with time and the introduction of antibacterial agents. Nowadays, the emerging issue in this field is the appearance of '''multiple drug-resistant (MDR) bacteria''' and '''extensive drug-resistant (XDR) bacteria'''. Yet the development of resistant strains of bacteria could be limited by the judicious use of antibiotics. In order to use the appropriate drug, knowing the antibiotic pattern of the invading bacteria is of importance. The routine process to identify causative organism in hospital, culturing and sensitivity testing for a specific antibiotic, is found to be sensitive.<br />
<br />
Bacterial infection may be further classified by where the infection occurs, into '''community-acquired infection''' and '''nosocomial infection'''. The strains of bacteria, infection site, and epidemiological transmission pathway all differ between them. Nosocomial infection is of increased importance. MDR or XDR are present in hospital environments such as MRSA (Methicillin-resistant ''Staphylococcus aureus'') and ''Acinetobacter''. Urinary tract infections, pneumopathy, and infections of surgery site are most common because of the formation of biofilm on the surface of catheters, endo-tubes, etc. What’s worse, due to the drug-resistance, diagnosis and treatment of bacterial nosocomial infection become a serious problem. It's urgent to develop new system of bacterial identification and drugs.<br />
<br />
==Quorum Sensing System in Gram Positive Bacteria==<br />
<br />
Gram-positive bacteria, characterized with a relatively thick layer of peptidylglycan, generally use peptides as quorum sensing molecules. These peptides are called '''autoinducing peptides (AIPs)'''; when produced by specialized AI synthase, they can be either transported from(outside?) the cells through a specific membrane-bound transporter, or processed and secreted directly from the membrane. A high concentration of extracellular AIPs indicates high cell density. By binding to its cognate membrane-bound sensor kinase or intracellular receptor, the quorum sensing signal is transmitted back and spread to other bacterial cells, creating an '''inter-cellular communication network'''. The cytoplasmic response regulator, which controls the downstream virulence factors and AI(AIP?) synthase, is phosphorylated by the histidine kinase receptor upon extracellular binding of AIPs, or is activated by the intracellular receptor-AIP complex itself (Figure 1).<br />
<br />
<br />
Together from a module-based point of view, the whole process of quorum sensing includes production, detection and response. Collectively these modules are termed a two-component system.<br />
<br />
<br />
Clinically important Gram-positive bacteria include ''Staphylococcus aureus'' and ''Streptococcus pneumoniae'', responsible for skin and respiratory infections respectively. ''S. aureus'' uses the agr as its quorum sensing system.<br />
<br />
[[File:NTU-Taida-background-5.jpg|700px|thumb|center|Figure.1]]<br />
<br />
==Routine Identification==<br />
Laboratory medicine (see also Visit[https://2013.igem.org/Team:NTU-Taida/Human_practice/Visit]) plays a crucial role in hospital and the identification of infecting bacteria are big part of it. According to the visit to professor Po-Ren Hsueh, a visiting staff in the department of laboratory medicine in NTU hospital, the routine identification of bacteria and sensitivity tests are mainly through the incubation in the plate. The method through mass spectrometry, having substantial advancement nowadays, can quickly excite proteins in bacteria, match in database and identify bacteria in 5 min, while methods via bio-chemical reactions require machines and chips (see figure below) including types for Gram positive, Gram negative, anaerobic bacteria, etc, and identify bacteria. However, these two methods detect mainly in protein levels, require expensive machines and cannot provide the antibiotic-sensitivity information making us back to the process of incubation.<br />
{|align='center'<br />
|[[File:NTU-Taida-project-background11.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background12.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background13.jpg|250px|center|thumb]]<br />
|}<br />
<br />
==Quorum Sensing System in Gram negative Bacteria==<br />
<br />
The cell wall of Gram-negative bacteria is composed of a relatively thin layer of peptidoglycan and an outer membrane which contains lipopolysaccharide (LPS). Due to its structure, quorum sensing molecules '''diffuse''' through the cell membrane and bind with '''intracellular receptors'''. <br />
[[File:NTU-Taida-background-3.jpg|||center|Figure.2]]<br />
<br />
Generally speaking, quorum sensing system in gram negative bacteria functions as follows (Take LasI/LasR system for example):<br />
<br />
The LasI gene encodes an '''autoinducer synthase(LasI)''', and this autoinducer synthase produces quorum sensing molecules(autoinducers) called '''acyl-homoserine lactone(AHLs)'''. Another gene LasR encodes for the '''response regulator of the autoinducers'''. Regulators bind with autoinducers and form complexes. They bind on target promoters, and then either activate or inhibit relevant down-stream genes.<br />
[[File:NTU-Taida-background-4.jpg|700px||center|Figure.3]]<br />
<br />
<br />
Under low bacterial concentration, target genes are under minimum expression (Figure a above), but as bacterial concentration elevates, AHL molecules begin to bind with the intracellular response regulators and promote the expression of target genes, many of them related to '''bacterial virulence''' or biofilm formation. Therefore, there is a close relationship between bacterial resistance and quorum sensing. Besides having species-specific quorum sensing system, many species of gram-negative bacteria share a type of quorum sensing molecule, the AI-2(autoinducer-2) molecule.<br />
<br />
==PQS system in ''Pseudomonas aeruginosa''==<br />
<br />
To date, it has been found that ''Pseudomonas aeruginosa'' has at least four quorum sensing systems: '''Las system''' (Las from e”las”tase), '''Rhl system''' (Rhl from “rh”amno”l”ipids), '''Qsc system''' (Qsc from “Q”uorum “s”ensing “c”ontroller ), and '''PQS system''' (PQS from “P”seudomonas “q”uinolone “s”ignal). In general, Las system is responsible for toxin expression; Rhl system is responsible for secretion system; Qsc system is as a negative regulator of Las system and Rhl system; PQS system is responsible for the virulence. The four systems also have interactions with each other.<br />
<br />
Among these four systems, Las, Rhl and Qsc system all contain an AHL (acyl -homoserine lactone) activated receptor. Las system and Qsc system use 12-C AHL as QS (Quorum Sensing) molecules; on the other hand, Rhl system prefers to use 4-C AHL as QS molecules.<br />
<br />
However, interestingly, PQS system is not activated through AHL, but a '''quinoline derivative''': 2-heptyl-3,4-dihydroxyquinoline (also called “PQS”). Once PQS binds to pqsR, pqsR ─ as a transcriptional factor ─ can further activates two operons: pqsABCDE and phnAB (phn from "ph"e"n"azine). These two operons encode the enzymes that can synthesize PQS, and pqsE can catalyze PQS to become phenazine. Importantly, these phenazine products have been demonstrated to be involved in '''virulence of the organisms'''. For example, the phenazine pyocyanin production can enhance the ability of Pseudomonas aeruginosa to colonize the lungs of cystic fibrosis patients.<br />
[[File:NTU-Taida-project-background14.jpg|200px|center|thumb|quinolone]]<br />
<br />
==Reference==<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Arul Jayaraman and Thomas K.Wood|Essay=Bacterial Quorum Sensing:Signals, Circuits, and Implications for Biofilms and Disease|Journal=Annu. Rev. Biomed. Eng. 2008. 10:145–67}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Rutherford,''et al''|Essay=Bacterial quorum sensing: its role in virulence and possibilities for its control|Journal=Cold Spring Harb Perspect Med. 2012 Nov 1;2(11)}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Antunes LCM, ''et al''|Essay=Quorum sensing in bacterial virulence|Journal=Microbiology(2010), 156, 2271–2282}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Lo´ pez D, ''et al''|Essay=Biofilms|Journal=Cold Spring Harb Perspect Biol 2010 ; 2:a000398}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jimenez PN, ''et al''|Essay=The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa|Journal=Microbiol. Mol. Biol. Rev. 2012, 76(1):46}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Kendra P. Rumbaugh|Essay=Quorum Sensing: Methods and Protocols|Journal=Methods in Molecular Biology, vol. 692}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jitesh A Soares and Brian MM Ahmer|Essay=Detection of acyl-homoserine lactones by Escherichia and Salmonella|Journal=Microbiology 2011, 14:188–193}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Hsueh PR, ''et al''|Essay=Consensus review of the epidemiology and appropriate antimicrobial therapy of complicated urinary tract infections in Asia-Pacific region|Journal=The British Infection Association 2011}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Vanessa Sperandio|Essay=SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen|Journal=Gut Microbes 1:6, 432-435; November/December 2010}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Dubern, ''et al''|Essay=Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species|Journal=Mol Biosyst (2008) vol. 4 (9) pp. 882}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Diggle, ''et al''|Essay=4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives|Journal=Int J Med Microbiol (2006) vol. 296 (2-3) pp. 83-91}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Steindler, ''et al''|Essay=Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors|Journal=FEMS Microbiol Lett (2007) vol. 266 (1) pp. 1-9}}<br />
<br />
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{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/IntroductionTeam:NTU-Taida/Project/Introduction2013-09-28T02:54:11Z<p>B00401107: /* Introduction of Our Project */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Introduction}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
==Introduction of Our Project==<br />
The final goal of our project is to '''real-time detect''' and '''identify drug-resistance bacterial strains''', which cause nosocomial infection from the hospital specimens.<br />
<br />
Nosocomial infections are those infections occur in hospitals. Comparing to communities, drug-resistant strains are more often found in hospitals. Moreover, nosocomial infections are easier to take place in the intensive care units than common wards. These two characteristics explain why nosocomial infections are usually fatal to those who are immune-compromised and hospitalized, if not treated in-time. However, it usually takes a long time from culturing to identifying bacteria strains, and we may lose the golden time to cure the patient. This is the problem we’re trying to solve, through the construction of an instant bacteria-drug-resistance identification system.<br />
<br />
We choose quorum sensing molecules as our target. Quorum sensing (QS) is a density-associated communication method for bacteria. It is usually species-specific, like dialects among people. After surveying many related researches, '''we reasonably assume that among the same bacterial species, those with drug-resistance and without drug-resistance, as well as those with different types of drug-resistance, their patterns of releasing QS molecules have quantitative difference'''. We plan to use our QS array - genetically modified ''E. coli'', to detect those differences in each QS molecule activation level, hoping to establish a profile ─ “antibiotic resistance” towards “pattern of quorum sensing molecule activation levels” ─ in order to instantaneously recognize drug-resistance strains. We would use a common opportunistic pathogen, ''Pseudomonas aeruginosa'' as a primary detection target. Tests will then expand to other bacterial species. Finally, by using these data, we might create a fast-and-safe array on a tiny chip, making nosocomial infection no more a nightmare.<br />
<br />
[[File:NTU-Taida-project-introduction-1.jpg|center|700px|thumb|Prototype of our array]]<br />
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{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/Team:NTU-TaidaTeam:NTU-Taida2013-09-28T02:31:39Z<p>B00401107: </p>
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<h2>NTU-Taida</h2><br />
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<td><a href="https://2013.igem.org/Team:NTU-Taida/Project/Introduction"><img src="/wiki/images/e/ed/NTU-Taida-mainpage-1.png" width="150px" alt=""></a></td><br />
<td><a href="https://2013.igem.org/Team:NTU-Taida/Modeling/Simple_Determinstic_Model"><img src="/wiki/images/4/49/NTU-Taida-mainpage-2.png" width="150px" alt=""></a></td><br />
<td><a href="https://2013.igem.org/Team:NTU-Taida/Result/AHL_Concentration"><img src="/wiki/images/e/e4/NTU-Taida-mainpage-3.png" width="150px" alt=""></a></td><br />
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<td><font size="4" color="#98b190"><b>Project</b></font></td><br />
<td><font size="4" color="#e1ba59"><b>Modeling</b></font></td><br />
<td><font size="4" color="#ed4f4f"><b>Results</b></font></td><br />
<td><font size="4" color="#6f91e5"><b>Human practice</b></font></td><br />
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{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar= }}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/BackgroundTeam:NTU-Taida/Project/Background2013-09-28T02:22:20Z<p>B00401107: /* Bacterial infection */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Background}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Bacterial infection==<br />
<br />
Bacterial infection is the invasion of bacteria into one’s body. They reproduce and multiply themselves, causing disease by local cellular injury, secretion of toxins, or antigen-antibody reaction in the host. The spectrum of bacteria changes with time and the introduction of antibacterial agent. Nowadays, the emerging issue in this field is the appearance of '''multiple drug-resistant (MDR) bacteria''' and '''extensive drug-resistant (XDR) bacteria'''. Yet the development of resistant strains of bacteria could be limited by the judicious use of antibiotics. In order to use the appropriate drug, knowing the antibiotic pattern of the invading bacteria is of importance. The routine process to identify causative organism in hospital, culturing and sensitivity testing for a specific antibiotic, is found to be sensitive.<br />
<br />
Bacterial infection may be further classified by where the infection occurs, into '''community-acquired infection''' and '''nosocomial infection'''. The strains of bacteria, infection site, and epidemiological transmission pathway all differ between them. Nosocomial infection is of increased importance. MDR or XDR are present in hospital environments such as MRSA (Methicillin-resistant ''Staphylococcus aureus'') and ''Acinetobacter''. Urinary tract infections, pneumopathy, and infections of surgery site are most common because of the formation of biofilm on the surface of catheters, endo-tubes, etc. What’s worse, because of the drug-resistance, diagnosis and treatment of bacterial nosocomial infection become a serious problem. The identification of bacteria and new drugs is required.<br />
<br />
==Quorum Sensing System in Gram Positive Bacteria==<br />
<br />
Gram-positive bacteria, characterized with a relatively thick layer of peptidylglycan, generally use peptides as quorum sensing molecules. These peptides are called '''autoinducing peptides (AIPs)'''; when produced by specialized AI synthase, they can be either transported from(outside?) the cells through a specific membrane-bound transporter, or processed and secreted directly from the membrane. A high concentration of extracellular AIPs indicates high cell density. By binding to its cognate membrane-bound sensor kinase or intracellular receptor, the quorum sensing signal is transmitted back and spread to other bacterial cells, creating an '''inter-cellular communication network'''. The cytoplasmic response regulator, which controls the downstream virulence factors and AI(AIP?) synthase, is phosphorylated by the histidine kinase receptor upon extracellular binding of AIPs, or is activated by the intracellular receptor-AIP complex itself (Figure 1).<br />
<br />
<br />
Together from a module-based point of view, the whole process of quorum sensing includes production, detection and response. Collectively these modules are termed a two-component system.<br />
<br />
<br />
Clinically important Gram-positive bacteria include ''Staphylococcus aureus'' and ''Streptococcus pneumoniae'', responsible for skin and respiratory infections respectively. ''S. aureus'' uses the agr as its quorum sensing system.<br />
<br />
[[File:NTU-Taida-background-5.jpg|700px|thumb|center|Figure.1]]<br />
<br />
==Routine Identification==<br />
Laboratory medicine (see also Visit[https://2013.igem.org/Team:NTU-Taida/Human_practice/Visit]) plays a crucial role in hospital and the identification of infecting bacteria are big part of it. According to the visit to professor Po-Ren Hsueh, a visiting staff in the department of laboratory medicine in NTU hospital, the routine identification of bacteria and sensitivity tests are mainly through the incubation in the plate. The method through mass spectrometry, having substantial advancement nowadays, can quickly excite proteins in bacteria, match in database and identify bacteria in 5 min, while methods via bio-chemical reactions require machines and chips (see figure below) including types for Gram positive, Gram negative, anaerobic bacteria, etc, and identify bacteria. However, these two methods detect mainly in protein levels, require expensive machines and cannot provide the antibiotic-sensitivity information making us back to the process of incubation.<br />
{|align='center'<br />
|[[File:NTU-Taida-project-background11.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background12.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background13.jpg|250px|center|thumb]]<br />
|}<br />
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==Quorum Sensing System in Gram negative Bacteria==<br />
<br />
The cell wall of Gram-negative bacteria is composed of a relatively thin layer of peptidoglycan and an outer membrane which contains lipopolysaccharide (LPS). Due to its structure, quorum sensing molecules '''diffuse''' through the cell membrane and bind with '''intracellular receptors'''. <br />
[[File:NTU-Taida-background-3.jpg|||center|Figure.2]]<br />
<br />
Generally speaking, quorum sensing system in gram negative bacteria functions as follows (Take LasI/LasR system for example):<br />
<br />
The LasI gene encodes an '''autoinducer synthase(LasI)''', and this autoinducer synthase produces quorum sensing molecules(autoinducers) called '''acyl-homoserine lactone(AHLs)'''. Another gene LasR encodes for the '''response regulator of the autoinducers'''. Regulators bind with autoinducers and form complexes. They bind on target promoters, and then either activate or inhibit relevant down-stream genes.<br />
[[File:NTU-Taida-background-4.jpg|700px||center|Figure.3]]<br />
<br />
<br />
Under low bacterial concentration, target genes are under minimum expression (Figure a above), but as bacterial concentration elevates, AHL molecules begin to bind with the intracellular response regulators and promote the expression of target genes, many of them related to '''bacterial virulence''' or biofilm formation. Therefore, there is a close relationship between bacterial resistance and quorum sensing. Besides having species-specific quorum sensing system, many species of gram-negative bacteria share a type of quorum sensing molecule, the AI-2(autoinducer-2) molecule.<br />
<br />
==PQS system in ''Pseudomonas aeruginosa''==<br />
<br />
To date, it has been found that ''Pseudomonas aeruginosa'' has at least four quorum sensing systems: '''Las system''' (Las from e”las”tase), '''Rhl system''' (Rhl from “rh”amno”l”ipids), '''Qsc system''' (Qsc from “Q”uorum “s”ensing “c”ontroller ), and '''PQS system''' (PQS from “P”seudomonas “q”uinolone “s”ignal). In general, Las system is responsible for toxin expression; Rhl system is responsible for secretion system; Qsc system is as a negative regulator of Las system and Rhl system; PQS system is responsible for the virulence. The four systems also have interactions with each other.<br />
<br />
Among these four systems, Las, Rhl and Qsc system all contain an AHL (acyl -homoserine lactone) activated receptor. Las system and Qsc system use 12-C AHL as QS (Quorum Sensing) molecules; on the other hand, Rhl system prefers to use 4-C AHL as QS molecules.<br />
<br />
However, interestingly, PQS system is not activated through AHL, but a '''quinoline derivative''': 2-heptyl-3,4-dihydroxyquinoline (also called “PQS”). Once PQS binds to pqsR, pqsR ─ as a transcriptional factor ─ can further activates two operons: pqsABCDE and phnAB (phn from "ph"e"n"azine). These two operons encode the enzymes that can synthesize PQS, and pqsE can catalyze PQS to become phenazine. Importantly, these phenazine products have been demonstrated to be involved in '''virulence of the organisms'''. For example, the phenazine pyocyanin production can enhance the ability of Pseudomonas aeruginosa to colonize the lungs of cystic fibrosis patients.<br />
[[File:NTU-Taida-project-background14.jpg|200px|center|thumb|quinolone]]<br />
<br />
==Reference==<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Arul Jayaraman and Thomas K.Wood|Essay=Bacterial Quorum Sensing:Signals, Circuits, and Implications for Biofilms and Disease|Journal=Annu. Rev. Biomed. Eng. 2008. 10:145–67}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Rutherford,''et al''|Essay=Bacterial quorum sensing: its role in virulence and possibilities for its control|Journal=Cold Spring Harb Perspect Med. 2012 Nov 1;2(11)}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Antunes LCM, ''et al''|Essay=Quorum sensing in bacterial virulence|Journal=Microbiology(2010), 156, 2271–2282}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Lo´ pez D, ''et al''|Essay=Biofilms|Journal=Cold Spring Harb Perspect Biol 2010 ; 2:a000398}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jimenez PN, ''et al''|Essay=The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa|Journal=Microbiol. Mol. Biol. Rev. 2012, 76(1):46}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Kendra P. Rumbaugh|Essay=Quorum Sensing: Methods and Protocols|Journal=Methods in Molecular Biology, vol. 692}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jitesh A Soares and Brian MM Ahmer|Essay=Detection of acyl-homoserine lactones by Escherichia and Salmonella|Journal=Microbiology 2011, 14:188–193}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Hsueh PR, ''et al''|Essay=Consensus review of the epidemiology and appropriate antimicrobial therapy of complicated urinary tract infections in Asia-Pacific region|Journal=The British Infection Association 2011}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Vanessa Sperandio|Essay=SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen|Journal=Gut Microbes 1:6, 432-435; November/December 2010}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Dubern, ''et al''|Essay=Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species|Journal=Mol Biosyst (2008) vol. 4 (9) pp. 882}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Diggle, ''et al''|Essay=4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives|Journal=Int J Med Microbiol (2006) vol. 296 (2-3) pp. 83-91}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Steindler, ''et al''|Essay=Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors|Journal=FEMS Microbiol Lett (2007) vol. 266 (1) pp. 1-9}}<br />
<br />
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{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/File:NTU-Taida-mainpage-project.gifFile:NTU-Taida-mainpage-project.gif2013-09-28T01:51:53Z<p>B00401107: </p>
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<div></div>B00401107http://2013.igem.org/File:NTU-Taida-mainpage-result.gifFile:NTU-Taida-mainpage-result.gif2013-09-28T01:51:30Z<p>B00401107: </p>
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<div></div>B00401107http://2013.igem.org/File:NTU-Taida-mainpage-modeling.gifFile:NTU-Taida-mainpage-modeling.gif2013-09-28T01:51:06Z<p>B00401107: </p>
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<div></div>B00401107http://2013.igem.org/File:NTU-Taida-mainpage-human_practice.gifFile:NTU-Taida-mainpage-human practice.gif2013-09-28T01:50:12Z<p>B00401107: </p>
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<div></div>B00401107http://2013.igem.org/Team:NTU-Taida/PartsTeam:NTU-Taida/Parts2013-09-28T00:37:18Z<p>B00401107: /* Note */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Part}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Note==<br />
Some plasmids are not submitted due to similar parts in registry or time limit while they are still important fragments in our projects and we still lists them below. <br />
<br />
Also, BBa_K575024 and BBa_K575033 submitted from the Northwestern help a lot.<br />
<br />
==Original Biobrick==<br />
<html><br />
<table class="tableizer-table"><br />
<tr class="tableizer-firstrow"><th>Name</th><th>Type</th><th>Description</th><th>Length</th></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157000"> BBa_K1157000</a></td><td>Regulatory</td><td>promoter sequence for PQS quorum sensing</td><td>341</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157001">BBa_K1157001</a></td><td>Coding</td><td>PQSR</td><td>999</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157003">BBa_K1157003</a></td><td>Coding</td><td>AbaR</td><td>597</td></tr><br />
</table><br />
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<br />
==Reporter==<br />
<html><br />
<table class="tableizer-table"><br />
<tr class="tableizer-firstrow"><th>Name</th><th>Type</th><th>Description</th><th>Length</th></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157005">BBa_K1157005</a></td><td>Reporter</td><td>Luciferase generator</td><td>1094</td></tr><br />
<tr><td>&nbsp;</td><td>Reporter</td><td>RBS-mTagBFP-tt</td><td>849</td></tr><br />
<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr><br />
<tr><td>&nbsp;</td><td>Reporter</td><td>RBS-mCherry-tt</td><td>858</td></tr><br />
<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td></tr><br />
<tr><td>&nbsp;</td><td>Reporter</td><td>RBS-GFP-tt</td><td>867</td></tr><br />
<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td></td></tr><br />
</table><br />
</html><br />
<br />
==Protein Generator==<br />
<html><br />
<table class="tableizer-table"><br />
<tr class="tableizer-firstrow"><th>Name</th><th>Type</th><th>Description</th><th>Length</th></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157007">BBa_K1157007</a></td><td>Coding</td><td>Quorum sensing receptor pqsR generator</td><td>1157</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157017">BBa_K1157017</a></td><td>Composite</td><td>pPQS-GFPmut3</td><td>1227</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157019">BBa_K1157019</a></td><td>Composite</td><td>Pc-PQSR</td><td>1200</td></tr><br />
<tr><td>&nbsp;</td><td>Composite</td><td>RBS-RhlR-tt</td><td>873</td></tr><br />
<tr><td>&nbsp;</td><td>Composite</td><td>&nbsp;</td><td>&nbsp;</td></tr><br />
<tr><td>&nbsp;</td><td>Composite</td><td>RBS-LasR-tt</td><td>867</td></tr><br />
<tr><td>&nbsp;</td><td>Composite</td><td>RBS-CinR-tt</td><td>931</td></tr><br />
<tr><td>&nbsp;</td><td>Composite</td><td>RBS-AbaR-tt</td><td>741</td></tr><br />
</table><br />
</html><br />
<br />
==Without positive feedback circuits==<br />
<html><br />
<table class="tableizer-table"><br />
<tr class="tableizer-firstrow"><th>Name</th><th>Type</th><th>Description</th><th>Length</th></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157010">BBa_K1157010</a></td><td>Composite</td><td>Pc-RhlR-mCherry</td><td>1871</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157016">BBa_K1157016</a></td><td>Composite</td><td>Pc-LasR-pLas-BFP</td><td>1960</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_KK575033">BBa_K575033</a></td><td>Composite</td><td>PRhl-GFP-Pc-RhlR</td><td>1600</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K575024">BBa_K575024</a></td><td>Composite</td><td>Plas-GFP-Pc-LasR</td><td>1701</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157008">BBa_K1157008</a></td><td>Composite</td><td>pLas-BFP-Pc-LasR</td><td>2018</td></tr><br />
<tr><td>&nbsp;</td><td>Composite</td><td>pPQS-GFP-Pc-PQSR</td><td>2401</td></tr><br />
</table><br />
</html><br />
<br />
==Positive Feedback circuit==<br />
<html><br />
<table class="tableizer-table"><br />
<tr class="tableizer-firstrow"><th>Name</th><th>Type</th><th>Description</th><th>Length</th></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157020">BBa_K1157020</a></td><td>Composite</td><td>Pc-RhlR-pRhl-RhlR-GFPmut3</td><td>2635</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157011">BBa_K1157011</a></td><td>Composite</td><td>Pc-RhlR-pRhl-RhlR-BFP</td><td>2620</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157012">BBa_K1157012</a></td><td>Composite</td><td>Pc-RhlR-pRhl-RhlR-luciferase</td><td>2851</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157018">BBa_K1157018</a></td><td>Composite</td><td>pRhl-RhlR-mCherry-Pc-RhlR</td><td>2629</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157021">BBa_K1157021</a></td><td>Composite</td><td>pRhl-RhlR-GFP-Pc-RhlR</td><td>2635</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157014">BBa_K1157014</a></td><td>Composite</td><td>pLas-LasR-GFPmut3-Pc-LasR</td><td>2727</td></tr><br />
</table><br />
</html><br />
<br />
==Negative Regulation==<br />
<html><br />
<table class="tableizer-table"><br />
<tr class="tableizer-firstrow"><th>Name</th><th>Type</th><th>Description</th><th>Length</th></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157013">BBa_K1157013</a></td><td>Composite</td><td>pCI-mCherry-pConst-RhlR-pRhl-RhlR-CI</td><td>3627</td></tr><br />
<tr><td><a href="http://parts.igem.org/Part:BBa_K1157015">BBa_K1157015</a></td><td>Composite</td><td>pConst-Rhl-pRhl-RhlR-CI-pCI-mCherry</td><td>3627</td></tr><br />
</table><br />
</html><br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Part}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/OverviewTeam:NTU-Taida/Project/Overview2013-09-28T00:26:54Z<p>B00401107: /* Overview */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Overview}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
=Overview=<br />
Our IGEM project aims to tailor an '''instant bacteria identification array'''. We chose '''Quorum sensing molecules (QS molecules)''' instead of traditional biochemical reactions as our main targets to achieve our goals. As a cell-cell communication pathway, Quorum sensing phenomenon regulates '''virulence gene expression''' and has recently been considered as a new target for therapeutic application. We proposed a novel method to identify bacteria by '''the expression pattern''' of many QS receptors from the intensity of fluorescent signals.<br />
<br />
For the sakes of sensitivity and the consideration of time, we underwent process of cloning and designed both '''positive feedback''' and '''negative regulation circuits''' insides plasmids containing quorum sensing receptors (or transcriptional regulator) conjugated with florescent proteins. These plasmids were transformed into E. Coli DH5α. They would act as '''biosensors''' when meeting quorum sensing molecules.<br />
<br />
We would like to identify bacterial strains both '''between species''' and '''within species'''. For Gram negative species, AHL is a common quorum sensing molecule. Different receptors, however, target different kinds of '''AHL (Acylhomoserine Lactone)''' depending on its carbon number of the acyl group. We targeted to construct an array of QS sensors, consisting of sensor for 4-carbon, 8-carbon, 12-carbon and 14-carbon AHL. Because QS sensors are also able to sense AHL molecules with '''a closer number of carbons''', this biosensor array can detects 2~14 carbon AHLs. In addition to AHL, we also developed '''novel biosensor—PQS''' for new type of quorum sensing molecule in iGem—'''Quinolones'''.<br />
<br />
To achieve a complete array, a lot of '''measurements''' are indispensable. We manipulated simple qualitative experiments for its property and the fluorescent protein expression via polyacrylamide gel electrophoresis stained by coomassie blue. Next, we bought molecules including AHL and Quinolones and utilized '''ELISA plate reader''' and '''flow cytometer''' to calibrate the '''standard diagram''' (intensity of florescent protein—time) of different biosensors added with series dilution of AHL in 96-well plate. At the third stage, the '''supernatant of bacteria''' (between species and within species) were taken into experiments. By replacement of AHL or Quinolones with the supernatant of bacteria, we depicted new curves, and compared it with each other and also standard diagram. With the efforts of the teams, we proved our idea. The responses of different strains of bacteria to our array varied greatly.<br />
<br />
To put it into practice, we aligned different Quorum sensing receptors circuits to form an array to test '''clinical samples''' like septum, blood, urine, etc. After collecting enough data of different clinical bacterial strains and build up a database, we hope to build up a new system for bacteria identification.<br />
<br />
[[File:NTU-Taida-overview-1.jpg|700px|thumb|center|Figure.3]]<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/OverviewTeam:NTU-Taida/Project/Overview2013-09-28T00:25:20Z<p>B00401107: /* Overview */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Overview}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
=Overview=<br />
Our IGEM project aims to tailor an '''instant bacteria identification array'''. We chose '''Quorum sensing molecules (QS molecules)''' instead of traditional biochemical reactions as our main targets to achieve our goals. As a cell-cell communication pathway, Quorum sensing phenomenon regulates '''virulence gene expression''' and has recently been considered as a new target for therapeutic application. We proposed a novel method to identify bacteria by '''the expression pattern''' of many QS receptors from the intensity of fluorescent signals.<br />
{|align='center'<br />
|[[File:NTU-Taida-overview-2.jpg|380px|thumb|center|LaSarre et al. Microbiol Mol Biol Rev (2013)]]<br />
|[[File:NTU-Taida-overview-3.jpg|350px|thumb|center|LaSarre et al. Microbiol Mol Biol Rev (2013)]]<br />
|}<br />
<br />
<br />
<br />
For the sakes of sensitivity and the consideration of time, we underwent process of cloning and designed both '''positive feedback''' and '''negative regulation circuits''' insides plasmids containing quorum sensing receptors (or transcriptional regulator) conjugated with florescent proteins. These plasmids were transformed into E. Coli DH5α. They would act as '''biosensors''' when meeting quorum sensing molecules.<br />
<br />
We would like to identify bacterial strains both '''between species''' and '''within species'''. For Gram negative species, AHL is a common quorum sensing molecule. Different receptors, however, target different kinds of '''AHL (Acylhomoserine Lactone)''' depending on its carbon number of the acyl group. We targeted to construct an array of QS sensors, consisting of sensor for 4-carbon, 8-carbon, 12-carbon and 14-carbon AHL. Because QS sensors are also able to sense AHL molecules with '''a closer number of carbons''', this biosensor array can detects 2~14 carbon AHLs. In addition to AHL, we also developed '''novel biosensor—PQS''' for new type of quorum sensing molecule in iGem—'''Quinolones'''.<br />
<br />
To achieve a complete array, a lot of '''measurements''' are indispensable. We manipulated simple qualitative experiments for its property and the fluorescent protein expression via polyacrylamide gel electrophoresis stained by coomassie blue. Next, we bought molecules including AHL and Quinolones and utilized '''ELISA plate reader''' and '''flow cytometer''' to calibrate the '''standard diagram''' (intensity of florescent protein—time) of different biosensors added with series dilution of AHL in 96-well plate. At the third stage, the '''supernatant of bacteria''' (between species and within species) were taken into experiments. By replacement of AHL or Quinolones with the supernatant of bacteria, we depicted new curves, and compared it with each other and also standard diagram. With the efforts of the teams, we proved our idea. The responses of different strains of bacteria to our array varied greatly.<br />
<br />
To put it into practice, we aligned different Quorum sensing receptors circuits to form an array to test '''clinical samples''' like septum, blood, urine, etc. After collecting enough data of different clinical bacterial strains and build up a database, we hope to build up a new system for bacteria identification.<br />
<br />
[[File:NTU-Taida-overview-1.jpg|700px|thumb|center|Figure.3]]<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/OverviewTeam:NTU-Taida/Project/Overview2013-09-28T00:24:56Z<p>B00401107: /* Overview */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Overview}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
=Overview=<br />
Our IGEM project aims to tailor an '''instant bacteria identification array'''. We chose '''Quorum sensing molecules (QS molecules)''' instead of traditional biochemical reactions as our main targets to achieve our goals. As a cell-cell communication pathway, Quorum sensing phenomenon regulates '''virulence gene expression''' and has recently been considered as a new target for therapeutic application. We proposed a novel method to identify bacteria by '''the expression pattern''' of many QS receptors from the intensity of fluorescent signals.<br />
{|align='center'<br />
|[[File:NTU-Taida-overview-2.jpg|380px|thumb|center|LaSarre et al. Microbiol Mol Biol Rev (2013)]]<br />
|[[File:NTU-Taida-overview-3.jpg|350px|thumb|center|LaSarre et al. Microbiol Mol Biol Rev (2013)]]<br />
|}<br />
<br />
<br />
<br />
For the sakes of sensitivity and the consideration of time, we underwent process of cloning and designed both '''positive feedback''' and '''negative regulation circuits''' insides plasmids containing quorum sensing receptors (or transcriptional regulator) conjugated with florescent proteins. These plasmids were transformed into E. Coli DH5α. They would act as '''biosensors''' when meeting quorum sensing molecules.<br />
<br />
We would like to identify bacterial strains both '''between species''' and '''within species'''. For Gram negative species, AHL is a common quorum sensing molecule. Different receptors, however, target different kinds of '''AHL (Acylhomoserine Lactone)''' depending on its carbon number of the acyl group. We targeted to construct an array of QS sensors, consisting of sensor for 4-carbon, 8-carbon, 12-carbon and 14-carbon AHL. Because QS sensors are also able to sense AHL molecules with '''a closer number of carbons''', this biosensor array can detects 2~14 carbon AHLs. In addition to AHL, we also developed '''novel biosensor—PQS''' for new type of quorum sensing molecule in iGem—'''Quinolones'''.<br />
<br />
To achieve a complete array, a lot of '''measurements''' are indispensable. We manipulated simple qualitative experiments for its property and the fluorescent protein expression via polyacrylamide gel electrophoresis stained by coomassie blue. Next, we bought molecules including AHL and Quinolones and utilized '''ELISA plate reader''' and '''flow cytometer''' to calibrate the '''standard diagram''' (intensity of florescent protein—time) of different biosensors added with series dilution of AHL in 96-well plate. At the third stage, the '''supernatant of bacteria''' (between species and within species) were taken into experiments. By replacement of AHL or Quinolones with the supernatant of bacteria, we depicted new curves, and compared it with each other and also standard diagram. With the efforts of the teams, we proved our idea. The responses of different strains of bacteria to our array varied greatly.<br />
<br />
To put it into practice, we aligned different Quorum sensing receptors circuits to form an array to test '''clinical samples''' like septum, blood, urine, etc. After collecting enough data of different clinical bacterial strains and build up a database, we hope to build up a new system for bacteria identification.<br />
<br />
[[File:NTU-Taida-overview-1.jpg|700px|thumb|center|Figure.3]]<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/OverviewTeam:NTU-Taida/Project/Overview2013-09-28T00:21:41Z<p>B00401107: /* Overview */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Overview}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
=Overview=<br />
Our IGEM project aims to tailor an '''instant bacteria identification array'''. We chose '''Quorum sensing molecules (QS molecules)''' instead of traditional biochemical reactions as our main targets to achieve our goals. As a cell-cell communication pathway, Quorum sensing phenomenon regulates '''virulence gene expression''' and has recently been considered as a new target for therapeutic application. We proposed a novel method to identify bacteria by '''the expression pattern''' of many QS receptors from the intensity of fluorescent signals.<br />
{|align='center'<br />
|[[File:NTU-Taida-overview-2.jpg|380px|thumb|center|LaSarre et al. Microbiol Mol Biol Rev (2013)]]<br />
|[[File:NTU-Taida-overview-3.jpg|350px|thumb|center|LaSarre et al. Microbiol Mol Biol Rev (2013)]]<br />
|}<br />
<br />
<br />
<br />
For the sakes of sensitivity and the consideration of time, we underwent process of cloning and designed both '''positive feedback''' and '''negative regulation circuits''' insides plasmids containing quorum sensing receptors (or transcriptional regulator) conjugated with florescent proteins. These plasmids were transformed into E. Coli DH5α. They would act as '''biosensors''' when meeting quorum sensing molecules.<br />
<br />
We would like to identify bacterial strains both '''between species''' and '''within species'''. For Gram negative species, AHL is a common quorum sensing molecule. Different receptors, however, target different kinds of '''AHL (Acylhomoserine Lactone)''' depending on its carbon number of the acyl group. We targeted to construct an array of QS sensors, consisting of sensor for 4-carbon, 8-carbon, 12-carbon and 14-carbon AHL. Because QS sensors are also able to sense AHL molecules with '''a closer number of carbons''', this biosensor array can detects 2~14 carbon AHLs. In addition to AHL, we also developed '''novel biosensor—PQS''' for new type of quorum sensing molecule in iGem—'''Quinolones'''.<br />
<br />
To achieve a complete array, a lot of '''measurements''' are indispensable. We manipulated simple qualitative experiments for its property and the fluorescent protein expression via polyacrylamide gel electrophoresis stained by coomassie blue. Next, we bought molecules including AHL and Quinolones and utilized '''ELISA plate reader''' and '''flow cytometer''' to calibrate the '''standard diagram''' (intensity of florescent protein—time) of different biosensors added with series dilution of AHL in 96-well plate. At the third stage, the '''supernatant of bacteria''' (between species and within species) were taken into experiments. By replacement of AHL or Quinolones with the supernatant of bacteria, we depicted new curves, and compared it with each other and also standard diagram. With the efforts of the teams, we proved our idea. The responses of different strains of bacteria to our array varied greatly.<br />
<br />
To put it into practice, we aligned different Quorum sensing receptors circuits to form an array to test '''clinical samples''' like septum, blood, urine, etc. After collecting enough data of different clinical bacterial strains and build up a database, we hope to build up a new system for bacteria identification.<br />
<br />
[[File:NTU-Taida-overview-1.jpg|700px|thumb|center|Figure.3]]<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/File:NTU-Taida-project-background14.jpgFile:NTU-Taida-project-background14.jpg2013-09-28T00:11:17Z<p>B00401107: </p>
<hr />
<div></div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/BackgroundTeam:NTU-Taida/Project/Background2013-09-28T00:10:28Z<p>B00401107: /* PQS system in Pseudomonas aeruginosa */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Background}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Bacterial infection==<br />
<br />
Bacterial infection is the invasion of bacteria into one’s body. They reproduce and multiply themselves, causing disease by local cellular injury, secretion of toxins, or antigen-antibody reaction in the host. The spectrum of bacteria changes with time and the introduction of antibacterial agent. Nowadays, the emerging issue in this field is the appearance of '''multiple drug-resistant (MDR) bacteria''' and '''extensive drug-resistant (XDR) bacteria'''. Yet the development of resistant strains of bacteria could be limited by the judicious use of antibiotics. In order to use the appropriate drug, knowing the antibiotic pattern of the invading bacteria is of importance. The routine process to identify causative organism in hospital, culturing and sensitivity testing for a specific antibiotic, is found to be sensitive.<br />
<br />
Bacterial infection may be further classified by where the infection occurs, into '''community-acquired infection''' and '''nosocomial infection'''. The strains of bacteria, infection site, and epidemiological transmission pathway all differ between them. Nosocomial infection is of increased importance. MDR or XDR are present in hospital environments such as MRSA (Methicillin-resistant ''Staphylococcus aureus'') and ''Acinetobacter''. The Table below is the susceptibility of antibiotics of clinical separated bacteria from NTUH (National Taiwan University Hospital) at 2012. Urinary tract infections, pneumopathy, and infections of surgery site are most common because of the formation of biofilm on the surface of catheters, endo-tubes, etc. What’s worse, because of the drug-resistance, diagnosis and treatment of bacterial nosocomial infection become a serious problem. The identification of bacteria and new drugs is required.<br />
<br />
==Quorum Sensing System in Gram Positive Bacteria==<br />
<br />
Gram-positive bacteria, characterized with a relatively thick layer of peptidylglycan, generally use peptides as quorum sensing molecules. These peptides are called '''autoinducing peptides (AIPs)'''; when produced by specialized AI synthase, they can be either transported from(outside?) the cells through a specific membrane-bound transporter, or processed and secreted directly from the membrane. A high concentration of extracellular AIPs indicates high cell density. By binding to its cognate membrane-bound sensor kinase or intracellular receptor, the quorum sensing signal is transmitted back and spread to other bacterial cells, creating an '''inter-cellular communication network'''. The cytoplasmic response regulator, which controls the downstream virulence factors and AI(AIP?) synthase, is phosphorylated by the histidine kinase receptor upon extracellular binding of AIPs, or is activated by the intracellular receptor-AIP complex itself (Figure 1).<br />
<br />
<br />
Together from a module-based point of view, the whole process of quorum sensing includes production, detection and response. Collectively these modules are termed a two-component system.<br />
<br />
<br />
Clinically important Gram-positive bacteria include ''Staphylococcus aureus'' and ''Streptococcus pneumoniae'', responsible for skin and respiratory infections respectively. ''S. aureus'' uses the agr as its quorum sensing system.<br />
<br />
[[File:NTU-Taida-background-5.jpg|700px|thumb|center|Figure.1]]<br />
<br />
==Routine Identification==<br />
Laboratory medicine (see also Visit[https://2013.igem.org/Team:NTU-Taida/Human_practice/Visit]) plays a crucial role in hospital and the identification of infecting bacteria are big part of it. According to the visit to professor Po-Ren Hsueh, a visiting staff in the department of laboratory medicine in NTU hospital, the routine identification of bacteria and sensitivity tests are mainly through the incubation in the plate. The method through mass spectrometry, having substantial advancement nowadays, can quickly excite proteins in bacteria, match in database and identify bacteria in 5 min, while methods via bio-chemical reactions require machines and chips (see figure below) including types for Gram positive, Gram negative, anaerobic bacteria, etc, and identify bacteria. However, these two methods detect mainly in protein levels, require expensive machines and cannot provide the antibiotic-sensitivity information making us back to the process of incubation.<br />
{|align='center'<br />
|[[File:NTU-Taida-project-background11.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background12.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background13.jpg|250px|center|thumb]]<br />
|}<br />
<br />
==Quorum Sensing System in Gram negative Bacteria==<br />
<br />
The cell wall of Gram-negative bacteria is composed of a relatively thin layer of peptidoglycan and an outer membrane which contains lipopolysaccharide (LPS). Due to its structure, quorum sensing molecules '''diffuse''' through the cell membrane and bind with '''intracellular receptors'''. <br />
[[File:NTU-Taida-background-3.jpg|||center|Figure.2]]<br />
<br />
Generally speaking, quorum sensing system in gram negative bacteria functions as follows (Take LasI/LasR system for example):<br />
<br />
The LasI gene encodes an '''autoinducer synthase(LasI)''', and this autoinducer synthase produces quorum sensing molecules(autoinducers) called '''acyl-homoserine lactone(AHLs)'''. Another gene LasR encodes for the '''response regulator of the autoinducers'''. Regulators bind with autoinducers and form complexes. They bind on target promoters, and then either activate or inhibit relevant down-stream genes.<br />
[[File:NTU-Taida-background-4.jpg|700px||center|Figure.3]]<br />
<br />
<br />
Under low bacterial concentration, target genes are under minimum expression (Figure a above), but as bacterial concentration elevates, AHL molecules begin to bind with the intracellular response regulators and promote the expression of target genes, many of them related to '''bacterial virulence''' or biofilm formation. Therefore, there is a close relationship between bacterial resistance and quorum sensing. Besides having species-specific quorum sensing system, many species of gram-negative bacteria share a type of quorum sensing molecule, the AI-2(autoinducer-2) molecule.<br />
<br />
==PQS system in ''Pseudomonas aeruginosa''==<br />
<br />
To date, it has been found that ''Pseudomonas aeruginosa'' has at least four quorum sensing systems: '''Las system''' (Las from e”las”tase), '''Rhl system''' (Rhl from “rh”amno”l”ipids), '''Qsc system''' (Qsc from “Q”uorum “s”ensing “c”ontroller ), and '''PQS system''' (PQS from “P”seudomonas “q”uinolone “s”ignal). In general, Las system is responsible for toxin expression; Rhl system is responsible for secretion system; Qsc system is as a negative regulator of Las system and Rhl system; PQS system is responsible for the virulence. The four systems also have interactions with each other.<br />
<br />
Among these four systems, Las, Rhl and Qsc system all contain an AHL (acyl -homoserine lactone) activated receptor. Las system and Qsc system use 12-C AHL as QS (Quorum Sensing) molecules; on the other hand, Rhl system prefers to use 4-C AHL as QS molecules.<br />
<br />
However, interestingly, PQS system is not activated through AHL, but a '''quinoline derivative''': 2-heptyl-3,4-dihydroxyquinoline (also called “PQS”). Once PQS binds to pqsR, pqsR ─ as a transcriptional factor ─ can further activates two operons: pqsABCDE and phnAB (phn from "ph"e"n"azine). These two operons encode the enzymes that can synthesize PQS, and pqsE can catalyze PQS to become phenazine. Importantly, these phenazine products have been demonstrated to be involved in '''virulence of the organisms'''. For example, the phenazine pyocyanin production can enhance the ability of Pseudomonas aeruginosa to colonize the lungs of cystic fibrosis patients.<br />
[[File:NTU-Taida-project-background14.jpg|200px|center|thumb|quinolone]]<br />
<br />
==Reference==<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Arul Jayaraman and Thomas K.Wood|Essay=Bacterial Quorum Sensing:Signals, Circuits, and Implications for Biofilms and Disease|Journal=Annu. Rev. Biomed. Eng. 2008. 10:145–67}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Rutherford,''et al''|Essay=Bacterial quorum sensing: its role in virulence and possibilities for its control|Journal=Cold Spring Harb Perspect Med. 2012 Nov 1;2(11)}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Antunes LCM, ''et al''|Essay=Quorum sensing in bacterial virulence|Journal=Microbiology(2010), 156, 2271–2282}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Lo´ pez D, ''et al''|Essay=Biofilms|Journal=Cold Spring Harb Perspect Biol 2010 ; 2:a000398}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jimenez PN, ''et al''|Essay=The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa|Journal=Microbiol. Mol. Biol. Rev. 2012, 76(1):46}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Kendra P. Rumbaugh|Essay=Quorum Sensing: Methods and Protocols|Journal=Methods in Molecular Biology, vol. 692}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jitesh A Soares and Brian MM Ahmer|Essay=Detection of acyl-homoserine lactones by Escherichia and Salmonella|Journal=Microbiology 2011, 14:188–193}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Hsueh PR, ''et al''|Essay=Consensus review of the epidemiology and appropriate antimicrobial therapy of complicated urinary tract infections in Asia-Pacific region|Journal=The British Infection Association 2011}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Vanessa Sperandio|Essay=SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen|Journal=Gut Microbes 1:6, 432-435; November/December 2010}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Dubern, ''et al''|Essay=Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species|Journal=Mol Biosyst (2008) vol. 4 (9) pp. 882}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Diggle, ''et al''|Essay=4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives|Journal=Int J Med Microbiol (2006) vol. 296 (2-3) pp. 83-91}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Steindler, ''et al''|Essay=Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors|Journal=FEMS Microbiol Lett (2007) vol. 266 (1) pp. 1-9}}<br />
<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/File:NTU-Taida-project-background13.jpgFile:NTU-Taida-project-background13.jpg2013-09-28T00:02:36Z<p>B00401107: </p>
<hr />
<div></div>B00401107http://2013.igem.org/File:NTU-Taida-project-background12.jpgFile:NTU-Taida-project-background12.jpg2013-09-27T23:58:01Z<p>B00401107: </p>
<hr />
<div></div>B00401107http://2013.igem.org/File:NTU-Taida-project-background11.jpgFile:NTU-Taida-project-background11.jpg2013-09-27T23:56:30Z<p>B00401107: </p>
<hr />
<div></div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/BackgroundTeam:NTU-Taida/Project/Background2013-09-27T23:55:26Z<p>B00401107: /* Routine Identification */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Background}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Bacterial infection==<br />
<br />
Bacterial infection is the invasion of bacteria into one’s body. They reproduce and multiply themselves, causing disease by local cellular injury, secretion of toxins, or antigen-antibody reaction in the host. The spectrum of bacteria changes with time and the introduction of antibacterial agent. Nowadays, the emerging issue in this field is the appearance of '''multiple drug-resistant (MDR) bacteria''' and '''extensive drug-resistant (XDR) bacteria'''. Yet the development of resistant strains of bacteria could be limited by the judicious use of antibiotics. In order to use the appropriate drug, knowing the antibiotic pattern of the invading bacteria is of importance. The routine process to identify causative organism in hospital, culturing and sensitivity testing for a specific antibiotic, is found to be sensitive.<br />
<br />
Bacterial infection may be further classified by where the infection occurs, into '''community-acquired infection''' and '''nosocomial infection'''. The strains of bacteria, infection site, and epidemiological transmission pathway all differ between them. Nosocomial infection is of increased importance. MDR or XDR are present in hospital environments such as MRSA (Methicillin-resistant ''Staphylococcus aureus'') and ''Acinetobacter''. The Table below is the susceptibility of antibiotics of clinical separated bacteria from NTUH (National Taiwan University Hospital) at 2012. Urinary tract infections, pneumopathy, and infections of surgery site are most common because of the formation of biofilm on the surface of catheters, endo-tubes, etc. What’s worse, because of the drug-resistance, diagnosis and treatment of bacterial nosocomial infection become a serious problem. The identification of bacteria and new drugs is required.<br />
<br />
==Quorum Sensing System in Gram Positive Bacteria==<br />
<br />
Gram-positive bacteria, characterized with a relatively thick layer of peptidylglycan, generally use peptides as quorum sensing molecules. These peptides are called '''autoinducing peptides (AIPs)'''; when produced by specialized AI synthase, they can be either transported from(outside?) the cells through a specific membrane-bound transporter, or processed and secreted directly from the membrane. A high concentration of extracellular AIPs indicates high cell density. By binding to its cognate membrane-bound sensor kinase or intracellular receptor, the quorum sensing signal is transmitted back and spread to other bacterial cells, creating an '''inter-cellular communication network'''. The cytoplasmic response regulator, which controls the downstream virulence factors and AI(AIP?) synthase, is phosphorylated by the histidine kinase receptor upon extracellular binding of AIPs, or is activated by the intracellular receptor-AIP complex itself (Figure 1).<br />
<br />
<br />
Together from a module-based point of view, the whole process of quorum sensing includes production, detection and response. Collectively these modules are termed a two-component system.<br />
<br />
<br />
Clinically important Gram-positive bacteria include ''Staphylococcus aureus'' and ''Streptococcus pneumoniae'', responsible for skin and respiratory infections respectively. ''S. aureus'' uses the agr as its quorum sensing system.<br />
<br />
[[File:NTU-Taida-background-5.jpg|700px|thumb|center|Figure.1]]<br />
<br />
==Routine Identification==<br />
Laboratory medicine (see also Visit[https://2013.igem.org/Team:NTU-Taida/Human_practice/Visit]) plays a crucial role in hospital and the identification of infecting bacteria are big part of it. According to the visit to professor Po-Ren Hsueh, a visiting staff in the department of laboratory medicine in NTU hospital, the routine identification of bacteria and sensitivity tests are mainly through the incubation in the plate. The method through mass spectrometry, having substantial advancement nowadays, can quickly excite proteins in bacteria, match in database and identify bacteria in 5 min, while methods via bio-chemical reactions require machines and chips (see figure below) including types for Gram positive, Gram negative, anaerobic bacteria, etc, and identify bacteria. However, these two methods detect mainly in protein levels, require expensive machines and cannot provide the antibiotic-sensitivity information making us back to the process of incubation.<br />
{|align='center'<br />
|[[File:NTU-Taida-project-background11.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background12.jpg|250px|center|thumb]]<br />
|[[File:NTU-Taida-project-background13.jpg|250px|center|thumb]]<br />
|}<br />
<br />
==Quorum Sensing System in Gram negative Bacteria==<br />
<br />
The cell wall of Gram-negative bacteria is composed of a relatively thin layer of peptidoglycan and an outer membrane which contains lipopolysaccharide (LPS). Due to its structure, quorum sensing molecules '''diffuse''' through the cell membrane and bind with '''intracellular receptors'''. <br />
[[File:NTU-Taida-background-3.jpg|||center|Figure.2]]<br />
<br />
Generally speaking, quorum sensing system in gram negative bacteria functions as follows (Take LasI/LasR system for example):<br />
<br />
The LasI gene encodes an '''autoinducer synthase(LasI)''', and this autoinducer synthase produces quorum sensing molecules(autoinducers) called '''acyl-homoserine lactone(AHLs)'''. Another gene LasR encodes for the '''response regulator of the autoinducers'''. Regulators bind with autoinducers and form complexes. They bind on target promoters, and then either activate or inhibit relevant down-stream genes.<br />
[[File:NTU-Taida-background-4.jpg|700px||center|Figure.3]]<br />
<br />
<br />
Under low bacterial concentration, target genes are under minimum expression (Figure a above), but as bacterial concentration elevates, AHL molecules begin to bind with the intracellular response regulators and promote the expression of target genes, many of them related to '''bacterial virulence''' or biofilm formation. Therefore, there is a close relationship between bacterial resistance and quorum sensing. Besides having species-specific quorum sensing system, many species of gram-negative bacteria share a type of quorum sensing molecule, the AI-2(autoinducer-2) molecule.<br />
<br />
==PQS system in ''Pseudomonas aeruginosa''==<br />
<br />
To date, it has been found that ''Pseudomonas aeruginosa'' has at least four quorum sensing systems: '''Las system''' (Las from e”las”tase), '''Rhl system''' (Rhl from “rh”amno”l”ipids), '''Qsc system''' (Qsc from “Q”uorum “s”ensing “c”ontroller ), and '''PQS system''' (PQS from “P”seudomonas “q”uinolone “s”ignal). In general, Las system is responsible for toxin expression; Rhl system is responsible for secretion system; Qsc system is as a negative regulator of Las system and Rhl system; PQS system is responsible for the virulence. The four systems also have interactions with each other.<br />
<br />
Among these four systems, Las, Rhl and Qsc system all contain an AHL (acyl -homoserine lactone) activated receptor. Las system and Qsc system use 12-C AHL as QS (Quorum Sensing) molecules; on the other hand, Rhl system prefers to use 4-C AHL as QS molecules.<br />
<br />
However, interestingly, PQS system is not activated through AHL, but a '''quinoline derivative''': 2-heptyl-3,4-dihydroxyquinoline (also called “PQS”). Once PQS binds to pqsR, pqsR ─ as a transcriptional factor ─ can further activates two operons: pqsABCDE and phnAB (phn from "ph"e"n"azine). These two operons encode the enzymes that can synthesize PQS, and pqsE can catalyze PQS to become phenazine. Importantly, these phenazine products have been demonstrated to be involved in '''virulence of the organisms'''. For example, the phenazine pyocyanin production can enhance the ability of Pseudomonas aeruginosa to colonize the lungs of cystic fibrosis patients.<br />
<br />
==Reference==<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Arul Jayaraman and Thomas K.Wood|Essay=Bacterial Quorum Sensing:Signals, Circuits, and Implications for Biofilms and Disease|Journal=Annu. Rev. Biomed. Eng. 2008. 10:145–67}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Rutherford,''et al''|Essay=Bacterial quorum sensing: its role in virulence and possibilities for its control|Journal=Cold Spring Harb Perspect Med. 2012 Nov 1;2(11)}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Antunes LCM, ''et al''|Essay=Quorum sensing in bacterial virulence|Journal=Microbiology(2010), 156, 2271–2282}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Lo´ pez D, ''et al''|Essay=Biofilms|Journal=Cold Spring Harb Perspect Biol 2010 ; 2:a000398}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jimenez PN, ''et al''|Essay=The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa|Journal=Microbiol. Mol. Biol. Rev. 2012, 76(1):46}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Kendra P. Rumbaugh|Essay=Quorum Sensing: Methods and Protocols|Journal=Methods in Molecular Biology, vol. 692}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jitesh A Soares and Brian MM Ahmer|Essay=Detection of acyl-homoserine lactones by Escherichia and Salmonella|Journal=Microbiology 2011, 14:188–193}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Hsueh PR, ''et al''|Essay=Consensus review of the epidemiology and appropriate antimicrobial therapy of complicated urinary tract infections in Asia-Pacific region|Journal=The British Infection Association 2011}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Vanessa Sperandio|Essay=SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen|Journal=Gut Microbes 1:6, 432-435; November/December 2010}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Dubern, ''et al''|Essay=Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species|Journal=Mol Biosyst (2008) vol. 4 (9) pp. 882}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Diggle, ''et al''|Essay=4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives|Journal=Int J Med Microbiol (2006) vol. 296 (2-3) pp. 83-91}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Steindler, ''et al''|Essay=Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors|Journal=FEMS Microbiol Lett (2007) vol. 266 (1) pp. 1-9}}<br />
<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/File:NTU-Taida-Human_practice-visit2.jpgFile:NTU-Taida-Human practice-visit2.jpg2013-09-27T23:50:45Z<p>B00401107: uploaded a new version of &quot;File:NTU-Taida-Human practice-visit2.jpg&quot;</p>
<hr />
<div></div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:46:34Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
{|align='center'<br />
|[[File:NTU-Taida-Human practice-visit1.jpg|400px|center|thumb]]<br />
|[[File:NTU-Taida-Human practice-visit2.jpg|400px|center|thumb]]<br />
|}<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:43:41Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
{|align='center'<br />
[[File:NTU-Taida-Human practice-visit1.jpg|400px|center|thumb]]<br />
[[File:NTU-Taida-Human practice-visit2.jpg|400px|center|thumb]]<br />
|}<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:40:03Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
[[File:NTU-Taida-Human practice-visit1.jpg|400px|center|thumb]]<br />
[[File:NTU-Taida-Human practice-visit2.jpg|400px|center|thumb]]<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:39:39Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
[[File:NTU-Taida-Human practice-visit1.jpg|400px|thumb]]<br />
[[File:NTU-Taida-Human practice-visit2.jpg|400px|thumb]]<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:39:01Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
[[File:NTU-Taida-Human practice-visit1.jpg|500px|thumb]]<br />
[[File:NTU-Taida-Human practice-visit2.jpg|400px|thumb]]<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:38:22Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
[[File:NTU-Taida-Human practice-visit1.jpg|500px|left|thumb]]<br />
[[File:NTU-Taida-Human practice-visit2.jpg|400px|right|thumb]]<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/File:NTU-Taida-Human_practice-visit2.jpgFile:NTU-Taida-Human practice-visit2.jpg2013-09-27T23:37:08Z<p>B00401107: uploaded a new version of &quot;File:NTU-Taida-Human practice-visit2.jpg&quot;</p>
<hr />
<div></div>B00401107http://2013.igem.org/File:NTU-Taida-Human_practice-visit2.jpgFile:NTU-Taida-Human practice-visit2.jpg2013-09-27T23:35:59Z<p>B00401107: </p>
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<div></div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:34:36Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
[[File:NTU-Taida-Human practice-visit1.jpg|500px|left|thumb]]<br />
[[File:NTU-Taida-Human practice-visit2.jpg|500px|right|thumb]]<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/File:NTU-Taida-Human_practice-visit1.jpgFile:NTU-Taida-Human practice-visit1.jpg2013-09-27T23:32:59Z<p>B00401107: </p>
<hr />
<div></div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:32:35Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
[[File:NTU-Taida-Human practice-visit1.jpg|500px|center|thumb]]<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Human_practice/VisitTeam:NTU-Taida/Human practice/Visit2013-09-27T23:31:46Z<p>B00401107: /* Introduction */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Department of Laboratory Medicine}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Introduction==<br />
<br />
Laboratory medicine is indispensable in modern medical science. Laboratory medicine can present scientific data to verify or rule out a certain diagnosis, guide and monitor treatment, and evaluate the severity and prognosis of a disease. It is also valuable in mass screening and can discover subjects with risk factors for early detection of diseases and treatment. The Department of Laboratory Medicine did not exist before World War II. At that time laboratory tests were performed not in a central lab, but in various small laboratories in clinical departments, by junior clinical doctors. The Department of Laboratory Diagnosis and the Department of Medical Technology of Medical College, National Taiwan University, were first established in August 1956, to provide laboratory tests for patients and education for students of medical college.<br />
<br />
The Department of Laboratory Medicine consists of the following divisions:<br />
#Stat laboratory<br />
#Biochemistry<br />
#Hematology<br />
#Virology<br />
#Microbiology<br />
#Transfusion & transplantation medicine<br />
#Phlebotomy & EKG<br />
#Clinical microscopy & cytology<br />
#Molecular diagnosis, immunology & quality control<br />
[[File:NTU-Taida-Human practice-visit1-jpg|500px|center|thumb]]<br />
<br />
==Organization==<br />
The Department of Laboratory Medicine consists of division of stat lab, biochemistry, hematology, virology, microbiology, transfusion & transplantation medicine, phlebotomy & electrocardiography (EKG), clinical microscopy & cytology, and molecular diagnosis, immunology & quality control.<br />
<br />
==Mission==<br />
Our department has highly qualified faculty and equipments, and is dedicated to providing high-quality laboratory tests to patients, professional consultations to clinicians, high-standard education to students, and cutting edge scientific research.<br />
<br />
==Goal==<br />
We are currently reforming the blood and specimen collection system of our hospital. We have introduced complete bedside bar code ID system in some of the wards and part of the outpatient phlebotomy stations, in order to decrease the risk of manual processes that may cause patient ID errors. In our laboratory we have also used new bar code registration and automatic transportation system to improve efficiency since March 2012. We are still working at improving the soft- and hard-ware of this new system, and expect that all the wards and outpatient units of our hospital would be equipped with this system in the near future.<br />
<br />
We are expanding the service items of our molecular diagnosis, hematology, virology, microbiology and biochemistry lab to meet the ever expanding need of clinical medicine and scientific research. We are executing quality-control programs to maintain a high- and constant-quality performance. We plan to seek lab accreditation from international accreditation association in the near future.<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/BackgroundTeam:NTU-Taida/Project/Background2013-09-27T23:28:04Z<p>B00401107: /* Bacterial infection */</p>
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<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Background}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
<br />
==Bacterial infection==<br />
<br />
Bacterial infection is the invasion of bacteria into one’s body. They reproduce and multiply themselves, causing disease by local cellular injury, secretion of toxins, or antigen-antibody reaction in the host. The spectrum of bacteria changes with time and the introduction of antibacterial agent. Nowadays, the emerging issue in this field is the appearance of '''multiple drug-resistant (MDR) bacteria''' and '''extensive drug-resistant (XDR) bacteria'''. Yet the development of resistant strains of bacteria could be limited by the judicious use of antibiotics. In order to use the appropriate drug, knowing the antibiotic pattern of the invading bacteria is of importance. The routine process to identify causative organism in hospital, culturing and sensitivity testing for a specific antibiotic, is found to be sensitive.<br />
<br />
Bacterial infection may be further classified by where the infection occurs, into '''community-acquired infection''' and '''nosocomial infection'''. The strains of bacteria, infection site, and epidemiological transmission pathway all differ between them. Nosocomial infection is of increased importance. MDR or XDR are present in hospital environments such as MRSA (Methicillin-resistant ''Staphylococcus aureus'') and ''Acinetobacter''. The Table below is the susceptibility of antibiotics of clinical separated bacteria from NTUH (National Taiwan University Hospital) at 2012. Urinary tract infections, pneumopathy, and infections of surgery site are most common because of the formation of biofilm on the surface of catheters, endo-tubes, etc. What’s worse, because of the drug-resistance, diagnosis and treatment of bacterial nosocomial infection become a serious problem. The identification of bacteria and new drugs is required.<br />
<br />
==Quorum Sensing System in Gram Positive Bacteria==<br />
<br />
Gram-positive bacteria, characterized with a relatively thick layer of peptidylglycan, generally use peptides as quorum sensing molecules. These peptides are called '''autoinducing peptides (AIPs)'''; when produced by specialized AI synthase, they can be either transported from(outside?) the cells through a specific membrane-bound transporter, or processed and secreted directly from the membrane. A high concentration of extracellular AIPs indicates high cell density. By binding to its cognate membrane-bound sensor kinase or intracellular receptor, the quorum sensing signal is transmitted back and spread to other bacterial cells, creating an '''inter-cellular communication network'''. The cytoplasmic response regulator, which controls the downstream virulence factors and AI(AIP?) synthase, is phosphorylated by the histidine kinase receptor upon extracellular binding of AIPs, or is activated by the intracellular receptor-AIP complex itself (Figure 1).<br />
<br />
<br />
Together from a module-based point of view, the whole process of quorum sensing includes production, detection and response. Collectively these modules are termed a two-component system.<br />
<br />
<br />
Clinically important Gram-positive bacteria include ''Staphylococcus aureus'' and ''Streptococcus pneumoniae'', responsible for skin and respiratory infections respectively. ''S. aureus'' uses the agr as its quorum sensing system.<br />
<br />
[[File:NTU-Taida-background-5.jpg|700px|thumb|center|Figure.1]]<br />
<br />
==Routine Identification==<br />
Laboratory medicine (see also Visit[https://2013.igem.org/Team:NTU-Taida/Human_practice/Visit]) plays a crucial role in hospital and the identification of infecting bacteria are big part of it. According to the visit to professor Po-Ren Hsueh, a visiting staff in the department of laboratory medicine in NTU hospital, the routine identification of bacteria and sensitivity tests are mainly through the incubation in the plate. The method through mass spectrometry, having substantial advancement nowadays, can quickly excite proteins in bacteria, match in database and identify bacteria in 5 min, while methods via bio-chemical reactions require machines and chips (see figure below) including types for Gram positive, Gram negative, anaerobic bacteria, etc, and identify bacteria. However, these two methods detect mainly in protein levels, require expensive machines and cannot provide the antibiotic-sensitivity information making us back to the process of incubation.<br />
<br />
==Quorum Sensing System in Gram negative Bacteria==<br />
<br />
The cell wall of Gram-negative bacteria is composed of a relatively thin layer of peptidoglycan and an outer membrane which contains lipopolysaccharide (LPS). Due to its structure, quorum sensing molecules '''diffuse''' through the cell membrane and bind with '''intracellular receptors'''. <br />
[[File:NTU-Taida-background-3.jpg|||center|Figure.2]]<br />
<br />
Generally speaking, quorum sensing system in gram negative bacteria functions as follows (Take LasI/LasR system for example):<br />
<br />
The LasI gene encodes an '''autoinducer synthase(LasI)''', and this autoinducer synthase produces quorum sensing molecules(autoinducers) called '''acyl-homoserine lactone(AHLs)'''. Another gene LasR encodes for the '''response regulator of the autoinducers'''. Regulators bind with autoinducers and form complexes. They bind on target promoters, and then either activate or inhibit relevant down-stream genes.<br />
[[File:NTU-Taida-background-4.jpg|700px||center|Figure.3]]<br />
<br />
<br />
Under low bacterial concentration, target genes are under minimum expression (Figure a above), but as bacterial concentration elevates, AHL molecules begin to bind with the intracellular response regulators and promote the expression of target genes, many of them related to '''bacterial virulence''' or biofilm formation. Therefore, there is a close relationship between bacterial resistance and quorum sensing. Besides having species-specific quorum sensing system, many species of gram-negative bacteria share a type of quorum sensing molecule, the AI-2(autoinducer-2) molecule.<br />
<br />
==PQS system in ''Pseudomonas aeruginosa''==<br />
<br />
To date, it has been found that ''Pseudomonas aeruginosa'' has at least four quorum sensing systems: '''Las system''' (Las from e”las”tase), '''Rhl system''' (Rhl from “rh”amno”l”ipids), '''Qsc system''' (Qsc from “Q”uorum “s”ensing “c”ontroller ), and '''PQS system''' (PQS from “P”seudomonas “q”uinolone “s”ignal). In general, Las system is responsible for toxin expression; Rhl system is responsible for secretion system; Qsc system is as a negative regulator of Las system and Rhl system; PQS system is responsible for the virulence. The four systems also have interactions with each other.<br />
<br />
Among these four systems, Las, Rhl and Qsc system all contain an AHL (acyl -homoserine lactone) activated receptor. Las system and Qsc system use 12-C AHL as QS (Quorum Sensing) molecules; on the other hand, Rhl system prefers to use 4-C AHL as QS molecules.<br />
<br />
However, interestingly, PQS system is not activated through AHL, but a '''quinoline derivative''': 2-heptyl-3,4-dihydroxyquinoline (also called “PQS”). Once PQS binds to pqsR, pqsR ─ as a transcriptional factor ─ can further activates two operons: pqsABCDE and phnAB (phn from "ph"e"n"azine). These two operons encode the enzymes that can synthesize PQS, and pqsE can catalyze PQS to become phenazine. Importantly, these phenazine products have been demonstrated to be involved in '''virulence of the organisms'''. For example, the phenazine pyocyanin production can enhance the ability of Pseudomonas aeruginosa to colonize the lungs of cystic fibrosis patients.<br />
<br />
==Reference==<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Arul Jayaraman and Thomas K.Wood|Essay=Bacterial Quorum Sensing:Signals, Circuits, and Implications for Biofilms and Disease|Journal=Annu. Rev. Biomed. Eng. 2008. 10:145–67}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Rutherford,''et al''|Essay=Bacterial quorum sensing: its role in virulence and possibilities for its control|Journal=Cold Spring Harb Perspect Med. 2012 Nov 1;2(11)}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Antunes LCM, ''et al''|Essay=Quorum sensing in bacterial virulence|Journal=Microbiology(2010), 156, 2271–2282}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Lo´ pez D, ''et al''|Essay=Biofilms|Journal=Cold Spring Harb Perspect Biol 2010 ; 2:a000398}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jimenez PN, ''et al''|Essay=The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa|Journal=Microbiol. Mol. Biol. Rev. 2012, 76(1):46}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Kendra P. Rumbaugh|Essay=Quorum Sensing: Methods and Protocols|Journal=Methods in Molecular Biology, vol. 692}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Jitesh A Soares and Brian MM Ahmer|Essay=Detection of acyl-homoserine lactones by Escherichia and Salmonella|Journal=Microbiology 2011, 14:188–193}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Hsueh PR, ''et al''|Essay=Consensus review of the epidemiology and appropriate antimicrobial therapy of complicated urinary tract infections in Asia-Pacific region|Journal=The British Infection Association 2011}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Vanessa Sperandio|Essay=SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen|Journal=Gut Microbes 1:6, 432-435; November/December 2010}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Dubern, ''et al''|Essay=Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species|Journal=Mol Biosyst (2008) vol. 4 (9) pp. 882}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Diggle, ''et al''|Essay=4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives|Journal=Int J Med Microbiol (2006) vol. 296 (2-3) pp. 83-91}}<br />
#{{:Team:NTU-Taida/Templates/Reference|Author=Steindler, ''et al''|Essay=Detection of quorum-sensing N-acyl homoserine lactone signal molecules by bacterial biosensors|Journal=FEMS Microbiol Lett (2007) vol. 266 (1) pp. 1-9}}<br />
<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/IntroductionTeam:NTU-Taida/Project/Introduction2013-09-27T23:25:59Z<p>B00401107: /* Introduction of Our Project */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Introduction}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
==Introduction of Our Project==<br />
The final goal of our project is to '''real-time detect''' and '''identify drug-resistance bacterial strains''', which cause nosocomial infection from the hospital specimens.<br />
<br />
Nosocomial infections are those infections occur in hospitals. Comparing to communities, resistant strains are more often found in hospitals. Moreover, nosocomial infection is easier to take place in the intensive care units than common wards. These two characteristics explain why nosocomial infections are usually fatal to those who are immune-compromised and hospitalized, if not treated in-time. However, it usually takes a long time from culturing to identifying bacteria strains, and we may lose the golden time to cure the patient. This is the problem we’re trying to solve, through the construction of an instant bacteria-resistance identification system.<br />
<br />
We choose quorum sensing molecules as our target. Quorum sensing (QS) is a density-associated communication method for bacteria. It is usually species-specific, like dialects among people. After surveying many related researches, '''we reasonably assume that among the same bacterial species, those with resistant strains and without resistant strains, as well as those with different types of resistance, their patterns of releasing QS molecules have quantitative difference'''. We plan to use our QS array - genetically modified E. coli, to detect those differences in each QS molecule activation level, hoping to establish a profile ─ “antibiotic resistance” towards “pattern of quorum sensing molecule activation levels” ─ in order to instantaneously recognize resistant strains. We would use a common opportunistic pathogen, ''Pseudomonas aeruginosa'' as a primary detection target. Tests will then expand to other bacterial species. Finally, by using these data, we might create a fast-and-safe array on a tiny chip, making nosocomial infection no more a nightmare.<br />
<br />
[[File:NTU-Taida-project-introduction-1.jpg|center|700px|thumb|Prototype of our array]]<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/File:NTU-Taida-project-introduction-1.jpgFile:NTU-Taida-project-introduction-1.jpg2013-09-27T23:24:29Z<p>B00401107: uploaded a new version of &quot;File:NTU-Taida-project-introduction-1.jpg&quot;</p>
<hr />
<div></div>B00401107http://2013.igem.org/File:NTU-Taida-project-introduction-1.jpgFile:NTU-Taida-project-introduction-1.jpg2013-09-27T23:22:15Z<p>B00401107: uploaded a new version of &quot;File:NTU-Taida-project-introduction-1.jpg&quot;</p>
<hr />
<div></div>B00401107http://2013.igem.org/File:NTU-Taida-project-introduction-1.jpgFile:NTU-Taida-project-introduction-1.jpg2013-09-27T23:21:26Z<p>B00401107: </p>
<hr />
<div></div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/IntroductionTeam:NTU-Taida/Project/Introduction2013-09-27T23:21:10Z<p>B00401107: /* Introduction of Our Project */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Introduction}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
==Introduction of Our Project==<br />
The final goal of our project is to '''real-time detect''' and '''identify drug-resistance bacterial strains''', which cause nosocomial infection from the hospital specimens.<br />
<br />
Nosocomial infections are those infections occur in hospitals. Comparing to communities, resistant strains are more often found in hospitals. Moreover, nosocomial infection is easier to take place in the intensive care units than common wards. These two characteristics explain why nosocomial infections are usually fatal to those who are immune-compromised and hospitalized, if not treated in-time. However, it usually takes a long time from culturing to identifying bacteria strains, and we may lose the golden time to cure the patient. This is the problem we’re trying to solve, through the construction of an instant bacteria-resistance identification system.<br />
<br />
We choose quorum sensing molecules as our target. Quorum sensing (QS) is a density-associated communication method for bacteria. It is usually species-specific, like dialects among people. After surveying many related researches, '''we reasonably assume that among the same bacterial species, those with resistant strains and without resistant strains, as well as those with different types of resistance, their patterns of releasing QS molecules have quantitative difference'''. We plan to use our QS array - genetically modified E. coli, to detect those differences in each QS molecule activation level, hoping to establish a profile ─ “antibiotic resistance” towards “pattern of quorum sensing molecule activation levels” ─ in order to instantaneously recognize resistant strains. We would use a common opportunistic pathogen, ''Pseudomonas aeruginosa'' as a primary detection target. Tests will then expand to other bacterial species. Finally, by using these data, we might create a fast-and-safe array on a tiny chip, making nosocomial infection no more a nightmare.<br />
<br />
[[File:NTU-Taida-project-introduction-1.jpg|center|700px|thumb]]<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/Team:NTU-Taida/Project/IntroductionTeam:NTU-Taida/Project/Introduction2013-09-27T23:19:22Z<p>B00401107: /* Introduction of Our Project */</p>
<hr />
<div>{{:Team:NTU-Taida/Templates/Header}}{{:Team:NTU-Taida/Templates/Navbar}}{{:Team:NTU-Taida/Templates/Sidebar|Title=Introduction}}{{:Team:NTU-Taida/Templates/ContentStart}}<br />
==Introduction of Our Project==<br />
The final goal of our project is to '''real-time detect''' and '''identify drug-resistance bacterial strains''', which cause nosocomial infection from the hospital specimens.<br />
<br />
Nosocomial infections are those infections occur in hospitals. Comparing to communities, resistant strains are more often found in hospitals. Moreover, nosocomial infection is easier to take place in the intensive care units than common wards. These two characteristics explain why nosocomial infections are usually fatal to those who are immune-compromised and hospitalized, if not treated in-time. However, it usually takes a long time from culturing to identifying bacteria strains, and we may lose the golden time to cure the patient. This is the problem we’re trying to solve, through the construction of an instant bacteria-resistance identification system.<br />
<br />
We choose quorum sensing molecules as our target. Quorum sensing (QS) is a density-associated communication method for bacteria. It is usually species-specific, like dialects among people. After surveying many related researches, '''we reasonably assume that among the same bacterial species, those with resistant strains and without resistant strains, as well as those with different types of resistance, their patterns of releasing QS molecules have quantitative difference'''. We plan to use our QS array - genetically modified E. coli, to detect those differences in each QS molecule activation level, hoping to establish a profile ─ “antibiotic resistance” towards “pattern of quorum sensing molecule activation levels” ─ in order to instantaneously recognize resistant strains. We would use a common opportunistic pathogen, ''Pseudomonas aeruginosa'' as a primary detection target. Tests will then expand to other bacterial species. Finally, by using these data, we might create a fast-and-safe array on a tiny chip, making nosocomial infection no more a nightmare.<br />
<br />
[[File:NTU-Taida-project-introduction-1|center|700px|thumb]]<br />
<br />
{{:Team:NTU-Taida/Templates/ContentEnd}}{{:Team:NTU-Taida/Templates/Footer|ActiveNavbar=Project, #nav-Modeling-Overview}}</div>B00401107http://2013.igem.org/Team:NTU-TaidaTeam:NTU-Taida2013-09-27T22:37:42Z<p>B00401107: </p>
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<h2>NTU-Taida</h2><br />
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<h2><a href="/Team:NTU-Taida/Project/Background">Enter</a></h2><br />
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