מימון עבור עבודה זו ניתן על ידי למדעי הטבע וההנדסה המועצה למחקר בקנדה (NSERC) וברשת ביו סנטינל נייר.

<ol>
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A., Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+a+catalytically+efficient+acidic+RNA-cleaving+deoxyribozyme.">Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozyme.</a> Nucleic Acids Res. 33, 7164-7175 (2005).</li><li>Rupcich, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quenching+of+fluorophore-labeled+DNA+oligonucleotides+by+divalent+metal+ions:+implications+for+selection,+design,+and+applications+of+signaling+aptamers+and+signaling+deoxyribozymes.">Quenching of fluorophore-labeled DNA oligonucleotides by divalent metal ions: implications for selection, design, and applications of signaling aptamers and signaling deoxyribozymes.</a> J. Am. Chem. Soc. 128, 780-790 (2005).</li><li>Shen, Y., Brennan, J. D., Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterizing+the+secondary+structure+and+identifying+functionally+essential+nucleotides+of+pH6DZ1,+a+fluorescence-signaling+and+RNA-cleaving+deoxyribozyme.">Characterizing the secondary structure and identifying functionally essential nucleotides of pH6DZ1, a fluorescence-signaling and RNA-cleaving deoxyribozyme.</a> Biochemistry. 44, 12066-12076 (2005).</li><li>Chiuman, W., Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Revitalization+of+six+abandoned+catalytic+DNA+species+reveals+a+common+three-way+junction+framework+and+diverse+catalytic+cores.">Revitalization of six abandoned catalytic DNA species reveals a common three-way junction framework and diverse catalytic cores.</a> J. Mol. Biol. 357, 748-754 (2006).</li><li>Chiuman, W., Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolution+of+high-branching+deoxyribozymes+from+a+catalytic+DNA+with+a+three-way+junction.">Evolution of high-branching deoxyribozymes from a catalytic DNA with a three-way junction.</a> Chem. Biol. 13, 1061-1069 (2006).</li><li>Shen, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Catalysis+and+rational+engineering+of+trans-acting+pH6DZ1,+an+RNA-cleaving+and+fluorescence-signaling+deoxyribozyme+with+a+four-way+junction+structure.">Catalysis and rational engineering of trans-acting pH6DZ1, an RNA-cleaving and fluorescence-signaling deoxyribozyme with a four-way junction structure.</a> Chem BioChem. 7, 1343-1348 (2006).</li><li>Ali, M. M., Kandadai, S. 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Chem. 85, 261-273 (2007).</li><li>Chiuman, W., Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+signaling+platforms+built+from+a+small+catalytic+DNA+and+doubly+labeled+fluorogenic+substrates.">Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates.</a> Nucleic Acids Res. 35, 401-405 (2007).</li><li>Chiuman, W., Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+fluorescent+sensors+engineered+with+catalytic+DNA+MgZ+based+on+a+non-classic+allosteric+design.">Simple fluorescent sensors engineered with catalytic DNA MgZ based on a non-classic allosteric design.</a> PLoS ONE. 2, e1224 (2007).</li><li>Shen, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Entrapment+of+fluorescence+signaling+DNA+enzymes+in+sol+gel-derived+materials+for+metal+ion+sensing.">Entrapment of fluorescence signaling DNA enzymes in sol gel-derived materials for metal ion sensing.</a> Anal. Chem. 79, 3494-3503 (2007).</li><li>Kandadai, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+an+RNA-cleaving+deoxyribozyme+with+optimal+activity+at+pH+5.">Characterization of an RNA-cleaving deoxyribozyme with optimal activity at pH 5.</a> Biochemistry. 48, 7383-7391 (2009).</li><li>Zhao, W., Brook, M. A., Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Periodic+assembly+of+nanospecies+on+repetitive+DNA+sequences+generated+on+gold+nanoparticles+by+rolling+circle+amplification.">Periodic assembly of nanospecies on repetitive DNA sequences generated on gold nanoparticles by rolling circle amplification.</a> Methods Mol. Biol. 474, 79-90 (2008).</li><li>Navani, N. K., Mok, W. 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אין ניגוד עניינים הצהיר.

רוב השיטות המקובלות לזיהוי חיידקים היום הם איטיים או (חיידקים קלאסי) או טכנית בדרישה (נוגדנים, PCR). לכן, אנו מאמינים כי הדור הבא של כלי איתור צריך לספק מהירות כלפי ופשטות. לצורך כך, יצרנו RNA-השחיטה ואת הקרינה, איתות DNAzyme שיכולים לשמש לפיתוח מבחני פשוטים לדווח נוכחות של חיידקים דרך הדור האות פלואורסצנטי. התכונות DNAzyme בדיקה, RFD-EC1, מופעל על ידי CEM הנוצר במהלך הצמיחה של א &#39; coli בתקשורת ובתרבות. מאז השיטה שלנו משתמשת בתערובות תאיים הגולמי של חיידק כיעד של איתור עוקף את מיצוי היעד מייגע וצעדים הגברה, ניתן להשתמש בו כדי להגדיר פשוט מאוד, &quot;תמהיל-and-לקרוא&quot; סוג של מבחני לגילוי חיידקי. השימוש DNAzyme שלנו אינו מוגבל בשיטה המבוססת על זיהוי הקרינה. לדוגמה, זיהוי colorimetric באמצעות אותה מערכת DNAzyme assay גלהיות מתוכנן בשיטה דיווחו בעבר כי מנצל הגברה מעגל מתגלגל יחד עם צבע אורגני. 32 אנו צופים את השימוש DNAzymes לגילוי חיידקי כמו השדרה אטרקטיבי ליצור biosensors חיידקים חדשים עם פשטות תפעולית גדולה יותר.

<table border="1" style=";text-align:right;direction:rtl"><tbody><tr><td> שם מגיב </td><td> חברה </td><td> מספר קטלוגי או מודל </td></tr><tr><td> אגר </td><td> BioShop קנדה </td><td> AGR003 </td></tr><tr><td> אמוניום persulfate (APS) </td><td> BioShop קנדה </td><td> AMP001 </td></tr><tr><td> Acrylamide / Bis-acrylamide (40%, 29:1) </td><td> BioShop קנדה </td><td> ACR004 </td></tr><tr><td> בור חומצה </td><td> BioShop קנדה </td><td> BOR001 </td></tr><tr><td> Bromophenol כחול </td><td> Sigma-Aldrich </td><td> B8026 </td></tr><tr><td> EDTA </td><td> א.מ. מדע </td><td> EXO539-1 </td></tr><tr><td> HCl </td><td> Sigma-Aldrich </td><td> 38281 </td></tr><tr><td> HEPES </td><td> Bioshop קנדה </td><td> HEP001 </td></tr><tr><td> LB מרק </td><td> Sigma-Aldrich </td><td> L3022 </td></tr><tr><td> MgCl 2 </td><td> EMDכימיקלים </td><td> B10149-34 </td></tr><tr><td> NaCl </td><td> BioShop קנדה </td><td> SOD002 </td></tr><tr><td> NaOAc </td><td> EMD כימיקלים </td><td> SXO255-1 </td></tr><tr><td> NaOH </td><td> EMD כימיקלים </td><td> SXO590-1 </td></tr><tr><td> SDS </td><td> BioShop קנדה </td><td> SDS001 </td></tr><tr><td> TEMED </td><td> BioShop קנדה </td><td> TEM001 </td></tr><tr><td> טריס בסיס </td><td> BioShop קנדה </td><td> BST666 </td></tr><tr><td> Tween 20 </td><td> Sigma-Aldrich </td><td> P9416 </td></tr><tr><td> אוריאה </td><td> BioShop קנדה </td><td> URE001 </td></tr><tr><td> Xylenecyanol FF </td><td> Sigma-Aldrich </td><td> X4126 </td></tr><tr><td> ה-DNA concentrator </td><td> Thermo Scientific </td><td> Savant DNA SpeedVac 120 </td></tr><tr><td> Millex יחידת המסנן </td><td> Millipore </td><td> SLGP033RS </td></tr><tr><td> ג&#39;ל טיפים העמסה </tד&gt; <td> Diamed </td><td> TEC200EX-K </td></tr><tr><td> ImageQuant תוכנה </td><td> מולקולרית דינמיקה </td><td> גרסה 5.0 </td></tr><tr><td> Kimwipes </td><td> קימברלי קלארק מקצועי </td><td> 34705 </td></tr><tr><td> מיני Vortexer </td><td> VWR </td><td> 58816-121 </td></tr><tr><td> Parafilm </td><td> Pechiney אריזות פלסטיק </td><td> PM996 </td></tr><tr><td> פטרי מנות </td><td> פישר סיינטיפיק </td><td> Fisherbrand 08-757-12 </td></tr><tr><td> Stripettor פלוס (פיפטה האקדח) </td><td> קורנינג </td><td> 07764714 </td></tr><tr><td> קוורץ cuvettes </td><td> וריאן Inc </td><td> 66-100216-00 </td></tr><tr><td> שאכר / חממה </td><td> ניו ברונסוויק מדעי </td><td> הסדרה הקלאסית C24 </td></tr><tr><td> טייפון סורק </td><td> GE Healthcare </td><td> 9200 משתנה מצב </td></tr><tr><td> סרכזת </td><td> Beckman Coulter </td><td> אלגרה X22-R </td></tr><tr><td> ספקטרופוטומטר UV </td><td> Thermo Scientific </td><td> GenesysUV 10 </td></tr><tr><td> הקרינה ספקטרופוטומטר </td><td> וריאן Inc </td><td> קרי ליקוי חמה </td></tr></tbody></table>

detection of bacteria using fluorogenic dnazymes

Outbreaks linked to food-borne and hospital-acquired pathogens account for millions of deaths and hospitalizations as well as colossal economic losses each and every year. Prevention of such outbreaks and minimization of the impact of an ongoing epidemic place an ever-increasing demand for analytical methods that can accurately identify culprit pathogens at the earliest stage. Although there is a large array of effective methods for pathogen detection, none of them can satisfy all the following five premier requirements embodied for an ideal detection method: high specificity (detecting only the bacterium of interest), high sensitivity (capable of detecting as low as a single live bacterial cell), short time-to-results (minutes to hours), great operational simplicity (no need for lengthy sampling procedures and the use of specialized equipment), and cost effectiveness. For example, classical microbiological methods are highly specific but require a long time (days to weeks) to acquire a definitive result.1 PCR- and antibody-based techniques offer shorter waiting times (hours to days), but they require the use of expensive reagents and/or sophisticated equipment.2-4 Consequently, there is still a great demand for scientific research towards developing innovative bacterial detection methods that offer improved characteristics in one or more of the aforementioned requirements. Our laboratory is interested in examining the potential of DNAzymes as a novel class of molecular probes for biosensing applications including bacterial detection.5
DNAzymes (also known as deoxyribozymes or DNA enzymes) are man-made single-stranded DNA molecules with the capability of catalyzing chemical reactions.6-8 These molecules can be isolated from a vast random-sequence DNA pool (which contains as many as 1016 individual sequences) by a process known as "in vitro selection" or "SELEX" (systematic evolution of ligands by exponential enrichment).9-16 These special DNA molecules have been widely examined in recent years as molecular tools for biosensing applications.6-8
Our laboratory has established in vitro selection procedures for isolating RNA-cleaving fluorescent DNAzymes (RFDs; Fig. 1) and investigated the use of RFDs as analytical tools.17-29 RFDs catalyze the cleavage of a DNA-RNA chimeric substrate at a single ribonucleotide junction (R) that is flanked by a fluorophore (F) and a quencher (Q). The close proximity of F and Q renders the uncleaved substrate minimal fluorescence. However, the cleavage event leads to the separation of F and Q, which is accompanied by significant increase of fluorescence intensity.
More recently, we developed a method of isolating RFDs for bacterial detection.5 These special RFDs were isolated to "light up" in the presence of the crude extracellular mixture (CEM) left behind by a specific type of bacteria in their environment or in the media they are cultured (Fig. 1). The use of crude mixture circumvents the tedious process of purifying and identifying a suitable target from the microbe of interest for biosensor development (which could take months or years to complete). The use of extracellular targets means the assaying procedure is simple because there is no need for steps to obtain intracellular targets.
Using the above approach, we derived an RFD that cleaves its substrate (FS1; Fig. 2A) only in the presence of the CEM produced by E. coli (CEM-EC).5 This E. coli-sensing RFD, named RFD-EC1 (Fig. 2A), was found to be strictly responsive to CEM-EC but nonresponsive to CEMs from a host of other bacteria (Fig. 3).
Here we present the key experimental procedures for setting up E. coli detection assays using RFD-EC1 and representative results.

Watch this Scientific Journal Video about Detection of Bacteria Using Fluorogenic DNAzymes at JoVE.com

Detection of Bacteria Using Fluorogenic DNAzymes

דיווחנו לאחרונה גישה חדשנית להפקת בדיקות DNAzyme fluorogenic כי ניתן להחיל על הקמת פשוט, &quot;תמהיל-and-לקרוא&quot; assay ניאון לגילוי חיידקי. אלו בדיקות דנ&quot;א מיוחד לזרז את המחשוף של מצע ה-DNA-RNA-chromophore שונה chimeric בנוכחות תערובת תאי גולמי (CEM) המיוצר על ידי חיידק מסוים, ובכך לתרגם את גילוי החיידק לדור אותות הקרינה. בדוח זה נתאר את הליכי הניסוי העיקריים שבהם בדיקה DNAzyme מסוים כונה &quot;RFD-EC1&quot; מועסק לצורך זיהוי של החיידק המודל,<emEscherichia coli&gt; (E. coli)</em&gt;.

זיהוי של חיידקים באמצעות DNAzymes Fluorogenic

Outbreaks linked to food-borne and hospital-acquired pathogens account for millions of deaths and hospitalizations as well as colossal economic losses ...

detection-of-bacteria-using-fluorogenic-dnazymes

Research

JoVE Journal

Immunology and Infection

18.8K Views.  McMaster University. דיווחנו לאחרונה גישה חדשנית להפקת בדיקות DNAzyme fluorogenic כי ניתן להחיל על הקמת פשוט, "תמהיל-and-לקרוא" assay ניאון לגילוי חיידקי. אלו בדיקות דנ"א מיוחד לזרז את המחשוף של מצע ה-DNA-RNA-chromophore שונה chimeric בנוכחות תערובת תאי גולמי (CEM) המיוצר על ידי חיידק מסוים, ובכך לתרגם את ...

Video: Detection of Bacteria Using Fluorogenic DNAzymes

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in situ hybridization (FISH) for rapid culture-independent detection of Salmonella spp. Cell-charged tapes can also be placed face-down on selective agar for solid-phase enrichment prior to detection. Alternatively, low-volume liquid enrichments (liquid surface miniculture) can be performed on the surface of the tape in non-selective broth, followed by FISH and analysis via flow cytometry. To begin, sterile adhesive tape is brought into contact with fresh produce, gentle pressure is applied, and the tape is removed, physically extracting microbes present on these surfaces. Tapes are mounted sticky-side up onto glass microscope slides and the sampled cells are fixed with 10% formalin (30 min) and dehydrated using a graded ethanol series (50, 80, and 95%; 3 min each concentration). Next, cell-charged tapes are spotted with buffer containing a Salmonella-targeted DNA probe cocktail and hybridized for 15 - 30 min at 55&deg;C, followed by a brief rinse in a washing buffer to remove unbound probe. Adherent, FISH-labeled cells are then counterstained with the DNA dye 4',6-diamidino-2-phenylindole (DAPI) and results are viewed using fluorescence microscopy. For solid-phase enrichment, cell-charged tapes are placed face-down on a suitable selective agar surface and incubated to allow in situ growth of Salmonella microcolonies, followed by FISH and microscopy as described above. For liquid surface miniculture, cell-charged tapes are placed sticky side up and a silicone perfusion chamber is applied so that the tape and microscope slide form the bottom of a water-tight chamber into which a small volume (&le; 500 &mu;L) of Trypticase Soy Broth (TSB) is introduced. The inlet ports are sealed and the chambers are incubated at 35 - 37&deg;C, allowing growth-based amplification of tape-extracted microbes. Following incubation, inlet ports are unsealed, cells are detached and mixed with vigorous back and forth pipetting, harvested via centrifugation and fixed in 10% neutral buffered formalin. Finally, samples are hybridized and examined via flow cytometry to reveal the presence of Salmonella spp. As described here, our "tape-FISH" approach can provide simple and rapid sampling and detection of Salmonella on tomato surfaces. We have also used this approach for sampling other types of fresh produce, including spinach and jalape&ntilde;o peppers.

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

This protocol describes a simple adhesive-tape-based approach for sampling of tomato and other fresh produce surfaces, followed by rapid whole cell detection of Salmonella using fluorescence in situ hybridization (FISH).

שילוב של הדגימה דבק קלטת מבוססי פלואורסצנטי באתרו הכלאה עבור איתור מהיר של סלמונלה על תוצרת טרייה

This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in ...

Multiplex Detection of Bacteria in Complex Clinical and Environmental Samples using Oligonucleotide-coupled Fluorescent Microspheres

Bacterial vaginosis (BV) is a recurring polymicrobial syndrome that is characterized by a change in the "normal" microbiota from Lactobacillus-dominated to a microbiota dominated by a number of bacterial species, including Gardnerella vaginalis, Atopobium vaginae, and others1-3. This condition is associated with a range of negative health outcomes, including HIV acquisition4, and it can be difficult to manage clinically5. Furthermore, diagnosis of BV has relied on the use of Gram stains of vaginal swab smears that are scored on various numerical criteria6,7. While this diagnostic is simple, inexpensive, and well suited to resource-limited settings, it can suffer from problems related to subjective interpretations and it does not give a detailed profile of the composition of the vaginal microbiota8. Recent deep sequencing efforts have revealed a rich, diverse vaginal microbiota with clear differences between samples taken from individuals that are diagnosed with BV compared to those individuals that are considered normal9,10, which has resulted in the identification of a number of potential targets for molecular diagnosis of BV11,12. These studies have provided a wealth of useful information, but deep sequencing is not yet practical as a diagnostic method in a clinical setting. We have recently described a method for rapidly profiling the vaginal microbiota in a multiplex format using oligonucleotide-coupled fluorescent beads with detection on a Luminex platform13. This method, like current Gram stain-based methods, is rapid and simple but adds the additional advantage of exploiting molecular knowledge arising from sequencing studies in probe design. This method therefore provides a way to profile the major microorganisms that are present in a vaginal swab that can be used to diagnose BV with high specificity and sensitivity compared to Gram stain while providing additional information on species presence and abundance in a semi-quantitative and rapid manner. This multiplex method is expandable well beyond the range of current quantitative PCR assays for particular organisms, which is currently limited to 5 or 6 different assays in a single sample14. Importantly, the method is not limited to the detection of bacteria in vaginal swabs and can be easily adapted to rapidly profile nearly any microbial community of interest. For example, we have recently begun to apply this methodology to the development of diagnostic tools for use in wastewater treatment plants.

We describe a multiplex method for the detection of microorganisms within a sample using oligonucleotide-coupled fluorescent beads. Amplicon from all organisms within a sample is hybridized to a panel of probe-coupled beads. A Luminex or Bio-Plex instrument is used to query each bead for bead type and hybridization signal.

Multiplex זיהוי של חיידקים דוגמאות מורכבות קלינית הסביבה באמצעות oligonucleotide מצמידים פלורסנט microspheres

Bacterial vaginosis (BV) is a recurring polymicrobial syndrome that is characterized by a change in the "normal" microbiota from Lactobacillus-dominated ...

Rapid Identification of Gram Negative Bacteria from Blood Culture Broth Using MALDI-TOF Mass Spectrometry

An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional identification requires the sub-culture of signaled blood culture broth with identification available only after colonies on solid agar have matured. MALDI-TOF MS is a reliable, rapid method for identification of the majority of clinically relevant bacteria when applied to colonies on solid media. The application of MALDI-TOF MS directly to blood culture broth is an attractive approach as it has potential to accelerate species identification of bacteria and improve clinical management. However, an important problem to overcome is the pre-analysis removal of interfering resins, proteins and hemoglobin&#160;contained in blood culture specimens which, if not removed, interfere with the MS spectra and can result in insufficient or low discrimination identification scores. In addition it is necessary to concentrate bacteria to develop spectra of sufficient quality. The presented method describes the concentration, purification, and extraction of Gram negative bacteria allowing for the early identification of bacteria from a signaled blood culture broth.

The application of matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) directly to blood culture broth expedites the identification of bacteria. The presented method is a rapid and reliable method for identification of Gram negative bacteria directly from blood culture broth.

זיהוי מהיר של חיידקים גראם שליליים מהדם תרבות מרק שימוש MALDI-TOF המוני ספקטרומטריית

An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional ...

In Situ Detection of Bacteria within Paraffin-embedded Tissues Using a Digoxin-labeled DNA Probe Targeting 16S rRNA

The presence of bacteria within the pocket epithelium and underlying connective tissue in gingival biopsies from patients with periodontitis has been reported using various methods, including electron microscopy, immunohistochemistry or immunofluorescence using bacteria-specific antibodies, and fluorescent in situ hybridization (FISH) using a fluorescence-labeled oligonucleotide probe. Nevertheless, these methods are not widely used due to technical limitation or difficulties. Here a method to localize bacteria within paraffin-embedded tissues using DIG-labeled DNA probes has been introduced. The paraffin-embedded tissues are the most common form of biopsy tissues available from pathology banks. Bacteria can be detected either in a species-specific or universal manner. Bacterial signals are detected as either discrete forms (coccus, rod, fusiform, and hairy form) of bacteria or dispersed forms. The technique allows other histological information to be obtained: the epithelia, connective tissue, inflammatory infiltrates, and blood vessels are well distinguished. This method can be used to study the role of bacteria in various diseases, such as periodontitis, cancers, and inflammatory immune diseases.

In Situ Detection of Bacteria within Paraffin-embedded Tissues Using a Digoxin-labeled DNA Probe Targeting 16S rRNA

Here a method to localize bacteria within paraffin-embedded tissues using DIG-labeled 16S rRNA-targeting DNA probes has been described. This protocol can be applied to study the role of bacteria in various diseases such as periodontitis, cancers, and inflammatory immune diseases.

באתרו איתור של חיידקים בתוך רקמות מוטבעות-פרפין באמצעות DNA בדיקה שכותרת Digoxin מיקוד 16S rRNA

The presence of bacteria within the pocket epithelium and underlying connective tissue in gingival biopsies from patients with periodontitis has been ...

Ultrasensitive Detection of Biomarkers by Using a Molecular Imprinting Based Capacitive Biosensor

The ability to detect and quantitate biomolecules in complex solutions has always been highly sought-after within natural science; being used for the detection of biomarkers, contaminants, and other molecules of interest. A commonly used technique for this purpose is the Enzyme-linked Immunosorbent Assay (ELISA), where often one antibody is directed towards a specific target molecule, and a second labeled antibody is used for the detection of the primary antibody, allowing for the absolute quantification of the biomolecule under study. However, the usage of antibodies as recognition elements limits the robustness of the method; as does the need of using labeled molecules. To overcome these limitations, molecular imprinting has been implemented, creating artificial recognition sites complementary to the template molecule, and obsoleting the necessity of using antibodies for initial binding. Further, for even higher sensitivity, the secondary labeled antibody can be replaced by biosensors relying on the capacitance for the quantification of the target molecule. In this protocol, we describe a method to rapidly and label-free detect and quantitate low-abundant biomolecules (proteins and viruses) in complex samples, with a sensitivity that is significantly better than commonly used detection systems such as the ELISA. This is all mediated by molecular imprinting in combination with a capacitance biosensor.

Here, we present a protocol for the detection and quantification of low abundant molecules in complex solutions using molecular imprinting in combination with a capacitance biosensor.

זיהוי העדינה של סמנים ביולוגיים באמצעות הטבעה מולקולרית מבוסס ביוסנסור קיבולי

The ability to detect and quantitate biomolecules in complex solutions has always been highly sought-after within natural science; being used for the ...

A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.

Fecal-oral transmission of acute gastroenteritis occurs from time to time, especially when people who handled food and water are infected by Salmonella spp./Shigella spp. The gold standard method for the detection of Salmonella spp./Shigella spp. is direct culture but this is labor-intensive and time-consuming. Here, we describe a high-throughput platform for Salmonella spp./Shigella spp. screening, using real-time polymerase chain reaction (PCR) combined with guided culture. There are two major stages: real-time PCR and the guided culture. For the first stage (real-time PCR), we explain each step of the method: sample collection, pre-enrichment, DNA extraction and real-time PCR. If the real-time PCR result is positive, then the second stage (guided culture) is performed: selective culture, biochemical identification and serological characterization. We also illustrate representative results generated from it. The protocol described here would be a valuable platform for the rapid, specific, sensitive and high-throughput screening of Salmonella spp./Shigella spp.

A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.

Salmonella spp./Shigella spp. are common pathogens attributed to diarrhea. Here, we describe a high-throughput platform for the screening of Salmonella spp./Shigella spp. using real-time PCR combined with guided culture.

פלטפורמה תפוקה גבוהה להקרנה של סלמונלה spp /שיגלה spp.

Fecal-oral transmission of acute gastroenteritis occurs from time to time, especially when people who handled food and water are infected by Salmonella ...

Assaying for Inorganic Polyphosphate in Bacteria

Inorganic polyphosphate (polyP) is a biological polymer found in cells from all domains of life, and is required for virulence and stress response in many bacteria. There are a variety of methods for quantifying polyP in biological materials, many of which are either labor-intensive or insensitive, limiting their usefulness. We present here a streamlined method for polyP quantification in bacteria, using a silica membrane column extraction optimized for rapid processing of multiple samples, digestion of polyP with the polyP-specific exopolyphosphatase ScPPX, and detection of the resulting free phosphate with a sensitive ascorbic acid-based colorimetric assay. This procedure is straightforward, inexpensive, and allows reliable polyP quantification in diverse bacterial species. We present representative polyP quantification from the Gram-negative bacterium (Escherichia coli), the Gram-positive lactic acid bacterium (Lactobacillus reuteri), and the mycobacterial species (Mycobacterium smegmatis). We also include a simple protocol for nickel affinity purification of mg quantities of ScPPX, which is not currently commercially available.

We describe a simple method for rapid quantification of inorganic polyphosphate in diverse bacteria, including Gram-negative, Gram-positive, and mycobacterial species.

Assaying עבור הפוליפוספאט אורגניים של חיידקים

Inorganic polyphosphate (polyP) is a biological polymer found in cells from all domains of life, and is required for virulence and stress response in many ...

Quantifying Human Norovirus Virus-like Particles Binding to Commensal Bacteria Using Flow Cytometry

Commensal bacteria are well established to impact infection of eukaryotic viruses. Direct binding between the pathogen and the host microbiome is responsible for altering infection for many of these viruses. Thus, characterizing the nature of virus-bacteria binding is a foundational step needed for elucidating the mechanism(s) by which bacteria alter viral infection. For human norovirus, commensal bacteria enhance B cell infection. The virus directly binds to these bacteria, indicating that this direct interaction is involved in the mechanism of infection enhancement. A variety of techniques can be used to quantify interactions between bacteria and viruses including scintillation counting of radiolabeled viruses and polymerase chain reaction (PCR). Both methods require the use of live virus, which may need to be generated in the laboratory. Currently, none of the established in vitro culture systems available for human norovirus are robust enough to allow for generation of highly concentrated viral stocks. In lieu of live virus, virus-like particles (VLPs) have been used to characterize the interactions between norovirus and bacteria. Herein a flow cytometry method is described with uses virus specific antibodies to quantify VLP binding to gram-negative and gram-positive bacteria. Inclusion of both bacteria only and isotype controls allowed for optimization of the assay to reduce background antibody binding and accurate quantification of VLP attachment to the bacteria tested. High VLP:bacterium ratios result in VLPs binding to large percentages of the bacterial population. However, when VLP quantities are decreased, the percent of bacteria bound also decreases. Ultimately, this method can be employed in future experiments elucidating the specific conditions and structural components that regulate norovirus:bacterial interactions.

The goal of this protocol is to quantify binding of the eukaryotic pathogen human norovirus to bacteria. After performing an initial virus-bacterium attachment assay, flow cytometry is used to detect virally-bound bacteria within the population.

כימות האדם Norovirus וירוס כריכת כריכה של חיידקים קומנדסאל באמצעות זרימה Cy, לנסות

Commensal bacteria are well established to impact infection of eukaryotic viruses. Direct binding between the pathogen and the host microbiome is ...

Models of Murine Vaginal Colonization by Anaerobically Grown Bacteria

The mammalian vagina can be colonized by many bacterial taxa. The human vaginal microbiome is often dominated by Lactobacillus species, but one-in-four women experience bacterial vaginosis, in which a low level of lactobacilli is accompanied by an overgrowth of diverse anaerobic bacteria. This condition has been associated with many health complications, including risks to reproductive and sexual health. While there is growing evidence showing the complex nature of microbial interactions in human vaginal health, the individual roles of these different anaerobic bacteria are not fully understood. This is complicated by the lack of adequate models to study anaerobically grown vaginal bacteria. Mouse models allow us to investigate the biology and virulence of these organisms in vivo. Other mouse models of vaginal bacterial inoculation have previously been described. Here, we describe methods for the inoculation of anaerobically grown bacteria and their viable recovery in conventionally raised C57Bl/6 mice. A new, less stressful procedural method for vaginal inoculation and washing is also described. Inoculation and viable recovery of Gardnerella are outlined in detail, and strategies for additional anaerobes such as Prevotella bivia and Fusobacterium nucleatum are discussed.

The protocol presents a mouse model of vaginal colonization with anaerobically cultured human vaginal bacteria. We focus on Gardnerella vaginalis,&#160;while including suggestions for Prevotella bivia and Fusobacterium nucleatum. This protocol can also be used as a guide for vaginal inoculations and viable recovery of other anaerobically grown bacteria.

מודלים של התיישבות נרתיקית מורין על ידי חיידקים שגודלו אנאירובית

The mammalian vagina can be colonized by many bacterial taxa. The human vaginal microbiome is often dominated by Lactobacillus species, but one-in-four ...

מעקב אחר פתוגן של איברים שלמים באמצעות כימות כתב פלואורסצנטי

High&#45;Resolution Three&#45;Dimensional Whole&#45;Organ Tomography of Microbial Infections

Most infections take place within three-dimensional host tissues with intricate anatomy and locally varying host physiology. The positioning of pathogen cells within this diverse environment significantly affects their stress levels, responses, fate, and contribution to the overall progression of the disease and treatment failure. However, due to the technical difficulties in locating &#181;m-sized pathogen cells within cm-sized host organs, this area of research has been relatively unexplored. Here, we present a method for addressing this challenge. We employ serial two-photon tomography and AI-enhanced image analysis to locate individual Salmonella cells throughout the entire spleen, liver lobes, and whole lymph nodes of infected mice. Using fluorescent reporters and in vivo antibody administration, the replication rate of single Salmonella cells, their local interaction with specific immune cells, and bacterial responses to antibiotics can be determined. These methodologies open avenues for a comprehensive examination of infections, their prevention, and treatment within the three-dimensional tissue context.

מחבר זרקור: חשיפת תגובות חיידקים לאנטיביוטיקה ולמערכת החיסון ברקמות

Here, we describe a procedure that enables organ-wide detection of pathogenic bacteria during infection and quantification of fluorescent reporter activities.

טומוגרפיה תלת-ממדית תלת-ממדית של איברים שלמים ברזולוציה גבוהה של זיהומים מיקרוביאליים

Most infections take place within three-dimensional host tissues with intricate anatomy and locally varying host physiology. The positioning of pathogen ...