Support by Centre National de la Recherche Scientifique (CNRS, UMR 6612 and 7339) is gratefully acknowledged.

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The authors have nothing to disclose.

ספקטרוסקופיה NMR היא שיטה יעילה למדידת ריכוזים של תרכובות כימיות בפתרון בצורה מאוד לשחזור ומדויק. עם זאת, כדי לקבל נתונים באיכות גבוהה יש צורך לדבוק בכללים מסוימים הנוגעים להכנת מדגם וניתוח. בקביעת ריכוזי המטבוליט ידי ספקטרוסקופיה NMR, לא הדור ולא הקבלה של אות NMR שולטת ?...

מודלים עכבריים כבר נוצלו בהרחבה בחקר מוח 1. מתאמי גנוטיפ, פנוטיפ נחקרו במוח עכבר וחולדה על ידי לימוד ביטוי גנים בRNA ו / או רמות חלבון מצד האחד, ופנוטיפים מורפולוגיים, תפקודיים, אלקטרו ו / או התנהגותי על 2-6 האחר. עם זאת, כדי להבין את המנגנונים המקשרים פנוטיפ לגנוטיפ לחלוטין, זה הכרחי כדי לחקור את האירועים המולקולריים במורד הזרם של ביטוי חלבון, כלומר. חילוף החומרים של מצעים ביוכימיים שעליו אנזימים לפעול 7. דרישה זו הובילה, על 10 עד 15 השנים האחרונות, לרנסנס של מחקר מטבולים בענפים רבים של 8,9 ביולוגיה. בעוד שמחקרים מטבוליים קלאסיים פעמים רבות מתמקדים בפרטים של מסלולים ספציפיים, גישת metabolomic החדשה מיועדת לחקירה כוללנית של הפרופיל המטבולי הגלובלי של הרקמה תחת שיקול.אחת תוצאות של תפיסה זו היא צורך ברור לכלים אנליטיים שלמזער את ההטיה לכיוון מסלולי מטבוליים ספציפיים ו / או סוגי תרכובות. עם זאת, assay ביוכימיים קלאסי מבוסס על תגובה כימית מסוימת של אנליטי ספציפי שצריך להיות מוגדרים לפני assay מבוצע. בניגוד לכך, טכניקות ספקטרוסקופיות כגון תהודה מגנטית ספקטרוסקופיה הגרעינית (NMR) וספקטרומטריית מסה (MS) (i) מבוססות על מאפיינים מסוימים מולקולריים (פיזיים) של תרכובות ביוכימיות, כל אחד מהם מעורר אותות אחד או כמה ברורים בספקטרום זוהה במהלך ניסוי אחד; וכן (ii) לזהות מספר רב של תרכובות שונות לכל ניסוי. לפיכך, כל ספקטרום מכיל מידע המשולב של מגוון רחב של מטבוליטים כל. מסיבה זו, שיטות ספקטרוסקופיות הם כלים נאותים לmetabolomics, כמו שאף בחירה לפני צריכה להיעשות לגבי אופי אנליטי כדי להימדד 8 </sup&gt;. כתוצאה מכך, הטכניקות הללו באופן טבעי להשאיל את עצמם ללימודי חיפושי נפט מכיוון שיקלו על זיהוי של שינויים מטבוליים בלתי צפויים במידה רבה. למרות ספקטרוסקופיה NMR וMS ניתן להשתמש לסירוגין לניתוח מטבוליטים רבים, כל שיטה הוא בעל יתרונות וחסרונות לאחרונה כי נבדקו 10 ספציפיים. בקצרה, ספקטרוסקופיה NMR יכולה בדרך כלל להתבצע מתמציות גולמיים ואינה דורשת הפרדת chromatographic של תרכובות מדגם לפני הניתוח. בניגוד לכך, MS עובד עם גז או כרומטוגרפיה נוזלית (GC או LC) הפרדה, למעט התפתחויות מסוימות האחרונות כגון הדמיה ספקטרומטריית מסה. בכמה מקרים מיוחדים, כגון הניתוח של סוכרים, הפרדת LC עשויה להיות הכרח עבור ספקטרוסקופיה NMR, כמו גם, כי קווי התהודה של סוכרים שונים חופפים באופן משמעותי בפרוטון (1 H) NMR ספקטרום. אף על פי כן, ספקטרוסקופיה H NMR 1 ללא chrהפרדת omatographic נשארה השיטה הפופולרית ביותר, כמעט אוניברסלי השימושית metabolomic NMR. באופן כללי, הכנת מדגם היא יותר זמן רב ומורכב עבור MS מאשר לספקטרוסקופיה NMR. בעיות חמורות בשל השפעות מטריצה ​​הן הרבה פחות נפוצות בספקטרוסקופיה NMR מאשר בטרשת הנפוצה שבו הם עלולים להוביל לאותות משמעותי מוחלשים. quantitation המטבוליט ניתן להשיג גם עם שיטה. עם זאת, תרכובות סטנדרטיים מרובות נדרשות עבור MS עקב שינויים בהשפעות מטריצה ​​ויעילות יינון בין מטבוליטים. לעומת זאת, רק אחד סטנדרטית לדגימה דרושה לניתוח ספקטרוסקופיות NMR כי בתנאי מדידה מתאימים, השיטה השנייה היא מהותית בזכות כמותיים לתגובת NMR ליניארי בקפדנות על ידי הגרעינים שנצפו. חסרון עיקרי של NMR הוא הרגישות הנמוכה יחסית שלה. MS, בLC-MS בפרט, הוא רגיש יותר מתמ&quot;ג על ידי צווים שונים של גודל; מסיבה זו, הטרשת הנפוצה היא להיות מועדפת על פני NMR לניתוח של תרכובות המתרחשות בריכוזים נמוכים מאוד. מצד השני, הטבע הורסות של ניסוי NMR הוא יתרון ברור על פני MS; בדרך זו, ניתן לבצע NMR שוב ושוב על אותו המדגם, למשל, לגרעיני NMR פעיל שונים כגון 1 H, זרחן 31 ב( 31 בP), פחמן -13 (C 13), פלואור-19 (19 F) וכו &#39;., כמו שאף חומר הנצרך על ידי NMR בניגוד למדידות MS. יכולים להיות מועסק NMR וMS הן במצבים שונים, כל אחד מהם להיות אופטימלי לזיהוי של תרכובות עם מאפיינים כימיים מסוימים. לדוגמא, ביום 31 בP NMR הוא לעתים קרובות מתאים יותר מ1 H NMR לניתוח של תרכובות פוספורילציה מרוכזות במתינות, אם כי מטבוליטים כמעט כל פוספורילציה גם מכילים פרוטונים. עם זאת, 1 אותות H NMR שלהם עשויים להיות מוסתרים על ידי 1 אותות H NMR מתרכובות אחרות, שאינה פוספורילציה, ואילו האחרוניםברור שאתה לא לגרום לאותות רקע ביום 31 בספקטרום P NMR. במצב אנלוגי, 19 ניתוח F NMR יש להעדיף לתרכובות פלואור, למשל, תרופות פלואור (אין אותות רקע ממטבוליטים אנדוגני), ואילו במקרה המיוחד של 13 C NMR הוא עניין כמעט אך ורק אם גורלו של 13 C- מבשרי חילוף חומרים אקסוגניים שכותרת צריך להיות אחרי, בשל השפע הטבעי הנמוך מאוד של איזוטופ 13 C (בערך 1%). ספקטרומטרים המוניים רבים לעבוד במצב או יונים שליליים או במצב יון חיובי. לכן, חשוב לדעת מראש את הניתוח אם היונים כדי לצפות חיוב או לשלילה יחויבו. אנו מתמקדים כאן בפרוטוקול לניתוח metabolome רקמת המוח על ידי H 1 ויום 31 בספקטרוסקופיה P NMR כי שיטה זו מניבה מספר גדול של ריכוזי המטבוליט חשובים בעלות נמוכה במונחים של זמן (i) דרוש למדגם הכנהnd (ii) מאמץ הנדרש כדי לכמת את המטבוליט. ניתן לבצע את כל הניסויים באמצעות הציוד של מעבדה כימיה רטובה סטנדרטית ומתקן ספקטרוסקופיה NMR ברזולוציה גבוהה. דרישות נוספות המתוארים בסעיף הפרוטוקול להלן.

<table border="0" cellpadding="0" cellspacing="0" width="921">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:281px;">Isoflurane</td>
			<td style="width:144px;">Virbac</td>
			<td style="width:180px;">Vetflurane</td>
			<td style="width:316px;">Anesthetic for animals</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Isoflurane vaporizer</td>
			<td>Ohmeda</td>
			<td>Isotec 3</td>
			<td>Newer model available: Isotec 4</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Scalpel, scissors, forceps, clamps</td>
			<td>Harvard Apparatus 
			Fisher Scientific</td>
			<td>various 
			various</td>
			<td>Surgical equipment for animals</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Freeze-clamp tool</td>
			<td>homebuilt</td>
			<td>n/a</td>
			<td>Tong with aluminium plates, to be inserted 
			in liquid nitrogen for cooling</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dewar</td>
			<td>Nalgene</td>
			<td>4150-4000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Liquid nitrogen</td>
			<td>Air Liquide</td>
			<td>n/a</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nitrogen gas</td>
			<td>Air Liquide</td>
			<td>n/a</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nitrogen evaporator</td>
			<td>Organomation Associates</td>
			<td>N-EVAP 111</td>
			<td>Can be replaced by homebuilt device</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mortar</td>
			<td>Sigma-Aldrich</td>
			<td>Z247472</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pestle</td>
			<td>Sigma-Aldrich</td>
			<td>Z247510</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tissue homogenizer</td>
			<td>Kinematica</td>
			<td>Polytron</td>
			<td>With test tubes fitting homogenizer shaft</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Electronic scale</td>
			<td>Sartorius</td>
			<td>n/a</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Methanol</td>
			<td>Sigma-Aldrich</td>
			<td>M3641</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Chloroform</td>
			<td>Sigma-Aldrich</td>
			<td>366910</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Glass centrifuge tubes</td>
			<td>Kimble</td>
			<td>45500-15, 45500-30</td>
			<td>Kimax 15-mL, 30-mL tube</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Microcentrifuge tubes</td>
			<td>Kimble</td>
			<td>45150-2</td>
			<td>Kimax 2-mL tube; should replace &#34;Eppen-dorf&#34; tube if compatible with centrifuge rotor</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">polystyrene pipettes</td>
			<td>Costar Corning</td>
			<td>Stripettes</td>
			<td>5 and 10-mL volumes</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Deuterochloroform</td>
			<td>Sigma-Aldrich</td>
			<td>431915</td>
			<td>99.96 % deuterated</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Deuterium oxide</td>
			<td>Sigma-Aldrich</td>
			<td>423459</td>
			<td>99.96 % deuterated</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Deuterium chloride</td>
			<td>Alpha Aesar</td>
			<td>42406</td>
			<td>20 % in deuterium oxide</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium deuteroxide</td>
			<td>Sigma-Aldrich</td>
			<td>164488</td>
			<td>30 % in deuterium oxide</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Lyophilizer</td>
			<td>Christ</td>
			<td>Alpha 1-2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cold centrifuge</td>
			<td>Heraeus</td>
			<td>Megafuge 16R</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pH meter</td>
			<td>Eutech Cybernetics</td>
			<td>Cyberscan</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">CDTA</td>
			<td>Sigma-Aldrich</td>
			<td>D0922</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cesium hydroxide</td>
			<td>Sigma-Aldrich</td>
			<td>516988</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NMR tubes</td>
			<td>Wilmad</td>
			<td>528-PP</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NMR stem coaxial insert</td>
			<td>Sigma-Aldrich</td>
			<td>Z278513</td>
			<td>By Wilmad</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NMR pipettes</td>
			<td>Sigma-Aldrich</td>
			<td>Z255688</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pipettes</td>
			<td>Eppendorf</td>
			<td>Research</td>
			<td>With tips for volumes from 0.5 to 1000 &#956;L</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pipet-Aid</td>
			<td>Drummond</td>
			<td>XP</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NMR spectrometer</td>
			<td>Bruker</td>
			<td>AVANCE 400</td>
			<td>including probe and other accessories</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NMR software</td>
			<td>Bruker</td>
			<td>TopSpin 1.3</td>
			<td>newer version available: Topspin 3.2</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Water-soluble standard compounds</td>
			<td>Sigma-Aldrich</td>
			<td>various</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Phospholipid standard compounds</td>
			<td>Avanti Polar Lipids 
			Doosan Serdary 
			Sigma-Aldrich</td>
			<td>various 
			various 
			various</td>
			<td>&#160; 
			Source for plasmalogens, but may be 
			&#60; 70 - 80 % purity</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Methylenediphosphonate</td>
			<td>Sigma-Aldrich</td>
			<td>M9508</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TSP-d4</td>
			<td>Sigma-Aldrich</td>
			<td>269913</td>
			<td></td>
		</tr>
	</tbody>
</table>

metabolomic analysis of rat brain by high resolution nuclear magnetic resonance spectroscopy of tissue extracts

Studies of gene expression on the RNA and protein levels have long been used to explore biological processes underlying disease. More recently, genomics and proteomics have been complemented by comprehensive quantitative analysis of the metabolite pool present in biological systems. This strategy, termed metabolomics, strives to provide a global characterization of the small-molecule complement involved in metabolism. While the genome and the proteome define the tasks cells can perform, the metabolome is part of the actual phenotype. Among the methods currently used in metabolomics, spectroscopic techniques are of special interest because they allow one to simultaneously analyze a large number of metabolites without prior selection for specific biochemical pathways, thus enabling a broad unbiased approach. Here, an optimized experimental protocol for metabolomic analysis by high-resolution NMR spectroscopy is presented, which is the method of choice for efficient quantification of tissue metabolites. Important strengths of this method are (i) the use of crude extracts, without the need to purify the sample and/or separate metabolites; (ii) the intrinsically quantitative nature of NMR, permitting quantitation of all metabolites represented by an NMR spectrum with one reference compound only; and (iii) the nondestructive nature of NMR enabling repeated use of the same sample for multiple measurements. The dynamic range of metabolite concentrations that can be covered is considerable due to the linear response of NMR signals, although metabolites occurring at extremely low concentrations may be difficult to detect. For the least abundant compounds, the highly sensitive mass spectrometry method may be advantageous although this technique requires more intricate sample preparation and quantification procedures than NMR spectroscopy. We present here an NMR protocol adjusted to rat brain analysis; however, the same protocol can be applied to other tissues with minor modifications.

כדי להשיג רזולוציה הטובה ביותר בספקטרום NMR חילוף חומרים של מוח ותמציות רקמות אחרות, זה כבר זמן רב מנהג נפוץ כדי להסיר או יוני מסכת מתכת (הכי חשוב: יוני פאראמגנטיים) קיימים בפתרוני תמצית. זו הושגה על ידי הוספת סוכן chelating כגון EDTA או CDTA לתמצית 19, או על ידי העברת התמצית...

Watch this Scientific Journal Video about Metabolomic Analysis of Rat Brain by High Resolution Nuclear Magnetic Resonance Spectroscopy of Tissue Extracts at JoVE.com

Metabolomic Analysis of Rat Brain by High Resolution Nuclear Magnetic Resonance Spectroscopy of Tissue Extracts

The neurochemistry of mammalian brain is changed in many neurological and systemic diseases. Characteristic profiles of cerebral metabolites can be efficiently obtained based on crude extracts of brain tissue. To this end, high-resolution NMR spectroscopy is employed, enabling detailed quantitative analysis of metabolite concentrations (metabolomics).

ניתוח metabolomic של מוח חולדה על ידי ספקטרוסקופיה בתהודה מגנטית הגרעינית ברזולוציה גבוהה של תמציות רקמות

Studies of gene expression on the RNA and protein levels have long been used to explore biological processes underlying disease. More recently, genomics ...

metabolomic-analysis-rat-brain-high-resolution-nuclear-magnetic

Research

JoVE Journal

Neuroscience

14.7K Views.  Aix-Marseille Université. The neurochemistry of mammalian brain is changed in many neurological and systemic diseases. Characteristic profiles of cerebral metabolites can be efficiently obtained based on crude extracts of brain tissue. To this end, high-resolution NMR spectroscopy is employed, enabling detailed quantitative analysis of metabolite concentrations (metabolomics).

Video: Metabolomic Analysis of Rat Brain by High Resolution Nuclear Magnetic Resonance Spectroscopy of Tissue Extracts

Magnetic Resonance Spectroscopy of live Drosophila melanogaster using Magic Angle Spinning

High-Resolution Magic Angle Spinning (HRMAS) proton magnetic resonance spectroscopy (1H-MRS) is a novel non-destructive technique that improves spectral line-widths and allows high-resolution spectra to be obtained from extracts, intact cells, cell cultures, and more importantly intact tissue to investigate relationships between metabolites and cellular processes. In vivo HRMAS 1H-MRS studies have yet to be reported in the live fruit fly Drosophila melanogaster. Drosophila, as a simpler genetic organism, allows the multiple biological functions and various evolutionarily conserved signaling pathways to be examined at the whole organism level and it is a useful model for investigating genetics and physiology. To this end, we developed and implemented an in vivo HRMAS 1H-MRS method to investigate live Drosophila at 14.1 T. Here, we outline an HRMAS 1H-MRS protocol for the molecular characterization of Drosophila with a conventional MR spectrometer equipped with an HRMAS probe. This technique is a novel, in vivo, non-destructive Drosophila metabolite measurement approach, which enables the identification of disease biomarkers and thus may contribute to novel therapeutic development.

Magnetic Resonance Spectroscopy of live Drosophila melanogaster using Magic Angle Spinning

This technique enables the use of high-resolution magic angle spinning proton MR spectroscopy (HRMAS 1H-MRS) for molecular characterization of live Drosophila melanogaster with a conventional 14.1 tesla spectrometer equipped with an HRMAS probe.

ספקטרוסקופיית תהודה מגנטית של חיים תסיסנית melanogaster באמצעות ספינינג זווית הקסם

High-Resolution Magic Angle Spinning (HRMAS) proton magnetic resonance spectroscopy (1H-MRS) is a novel non-destructive technique that improves spectral ...

High-resolution Functional Magnetic Resonance Imaging Methods for Human Midbrain

Functional MRI (fMRI) is a widely used tool for non-invasively measuring correlates of human brain activity. However, its use has mostly been focused upon measuring activity on the surface of cerebral cortex rather than in subcortical regions such as midbrain and brainstem. Subcortical fMRI must overcome two challenges: spatial resolution and physiological noise. Here we describe an optimized set of techniques developed to perform high-resolution fMRI in human SC, a structure on the dorsal surface of the midbrain; the methods can also be used to image other brainstem and subcortical structures.
High-resolution (1.2 mm voxels) fMRI of the SC requires a non-conventional approach. The desired spatial sampling is obtained using a multi-shot (interleaved) spiral acquisition1. Since, T2* of SC tissue is longer than in cortex, a correspondingly longer echo time (TE ~ 40 msec) is used to maximize functional contrast. To cover the full extent of the SC, 8-10 slices are obtained. For each session a structural anatomy with the same slice prescription as the fMRI is also obtained, which is used to align the functional data to a high-resolution reference volume.
In a separate session, for each subject, we create a high-resolution (0.7 mm sampling) reference volume using a T1-weighted sequence that gives good tissue contrast. In the reference volume, the midbrain region is segmented using the ITK-SNAP software application2. This segmentation is used to create a 3D surface representation of the midbrain that is both smooth and accurate3. The surface vertices and normals are used to create a map of depth from the midbrain surface within the tissue4.
Functional data is transformed into the coordinate system of the segmented reference volume. Depth associations of the voxels enable the averaging of fMRI time series data within specified depth ranges to improve signal quality. Data is rendered on the 3D surface for visualization.
In our lab we use this technique for measuring topographic maps of visual stimulation and covert and overt visual attention within the SC1. As an example, we demonstrate the topographic representation of polar angle to visual stimulation in SC.

This article describes techniques to perform high-resolution functional magnetic resonance imaging with 1.2 mm sampling in human midbrain and subcortical structures using a 3T scanner. Use of these techniques to resolve topographic maps of visual stimulation in the human superior colliculus (SC) is given as an example.

ברזולוציה גבוהה תהודה מגנטית פונקציונלית שיטות המוח התיכון האדם

Functional MRI (fMRI) is a widely used tool for non-invasively measuring correlates of human brain activity. However, its use has mostly been focused upon ...

Micron-scale Resolution Optical Tomography of Entire Mouse Brains with Confocal Light Sheet Microscopy

Understanding the architecture of mammalian brain at single-cell resolution is one of the key issues of neuroscience. However, mapping neuronal soma and projections throughout the whole brain is still challenging for imaging and data management technologies. Indeed, macroscopic volumes need to be reconstructed with high resolution and contrast in a reasonable time, producing datasets in the TeraByte range. We recently demonstrated an optical method (confocal light sheet microscopy, CLSM) capable of obtaining micron-scale reconstruction of entire mouse brains labeled with enhanced green fluorescent protein (EGFP). Combining light sheet illumination and confocal detection, CLSM allows deep imaging inside macroscopic cleared specimens with high contrast and speed. Here we describe the complete experimental pipeline to obtain comprehensive and human-readable images of entire mouse brains labeled with fluorescent proteins. The clearing and the mounting procedures are described, together with the steps to perform an optical tomography on its whole volume by acquiring many parallel adjacent stacks. We showed the usage of open-source custom-made software tools enabling stitching of the multiple stacks and multi-resolution data navigation. Finally, we illustrated some example of brain maps: the cerebellum from an L7-GFP transgenic mouse, in which all Purkinje cells are selectively labeled, and the whole brain from a thy1-GFP-M mouse, characterized by a random sparse neuronal labeling.

In this article we describe the full experimental procedure to reconstruct, with high resolution, the fine brain anatomy of fluorescently labeled mouse brains. The described protocol includes sample preparation and clearing, specimen mounting for imaging, data post-processing and multi-scale visualization.

מיקרון בקנה מידת רזולוציה אופטית טומוגרפיה של מוח עכבר השלם עם מיקרוסקופית גיליון Confocal אור

Understanding the architecture of mammalian  brain at single-cell resolution is one of the key issues of neuroscience.  However, mapping neuronal soma and ...

The Use of Magnetic Resonance Spectroscopy as a Tool for the Measurement of Bi-hemispheric Transcranial Electric Stimulation Effects on Primary Motor Cortex Metabolism

Transcranial direct current stimulation (tDCS) is a neuromodulation technique that has been increasingly used over the past decade in the treatment of neurological and psychiatric disorders such as stroke and depression. Yet, the mechanisms underlying its ability to modulate brain excitability to improve clinical symptoms remains poorly understood 33. To help improve this understanding, proton magnetic resonance spectroscopy (1H-MRS) can be used as it allows the in vivo quantification of brain metabolites such as &#947;-aminobutyric acid (GABA) and glutamate in a region-specific manner 41. In fact, a recent study demonstrated that 1H-MRS is indeed a powerful means to better understand the effects of tDCS on neurotransmitter concentration 34. This article aims to describe the complete protocol for combining tDCS (NeuroConn MR compatible stimulator) with 1H-MRS at 3 T using a MEGA-PRESS sequence. We will describe the impact of a protocol that has shown great promise for the treatment of motor dysfunctions after stroke, which consists of bilateral stimulation of primary motor cortices 27,30,31. Methodological factors to consider and possible modifications to the protocol are also discussed.

This article aims to describe a basic protocol for combining transcranial direct current stimulation (tDCS) with proton magnetic resonance spectroscopy (1H-MRS) measurements to investigate the effects of bilateral stimulation on primary motor cortex metabolism.

השימוש בספקטרוסקופיה בתהודה מגנטית ככלי למדידה של השפעות דו חצי מוח Transcranial חשמלי גירוי על יסודי Motor Cortex מטבוליזם

Transcranial direct current stimulation (tDCS) is a neuromodulation technique that has been increasingly used over the past decade in the treatment of ...

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has been heavily studied. While many imaging studies treat the hippocampus as a single unitary neuroanatomical structure, it is, in fact, composed of several subfields that have a complex three-dimensional geometry. As such, it is known that these subfields perform specialized functions and are differentially affected through the course of different disease states. Magnetic resonance (MR) imaging can be used as a powerful tool to interrogate the morphology of the hippocampus and its subfields. Many groups use advanced imaging software and hardware (&#62;3T) to image the subfields; however this type of technology may not be readily available in most research and clinical imaging centers. To address this need, this manuscript provides a detailed step-by-step protocol for segmenting the full anterior-posterior length of the hippocampus and its subfields: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus (DG), strata radiatum/lacunosum/moleculare (SR/SL/SM), and subiculum. This protocol has been applied to five subjects (3F, 2M; age 29-57, avg. 37). Protocol reliability is assessed by resegmenting either the right or left hippocampus of each subject and computing the overlap using the Dice&#39;s kappa metric. Mean Dice&#39;s kappa (range) across the five subjects are: whole hippocampus, 0.91 (0.90-0.92); CA1, 0.78 (0.77-0.79); CA2/CA3, 0.64 (0.56-0.73); CA4/dentate gyrus, 0.83 (0.81-0.85); strata radiatum/lacunosum/moleculare, 0.71 (0.68-0.73); and subiculum 0.75 (0.72-0.78). The segmentation protocol presented here provides other laboratories with a reliable method to study the hippocampus and hippocampal subfields in vivo using commonly available MR tools.

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

The goal of this manuscript is to study the hippocampus and hippocampal subfields using MRI. The manuscript describes a protocol for segmenting the hippocampus and five hippocampal substructures: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus, strata radiatum/lacunosum/moleculare, and subiculum.

ברזולוציה גבוהה<em&gt; In vivo</em&gt; פרוטוקול פילוח ידני לאדם בהיפוקמפוס תת תחומים באמצעות הדמיה בתהודה מגנטית 3T

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has ...

High-resolution Structural Magnetic Resonance Imaging of the Human Subcortex In Vivo and Postmortem

The focus of this study was to test the resolution limits of structural MRI of a postmortem brain compared to living human brains. The resolution of structural MRI in vivo is ultimately limited by physiological noise, including pulsation, respiration and head movement. Although imaging hardware continues to improve, it is still difficult to resolve structures on the millimeter scale. For example, the primary visual sensory pathways synapse at the lateral geniculate nucleus (LGN), a visual relay and control nucleus in the thalamus that normally is organized into six interleaved monocular layers. Neuroimaging studies have not been able to reliably distinguish these layers due their small size that are less than 1 mm thick.
The resolving limit of structural MRI, in a postmortem brain was tested using multiple images averaged over a long duration (~24 h). The purpose was to test whether it was possible to resolve the individual layers of the LGN in the absence of physiological noise. A proton density (PD)1 weighted pulse sequence was used with varying resolution and other parameters to determine the minimum number of images necessary to be registered and averaged to reliably distinguish the LGN and other subcortical regions. The results were also compared to images acquired in living human brains. In vivo subjects were scanned in order to determine the additional effects of physiological noise on the minimum number of PD scans needed to differentiate subcortical structures, useful in clinical applications.

High-resolution Structural Magnetic Resonance Imaging of the Human Subcortex In Vivo and Postmortem

Here we present a protocol to determine the minimum number images that needed to be registered and averaged to resolve subcortical structures and test whether the individual layers of the LGN could be resolved in the absence of physiological noise.

הדמיית תהודה מגנטית מבנית ברזולוציה גבוהה של תת-הקליפה&quot; האדם<I&gt; In vivo</I&gt; ולאחר המוות

The focus of this study was to test the resolution limits of structural MRI of a postmortem brain compared to living human brains. The resolution of ...

Functional Magnetic Resonance Spectroscopy at 7 T in the Rat Barrel Cortex During Whisker Activation

Nuclear magnetic resonance (NMR) spectroscopy offers the opportunity to measure cerebral metabolite contents in vivo and noninvasively. Thanks to technological developments over the last decade and the increase in magnetic field strength, it is now possible to obtain good resolution spectra in vivo in the rat brain. Neuroenergetics (i.e., the study of brain metabolism) and, especially, metabolic interactions between the different cell types have attracted more and more interest in recent years. Among these metabolic interactions, the existence of a lactate shuttle between neurons and astrocytes is still debated. It is, thus, of great interest to perform functional proton magnetic resonance spectroscopy (1H-MRS) in a rat model of brain activation and monitor lactate. However, the methyl lactate peak overlaps lipid resonance peaks and is difficult to quantify. The protocol described below allows metabolic and lactate fluctuations to be monitored in an activated brain area. Cerebral activation is obtained by whisker stimulation and 1H-MRS is performed in the corresponding activated barrel cortex, whose area is detected using blood-oxygen-level-dependent functional magnetic resonance imaging (BOLD fMRI). All steps are fully described: the choice of anesthetics, coils, and sequences, achieving efficient whisker stimulation directly in the magnet, and data processing.

After checking by blood-oxygen-level-dependent functional magnetic resonance imaging (BOLD fMRI) that the corresponding somatosensory barrel field cortex area (called S1BF) is correctly activated, the main goal of this study is to quantify lactate content fluctuations in the activated rat brains by localized proton magnetic resonance spectroscopy (1H-MRS) at 7 T.

ספקטרוסקופיה תהודה מגנטית תפקודית-7 T בקליפת חבית חולדה במהלך ההפעלה שפם

Nuclear magnetic resonance (NMR) spectroscopy offers the opportunity to measure cerebral metabolite contents in vivo and noninvasively. Thanks to ...

High-Resolution 3D Imaging of Rabies Virus Infection in Solvent-Cleared Brain Tissue

The visualization of infection processes in tissues and organs by immunolabeling is a key method in modern infection biology. The ability to observe and study the distribution, tropism, and abundance of pathogens inside of organ tissues provides pivotal data on disease development and progression. Using conventional microscopy methods, immunolabeling is mostly restricted to thin sections obtained from paraffin-embedded or frozen samples. However, the limited 2D image plane of these thin sections may lead to the loss of crucial information on the complex structure of an infected organ and the cellular context of the infection. Modern multicolor, immunostaining-compatible tissue clearing techniques now provide a relatively fast and inexpensive way to study high-volume 3D image stacks of virus-infected organ tissue. By exposing the tissue to organic solvents, it becomes optically transparent. This matches the sample&#8217;s refractive indices and eventually leads to a significant reduction of light scattering. Thus, in combination with long free working distance objectives, large tissue sections up to 1 mm in size can be imaged by conventional confocal laser scanning microscopy (CLSM) at high resolution. Here, we describe a protocol to apply deep-tissue imaging after tissue clearing to visualize rabies virus distribution in infected brains in order to study topics like virus pathogenesis, spread, tropism, and neuroinvasion.

Novel, immunostaining-compatible tissue clearing techniques like the ultimate 3D imaging of solvent-cleared organs allow the 3D visualization of rabies virus brain infection and its complex cellular environment. Thick, antibody-labeled brain tissue slices are made optically transparent to increase imaging depth and to enable 3D analysis by confocal laser scanning microscopy.

ברזולוציה גבוהה 3D הדמיה של זיהום וירוס כלבת ברקמת המוח נקי ממס

The visualization of infection processes in tissues and organs by immunolabeling is a key method in modern infection biology. The ability to observe and ...

Preparation of Newborn Rat Brain Tissue for Ultrastructural Morphometric Analysis of Synaptic Vesicle Distribution at Nerve Terminals

Our laboratory and many others have exploited the high resolving power of transmission electron microscopy to study the morphology and spatial organization of synaptic vesicles. In order to obtain high-quality electron micrographs that can yield the degree of morphological detail necessary for quantitative analysis of pre-synaptic vesicle distribution, optimal specimen preparation is critical. Chemical fixation is the first step in the process of specimen preparation, and of utmost importance to preserve fine ultrastructure. Vascular fixation with a glutaraldehyde-formaldehyde solution, followed by treatment of vibratome-sectioned specimens with osmium tetroxide, stabilizes the maximum number of molecules, especially proteins and lipids, and results in superior conservation of ultrastructure. Tissue is then processed with counterstaining, sequential dehydration and resin-embedding. En bloc staining with uranyl acetate (i.e., staining of vibratome-sectioned tissue before resin embedding) enhances endogenous contrast and stabilizes cell components against extraction during specimen processing. Contrast can be further increased by applying uranyl acetate as a post-stain on ultrathin sections. Double-staining of ultrathin sections with lead citrate after uranyl acetate treatment also improves image resolution, by intensifying electron-opacity of nucleic acid-containing structures through selective binding of lead to uranyl acetate. Transmission electron microscopy is a powerful tool for characterization of the morphological details of synaptic vesicles and quantification of their size and spatial organization in the terminal bouton. However, because it uses fixed tissue, transmission electron microscopy can only provide indirect information regarding living or evolving processes. Therefore, other techniques should be considered when the main objective is to study dynamic or functional aspects of synaptic vesicle trafficking and exocytosis.

We describe procedures for processing newborn rat brain tissue to obtain high-resolution electron micrographs for morphometric analysis of synaptic vesicle distribution at nerve terminals. The micrographs obtained with these methods can also be used to study the morphology of a number of other cellular components and their dimensional structural relationships.

הכנת התינוק היילוד רקמת המוח עבור ניתוח בדיקת מבנית באולטרסאונד של הפצת שלפוחית סינפטית במסופי העצבים

Our laboratory and many others have exploited the high resolving power of transmission electron microscopy to study the morphology and spatial ...

A Hydrophobic Tissue Clearing Method for Rat Brain Tissue

Hydrophobic tissue clearing methods are easily adjustable, fast, and low-cost procedures that allows for the study of a molecule of interest in unaltered tissue samples. Traditional immunolabeling procedures require cutting the sample into thin sections, which restricts the ability to label and examine intact structures. However, if brain tissue can remain intact during processing, structures and circuits can remain intact for the analysis. Previously established clearing methods take significant time to completely clear the tissue, and the harsh chemicals can often damage sensitive antibodies. The iDISCO method quickly and completely clears tissue, is compatible with many antibodies, and requires no special lab equipment. This technique was initially validated for the use in mice tissue, but the current protocol adapts this method to image hemispheres of control and transgenic rat brains. In addition to this, the present protocol also makes several adjustments to preexisting protocol to provide clearer images with less background staining. Antibodies for Iba-1 and tyrosine hydroxylase were validated in the HIV-1 transgenic rat and in F344/N control rats using the present hydrophobic tissue clearing method. The brain is an interwoven network, where structures work together more often than separately of one another. Analyzing the brain as a whole system as opposed to a combination of individual pieces is the greatest benefit of this whole brain clearing method.

Here we present a hydrophobic tissue clearing method that allows for the viewing of target molecules as part of intact brain structures. This technique has now been validated for F344/N control and HIV-1 transgenic rats of both sexes.

שיטת ניקוי רקמות הידרופובית לרקמת מוח חולדה

Hydrophobic tissue clearing methods are easily adjustable, fast, and low-cost procedures that allows for the study of a molecule of interest in unaltered ...