המחברים רוצה להודות נתן ג'ונסון על סיועו בהכנת הדמויות. מחקר זה נתמך על ידי תוכנית פאן-טכנולוגיות אשר ממומן על ידי של משרד האנרגיה האמריקני של Office הביולוגיים ומחקר סביבתי (תכנית גנומית של המדע), Microbiomes המעבר (מנטה) מעבדה מכוונות פיתוח מחקר היזמה המעבדה הלאומית הפסיפי, כמו גם את נבחרת מוסדות של הבריאות הלאומי מכון בריאות למדעי הסביבה (R01 ES022190) ו- NIH (P42 ES027704). KEBJ הייתי רוצה להודות R21 HD084788 עבור תמיכה כספית לפתח ולאמת טכניקות החילוץ רומן רב-omic. עבודה זו בוצעה ב W. R. ויילי סביבתיים מולקולרית מדעי מעבדה (EMSL), מתקן משתמש המדעי לאומי DOE-הפסיפי הלאומי מעבדה (PNNL). PNNL הוא מעבדה לאומית רב התוכנית המופעלת ע י Battelle על האלמונית תחת חוזה דה-AC06-76RL01830.

<ol>
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המחברים מצהירים כי יש להם אינטרסים כלכליים אין מתחרים.

חשוב לציין כי לא כל המעבדות יהיו זמינות ציוד אז שיטות מסוימות, לדוגמה השלב פירוק, ניתן להתאים. כאן אנו משתמשים vortexing sonicating, אולם השימוש מכה חרוז גדול 50 מ ל יעבוד. אם איזה שהוא לופילייזר עם טמפרטורת אספן מסוגל-105 מעלות צלזיוס אינה זמינה, יכולים להיות מיובש דגימות תחת זרם חנקן. גם סוגי אדמה להשת?...

הערכת קהילות מיקרוביאלית בקרקע יש השלכות חשובות להבנת שינוי האקלים ורכיבה פחמן. מחקרים שנעשו לאחרונה הראו אולם קשיים, כגון חוסר הגנום ברצף עבור microbiota בסוגים שונים של אדמה והפונקציה לא ידוע של החלבונים זוהה רבים. כתוצאה אתגרים בשל קרקע להיות הקהילה מיקרוביאלי המורכבים ביותר הידוע עד כה1,2,3. ניתוח רב-omic, המשלבים נובע metagenomic ', ' metatranscriptomic ', ' metaproteomic ', metabolomic, lipidomic מחקרים, יושמו לאחרונה במחקרים קרקע רבים כדי להשיג הבנה טובה יותר לתוך החיידקים ההווה, תוך קבלת מידע מקיף אודות השינויים המולקולריים המתרחשים בשל הסביבה לפליטת1,4,5. אתגר אחד עם מחקרים מולטי-omic זה ספקטרומטר מסה (MS)-לפי מידות metaproteomic, metabolomic ו- lipidomic מצריכים בדרך כלל תהליך החילוץ ספציפיים עבור כל omic להיות MS התואם6,7 , 8 , 9. אלה נהלים מדויקים להפוך ביישום שלהם מאוד קשה או בלתי אפשרי כאשר רק כמות מוגבלת של המדגם הינו זמין. האתגרים הללו עוררו אותנו לחקור בו זמנית מטבוליט, חלבונים, שומנים בדם החילוץ (MPLEx) שיטה מסוגלת באמצעות אמצעי אחסון מדגם קטן או גושים, שיפור דיוק, מתן דגימת מהר יותר, ההכנות כל שלושה ניתוחים 10. נכון להיום, ישנם הליכים החילוץ אין קרקע חלופית להשגת כל המטרות הללו.
כדי לאפשר ריבוי העולמית-omic ניתוחים של דגימת אדמה יחיד, פרוטוקול החילוץ בממיסים אורגניים המבוססים על כלורופורם, מתנול, הפרדות צבע המים היה שימוש10. שיטה זו פותחה במקור עבור סך השומנים עקירות9,11 , ולאחרונה תוקן על החילוץ סימולטני של מטבוליטים, חלבונים, שומנים מדגם יחיד12,13 ,14,15,16,17,18,19,20,21,22, 23,24,25,26,27,28,29,30, שמאפשר הכמות המדגם פחות, השתנות ניסיוני10. פרוטוקול MPLEx, כלורופורם אינה miscible עם מים, אשר מספק את הבסיס עבור triphasic כימי ההפרדה של מדגם המרכיבים לתוך שברים נפרדים. פזה מימית בראש מכיל ולכן מטבוליטים הידרופיליות, ואחריו דיסק חלבון, ואז שכבה השומנים בשלב כלורופורם התחתון (איור 1). MPLEx מוחל על רוב קרקעות, חלקיקי הלכלוך מצטבר בתחתית מאוד של הצינורות דגימה, יכול להיות מושלך לאחר שנאספו כל השכבות. כל סוג הקרקע עשויות להיות שונות, עם זאת, ובשנת אדמה מאוד אורגני כגון כבול, שפכי אדמה נשאר השכבה האמצעית לא נופל לתחתית הצינור הדגימה. MPLEx מספקת מספר יתרונות כאשר בידוד המולקולה מספר סוגי מדגם זהה כגון כמויות מדגם קטן 1) יכול לשמש עבור ניתוחים רב-omic, 2) מולטי-omic ושילוב הירידה מדגם זהה השתנות ניסיוני הכולל, ואת 3) ניתן להכין במספרים גדולים של דגימות מהר יותר תפוקה גבוהה יותר מחקרים10. יחד יתרונות אלה הם חיוני למתן יותר יכולות מדידה להערכת דגימות. אדמה וקהילות מיקרוביאלי מורכבים שלהם.

<table>
	<tbody>
		<tr>
			<td>Chloroform</td>
			<td>Sigma-Aldrich</td>
			<td>650498</td>
			<td>Stored at -20&#176;C !Caution chloroform has acute potential health effects, skin irritation and possible chemical burns, irritation to the respiratory system, may affect the kidneys, liver, heart. Wear suitable protective glasses, clothing and gloves, work in a fume hood.</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Sigma-Aldrich</td>
			<td>34860</td>
			<td>Stored at -20&#176;C !Caution Methanol may cause respiratory tract, skin and eye irritation, may damage the nerves, kidneys and liver. Wear suitable protective glasses, clothing and gloves, work in a fume hood.</td>
		</tr>
		<tr>
			<td>Purified water from Millipore</td>
			<td>Milli-Q</td>
			<td></td>
			<td>Water purification system.</td>
		</tr>
		<tr>
			<td>Sodium dodecyl sulfate</td>
			<td>Sigma-Aldrich</td>
			<td>L6026</td>
			<td>!Caution SDS causes acute toxicity and is flammable. It is a skin, eye and airway irritant. Wear gloves and safety glasses.</td>
		</tr>
		<tr>
			<td>Soil protein extraction kit</td>
			<td>MoBio, NoviPure Soil Protein Extraction Kit, Qiagen</td>
			<td>30000-20</td>
			<td></td>
		</tr>
		<tr>
			<td>DL-dithiothreitol</td>
			<td>Sigma-Aldrich</td>
			<td>43815</td>
			<td></td>
		</tr>
		<tr>
			<td>1M Trizma HCL</td>
			<td>Sigma-Aldrich</td>
			<td>T2694</td>
			<td></td>
		</tr>
		<tr>
			<td>Trichloroacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>T0699</td>
			<td>!Caution TCA is caustic, toxic and may cause skin burns. Wear gloves and safety glasses.</td>
		</tr>
		<tr>
			<td>Acetone</td>
			<td>Sigma-Aldrich</td>
			<td>650501</td>
			<td>Stored at -20&#176;C !Caution Acetone may cause respiratory tract and skin and eye irritation. Flammable liquid and vapor. Wear safety glasses gloves and a lab coat, work in a fume hood.</td>
		</tr>
		<tr>
			<td>Urea</td>
			<td>Sigma-Aldrich</td>
			<td>208884</td>
			<td>!Caution Urea is an eye and skin irritant, use gloves and safety glasses</td>
		</tr>
		<tr>
			<td>Ammonium bicarbonate</td>
			<td>Fluka</td>
			<td>09830</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin</td>
			<td>Promega</td>
			<td>V528A</td>
			<td>20&#181;g vials</td>
		</tr>
		<tr>
			<td>Bicinchoninic acid protein assay kit</td>
			<td>Pierce</td>
			<td>23227</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium Formate</td>
			<td>Sigma-Aldrich</td>
			<td>09735</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetonitrile</td>
			<td>Sigma-Aldrich</td>
			<td>34998</td>
			<td>!Caution Acetonitrile is a skin and eye irritant. Highly flammable. Wear gloves and safety glasses. Work in a fume hood.</td>
		</tr>
		<tr>
			<td>Trifluoroacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>T6508</td>
			<td>!Caution TFA is extremely hazardous in case of skin contact, eye contact, ingestion and inhalation. May produce tissue damage particularly on mucous membranes of eyes, mouth and respiratory tract. Skin contact may produce burns. Wear gloves, lab coat, safety glasses and work in a fume hood.</td>
		</tr>
		<tr>
			<td>Methoxyamine hydrochloride</td>
			<td>Sigma-Aldrich</td>
			<td>226904</td>
			<td>!Caution Methoxyamine hydrochloride causes severe burns and serious damage to eyes, may cause sensitization by skin contact. Wear safety glasses, gloves and lab coat, work in a fume hood.</td>
		</tr>
		<tr>
			<td>Pyridine</td>
			<td>Sigma-Aldrich</td>
			<td>270970</td>
			<td>!Caution Pyridine can cause skin and eye irritation, central nervous system depression. Vapor may cause flash fire. Wear safety glasses, gloves and lab coat, work in a fume hood.</td>
		</tr>
		<tr>
			<td>N-Methyl-N-(trimethylsilyl)trifluoroacetamide with 1% trimethylchlorosilane</td>
			<td>Sigma-Aldrich</td>
			<td>69478</td>
			<td>!Caution MSTFA + 1% TMCS can cause skin corrosion, serious eye damage and specific target organ toxicity. Flammable liquid and vapor. Wear safety glasses, gloves and lab coat, work in a fume hood.</td>
		</tr>
		<tr>
			<td>Potassium chloride</td>
			<td>Sigma-Aldrich</td>
			<td>P9541</td>
			<td></td>
		</tr>
		<tr>
			<td>Milli-Q water purification system</td>
			<td>Millipore</td>
			<td></td>
			<td>model MPGP04001</td>
		</tr>
		<tr>
			<td>Vortex</td>
			<td>Scientific Industries</td>
			<td>SI-0236</td>
			<td>Vortex Genie 2</td>
		</tr>
		<tr>
			<td>Probe sonicator</td>
			<td>FisherBrand</td>
			<td></td>
			<td>model FB505</td>
		</tr>
		<tr>
			<td>Refrigerated centrifuge</td>
			<td>Eppendorf</td>
			<td></td>
			<td>model 5810R</td>
		</tr>
		<tr>
			<td>50mL tube swinging bucket rotor</td>
			<td>Eppendorf</td>
			<td>A-4-44</td>
			<td></td>
		</tr>
		<tr>
			<td>50mL fixed angle rotor</td>
			<td>Eppendorf</td>
			<td>FA-45-6-30</td>
			<td></td>
		</tr>
		<tr>
			<td>Balance</td>
			<td>OHAUS</td>
			<td></td>
			<td>model V22PWE150IT</td>
		</tr>
		<tr>
			<td>Serological pipette controller</td>
			<td>Eppendorf</td>
			<td>12-654-100</td>
			<td></td>
		</tr>
		<tr>
			<td>10mL, 25mL glass serological pipettes</td>
			<td>FisherBrand</td>
			<td>13-678-27F, 13-678-36D</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermomixer with Thermotop</td>
			<td>Eppendorf</td>
			<td>5382000015, 5308000003</td>
			<td></td>
		</tr>
		<tr>
			<td>0.9 &#8211; 2.0 mm blend stainless steel beads</td>
			<td>NextAdvance</td>
			<td>SSB14B</td>
			<td></td>
		</tr>
		<tr>
			<td>0.15 mm garnet beads</td>
			<td>MoBio</td>
			<td>13122-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnetic stir plate</td>
			<td>FisherBrand</td>
			<td>11-100-16SH</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnetic stir bar</td>
			<td>FisherBrand</td>
			<td>14512130</td>
			<td></td>
		</tr>
		<tr>
			<td>pH paper strips, pH range 0&#8211;14</td>
			<td>FisherBrand</td>
			<td>M95903</td>
			<td></td>
		</tr>
		<tr>
			<td>15mL, 50mL conical polypropylene centrifuge tube</td>
			<td>Genesee Scientific</td>
			<td>21-103 21-108</td>
			<td>chloroform compatible</td>
		</tr>
		<tr>
			<td>50mL vortex attachment</td>
			<td>MoBio</td>
			<td>13000-V1-50</td>
			<td></td>
		</tr>
		<tr>
			<td>Ice bucket</td>
			<td>FisherBrand</td>
			<td>02-591-44</td>
			<td></td>
		</tr>
		<tr>
			<td>27.25x70mm glass vials</td>
			<td>FisherBrand</td>
			<td>03-339-22K</td>
			<td></td>
		</tr>
		<tr>
			<td>Breathe Easier plate membranes</td>
			<td>Midwest Scientific</td>
			<td>BERM-2000</td>
			<td></td>
		</tr>
		<tr>
			<td>Alcohol wipes</td>
			<td>Diversified Biotech</td>
			<td>BPWP-1000</td>
			<td></td>
		</tr>
		<tr>
			<td>Heater shaker incubator</td>
			<td>Benchmark, Incu-Shaker Mini</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Analog rotisserie tube rotator</td>
			<td>SoCal BioMed, LLC</td>
			<td>82422001</td>
			<td></td>
		</tr>
		<tr>
			<td>Filter-Aided-Sample-Prep kit</td>
			<td>FASP; Expedeon</td>
			<td>44250</td>
			<td></td>
		</tr>
		<tr>
			<td>Microplate reader</td>
			<td>Biotek, EPOCH</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>-20 Degree Celsius Freezer</td>
			<td>Fisher</td>
			<td>13986149</td>
			<td></td>
		</tr>
		<tr>
			<td>-80 Degree Celsius Freezer</td>
			<td>Stirling Ultracold</td>
			<td>SU78OUE</td>
			<td></td>
		</tr>
		<tr>
			<td>Q-Exactive ion trap mass spectrometer</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent 7890A gas chromatograph coupled with a single quadrupole 5975C mass spectrometer</td>
			<td>Agilent Technologies, Inc.</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>LTQ-Orbitrap Velo</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Waters NanoEquityTM UPLC system</td>
			<td>Millford, MA</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>250mL media bottle</td>
			<td>FisherBrand</td>
			<td>1395-250</td>
			<td></td>
		</tr>
		<tr>
			<td>Waters vial</td>
			<td>Waters</td>
			<td>186002805</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass MS sample vial and inserts</td>
			<td>MicroSolv</td>
			<td>9502S-WCV, 9502S-02ND</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass HPLC vial and snap caps</td>
			<td>MicroSolv</td>
			<td>9512C-0DCV, 9502C-10C-B</td>
			<td></td>
		</tr>
		<tr>
			<td>HPLC 96-well plate</td>
			<td>Agilent</td>
			<td>5042-6454</td>
			<td></td>
		</tr>
		<tr>
			<td>Large glass vial 27.25x70mm</td>
			<td>FisherBrand</td>
			<td>03-339-22K</td>
			<td></td>
		</tr>
		<tr>
			<td>Lyophilizer</td>
			<td>Labconco</td>
			<td>7934021</td>
			<td></td>
		</tr>
		<tr>
			<td>Polished stainless steel flat head spatula</td>
			<td>Spoonula; FisherBrand</td>
			<td>14-375-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Kim wipes</td>
			<td>Kimberly-Clark</td>
			<td>34721</td>
			<td></td>
		</tr>
		<tr>
			<td>XBridge C18, 250x4.6 mm, 5 &#956;M with 4.6x20 mm guard column</td>
			<td>Waters</td>
			<td>186003117, 186003064</td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent 1100 series HPLC system</td>
			<td>Agilent Technologies</td>
			<td>G1380-90000</td>
			<td></td>
		</tr>
		<tr>
			<td>1.7mL centrifuge tube</td>
			<td>Sorenson</td>
			<td>11700</td>
			<td></td>
		</tr>
		<tr>
			<td>Hamilton Glass Syringes, 5mL, 50&#181;L and 250&#181;L</td>
			<td>Hamilton</td>
			<td>81517, 80975, 81175</td>
			<td></td>
		</tr>
		<tr>
			<td>Pasteur Pipettes</td>
			<td>FisherBrand</td>
			<td>13-678-20A</td>
			<td></td>
		</tr>
		<tr>
			<td>Pasteur Pipette Bulbs</td>
			<td>Sigma-Aldrich</td>
			<td>Z111597</td>
			<td></td>
		</tr>
		<tr>
			<td>Bath Sonicator</td>
			<td>Branson 1800 Ultrasonic Cleaner</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum Centrifuge</td>
			<td colspan="2">Labconco Centrivap Acid-Resistant Concentrator System</td>
			<td></td>
		</tr>
		<tr>
			<td>MicroSpin Columns, C18 Silica</td>
			<td>The Nest Group</td>
			<td>SEM SS18V</td>
			<td></td>
		</tr>
	</tbody>
</table>

the mplex protocol for multi-omic analyses of soil samples

ספקטרומטר מסה (MS)-מבוסס metaproteomic משולב, metabolomic ו- lipidomic (multi-omic) מחקרים משנים צורה של היכולת שלנו להבין ולאפיין קהילות חיידקים במערכות ביולוגיות וסביבתיות. מדידות אלה אפילו אתם מאפשרים ניתוח משופרת הקהילות מיקרוביאלית בקרקע מורכבים, אשר הם הכי מערכות מורכבות מיקרוביאלי ידוע עד כה. ניתוח רב-omic, אולם בעל מדגם הכנה אתגרים, מאז נפרד עקירות נדרשים בדרך כלל עבור כל מחקר omic, במיתון מגביר את זמן הכנה ואת משך דגימת נדרש. כדי לטפל מגבלה זו, שיטה 3 ב- 1 על החילוץ סימולטני של מטבוליטים, חלבונים ושומנים (MPLEx) מן הקרקע באותה דגימת זרע נוצר על ידי התאמת בגישה ממס מבוסס. פרוטוקול זה MPLEx הוכיחה להיות פשוטה וגם חזקים עבור סוגי דגימה רבים, גם כאשר מנוצל עבור כמויות מוגבלות של דגימות. אדמה מורכבים. שיטת MPLEx זמין במידה רבה גם את המידות מהירה multi-omic הדרושים כדי להשיג הבנה טובה יותר של חברי כל הקהילה מיקרוביאלי, תוך הערכת את השינויים המתרחשים בעת לפליטת ביולוגי וסביבתי.

כאשר פרוטוקול MPLEx שימש כדי לחלץ מולקולות של קנזס ערבה יליד האדמה (קרקע Mollisol), הבדיקות triplicate מספק תוצאות עבור 3376 פפטידים, ליפידים 105 ו 102 קוטבי מטבוליטים (כל המזהים הייחודיים). בזמן פרוטוקול MPLEx הייתה ומבוססת לחילוץ כללי של ליפידים, מטבוליטים12,13</su...

Watch this Scientific Journal Video about The MPLEx Protocol for Multi-omic Analyses of Soil Samples at JoVE.com

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

פרוטוקול מוצג עבור חילוץ מטבוליטים, חלבונים ושומנים דגימת אדמה אחד בו זמנית, המאפשר דגימת מופחתת הכנה פעמים ולאפשר מולטי-omic ניתוחים ספקטרומטר מסה של דגימות עם כמויות מוגבלות.

פרוטוקול MPLEx עבור ניתוחים מולטי-omic של דגימות אדמה

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and ...

the-mplex-protocol-for-multi-omic-analyses-of-soil-samples

Universidad de Cartagena UDEC

Research

JoVE Journal

Chemistry

10.8K Views.  Pacific Northwest National Laboratory. פרוטוקול מוצג עבור חילוץ מטבוליטים, חלבונים ושומנים דגימת אדמה אחד בו זמנית, המאפשר דגימת מופחתת הכנה פעמים ולאפשר מולטי-omic ניתוחים ספקטרומטר מסה של דגימות עם כמויות מוגבלות.

Video: The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities1,2. Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils3-8. A large variety of these peptides is commercially available.
This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a &#34;beads on a string&#34;-like structure by this process.9 The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

This paper describes the formation of highly ordered peptide-based structures by the spontaneous process of self-assembly. The method utilizes commercially available peptides and common lab equipment. This technique can be applied to a large variety of peptides and may lead to the discovery of new peptide-based assemblies.

היווצרות של מבני Biomolecular הוזמנו על ידי ההרכבה העצמית של פפטידים קצרים

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control ...

Transport of Surface-modified Carbon Nanotubes through a Soil Column

Carbon nanotubes (CNTs) are widely manufactured nanoparticles, which are being utilized in a number of consumer products, such as sporting goods, electronics and biomedical applications. Due to their accelerating production and use, CNTs constitute a potential environmental risk if they are released to soil and groundwater systems. It is therefore essential to improve the current understanding of environmental fate and transport of CNTs. The transport and retention of CNTs in both natural and artificial media have been reported in literature, but the findings widely vary and are thus not conclusive. There are a number of physical and chemical parameters responsible for variation in retention and transport. In this study, a complete procedure of selected multiwalled carbon nanotubes (MWCNTs) is presented starting from their surface modification to a complete set of laboratory column experiments at critical physical and chemical scenarios. Results indicate that the stability of the commercially available MWCNTs are critical with their attached surface functional group which can also influence the transport and retention of MWCNT through the surrounding medium.

Surface properties of a nanoparticle are important for their interaction with the surrounding medium. Therefore the surface modification of carbon nanotubes can be critical for their transport and retention through porous media. Here, lab scale column experiments are used to understand the possible transport and retention of these nanoparticles.

הובלה של פחמן-שונה Surface דרך טור קרקע

Carbon nanotubes (CNTs) are widely manufactured nanoparticles, which are being utilized in a number of consumer products, such as sporting goods, ...

A Direct, Early Stage Guanidinylation Protocol for the Synthesis of Complex Aminoguanidine-containing Natural Products

The guanidine functional group, displayed most prominently in the amino acid arginine, one of the fundamental building blocks of life, is an important structural element found in many complex natural products and pharmaceuticals. Owing to the continual discovery of new guanidine-containing natural products and designed small molecules, rapid and efficient guanidinylation methods are of keen interest to synthetic and medicinal organic chemists. Because the nucleophilicity and basicity of guanidines can affect subsequent chemical transformations, traditional, indirect guanidinylation is typically pursued. Indirect methods commonly employ multiple protection steps involving a latent amine precursor, such as an azide, phthalimide, or carbamate. By circumventing these circuitous methods and employing a direct guanidinylation reaction early in the synthetic sequence, it was possible to forge the linear terminal guanidine containing backbone of clavatadine A to realize a short and streamlined synthesis of this potent factor XIa inhibitor. In practice, guanidine hydrochloride is elaborated with a carefully constructed protecting array that is optimized to survive the synthetic steps to come. In the preparation of clavatadine A, direct guanidinylation of a commercially available diamine eliminated two unnecessary steps from its synthesis. Coupled with the wide variety of known guanidine protecting groups, direct guanidinylation evinces a succinct and efficient practicality inherent to methods that find a home in a synthetic chemist&#39;s toolbox.

Here, we present a protocol for direct, early stage guanidinylation that enables rapid total synthesis of aminoguanidine-containing small organic molecules. An advanced synthetic intermediate used in the synthesis of a blood coagulation factor XIa inhibitor was prepared using this protocol.

ישיר, בשלבים מוקדמים Guanidinylation פרוטוקול לסינתזה של מוצרים טבעיים Aminoguanidine המכיל קומפלקס

The guanidine functional group, displayed most prominently in the amino acid arginine, one of the fundamental building blocks of life, is an important ...

Protocol for the Synthesis of Ortho-trifluoromethoxylated Aniline Derivatives

Molecules bearing trifluoromethoxy (OCF3) group often show desired pharmacological and biological properties. However, facile synthesis of trifluoromethoxylated aromatic compounds remains a formidable challenge in organic synthesis. Conventional approaches often suffer from poor substrate scope, or require use of highly toxic, difficult-to-handle, and/or thermally labile reagents. Herein, we report a user-friendly protocol for the synthesis of methyl 4-acetamido-3-(trifluoromethoxy)benzoate using 1-trifluoromethyl-1,2-benziodoxol-3(1H)-one (Togni reagent II). Treating methyl 4-(N-hydroxyacetamido)benzoate (1a) with Togni reagent II in the presence of a catalytic amount of cesium carbonate (Cs2CO3) in chloroform at RT afforded methyl 4-(N-(trifluoromethoxy)acetamido)benzoate (2a). This intermediate was then converted to the final product methyl 4-acetamido-3-(trifluoromethoxy)benzoate (3a) in nitromethane at 120 &#176;C. This procedure is general and can be applied to the synthesis of a broad spectrum of ortho-trifluoromethoxylated aniline derivatives, which could serve as useful synthetic building blocks for the discovery and development of new pharmaceuticals, agrochemicals, and functional materials.

Protocol for the Synthesis of Ortho-trifluoromethoxylated Aniline Derivatives

An operationally simple procedure for the synthesis of ortho-trifluoromethoxylated aniline derivatives via a two-step sequence of O-trifluoromethylation of N-aryl-N-hydroxyacetamide followed by thermally induced intramolecular OCF3-migration is reported.

פרוטוקול לסינתזה של<em&gt; Ortho</em&gt; נגזרי אנילין -trifluoromethoxylated

Molecules bearing trifluoromethoxy (OCF3) group often show desired pharmacological and biological properties. However, facile synthesis of ...

A Protocol for the Production of Gliadin-cyanoacrylate Nanoparticles for Hydrophilic Coating

This article presents a protocol for the production of protein-based nanoparticles that changes the hydrophobic surface to hydrophilic by a simple spray coating. These nanoparticles are produced by the polymerization reaction of alkyl cyanoacrylate on the surface of cereal protein (gliadin) molecules. Alkyl cyanoacrylate is a monomer that instantly polymerizes at RT when it is applied to the surface of materials. Its polymerization reaction is initiated by the trace amounts of weakly basic or nucleophilic species on the surface, including moisture. Once polymerized, the polymerized alkyl cyanoacrylates show a strong affinity with the object materials because nitrile groups are in the backbone of poly (alkyl cyanoacrylate). Proteins also work as initiator for this polymerization because they contain amine groups that can initiate the polymerization of cyanoacrylate. If aggregated protein is used as an initiator, protein aggregate is surrounded by the hydrophobic poly(alkyl cyanoacrylate) chains after the polymerization reaction of alkyl cyanoacrylate. By controlling the experimental condition, particles in the nanometer range are produced. The produced nanoparticles readily adsorb to the surface of most materials including glass, metals, plastics, wood, leather, and fabrics. When the surface of a material is sprayed with the produced nanoparticle suspension and rinsed with water, the micellar structure of nanoparticle changes its conformation, and the hydrophilic proteins are exposed to the air. As a result, the nanoparticle-coated surface changes to hydrophilic.

This article presents a protocol for the production of protein-based nanoparticles that changes the hydrophobic surface to hydrophilic. The produced nanoparticle is an assembly of gliadin-cyanoacrylate diblock copolymers. Spray coating with the produced nanoparticle changes the surface of target material to a hydrophilic surface.

פרוטוקול עבור ההפקה של חלקיקי גליאדין-cyanoacrylate לציפוי הידרופיליות

This article presents a protocol for the production of protein-based nanoparticles that changes the hydrophobic surface to hydrophilic by a simple spray ...

A Simple and Efficient Protocol for the Catalytic Insertion Polymerization of Functional Norbornenes

Norbornene can be polymerized by a variety of mechanisms, including insertion polymerization whereby the double bond is polymerized and the bicyclic nature of the monomer is conserved. The resulting polymer, polynorbornene, has a very high glass transition temperature, Tg, and interesting optical and electrical properties. However, the polymerization of functional norbornenes by this mechanism is complicated by the fact that the endo substituted norbornene monomer has, in general, a very low reactivity. Furthermore, the separation of the endo substituted monomer from the exo monomer is a tedious task. Here, we present a simple protocol for the polymerization of substituted norbornenes (endo:exo ca. 80:20) bearing either a carboxylic acid or a pendant double bond. The process does not require that both isomers be separated, and proceeds with low catalyst loadings (0.01 to 0.02 mol%). The polymer bearing pendant double bonds can be further transformed in high yield, to afford a polymer bearing pendant epoxy groups. These simple procedures can be applied to prepare polynorbornenes with a variety of functional groups, such as esters, alcohols, imides, double bonds, carboxylic acids, bromo-alkyls, aldehydes and anhydrides.

We describe the catalytic insertion polymerization of 5-norbornene-2-carboxylic acid and 5-vinyl-2-norbornene to form functional polymers with a very high glass transition temperature.

פרוטוקול פשוט ויעיל עבור פילמור קטליטי קלטי Norbornenes פונקציונלית

Norbornene can be polymerized by a variety of mechanisms, including insertion polymerization whereby the double bond is polymerized and the bicyclic ...

A Protocol for Safe Lithiation Reactions Using Organolithium Reagents

Organolithium reagents are powerful tools in the synthetic chemist&#39;s toolbox. However, the extreme pyrophoric nature of the most reactive reagents warrants proper technique, thorough training, and proper personal protective equipment. To aid in the training of researchers using organolithium reagents, a thorough, step-by-step protocol for the safe and effective use of tert-butyllithium on an inert gas line or within a glovebox is described. As a model reaction, preparation of lithium tert-butyl amide by the reaction of tert-butyl amine with one equivalent of tert-butyl lithium is presented.

The safe and proper use of organolithium reagents is described.

פרוטוקול תגובות בטוח Lithiation באמצעות ריאגנטים Organolithium

Organolithium reagents are powerful tools in the synthetic chemist&#39;s toolbox. However, the extreme pyrophoric nature of the most reactive reagents ...

An Optimized Protocol for the Efficient Radiolabeling of Gold Nanoparticles by Using a 125I-labeled Azide Prosthetic Group

Here, we demonstrate a detailed protocol for the radiosynthesis of a 125I-labeled azide prosthetic group and its application to the efficient radiolabeling of DBCO-group-functionalized gold nanoparticles using a copper-free click reaction. Radioiodination of the stannylated precursor (2) was carried out by using [125I]NaI and chloramine T as an oxidant at room temperature for 15 min. After HPLC purification of the crude product, the purified 125I-labeled azide (1) was obtained with high radiochemical yield (75 &plusmn; 10%, n = 8) and excellent radiochemical purity (&gt;99%). For the synthesis of radiolabeled 13-nm-sized gold nanoparticles, the DBCO-functionalized gold nanoparticles (3) were prepared by using a thiolated polyethylene glycol polymer. A copper-free click reaction between 1 and 3 gave the 125I-labeled gold nanoparticles (4) with more than 95% of radiochemical yield as determined by radio-thin-layer chromatography (radio-TLC). These results clearly indicate that the present radiolabeling method using a strain-promoted copper-free click reaction will be useful for the efficient and convenient radiolabeling of DBCO-group-containing nanomaterials.

An Optimized Protocol for the Efficient Radiolabeling of Gold Nanoparticles by Using a 125I-labeled Azide Prosthetic Group

A detailed procedure for the synthesis of a 125I-labeled azide and the radiolabeling of dibenzocyclooctyne (DBCO)-group-conjugated, 13-nm-sized gold nanoparticles using a copper-free click reaction is described.

פרוטוקול אופטימיזציה עבור Radiolabeling היעיל של חלקיקי זהב על ידי שימוש<sup&gt; 125</sup&gt; שכותרתו לי אזיד תותבת קבוצה

Here, we demonstrate a detailed protocol for the radiosynthesis of a 125I-labeled azide prosthetic group and its application to the efficient ...

Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism

Solid-phase synthesis has been used to obtain canonical and modified polymers of nucleic acids, specifically of DNA or RNA, which has made it a popular methodology for applications in various fields and for different research purposes. The procedure described herein focuses on the synthesis, purification, and characterization of dodecamers of RNA 5&#39;-[CUA CGG AAU CAU]-3&#39; containing zero, one, or two modifications located at the C2&#39;-O-position. The probes are based on 2-thiophenylmethyl groups, incorporated into RNA nucleotides via standard organic synthesis and introduced into the corresponding oligonucleotides via their respective phosphoramidites. This report makes use of phosphoramidite chemistry via the four canonical nucleobases (Uridine (U), Cytosine (C), Guanosine (G), Adenosine (A)), as well as 2-thiophenylmethyl functionalized nucleotides modified at the 2&#39;-O-position; however, the methodology is amenable for a large variety of modifications that have been developed over the years. The oligonucleotides were synthesized on a controlled-pore glass (CPG) support followed by cleavage from the resin and deprotection under standard conditions, i.e., a mixture of ammonia and methylamine (AMA) followed by hydrogen fluoride/triethylamine/N-methylpyrrolidinone. The corresponding oligonucleotides were purified via polyacrylamide electrophoresis (20% denaturing) followed by elution, desalting, and isolation via reversed-phase chromatography (Sep-pak, C18-column). Quantification and structural parameters were assessed via ultraviolet-visible (UV-vis) and circular dichroism (CD) photometric analysis, respectively. This report aims to serve as a resource and guide for beginner and expert researchers interested in embarking in this field. It is expected to serve as a work-in-progress as new technologies and methodologies are developed. The description of the methodologies and techniques within this document correspond to a DNA/RNA synthesizer (refurbished and purchased in 2013) that uses phosphoramidite chemistry.

Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism

This article provides a detailed procedure on the solid-phase synthesis, purification, and characterization of dodecamers of RNA modified at the C2&#39;-O-position. UV-vis and circular dichroism photometric analyses are used to quantify and characterize structural aspects, i.e., single-strands or double-strands.

Protocol עבור שלב מוצק סינתזה של אוליגומרים של רנ&quot;א המכיל 2 &#39;<em&gt; הו</em&gt; שינוי ואפיון של תיאופנילמתיל באמצעות דיכרואיזם מעגלי

Solid-phase synthesis has been used to obtain canonical and modified polymers of nucleic acids, specifically of DNA or RNA, which has made it a popular ...

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles (PPAs) and Related Biomaterials

Polyamine-based Peptide Amphiphiles (PPAs) are a new class of self-assembling amphiphilic biomaterials-related to the peptide amphiphiles (PAs). Traditional PAs possess charged amino acids as solubilizing groups (lysine, arginine), which are directly connected to a lipid segment or can contain a linker region made of neutral amino acids. Tuning the peptide sequence of PAs can yield diverse morphologies. Similarly, PPAs possess a hydrophobic segment and neutral amino acids, but also contain polyamine molecules as water solubilizing (hydrophilic) groups. As is the case with PAs, PPAs can also self-assemble into diverse morphologies, including small rods, twisted nano-ribbons, and fused nano-sheets, when dissolved in water. However, the presence of both primary and secondary amines on a single polyamine molecule poses a significant challenge when synthesizing PPAs. In this paper, we show a simple protocol, based on literature precedents, to achieve a facile synthesis of PPAs using solid phase peptide synthesis (SPPS). This protocol can be extended to the synthesis of PAs and other similar systems. We also illustrate the steps that are needed for cleavage from the resin, identification, and purification.

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles PPAs and Related Biomaterials

The synthesis of polyamine-based peptide amphiphiles (PPAs) is a significant challenge due to the presence of multiple amine nitrogens, which requires judicious use of protecting groups to mask these reactive functionalities. In this paper, we describe a facile method for the preparation of these new class of self-assembling molecules.

פרוטוקול MPLEx עבור ניתוחים מולטי-omic של דגימות אדמה

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היווצרות של מבני Biomolecular הוזמנו על ידי ההרכבה העצמית של פפטידים קצרים

הובלה של פחמן-שונה Surface דרך טור קרקע

ישיר, בשלבים מוקדמים Guanidinylation פרוטוקול לסינתזה של מוצרים טבעיים Aminoguanidine המכיל קומפלקס

פרוטוקול לסינתזה של

פרוטוקול עבור ההפקה של חלקיקי גליאדין-cyanoacrylate לציפוי הידרופיליות

פרוטוקול פשוט ויעיל עבור פילמור קטליטי קלטי Norbornenes פונקציונלית

פרוטוקול תגובות בטוח Lithiation באמצעות ריאגנטים Organolithium

פרוטוקול אופטימיזציה עבור Radiolabeling היעיל של חלקיקי זהב על ידי שימוש

Protocol עבור שלב מוצק סינתזה של אוליגומרים של רנ"א המכיל 2 '

פרוטוקול נתיישב לסינתזה של הרכבה עצמית מבוסס פוליאמין פפטיד חומרים פעילי שטח (PPAs), Biomaterials קשורים