Difference between revisions of "Team:USTC"

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                     <a href="#Overview" class="white-text active waves-effect waves-light">Overview</a>
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                     <a href="#ROSE" class="white-text waves-effect waves-light">ROSE</a>
 
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                     <a href="#CACCI" class="white-text waves-effect waves-light">CACCI</a>
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                             <h3><b>NDM: Nanomachine Detecting Microbiotics</b></h3>
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                             <p>Abusing antibiotics has caused severe antibiotics contamination and resistance issues worldwide. Therefore, we USTC develop a device NDM with OD detector and optical interference path, recognition program based on RasberryPi and Arduino to detect antibiotics in natural water bodies. In NDM, there are two bacterial systems for measurement: ROSE, an engineered bacterial reporter system integrated with permeability modification, logic amplification circuit and quorum sensing, is able to adjust EGFP expression level, and NDM reads fluorescence intensity from ROSE to send results in high resolution. CACCI, chemotaxis and transmembrane protein-modified bacteria, are chemically covalently adhered to a polymer membrane. Deformation caused by CACCI motility can be recognized with optical interference and the interference pattern recognition program inside NDM will analyze the deformation, thus antibiotic situation in sample can be accurately told. Hope with our project, antibiotics issues can be solved in an accelerated way. </p>
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                        <h3>Contact us:<br/></h3>
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                        <a href="http://weibo.com/3929719655/fans?topnav=1&wvr=6&mod=message&need_filter=1">Weibo</a>
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                             <h3><b id="OverviewNDM" class="scrollspy">NDM:</b><br /><b>Nanomachine Detecting Microbiotics</b></h3>
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                        <a href="https://www.facebook.com/2014ustcchinaigem?ref=bookmarks">Facebook</a>
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                             <p>
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                                Abusing antibiotics has caused severe antibiotics contamination and resistance issues worldwide. Therefore, we USTC develop a device NDM with OD detector and optical interference path, recognition program based on RasberryPi and Arduino to detect antibiotics in natural water bodies.
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                        <a href="mailto:ustc.igem.2015@gmail.com">ustc.igem.2015@gmail.com</a>
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                                <br /> In NDM, there are two bacterial systems for measurement:
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                                <b id="OverviewROSE" class="scrollspy">ROSE</b>, an engineered bacterial reporter system integrated with permeability modification, logic amplification circuit and quorum sensing, is able to adjust EGFP expression level, and NDM reads fluorescence intensity from ROSE to send results in high resolution.
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                             <a href="#">Read More ...</a>
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                                <br />
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                                <br />
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                                <b id="OverviewCACCI" class="scrollspy">CACCI</b>, chemotaxis and transmembrane protein-modified bacteria, are chemically covalently adhered to a polymer membrane. Deformation caused by CACCI motility can be recognized with optical interference and the interference pattern recognition program inside NDM will analyze the deformation, thus antibiotic situation in sample can be accurately told.
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                                <br /> Hope with our project, antibiotics issues can be solved in an accelerated way.
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                                    <a href="#OverviewNDM">Overview:NDM</a>
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                            <p>Our notebook has three sections: </p>
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                                <li>Timeline:The record of our laboratory progress;
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                                 <li>Bibliography: The collection of literatures;
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                                    <a href="#OverviewROSE">Overview:ROSE</a>
 
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                                 <li>Protocols:The experimental standards we applied.</li>
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                                    <a href="#OverviewCACCI">Overview:CACCI</a>
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                            <br>
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                            <p>We sincerely hope that you can gain something from our notes. If you have doubt of anything, please contact us!</p>
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                             <p>In our modeling efforts, we followed closely on our major 2 sub-projects, Color Imaging and Motion Control and their experimental connection. Conjugation Combing all the above, came the C. imager Modeling.</p>
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                            <h3 id="what-is-antibiotics-" class="scrollspy">What is Antibiotics?</h3>
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                             <p>Antibiotics, or microbiotics, in narrow sense, are a various type of artificially constructed or naturally existing chemicals containing the capability of killing bactiera or inhibiting their growth, which are implemented widespreadly around the world. Patients who got bactieral or protozoan infection from surgical wound like war field, empyrosis and previously regarding severe diseases such as general cold, tuberculosis(TB), sexual transmitted diseases(STD), dysentery, anthrax, even cancer and so forth are able to cure treating with antibiotic substances. Since the discovery of penicillin by British biologists Alexander Flaming in 1929, the antibiotic family has been enlarged a lot. With properly administration of antibiotics, millions of people were saved in evidently alleviated symptom. There was a time when antibiotics, along with oil source for automobile, was indispensable for human beings.</p>
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                             <a href="#">Read More ...</a>
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                            <p>Antibiotic substances containing several mechanism, rendering them to kill and inhibit bactieral growth in their own ways. Those mechanisms including:</p>
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                            <ul class="collection">
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                                <li class="collection-item">inhibit the synthesis of cell wall.</li>
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                                <li class="collection-item">influence the function of cell membrane.</li>
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                                <li class="collection-item">inhibit the biosynthesis of nucleic acid.</li>
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                                <li class="collection-item">inhibit the biosynthesis of proteins.</li>
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                            </ul>
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                            <p><img src="https://upload.wikimedia.org/wikipedia/commons/0/08/Antibiotics_Mechanisms_of_action.png" alt="From TheMedSchool">
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                                <br>Classes catogorization based on chemical structure including:</p>
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                            <ul class="collection">
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                                <li class="collection-item">Beta-lactam</li>
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                                <li class="collection-item">Aminoglycoside</li>
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                                <li class="collection-item">Amide alcohol</li>
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                                <li class="collection-item">Macrolide</li>
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                                <li class="collection-item">Polypetide</li>
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                                <li class="collection-item">Tetracycline</li>
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                                <li class="collection-item">Sulfonamides</li>
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                                <li class="collection-item">Quinolones</li>
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                                <li class="collection-item">Polymyxin</li>
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                                <li class="collection-item">Trimethprim</li>
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                                <li class="collection-item">Nitrofuran etc.</li>
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                            <p><img src="image/55572f8e4a771.jpg" alt=""></p>
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                            <p>Ordered formal course of treatment, these antibiotic would effectly treat
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                                <br>gonorrhea, MRSA and pseudomonal infections respectively.</p>
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                            <br/>
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                            <p>However, treating with microbiotics may be associated with a rang of side effects, from some mild including gastrointestinal upset, diarrhea to severe like hearing loss, kidney damage. Some speculation from scientists postulated that exposition of high concentration utilization of antibiotics alter the host microbiota, especially the familiy of the probiotics, and this has been associated with chronic diseases.</p>
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                            <br />
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                            <p>The prodcution of antibiotics in pharmceutical companies explosively expanded these years. Articifical synthesis of sulfonamides, quinolones and oxazolidinones enrich the categories of antibiotics.</p>
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                            <h3 id="antimicrobial-resistance-and-abuses" class="scrollspy">Antimicrobial Resistance and Abuses</h3>
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                            <p>As the matter of fact, microbiotics, the great saver of our life, is now putting us in potentially tremendous disaster both environmentally and physiologically. </p>
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                            <br />
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                            <p>Emergence of antimicrobial resistance is theoratically predictable by evolutionary potential. The antibiotic treatment may select for bacterial strains physiologically improved of their cell bodies or genetically enhanced capacity of mutagenesis and gene horizontal transfer like conjugation.</p>
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                            <p>Because of such horizontal genetic exchange, nowadays, efficacy loss may attribute to the emergence of many antimicrobrial-resistent strains. For instance, tuberculosis(TB) in China becomes more difficult with administration with previous antibiotic substances owing to elevating level of antimicribrial resistence, which raised great challenge on Chinese public health. Besides, the discovery of NDM-1(New Delhi Metallo-beta-lactamase) in <em>Klebsiella pneumoniae</em> from a Swedish patient of Indian origin in 2008 once may contribute to severe disaster on that broad of beta-lactan antibiotics.</p>
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                            <br />
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                            <p>Though, antimicrobial resistance can be transferred through evolutionary theory, main contribution of increasing antibiotic resistance comes from individuals' inappropriate antibiotics treatment, overuse of antibiotics without prescription from professional doctor, instead from self-prescription.</p>
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                            <p><img src="image/1438322045x-954498856.jpg" alt="图片名称"></p>
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                            <p>Demonstrably, attribution of antibiotic resistance not only from clinically, but from agriculture and animal husbandry. In China, the overuse of antibiotics for animal is the same serious as the clinical therapy. In farms or hospitals, solution containing antibiotics directly emittes to river, which potentially strongly influence the ecological equilibrium of bactierial colonies and sidelong threaten public health.</p>
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                            <h3 id="antibiotics-production-and-contamination-in-china" class="scrollspy">Antibiotics Production and Contamination in China</h3>
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                             <p>Because individuals neglecting antibiotic emission, rivers in China now encounter extremely antibiotic contamination.</p>
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                            <p><img src="image/1438323729x-1566638187.png" alt="图片名称"></p>
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                            <p>According to the latest research from <em>Chinese Academy of Science</em> published on ACS Environmental Science and Technology, China used 162,000 tons of antibiotic substances for human(48%) and animal(52%) in 2013, which is tenfold usage of USA and antibiotic substances in high concentration can be detected from many river basins that may potentially harmful to public health and environment. In their professional evaluation, antibiotics can be detected in all rivers in China in different degree. </p>
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                            <p><img src="image/1438322929x-1566638187.png" alt="图片名称"></p>
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                            <p>Among these rivers, the Pearl River Basin in South China and Hai River Basin in North China received the highest antibiotics emission. More than 36 common antibiotic substances were discovered in these rivers, one of them, for example, in the Pearl River Basin, amoxicillin was found at 3384 ng/L and fluprofen at 2867 ng/L. Though lack of standard ranking on antibiotic contamination, according to environmental scienctists from CAS, antibiotic substances concentration more than 1000 ng/L is relatively extremely high, based on Europe Union Standard.</p>
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                            <br />
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                            <p>Now, many technology including ELISA, Delvotest, HPLC-MS/MS, CE and Quantum Dot are able to detect antibiotic concentration in river sample, however much of their have much dificiencies, including:</p>
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                            <ul class="collection">
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                                <li class="collection-item">Not portable, many big and automatic equipments are indispensable for concentration detection.</li>
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                                <li class="collection-item">Complicated Routine, which requires traned personnel to conduct experiment. However, facing that large scale contamination, complicated routine and trained personnel cannot be satisfied at all districts, so do it in many developing and undeveloped countries and districts.</li>
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                                <li class="collection-item">Recent technology is still not sensitive enough and sometimes time consuming.</li>
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                            </ul>
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                            <p>Consequently, this year we iGEM constructed NDM, which is abbreviated from Nanomachine detecting microbiotics. Using NDM based on mechanism of GFP reporter, chemotaxis and interference, a portable and accurate device is established to encounter the issues today.</p>
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                            <p><a onclick="$(document).scrollTop(0)">Top</a></p>
 
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                                    <a href="#what-is-antibiotics-">What is Antibiotics? </a>
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                                    <a href="#antimicrobial-resistance-and-abuses">Antimicrobial Resistance <br/>and Abuses</a>
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                            <p>We strongly hold a belief that it is our arduous responsibility to not only develop synthetic biology by working on a project day and night but teach and enlighten the public to be intrigued in biology and understand what scientists are doing on genetic engineering and other biology technology so that the public is capable of judging whether genetically modified organism (GMO) is safe and personalized gene sequencing and therapy are reliable enough...</p>
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                                    <a href="#antibiotics-production-and-contamination-in-china">Antibiotics Production <br/>and Contamination in China</a>
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Revision as of 14:11, 28 August 2015

NDM:
Nanomachine Detecting Microbiotics

Abusing antibiotics has caused severe antibiotics contamination and resistance issues worldwide. Therefore, we USTC develop a device NDM with OD detector and optical interference path, recognition program based on RasberryPi and Arduino to detect antibiotics in natural water bodies.

In NDM, there are two bacterial systems for measurement:

ROSE, an engineered bacterial reporter system integrated with permeability modification, logic amplification circuit and quorum sensing, is able to adjust EGFP expression level, and NDM reads fluorescence intensity from ROSE to send results in high resolution.

CACCI, chemotaxis and transmembrane protein-modified bacteria, are chemically covalently adhered to a polymer membrane. Deformation caused by CACCI motility can be recognized with optical interference and the interference pattern recognition program inside NDM will analyze the deformation, thus antibiotic situation in sample can be accurately told.
Hope with our project, antibiotics issues can be solved in an accelerated way.

What is Antibiotics?

Antibiotics, or microbiotics, in narrow sense, are a various type of artificially constructed or naturally existing chemicals containing the capability of killing bactiera or inhibiting their growth, which are implemented widespreadly around the world. Patients who got bactieral or protozoan infection from surgical wound like war field, empyrosis and previously regarding severe diseases such as general cold, tuberculosis(TB), sexual transmitted diseases(STD), dysentery, anthrax, even cancer and so forth are able to cure treating with antibiotic substances. Since the discovery of penicillin by British biologists Alexander Flaming in 1929, the antibiotic family has been enlarged a lot. With properly administration of antibiotics, millions of people were saved in evidently alleviated symptom. There was a time when antibiotics, along with oil source for automobile, was indispensable for human beings.


Antibiotic substances containing several mechanism, rendering them to kill and inhibit bactieral growth in their own ways. Those mechanisms including:

  • inhibit the synthesis of cell wall.
  • influence the function of cell membrane.
  • inhibit the biosynthesis of nucleic acid.
  • inhibit the biosynthesis of proteins.

From TheMedSchool
Classes catogorization based on chemical structure including:

  • Beta-lactam
  • Aminoglycoside
  • Amide alcohol
  • Macrolide
  • Polypetide
  • Tetracycline
  • Sulfonamides
  • Quinolones
  • Polymyxin
  • Trimethprim
  • Nitrofuran etc.

Ordered formal course of treatment, these antibiotic would effectly treat
gonorrhea, MRSA and pseudomonal infections respectively.


However, treating with microbiotics may be associated with a rang of side effects, from some mild including gastrointestinal upset, diarrhea to severe like hearing loss, kidney damage. Some speculation from scientists postulated that exposition of high concentration utilization of antibiotics alter the host microbiota, especially the familiy of the probiotics, and this has been associated with chronic diseases.


The prodcution of antibiotics in pharmceutical companies explosively expanded these years. Articifical synthesis of sulfonamides, quinolones and oxazolidinones enrich the categories of antibiotics.



Antimicrobial Resistance and Abuses

As the matter of fact, microbiotics, the great saver of our life, is now putting us in potentially tremendous disaster both environmentally and physiologically.


Emergence of antimicrobial resistance is theoratically predictable by evolutionary potential. The antibiotic treatment may select for bacterial strains physiologically improved of their cell bodies or genetically enhanced capacity of mutagenesis and gene horizontal transfer like conjugation.


Because of such horizontal genetic exchange, nowadays, efficacy loss may attribute to the emergence of many antimicrobrial-resistent strains. For instance, tuberculosis(TB) in China becomes more difficult with administration with previous antibiotic substances owing to elevating level of antimicribrial resistence, which raised great challenge on Chinese public health. Besides, the discovery of NDM-1(New Delhi Metallo-beta-lactamase) in Klebsiella pneumoniae from a Swedish patient of Indian origin in 2008 once may contribute to severe disaster on that broad of beta-lactan antibiotics.


Though, antimicrobial resistance can be transferred through evolutionary theory, main contribution of increasing antibiotic resistance comes from individuals' inappropriate antibiotics treatment, overuse of antibiotics without prescription from professional doctor, instead from self-prescription.

图片名称

Demonstrably, attribution of antibiotic resistance not only from clinically, but from agriculture and animal husbandry. In China, the overuse of antibiotics for animal is the same serious as the clinical therapy. In farms or hospitals, solution containing antibiotics directly emittes to river, which potentially strongly influence the ecological equilibrium of bactierial colonies and sidelong threaten public health.



Antibiotics Production and Contamination in China

Because individuals neglecting antibiotic emission, rivers in China now encounter extremely antibiotic contamination.

图片名称

According to the latest research from Chinese Academy of Science published on ACS Environmental Science and Technology, China used 162,000 tons of antibiotic substances for human(48%) and animal(52%) in 2013, which is tenfold usage of USA and antibiotic substances in high concentration can be detected from many river basins that may potentially harmful to public health and environment. In their professional evaluation, antibiotics can be detected in all rivers in China in different degree.

图片名称

Among these rivers, the Pearl River Basin in South China and Hai River Basin in North China received the highest antibiotics emission. More than 36 common antibiotic substances were discovered in these rivers, one of them, for example, in the Pearl River Basin, amoxicillin was found at 3384 ng/L and fluprofen at 2867 ng/L. Though lack of standard ranking on antibiotic contamination, according to environmental scienctists from CAS, antibiotic substances concentration more than 1000 ng/L is relatively extremely high, based on Europe Union Standard.


Now, many technology including ELISA, Delvotest, HPLC-MS/MS, CE and Quantum Dot are able to detect antibiotic concentration in river sample, however much of their have much dificiencies, including:

  • Not portable, many big and automatic equipments are indispensable for concentration detection.
  • Complicated Routine, which requires traned personnel to conduct experiment. However, facing that large scale contamination, complicated routine and trained personnel cannot be satisfied at all districts, so do it in many developing and undeveloped countries and districts.
  • Recent technology is still not sensitive enough and sometimes time consuming.

Consequently, this year we iGEM constructed NDM, which is abbreviated from Nanomachine detecting microbiotics. Using NDM based on mechanism of GFP reporter, chemotaxis and interference, a portable and accurate device is established to encounter the issues today.

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