המחברים מעריך ד ר פרדריק Fellouse מן המעבדה Sidhu עבור תגובות ביקורתיות של Kunkel שיטה מבוססת phage Fab סינתטי ספריית הבנייה. המחברים מעריך את גברת משה סגל Pavlenco וחברים אחרים מן המעבדה Sidhu לעזרה יקר של הכנת יעילות גבוהה אלקטרו-המוסמכת תאים e. coli , באיכות גבוהה דו-ssDNA. עבודה זו נתמכה על ידי קרן מדעי הטבע הלאומי של סין (מענק מס: 81572698, 31771006) DW, על ידי אוניברסיטת ShanghaiTech (מענק מס: F-0301 בשידור-13-005) כדי מעבדה של נוגדן הנדסה.

<ol>
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P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IMGT+unique+numbering+for+immunoglobulin+and+T+cell+receptor+variable+domains+and+Ig+superfamily+V-like+domains.">IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains.</a> Dev Comp Immunol. 27 (1), 55-77 (2003).</li><li>Graille, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complex+between+Peptostreptococcus+magnus+protein+L+and+a+human+antibody+reveals+structural+convergence+in+the+interaction+modes+of+Fab+binding+proteins.">Complex between Peptostreptococcus magnus protein L and a human antibody reveals structural convergence in the interaction modes of Fab binding proteins.</a> Structure. 9 (8), 679-687 (2001).</li><li>Graille, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crystal+structure+of+a+Staphylococcus+aureus+protein+A+domain+complexed+with+the+Fab+fragment+of+a+human+IgM+antibody:+structural+basis+for+recognition+of+B-cell+receptors+and+superantigen+activity.">Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity.</a> Proc Natl Acad Sci U S A. 97 (10), 5399-5404 (2000).</li><li>Huang, R., Fang, P., Kay, B. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improvements+to+the+Kunkel+mutagenesis+protocol+for+constructing+primary+and+secondary+phage-display+libraries.">Improvements to the Kunkel mutagenesis protocol for constructing primary and secondary phage-display libraries.</a> Methods. 58 (1), 10-17 (2012).</li><li>Chen, G., Sidhu, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+generation+of+synthetic+antibody+libraries+for+phage+display.">Design and generation of synthetic antibody libraries for phage display.</a> Methods Mol Biol. 1131, 113-131 (2014).</li><li>Padlan, E. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anatomy+of+the+antibody+molecule.">Anatomy of the antibody molecule.</a> Mol Immunol. 31 (3), 169-217 (1994).</li><li>Virnekas, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trinucleotide+phosphoramidites:+ideal+reagents+for+the+synthesis+of+mixed+oligonucleotides+for+random+mutagenesis.">Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis.</a> Nucleic Acids Res. 22 (25), 5600-5607 (1994).</li><li>Fellouse, F. A., Sidhu, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Making and Using Antibodies: A Practical Handbook. , 157-180 (2006).</li><li>Fantini, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessment+of+antibody+library+diversity+through+next+generation+sequencing+and+technical+error+compensation.">Assessment of antibody library diversity through next generation sequencing and technical error compensation.</a> PLoS One. 12 (5), e0177574 (2017).</li><li>Glanville, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deep+sequencing+in+library+selection+projects:+what+insight+does+it+bring?.">Deep sequencing in library selection projects: what insight does it bring?.</a> Curr Opin Struct Biol. 33, 146-160 (2015).</li><li>Perelson, A. 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המחברים אין לחשוף.

כדי לבנות גיוון גבוהה, המוצג phage ספריות Fab, בקרת איכות נקודות ביקורת יש צורך לעקוב אחר השלבים השונים של תהליך הבנייה, לרבות את כשירות של תאים אלקטרו-מוסמך, איכות של תבנית דו-ssDNA, היעילות של CCC-dsDNA סינתזה, כייל נוגדנים לאחר אלקטרופורציה קיפול Fab, חומצת אמינו המגוון של Cdr על ידי ניתוח רצף של Fab-phage ש...

mAbs יש שימושים רחב החל מחקר בסיסי אבחון המחלה, הרפוי. נכון לשנת 2016, mAbs יותר מ- 60 אושרו על ידי ארצות הברית המזון סמים המינהל (USFDA) לטיפול קלינית של מחלות אוטואימוניות, סרטן, מחלות זיהומיות1,2.
בשנת 1975, קולר, מילשטיין דיווח טכניקה לדור רציפה של נוגדנים היחודיות המשובטים יחיד ממקור הסלולר המכונה 'hybridomas', טכניקה זו לאחר מכן הפכה לאבן פינה ברפואה ובתעשייה3 ,4. דור של mAbs בשיטה זו דורש צעדים שונים כולל ייצור אנטיגן, חיסון עכבר, מיצוי של B לימפוציטים, פיוז'ן של תאי B עם תאי מיאלומה כדי ליצור תאים ליפידים בן אלמוות, שיבוט בחירה, ליישומים טיפוליים, האנשה נדרש להימנע אנטי-העכבר אנושית נוגדנים (חמה)4,5. עם זאת, לטכנולוגיה הזו, אנטיגנים כולל רעלנים, פתוגנים של חלבונים גבוהה שנשמרת אינם יעילים יחסית מפעילה ויוו תגובה חיסונית mAb הפקה5.
בשנת 1978, האצ'יסון. et al. דיווח על השימוש oligonucleotide ישירה מוטגנזה מכוונת של משקע וירוס חד גדילי bacteriophage6. בשנת 1985, סמית דיווחו שברי גנים זרים יכולים להיות התמזגו במסגרת עם הגן קידוד phage המעיל החלבון השלישי ובכך ניתן להציג על פני phage מבלי להתפשר על שלה infectivity7. אלה חלוצי עבודות הניח בסיס לבנייה עוקבות של נוגדן המוצג phage בספריות תמים החיסון, וטפסים סינתטיים עם התבניות של המקטע משתנה יחיד-שרשרת (scFv) וגם אנטיגן מחייב פרגמנט (Fab) עבור טיפולית mAb פיתוח8,9. מ מנקודת מבט טכנית, פיתוח נוגדן מבוסס התצוגה phage מציעה גישה המשלימה לפיתוח מבוסס-ליפידים mAb שיכול לעזור לעקוף את המגבלות שאנטיגנים מסוימים יכול להוות, האנשה לעבד את זה ליפידים-derived נוגדנים לעיתים קרובות דורשים5. החל 2016, mAbs, נגזר תצוגה ל- 6 phage אושרו במשק לרבות Humira, לאחד mAbs המצליח ביותר משמש לטיפול בדלקת מפרקים שגרונית, מועמדים רבים של נוגדן נגזר התצוגה phage הינם כרגע בשלבים שונים של ניסויים קליניים החקירה10.
לספריות החיסון ותמימה phage נוגדן, המגוון של משלימים את החסר-קביעת אזורים (Cdr) בשרשרת קל וכבד נגזר מן הרפרטואר החיסון הטבעי (כלומר, מתאי B). לעומת זאת, המגוון של Cdr בספריות נוגדן phage סינתטית היא מלאכותית לחלוטין. גישות סינתטי בניית הספרייה לספק שליטה מדויקת על העיצוב של רצף גיוון להציע הזדמנויות ללימודים מכניסטית של נוגדן מבנה, לתפקד11,12. יתר על כן, ניתן למטב את המסגרת עבור ספריות סינתטי לפני הבנייה הספריה כדי להקל על במורד הזרם, בפיתוח תעשייתי רחב היקף11,12.
בשנת 1985, Kunkel דיווח בגישה מוטגנזה מכוונת המבוססים על תבנית חד גדילי הדנ א (ssDNA) כדי להציג את האתר מכוון מוטציות לתוך M13 bacteriophage ביעילות13. גישה זו היה שימוש נרחב לאחר מכן להקמת ספריות phage המוצג. Oligonucleotides DNA מסונתז כימית שנועד להציג את המגוון לתוך Fab Cdr משולבים של phagemid עם תבנית עמוד השדרה של נוגדן. בתהליך זה, phagemid מבוטאת ssDNA המכילים אורציל (דו-ssDNA), oligonucleotides הם annealed אל Cdr והרחבה לסנתז DNA גדילי כפול (dsDNA) בנוכחות T7 DNA פולימראז ו T4 DNA ליגאז. לבסוף, ds-DNA שנוצר יכול להיות מוחדרים Escherichia coli מאת אלקטרופורציה.
גיוון גבוהה, ספריית המוצג phage הבנייה, מתח גבוה אלקטרופורציה תערובת שני תאים אלקטרו-מוסמך, covalently dsDNA עגול סגור (CCC-dsDNA) צריך להיות מוכן בקפידה. . Sidhu et al. ששינה את הכנת תאים אלקטרו-המוסמכת ודנ א שיטות מסורתיות, ספריה משופרת באופן משמעותי גיוון14.
ב פרוטוקול זה, אנו מתארים שיטה לבנייה של ספריות Fab המוצג phage סינתטי עם הבדלים של 109-1010 השגה עם אלקטרופורציה יחיד. איור 1 מציג סקירה של ספריית הבנייה כולל: 1) הכנה תא אלקטרו-המוסמכת יעילות גבוהה; 2) הפקת דו-ssDNA; 3) השיטה של Kunkel המבוסס על oligonucleotide מכוון מוטגנזה מכוונת; 4) אלקטרופורציה, חישוב של גודל הספרייה; 5) חלבון A/L-מבוסס אליסה לקיפול והערכה פונקציונלי; ו- 6) ניתוח רצף הדנ א של גיוון. כל ריאגנטים, זנים, ציוד מפורטים בטבלה של החומר. טבלה 1 מציגה את הכיוונון מגיב.

<table>
	<tbody>
		<tr>
			<td>Reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1.0 M H3PO4</td>
			<td>Fisher</td>
			<td>AC29570</td>
			<td></td>
		</tr>
		<tr>
			<td>1.0 M Tris, pH 8.0</td>
			<td>Invitrogen</td>
			<td>15568-025</td>
			<td></td>
		</tr>
		<tr>
			<td>10 mM ATP</td>
			<td>Invitrogen</td>
			<td>18330-019</td>
			<td></td>
		</tr>
		<tr>
			<td>100 mM dithiothreitol</td>
			<td>Fisher</td>
			<td>BP172</td>
			<td></td>
		</tr>
		<tr>
			<td>100 mM dNTP mix</td>
			<td>GE Healthcare</td>
			<td>28-4065-60</td>
			<td>solution containing 25 mM each of dATP, dCTP, dGTP and dTTP.</td>
		</tr>
		<tr>
			<td>3,3&#8217;,5,5&#8217;-tetramethylbenzidine (TMB)</td>
			<td>Kirkegaard &#38; Perry Laboratories Inc</td>
			<td>50-76-02</td>
			<td></td>
		</tr>
		<tr>
			<td>50X TAE</td>
			<td>Invitrogen</td>
			<td>24710030</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Fisher</td>
			<td>BP160</td>
			<td></td>
		</tr>
		<tr>
			<td>Carbenicillin, carb</td>
			<td>Sigma</td>
			<td>C1389</td>
			<td>100 mg/mL in water,&#160; 0.22 &#956;m filter-sterilize, work concentration: 100 &#956;g/mL.</td>
		</tr>
		<tr>
			<td>Chloramphenicol, cmp</td>
			<td>Sigma</td>
			<td>C0378</td>
			<td>100 mg/mL in ethanol, 0.22 &#956;m filter-sterilize, work concentration: 10 &#956;g/mL.</td>
		</tr>
		<tr>
			<td>EDTA 0.5 M, pH 8.0</td>
			<td>Invitrogen</td>
			<td>AM9620G</td>
			<td></td>
		</tr>
		<tr>
			<td>Granulated agar</td>
			<td>VWR</td>
			<td>J637-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>H2O2 peroxidase substrate</td>
			<td>Kirkegaard &#38; Perry Laboratories Inc</td>
			<td>50-65-02</td>
			<td></td>
		</tr>
		<tr>
			<td>K2HPO4</td>
			<td>Sigma</td>
			<td>795488</td>
			<td></td>
		</tr>
		<tr>
			<td>Kanamycin, kan</td>
			<td>Fisher</td>
			<td>AC61129</td>
			<td>50 mg/mL in water,&#160; 0.22 &#956;m filter-sterilize, work concentration: 50 &#956;g/mL.</td>
		</tr>
		<tr>
			<td>KH2PO4</td>
			<td>Sigma</td>
			<td>P2222</td>
			<td></td>
		</tr>
		<tr>
			<td>Na2HPO4</td>
			<td>Sigma</td>
			<td>94046</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Alfa Aesar</td>
			<td>U19C015</td>
			<td></td>
		</tr>
		<tr>
			<td>Nanodrop</td>
			<td>Fisher</td>
			<td>ND2000C</td>
			<td></td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td>Fisher</td>
			<td>SS256</td>
			<td>! CAUTION NaOH causes burns.</td>
		</tr>
		<tr>
			<td>NON-Fat Powdered Milk</td>
			<td>Sangon Biotech</td>
			<td>A600669</td>
			<td></td>
		</tr>
		<tr>
			<td>PEG-8000</td>
			<td>Fisher</td>
			<td>BP233</td>
			<td></td>
		</tr>
		<tr>
			<td>Protein A-HRP conjugate</td>
			<td>Invitrogen</td>
			<td>101123</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAprep Spin M13 Kit</td>
			<td>Qiagen</td>
			<td>22704</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAquick Gel Extraction Kit</td>
			<td>Qiagen</td>
			<td>28706</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAquick PCR Purification Kit</td>
			<td>Qiagen</td>
			<td>28104</td>
			<td></td>
		</tr>
		<tr>
			<td>Recombinant Protein L</td>
			<td>Fisher</td>
			<td>77679</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA polymerase</td>
			<td>New England Biolabs</td>
			<td>M0203S</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 polynucleotide kinase</td>
			<td>New England Biolabs</td>
			<td>M0201S</td>
			<td></td>
		</tr>
		<tr>
			<td>T7 DNA polymerase</td>
			<td>New England Biolabs</td>
			<td>M0274S</td>
			<td></td>
		</tr>
		<tr>
			<td>Tetracycline, tet</td>
			<td>Sigma</td>
			<td>T7660</td>
			<td>50 mg/mL in water, 0. 22 &#956;m filter-sterilize, work concentration: 10 &#956;g/mL.</td>
		</tr>
		<tr>
			<td>Tryptone</td>
			<td>Fisher</td>
			<td>0123-07-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Sigma</td>
			<td>P2287</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultrapure glycerol</td>
			<td>Invitrogen</td>
			<td>15514-011</td>
			<td></td>
		</tr>
		<tr>
			<td>Uridine</td>
			<td>Sigma</td>
			<td>U3750</td>
			<td>25 mg/mL in ethanol, work concentration: 0.25 &#956;g/mL.</td>
		</tr>
		<tr>
			<td>Yeast extract</td>
			<td>VWR</td>
			<td>DF0127-08</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company </td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Strains</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>E.coli CJ236</td>
			<td>New England Biolabs</td>
			<td>E4141</td>
			<td>Genotype: dut-&#160; ung-&#160; thi-1 relA1 spoT1 mcrA/pCJ105(F&#39; camr). Used for preparation of dU-ssDNA.</td>
		</tr>
		<tr>
			<td>E.coli SS320</td>
			<td>Lucigen</td>
			<td>60512</td>
			<td>Genotype: [F&#39;proAB+lacIq lacZ&#916;M15 Tn10 (tetr)] hsdR mcrB araD139 &#916;(araABC-leu)7679 &#916;lacX74 galUgalK rpsL thi. Optimized for high-efficiency electroporation and filamentous bacteriophage production.</td>
		</tr>
		<tr>
			<td>M13KO7</td>
			<td>New England Biolabs</td>
			<td>N0315S</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company </td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>0.2-cm gap electroporation cuvette</td>
			<td>BTX</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>96-well 2mL Deep-well plates</td>
			<td>Fisher</td>
			<td>278743</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well Maxisorp immunoplates</td>
			<td>Nunc</td>
			<td>151759</td>
			<td></td>
		</tr>
		<tr>
			<td>Baffled flasks</td>
			<td>Corning</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Benchtop centrifuge</td>
			<td>Eppendorf</td>
			<td>5811000096</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge bottles</td>
			<td>Nalgene</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>ECM-630 electroporator</td>
			<td>BTX</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Magnetic stir bars</td>
			<td>Nalgene</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Thermo Fisher centrifuge</td>
			<td>Fisher</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>High speed shaker</td>
			<td>TAITEK</td>
			<td>MBR-034P</td>
			<td></td>
		</tr>
		<tr>
			<td>Microplate shaker</td>
			<td>QILINBEIER</td>
			<td>QB-9002</td>
			<td></td>
		</tr>
		<tr>
			<td>Liquid handler for 96 and 384 wells</td>
			<td>RAININ</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mutil-channel pipette</td>
			<td>RAININ</td>
			<td>E4XLS</td>
			<td></td>
		</tr>
		<tr>
			<td>Amicon concentrator</td>
			<td>Merck</td>
			<td>UFC803096</td>
			<td></td>
		</tr>
	</tbody>
</table>

construction of synthetic phage displayed fab library with tailored diversity

הביקוש נוגדנים חד-שבטיים (mAbs) מחקר בסיסי ורפואה הולך וגדל מדי שנה. ליפידים הטכנולוגיה כבר השיטה הדומיננטית לפיתוח mAb מאז את הדו ח הראשון שלה בשנת 1975. כמו טכנולוגיה חלופית, שיטות תצוגה phage לפיתוח mAb הן יותר ויותר אטרקטיבי מאז Humira, הנוגדן הראשון נגזר phage ואחד mAbs הנמכר, אושרה לטיפול קליני של דלקת מפרקים שגרונית בשנת 2002. חיה-שאינו מבוסס טכנולוגיית פיתוח mAb, התצוגה phage עוקף אנטיגן immunogenicity, האנשה ותחזוקה בעלי חיים הדרושים של ליפידים מסורתי המבוסס על טכנולוגיית פיתוח נוגדן. ב פרוטוקול זה, אנו מתארים שיטה לבנייה של ספריות Fab המוצג phage סינתטי עם הבדלים של 109-1010 השגה עם אלקטרופורציה יחיד. פרוטוקול זה מורכב: 1) הכנה תא אלקטרו-המוסמכת יעילות גבוהה; 2) הפקת המכילות אורציל דנ א חד גדילי (דו-ssDNA); 3) השיטה של Kunkel המבוסס על oligonucleotide מכוון מוטגנזה מכוונת; 4) אלקטרופורציה, חישוב של גודל הספרייה; 5) חלבון מבוססת על A/L מקושרים-אנזים immunosorbent assay (אליסה) לקיפול והערכה פונקציונלי; ו- 6) ניתוח רצף הדנ א של גיוון.

בעקבות את תרשים זרימה הקמת ספריה ללונג (ראה איור 1), הכנו המסייע M13KO7 תאים אלקטרו-המוסמכת של e. coli SS320 phage מראש נגוע. היעילות של תאים אלקטרו-המוסמכת אלה מוערך כמו 2 X 109 cfu/µg כאשר עמוד השדרה Fab phagemid לבנייה הספרייה שימשה (איור 4).
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Watch this Scientific Journal Video about Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity at JoVE.com

Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity

פרוטוקול זה מתאר הליך מפורט להקמת ספרייה המוצג phage נוגדן סינתטי עם גיוון מחויטת. נוגדנים סינתטי יש יישומים רבים של מחקר בסיסי אבחון המחלה, הרפוי.

בניית Phage סינתטי מוצגת ספריית Fab עם גיוון המותאמים

Demand for monoclonal antibodies (mAbs) in basic research and medicine is increasing yearly. Hybridoma technology has been the dominant method for mAb ...

construction-synthetic-phage-displayed-fab-library-with-tailored

Research

JoVE Journal

Immunology and Infection

13.5K Views.  ShanghaiTech University. פרוטוקול זה מתאר הליך מפורט להקמת ספרייה המוצג phage נוגדן סינתטי עם גיוון מחויטת. נוגדנים סינתטי יש יישומים רבים של מחקר בסיסי אבחון המחלה, הרפוי.

Video: Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity

'Bioluminescent' Reporter Phage for the Detection of Category A Bacterial Pathogens

Yersinia pestis and Bacillus anthracis are Category A bacterial pathogens that are the causative agents of the plague and anthrax, respectively 1. Although the natural occurrence of both diseases&#39; is now relatively rare, the possibility of terrorist groups using these pathogens as a bioweapon is real. Because of the disease&#39;s inherent communicability, rapid clinical course, and high mortality rate, it is critical that an outbreak be detected quickly. Therefore methodologies that provide rapid detection and diagnosis are essential to ensure immediate implementation of public health measures and activation of crisis management.
Recombinant reporter phage may provide a rapid and specific approach for the detection of Y. pestis and B. anthracis. The Centers for Disease Control and Prevention currently use the classical phage lysis assays for the confirmed identification of these bacterial pathogens 2-4. These assays take advantage of naturally occurring phage which are specific and lytic for their bacterial hosts. After overnight growth of the cultivated bacterium in the presence of the specific phage, the formation of plaques (bacterial lysis) provides a positive identification of the bacterial target. Although these assays are robust, they suffer from three shortcomings: 1) they are laboratory based; 2) they require bacterial isolation and cultivation from the suspected sample, and 3) they take 24-36 h to complete. To address these issues, recombinant &#34;light-tagged&#34; reporter phage were genetically engineered by integrating the Vibrio harveyi luxAB genes into the genome of Y. pestis and B. anthracis specific phage 5-8. The resulting luxAB reporter phage were able to detect their specific target by rapidly (within minutes) and sensitively conferring a bioluminescent phenotype to recipient cells. Importantly, detection was obtained either with cultivated recipient cells or with mock-infected clinical specimens 7.
For demonstration purposes, here we describe the method for the phage-mediated detection of a known Y. pestis isolate using a luxAB reporter phage constructed from the CDC plague diagnostic phage &#934;A1122 6,7 (Figure 1). A similar method, with minor modifications (e.g. change in growth temperature and media), may be used for the detection of B. anthracis isolates using the B. anthracis reporter phage W&#946;::luxAB 8. The method describes the phage-mediated transduction of a biolumescent phenotype to cultivated Y. pestis cells which are subsequently measured using a microplate luminometer. The major advantages of this method over the traditional phage lysis assays is the ease of use, the rapid results, and the ability to test multiple samples simultaneously in a 96-well microtiter plate format.
<img alt="Figure 1" src="/files/ftp_upload/2740/2740fig1.jpg" /> 
Figure 1. Detection schematic. The phage are mixed with the sample, the phage infects the cell, luxAB are expressed, and the cell bioluminesces. Sample processing is not necessary; the phage and cells are mixed and subsequently measured for light.

A simple method for the identification of priority bacterial pathogens is to use genetically engineered reporter phage. These reporter phage, which are specific to their particular host species, are capable of rapidly transducing a bioluminescent signal response to host cells. Herein, we describe the use of reporter phage for the detection of Yersinia pestis.

&quot;Bioluminescent&quot; כתב phage לצורך זיהוי של קטגוריה פתוגנים חיידקיים

Yersinia pestis and Bacillus anthracis are Category A bacterial pathogens that are the causative agents of the plague and anthrax, respectively 1. ...

Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy

During the last few years scientists became increasingly aware that average data obtained from microbial population based experiments are not representative of the behavior, status or phenotype of single cells. Due to this new insight the number of single cell studies rises continuously (for recent reviews see 1,2,3). However, many of the single cell techniques applied do not allow monitoring the development and behavior of one specific single cell in time (e.g. flow cytometry or standard microscopy).
Here, we provide a detailed description of a microscopy method used in several recent studies 4, 5, 6, 7, which allows following and recording (fluorescence of) individual bacterial cells of Bacillus subtilis and Streptococcus pneumoniae through growth and division for many generations. The resulting movies can be used to construct phylogenetic lineage trees by tracing back the history of a single cell within a population that originated from one common ancestor. This time-lapse fluorescence microscopy method cannot only be used to investigate growth, division and differentiation of individual cells, but also to analyze the effect of cell history and ancestry on specific cellular behavior. Furthermore, time-lapse microscopy is ideally suited to examine gene expression dynamics and protein localization during the bacterial cell cycle. The method explains how to prepare the bacterial cells and construct the microscope slide to enable the outgrowth of single cells into a microcolony. In short, single cells are spotted on a semi-solid surface consisting of growth medium supplemented with agarose on which they grow and divide under a fluorescence microscope within a temperature controlled environmental chamber. Images are captured at specific intervals and are later analyzed using the open source software ImageJ.

Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy

This protocol provides a step-by-step procedure to monitor single cell behavior of different bacteria in time using automated fluorescence time-lapse microscopy. Furthermore, we provide guidelines how to analyze the microscopy images.

תא הדמיה חיה של Bacillus subtilis ו Streptococcus pneumoniae באמצעות מיקרוסקופית אוטומטי זמן לשגות

During the last few years scientists became increasingly aware that average data obtained from microbial population based experiments are not ...

Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography

Viruses, particularly bacteriophages (phages), are the most numerous biological entities on Earth1,2. Viruses modulate host cell abundance and diversity, contribute to the cycling of nutrients, alter host cell phenotype, and influence the evolution of both host cell and viral communities through the lateral transfer of genes 3. Numerous studies have highlighted the staggering genetic diversity of viruses and their functional potential in a variety of natural environments. 
Metagenomic techniques have been used to study the taxonomic diversity and functional potential of complex viral assemblages whose members contain single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and RNA genotypes 4-9. Current library construction protocols used to study environmental DNA-containing or RNA-containing viruses require an initial nuclease treatment in order to remove nontargeted templates 10. However, a comprehensive understanding of the collective gene complement of the virus community and virus diversity requires knowledge of all members regardless of genome composition. Fractionation of purified nucleic acid subtypes provides an effective mechanism by which to study viral assemblages without sacrificing a subset of the community&#x2019;s genetic signature. 
Hydroxyapatite, a crystalline form of calcium phosphate, has been employed in the separation of nucleic acids, as well as proteins and microbes, since the 1960s11. By exploiting the charge interaction between the positively-charged Ca2+ ions of the hydroxyapatite and the negatively charged phosphate backbone of the nucleic acid subtypes, it is possible to preferentially elute each nucleic acid subtype independent of the others. We recently employed this strategy to independently fractionate the genomes of ssDNA, dsDNA and RNA-containing viruses in preparation of DNA sequencing 12. Here, we present a method for the fractionation and recovery of ssDNA, dsDNA and RNA viral nucleic acids from mixed viral assemblages using hydroxyapatite chromotography.

We describe an efficient method to separate single-stranded DNA, double-stranded DNA and RNA molecules from environmental viral communities. Nucleic acids are fractionated using hydroxyapatite chromatography with increasing concentrations of phosphate-containing buffers. This method permits the isolation of all viral nucleic acid types from environmental samples.

ההפרדה של ה-DNA חד גדילי, פעמיים תקועים DNA ו-RNA מהקהילה ויראלי הסביבה באמצעות כרומטוגרפיה hydroxyapatite

Viruses, particularly bacteriophages (phages), are the most numerous biological entities on Earth1,2.  Viruses modulate host cell abundance and diversity, ...

Following Cell-fate in E. coli After Infection by Phage Lambda

The system comprising bacteriophage (phage) lambda and the bacterium E. coli has long served as a paradigm for cell-fate determination1,2. Following the simultaneous infection of the cell by a number of phages, one of two pathways is chosen: lytic (virulent) or lysogenic (dormant)3,4. We recently developed a method for fluorescently labeling individual phages, and were able to examine the post-infection decision in real-time under the microscope, at the level of individual phages and cells5. Here, we describe the full procedure for performing the infection experiments described in our earlier work5. This includes the creation of fluorescent phages, infection of the cells, imaging under the microscope and data analysis. The fluorescent phage is a "hybrid", co-expressing wild- type and YFP-fusion versions of the capsid gpD protein. A crude phage lysate is first obtained by inducing a lysogen of the gpD-EYFP (Enhanced Yellow Fluorescent Protein) phage, harboring a plasmid expressing wild type gpD. A series of purification steps are then performed, followed by DAPI-labeling and imaging under the microscope. This is done in order to verify the uniformity, DNA packaging efficiency, fluorescence signal and structural stability of the phage stock. The initial adsorption of phages to bacteria is performed on ice, then followed by a short incubation at 35&deg;C to trigger viral DNA injection6. The phage/bacteria mixture is then moved to the surface of a thin nutrient agar slab, covered with a coverslip and imaged under an epifluorescence microscope. The post-infection process is followed for 4 hr, at 10 min interval. Multiple stage positions are tracked such that ~100 cell infections can be traced in a single experiment. At each position and time point, images are acquired in the phase-contrast and red and green fluorescent channels. The phase-contrast image is used later for automated cell recognition while the fluorescent channels are used to characterize the infection outcome: production of new fluorescent phages (green) followed by cell lysis, or expression of lysogeny factors (red) followed by resumed cell growth and division. The acquired time-lapse movies are processed using a combination of manual and automated methods. Data analysis results in the identification of infection parameters for each infection event (e.g. number and positions of infecting phages) as well as infection outcome (lysis/lysogeny). Additional parameters can be extracted if desired.

Following Cell-fate in E. coli After Infection by Phage Lambda

This article describes the procedure for preparing a fluorescently-labeled version of bacteriophage lambda, infection of E. coli bacteria, following the infection outcome under the microscope, and analysis of infection results.

בעקבות Cell-גורל ב<em&gt; א coli</em&gt; לאחר זיהום על ידי phage מבדה

The system comprising bacteriophage (phage) lambda and the bacterium E. coli has long served as a paradigm for cell-fate determination1,2. Following the ...

Imaging of HIV-1 Envelope-induced Virological Synapse and Signaling on Synthetic Lipid Bilayers

Human immunodeficiency virus type 1 (HIV-1) infection occurs most efficiently via cell to cell transmission2,10,11. This cell to cell transfer between CD4+ T cells involves the formation of a virological synapse (VS), which is an F-actin-dependent cell-cell junction formed upon the engagement of HIV-1 envelope gp120 on the infected cell with CD4 and the chemokine receptor (CKR) CCR5 or CXCR4 on the target cell 8. In addition to gp120 and its receptors, other membrane proteins, particularly the adhesion molecule LFA-1 and its ligands, the ICAM family, play a major role in VS formation and virus transmission as they are present on the surface of virus-infected donor cells and target cells, as well as on the envelope of HIV-1 virions1,4,5,6,7,13. VS formation is also accompanied by intracellular signaling events that are transduced as a result of gp120-engagement of its receptors. Indeed, we have recently showed that CD4+ T cell interaction with gp120 induces recruitment and phosphorylation of signaling molecules associated with the TCR signalosome including Lck, CD3&zeta;, ZAP70, LAT, SLP-76, Itk, and PLC&gamma;15.
In this article, we present a method to visualize supramolecular arrangement and membrane-proximal signaling events taking place during VS formation. We take advantage of the glass-supported planar bi-layer system as a reductionist model to represent the surface of HIV-infected cells bearing the viral envelope gp120 and the cellular adhesion molecule ICAM-1. The protocol describes general procedures for monitoring HIV-1 gp120-induced VS assembly and signal activation events that include i) bi-layer preparation and assembly in a flow cell, ii) injection of cells and immunofluorescence staining to detect intracellular signaling molecules on cells interacting with HIV-1 gp120 and ICAM-1 on bi-layers, iii) image acquisition by TIRF microscopy, and iv) data analysis. This system generates high-resolution images of VS interface beyond that achieved with the conventional cell-cell system as it allows detection of distinct clusters of individual molecular components of VS along with specific signaling molecules recruited to these sub-domains.

This article describes a method to visualize formation of an HIV-1 envelope-induced virological synapse on glass supported planar bilayers by total internal reflection fluorescence (TIRF) microscopy. The method can also be combined with immunofluorescence staining to detect activation and redistribution of signaling molecules that occur during HIV-1 envelope-induced virological synapse formation.

הדמיה של HIV-1 מעטפה הנגרמת סינפסה Virological והאיתות על bilayers שומנים סינתטי

Human immunodeficiency virus type 1 (HIV-1) infection occurs most efficiently via cell to cell transmission2,10,11. This cell to cell transfer between ...

Scalable High Throughput Selection From  Phage-displayed Synthetic Antibody Libraries

The demand for antibodies that fulfill the needs of both basic and clinical research applications is high and will dramatically increase in the future. However, it is apparent that traditional monoclonal technologies are not alone up to this task. This has led to the development of alternate methods to satisfy the demand for high quality and renewable affinity reagents to all accessible elements of the proteome. Toward this end, high throughput methods for conducting selections from phage-displayed synthetic antibody libraries have been devised for applications involving diverse antigens and optimized for rapid throughput and success. Herein, a protocol is described in detail that illustrates with video demonstration the parallel selection of Fab-phage clones from high diversity libraries against hundreds of targets using either a manual 96 channel liquid handler or automated robotics system. Using this protocol, a single user can generate hundreds of antigens, select antibodies to them in parallel and validate antibody binding within 6-8 weeks. Highlighted are: i) a viable antigen format, ii) pre-selection antigen characterization, iii) critical steps that influence the selection of specific and high affinity clones, and iv) ways of monitoring selection effectiveness and early stage antibody clone characterization. With this approach, we have obtained synthetic antibody fragments (Fabs) to many target classes including single-pass membrane receptors, secreted protein hormones, and multi-domain intracellular proteins. These fragments are readily converted to full-length antibodies and have been validated to exhibit high affinity and specificity. Further, they have been demonstrated to be functional in a variety of standard immunoassays including Western blotting, ELISA, cellular immunofluorescence, immunoprecipitation and related assays. This methodology will accelerate antibody discovery and ultimately bring us closer to realizing the goal of generating renewable, high quality antibodies to the proteome.

A method is described with visual accompaniment for conducting scalable, high throughput selections from phage-displayed combinatorial synthetic antibody libraries against hundreds of antigens simultaneously. Using this parallel approach, we have isolated antibody fragments that exhibit high affinity and specificity for diverse antigens that are functional in standard immunoassays.

גבוהה Scalable תפוקה בחירה מספריות נוגדן סינטטיים-מוצג הפאג

The demand for antibodies that fulfill the needs of both basic and clinical research applications is high and will dramatically increase in the future. ...

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysis by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.

Here, we present phenomic approaches for the functional characterization of putative phage genes. Techniques include a developed assay capable of monitoring host anabolic metabolism, the Multi-phenotype Assay Plates (MAPs), in addition to the established method of metabolomics, capable of measuring effects to catabolic metabolism.

Phenomics הפאג: גישות פיזיולוגיות לאפיין חלבונים חדשים ויראלי

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage ...

Anti-virulent Disruption of Pathogenic Biofilms using Engineered Quorum-quenching Lactonases

The rapid emergence of multi-drug resistant bacteria has accelerated the need for novel therapeutic approaches to counter life-threatening infections. The persistence of bacterial infection is often associated with quorum-sensing-mediated biofilm formation. Thus, the disruption of this signaling circuit presents an attractive anti-virulence strategy. Quorum-quenching lactonases have been reported to be effective disrupters of quorum-sensing circuits. However, there have been very few reports of the effective use of these enzymes in disrupting bacterial biofilm formation. This protocol describes a method to disrupt biofilm formation in a clinically relevant A. baumannii S1 strain through the use of an engineered quorum-quenching lactonase. Acinetobacter baumannii is a major human pathogen implicated in serious hospital-acquired infections globally and its virulence is attributed predominantly to its biofilm's tenacity. The engineered lactonase treatment achieved significant A. baumannii S1 biofilm reduction. This study also showed the possibility of using engineered quorum-quenching enzymes in future treatment of biofilm-mediated bacterial diseases. Lastly, the method may be used to evaluate the competency of promising quorum-quenching enzymes.

Quorum-quenching enzymes are anti-virulent and anti-bacterial options that can mitigate pathogenesis without risk of incurring resistance, by preventing the expression of virulence factors and genes associated with antibiotic resistance and biofilm formation. In this study, we report a method that demonstrates the efficacy of quorum-quenching enzymes in bacterial biofilm disruption.

שיבוש אנטי-ארסי של Biofilms פתוגניים באמצעות Lactonases תכנון הנדסי Quorum-מרווה

The rapid emergence of multi-drug resistant bacteria has accelerated the need for novel therapeutic approaches to counter life-threatening infections. The ...

Analysis of Lymphocyte Extravasation Using an In Vitro Model of the Human Blood-brain Barrier

Lymphocyte extravasation into the central nervous system (CNS) is critical for immune surveillance. Disease-related alterations of lymphocyte extravasation might result in pathophysiological changes in the CNS. Thus, investigation of lymphocyte migration into the CNS is important to understand inflammatory CNS diseases and to develop new therapy approaches. Here we present an in vitro model of the human blood-brain barrier to study lymphocyte extravasation. Human brain microvascular endothelial cells (HBMEC) are confluently grown on a porous polyethylene terephthalate transwell insert to mimic the endothelium of the blood-brain barrier. Barrier function is validated by zonula occludens immunohistochemistry, transendothelial electrical resistance (TEER) measurements as well as analysis of evans blue permeation. This model allows investigation of the diapedesis of rare lymphocyte subsets such as CD56brightCD16dim/- NK cells. Furthermore, the effects of other cells, cytokines and chemokines, disease-related alterations, and distinct treatment regimens on the migratory capacity of lymphocytes can be studied. Finally, the impact of inflammatory stimuli as well as different treatment regimens on the endothelial barrier can be analyzed.

Analysis of Lymphocyte Extravasation Using an In Vitro Model of the Human Blood-brain Barrier

Here, we describe a human blood-brain barrier model enabling to investigate lymphocyte transmigration into the central nervous system in vitro.

ניתוח של לימפוציטים extravasation שימוש<em&gt; במבחנה</em&gt; דגם של מחסום אנושי דם-מוח

Lymphocyte extravasation into the central nervous system (CNS) is critical for immune surveillance. Disease-related alterations of lymphocyte ...

Overlapping Peptide Library to Map Qa-1 Epitopes in a Protein

Qa-1 (HLA-E in human) belongs to a group of non-classical major histocompatibility complex 1b (MHC-Ib) molecules. Recent data suggest that Qa-1 molecules play important roles in surveying cells for structural and functional integrity, inducing immune regulation, and limiting immune responses to viral infections. Additionally, functional augmentation of Qa-1-restricted CD8+ T cells through epitope immunization has shown therapeutic effects in several autoimmune disease animal models, e.g. experimental allergic encephalomyelitis, collagen-induced arthritis, and non-obese diabetes. Therefore, there is an urgent need for a method that can efficiently and quickly identify functional Qa-1 epitopes in a protein. Here, we describe a protocol that utilizes Qa-1-restricted CD8+ T cell lines specific for an overlapping peptide (OLP) library for determining Qa-1 epitopes in a protein. This OLP library contains 15-mer overlapping peptides that cover the whole length of a protein, and adjacent peptides overlap by 11 amino acids. Using this protocol, we recently identified a 9-mer Qa-1 epitope in myelin oligodendrocyte glycoprotein (MOG). This newly mapped MOG Qa-1 epitope was shown to induce epitope-specific, Qa-1-restricted CD8+ T cells that enhanced myelin-specific immune regulation. Therefore, this protocol is useful for future investigation of novel targets and functions of Qa-1-restricted CD8+ T cells.

Qa-1 (HLA-E in human) belongs to a group of non-classical major histocompatibility complex 1b molecules. Immunization with Qa-1-binding epitopes has been shown to augment tissue-specific immune regulation and ameliorate several autoimmune diseases. Herein we describe an overlapping peptide library strategy for the identification of Qa-1 epitopes in a protein.

ספריית פפטיד חופפים למפות Epitopes Qa-1 בחלבון

Qa-1 (HLA-E in human) belongs to a group of non-classical major histocompatibility complex 1b (MHC-Ib) molecules. Recent data suggest that Qa-1 molecules ...