المؤلفان بالشكر سلمان Khetani ، ألن جاريد ، Flaim كريس وDerfus أوستن لإجراء مناقشات مفيدة خلال عملية تصميم هذا الجهاز. وأيد هذا العمل من قبل مؤسسة العلوم الوطنية كلية المبكر برنامج التطوير المهني والمعاهد الوطنية للصحة المعهد / الوطني للسكري وأمراض الجهاز الهضمي والكلى ، ومؤسسة ديفيد ولوسيل باكارد. كان مدعوما من قبل L. EEH روث الجائزة الوطنية كيرشتاين دائرة البحوث.

إعداد الثقافات الخلية : <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> تبدأ مع قطع السليكون مغلفة مع البلازما المعاملة البوليسترين. </li><li style=";text-align:right;direction:rtl"> قطع معطف مع البروتينات المصفوفة خارج الخلية المناسبة لدعم مرفق من نوع من الخلايا المطلوبة. لخلايا الكبد ، يحضن في 50 جم / مل 1 - الكولاجين الحل عند 37 درجة مئوية لمدة 45 دقيقة. لالليفية 3T3 ، هناك حاجة إلى أي مصفوفة. </li><li style=";text-align:right;direction:rtl"> تأمين قطع الغيار مع أجزاء مكملة في التكوين للإتصال به. </li><li style=";text-align:right;direction:rtl"> نقع في الإيثانول 70 ٪ لمدة لا تقل عن 10 دقيقة لتعقيم. شطف 2X في DDH 2 O ، و1X في وسائل الإعلام ثقافة الخلية. </li><li style=";text-align:right;direction:rtl"> خلايا البذور بتركيز 500000 خلية / مل في مستنبت المناسبة. 1 مل في استخدام كل بئر من لوحة الثقافة 12 - جيدا. </li><li style=";text-align:right;direction:rtl"> احتضان لمدة 1 ساعة ، ويهز كل 15 دقيقة لاعادة تعليق الخلايا بالتساوي. </li><li style=";text-align:right;direction:rtl"> إذا كان أحادي الطبقة متموجة لم يتحقق بعد 1 ساعة ، نضح تعليق الخلية والبذر مع تكرار توقف الطازجة. كرر حتى تحقق كثافة الخلية المطلوبة. </li><li style=";text-align:right;direction:rtl"> إزالة أجزاء مكملة. نقل أجزاء من الآبار العذبة واحتضان بين عشية وضحاها للسماح للخلايا على الالتزام الكامل وانتشارها. </li><li style=";text-align:right;direction:rtl"> نموذج الاشتراك في الثقافات تأمين قطع الغيار المناسبة في الفجوة أو تكوين الاتصال. قد يتغير في أي لحظة التكوين المطلوب خلال الثقافة. </li><li style=";text-align:right;direction:rtl"> عند تغيير وسائل الإعلام ، أن تحرص على ترك الخلايا الجافة لأقل وقت ممكن ، ويفضل أن يكون مجرد ثانية أو اثنتين. استخلاص السوائل مع يد واحدة واستبدالها فورا باستخدام وسائل الإعلام من جهة أخرى. </li></ol> قطع السيليكون تجهيز لإعادة الاستخدام : <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> الشريط الخلايا التي تمرغ في التبييض والشطف بالماء. </li><li style=";text-align:right;direction:rtl"> تسمح أجزاء حتى يجف تماما. نقع في التولوين لمدة 2 ساعة لتجريد البوليسترين. </li><li style=";text-align:right;direction:rtl"> النظيفة في حل البيرانا (1:2 H 2 O 2 : H 2 SO 4) تسخينه إلى 120 درجة مئوية. </li><li style=";text-align:right;direction:rtl"> شطف لمدة 15 دقيقة في ظل التدفق المستمر للDDH 2 O. إذا كنت لا يذهبون إلى إيداع البوليسترين على الفور ، وتخزين قطع الغيار في المياه. </li><li style=";text-align:right;direction:rtl"> حل البوليسترين في التولوين عند 100 ملغ / مل. في دوامة المخروطية البولي بروبلين لحوالي 1 ساعة أو حتى ، حلت بالكامل. مطلوب أكثر قليلا من 1 مل من حل لكل أجزاء 10. </li><li style=";text-align:right;direction:rtl"> حل تدور حول قطع البوليسترين معطف السيليكون الفردية في 2400 دورة في الدقيقة لمدة 30 ثانية. </li><li style=";text-align:right;direction:rtl"> أخبز لمدة لا تقل عن 5 درجة مئوية في ح 120 </li><li style=";text-align:right;direction:rtl"> علاج الأوكسجين مع البلازما (200 mTorr ، 200 م) لمدة 1 دقيقة. </li></ol>

<ol>
	<li>Hui, E. E., Bhatia, S. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Micromechanical+control+of+cell-cell+interactions.">Micromechanical control of cell-cell interactions.</a> Proceedings of the National Academy of Sciences. 104, 5722-5726 (2007).</li><li>Bhatia, S. N., Balis, U. J., Yarmush, M. L., Toner, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+cell-cell+interactions+in+preservation+of+cellular+phenotype:+cocultivation+of+hepatocytes+and+nonparenchymal+cells.">Effect of cell-cell interactions in preservation of cellular phenotype: cocultivation of hepatocytes and nonparenchymal cells.</a> The FASEB Journal. 13, 1883-1900 (1999).</li><li>El-Ali, J., Sorger, P. K., Jensen, K. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cells+on+Chips.">Cells on Chips.</a> Nature. 442, 403-411 (2006).</li></ol>

The authors have nothing to disclose.

هذا النظام هو فريد من نوعه من حيث أنه يتيح التنظيم المكاني للأنسجة لمعالجته بشكل حيوي على المستوى الخلوي. وبالتالي ، مكن هذا الجهاز عددا من التجارب البيولوجية الرواية ، والتي تمتد موضوعات مثل إشارات بين الخلايا الديناميات ، اتصل بوساطة مقابل إشارة للذوبان ، وقرارات مصير الخلية...

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		<th>Material Name</th>
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<td>Silicon Comb Substrates</td>
<td>Tool</td>
<td>N/A</td>
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<td>Parts are available for collaborative research projects. Please contact Elliot Hui (eehui @ alum . mit . edu) or Sangeeta Bhatia (sbhatia @ mit . edu).</td>
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silicon microchips for manipulating cell-cell interaction

يتم التعرف على دور المكروية الخليوي بانه حاسم في تحديد مصير الخلايا والأنسجة وظيفة في جميع الثدييات تقريبا من التنمية إلى التحول إلى أورام خبيثة. على وجه الخصوص ، وقد تورط التفاعل مع سدى المجاورة في عدد كبير من الظواهر البيولوجية ، إلا أن التقنيات التقليدية تحد من القدرة على استجواب العناصر المكانية والدينامية لهذه التفاعلات. اعادة التشكيل في الثقافة الميكرو ميكانيكية (RC) ، ونحن توظيف ركيزة السيليكون مجهريا مع أجزاء متحركة لمراقبة حيوي خلية خلية التفاعلات من خلال إعادة الميكانيكية. سابقا ، وقد تم تطبيق هذا الأسلوب لتحقيق الاتصال بين الخلايا في الثقافات المشتركة لخلايا الكبد والخلايا غير متني ، مما يدل على الوقت التي تعتمد على التفاعل وعلى نطاق محدود للإشارة للذوبان 1. هنا ، نحن تصف بالتفصيل إعداد واستخدام نظام المنسق المقيم. نبدأ من خلال البرهنة على التعامل مع أجزاء الجهاز باستخدام الملقط ، بما في ذلك التي تحرك بين الفجوة وتكوينات الاتصال (السكان خلية مفصولة فجوة 80 ميكرومتر الضيقة ، أو في اتصال حميم المباشر). المقبل ، ونحن بالتفصيل عملية تحضير ركائز للثقافة ، وبذر الخلية عملية متعددة الخطوات المطلوبة للحصول على monolayers الخلية متموجة. باستخدام المجهر العيش ، ثم نوضح في الوقت الحقيقي التلاعب في الخلايا بين تكوينات مختلفة التجريبية الممكنة. أخيرا ، علينا أن نظهر الخطوات المطلوبة من أجل تجديد سطح الجهاز لإعادة الاستخدام : التولوين وتنظيف سمكة البيرانا ، طلاء البوليسترين ، والأكسجين العلاج البلازما.

Watch this Scientific Journal Video about Silicon Microchips for Manipulating Cell-cell Interaction at JoVE.com

Silicon Microchips for Manipulating Cell-cell Interaction

توضح هذه المقالة نهج التجريبي لتنظيم دينامية خلية خلية التفاعلات بين الخلايا الملتصقة على نطاق ميكرون. ويتضح من الاتصالات بين الخلايا التلاعب بين خلايا الكبد والخلايا اللحمية. المنصة المتقدمة تمكن التحقيق من خلية خلية التفاعلات في مجموعة متنوعة من العمليات البيولوجية ، بما في ذلك تطوير والمرضية.

السيليكون لمعالجة الرقائق خلية خلية التفاعل

The role of the cellular microenvironment is recognized as crucial in determining cell fate and function in virtually all mammalian tissues from ...

silicon-microchips-for-manipulating-cell-cell-interaction

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Biology

10.7K Views.  MIT - Massachusetts Institute of Technology. توضح هذه المقالة نهج التجريبي لتنظيم دينامية خلية خلية التفاعلات بين الخلايا الملتصقة على نطاق ميكرون. ويتضح من الاتصالات بين الخلايا التلاعب بين خلايا الكبد والخلايا اللحمية. المنصة المتقدمة تمكن التحقيق من خلية خلية التفاعلات في مجموعة متنوعة من العمليات ال...

Video: Silicon Microchips for Manipulating Cell-cell Interaction

Using Laser Tweezers For Manipulating Isolated Neurons In Vitro

In this paper and video, we describe the protocols used in our laboratory to study the targeting preferences of regenerating cell processes of adult retinal neurons in vitro. Procedures for preparing retinal cell cultures start with the dissection, digestion and trituration of the retina, and end with the plating of isolated retinal cells on dishes made especially for use with laser tweezers. These dishes are divided into a cell adhesive half and a cell repellant half. The cell adhesive side is coated with a layer of Sal-1 antibodies, which provide a substrate upon which our cells grow. Other adhesive substrates could be used for other cell types. The cell repellant side is coated with a thin layer of poly-HEMA. The cells plated on the poly-HEMA side of the dish are trapped with the laser tweezers, transported and then placed adjacent to a cell on the Sal-1 side to create a pair. Formation of cell groups of any size should be possible with this technique. "Laser-tweezers-controlled micromanipulation" means that the investigator can choose which cells to move, and the desired distance between the cells can be standardized. Because the laser beam goes through transparent surfaces of the culture dish, cell selection and placement are done in an enclosed, sterile environment. Cells can be monitored by video time-lapse and used with any cell biological technique required. This technique may help investigations of cell-cell interactions.

This video describes the manipulation of cultured neurons using laser tweezers in vitro.

باستخدام الملقط ليزر لمعالجة الخلايا العصبية معزولة في المختبر

In this paper and video, we describe the protocols used in our laboratory to study the targeting preferences of regenerating cell processes of adult ...

Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein 1. The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification.
HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH4)2SO4). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) 2. As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter 3. Automated column scouting allows for an efficient approach for determining which HIC media should be employed for future, more exhaustive optimization experiments and protein purification runs 4.
The specific protein being purified here is recombinant green fluorescent protein (GFP); however, the approach may be adapted for purifying other proteins with one or more hydrophobic surface regions. GFP serves as a useful model protein, due to its stability, unique light absorbance peak at 397 nm, and fluorescence when exposed to UV light 5. Bacterial lysate containing wild type GFP was prepared in a high-salt buffer, loaded into a Bio-Rad DuoFlow medium pressure liquid chromatography system, and adsorbed to HiTrap HIC columns containing different HIC media. The protein was eluted from the columns and analyzed by in-line and post-run detection methods. Buffer blending, dynamic sample loop injection, sequential column selection, multi-wavelength analysis, and split fraction eluate collection increased the functionality of the system and reproducibility of the experimental approach.

An automated method for identifying suitable hydrophobic interaction chromatography (HIC) media to be used in the process of protein purification is presented. The method utilizes a medium-pressure liquid chromatography system including automated buffer blending, dynamic sample loop injection, sequential column selection, multi-wavelength analysis, and split fraction eluate collection.

آلية التفاعل اللوني مسعور اختيار عمود للاستخدام في تنقية البروتين

In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction ...

A Liquid Phase Affinity Capture Assay Using Magnetic Beads to Study Protein-Protein Interaction: The Poliovirus-Nanobody Example

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. Provided that one protein can be tagged and another protein labeled, this method can be implemented for the investigation of protein-protein interactions. It is based on one hand on the recognition of the tagged protein by cobalt coated magnetic beads and on the other hand on the interaction between the tagged protein and a second specific protein that is labeled. First, the labeled and tagged proteins are mixed and incubated at room temperature. The magnetic beads, that recognize the tag, are added and the bound fraction of labeled protein is separated from the unbound fraction using magnets. The amount of labeled protein that is captured can be determined in an indirect way by measuring the signal of the labeled protein remained in the unbound fraction. The described liquid phase affinity assay is extremely useful when conformational conversion sensitive proteins are assayed. The development and application of the assay is demonstrated for the interaction between poliovirus and poliovirus recognizing nanobodies1. Since poliovirus is sensitive to conformational conversion2 when attached to a solid surface (unpublished results), the use of ELISA is limited and a liquid phase based system should therefore be preferred. An example of a liquid phase based system often used in polioresearch3,4 is the micro protein A-immunoprecipitation test5. Even though this test has proven its applicability, it requires an Fc-structure, which is absent in the nanobodies6,7. However, as another opportunity, these interesting and stable single-domain antibodies8 can be easily engineered with different tags. The widely used (His)6-tag shows affinity for bivalent ions such as nickel or cobalt, which can on their turn be easily coated on magnetic beads. We therefore developed this simple quantitative affinity capture assay based on cobalt coated magnetic beads. Poliovirus was labeled with 35S to enable unhindered interaction with the nanobodies and to make a quantitative detection feasible. The method is easy to perform and can be established with a low cost, which is further supported by the possibility of effectively regenerating the magnetic beads.

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. It is a reliable technique based on the interaction between magnetic beads and tagged proteins (e.g. nanobodies) on one hand and the affinity between the tagged protein and a second, labeled protein (e.g. poliovirus) on the other.

تقارب المرحلة السائلة الفحص التقاطها باستخدام الخرز المغناطيسي لدراسة البروتين البروتين التفاعل: المثال فيروس شلل الأطفال، Nanobody

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. Provided that one protein can be tagged and another protein ...

Manipulating the Murine Lacrimal Gland

The lacrimal gland (LG) secretes aqueous tears necessary for maintaining the structure and function of the cornea, a transparent tissue essential for vision. In the human a single LG resides in the orbit above the lateral end of each eye delivering tears to the ocular surface through 3 - 5 ducts. The mouse has three pairs of major ocular glands, the most studied of which is the exorbital lacrimal gland (LG) located anterior and ventral to the ear. Similar to other glandular organs, the LG develops through the process of epithelial branching morphogenesis in which a single epithelial bud within a condensed mesenchyme undergoes multiple rounds of bud and duct formation to form an intricate interconnected network of secretory acini and ducts. This elaborate process has been well documented in many other epithelial organs such as the pancreas and salivary gland. However, the LG has been much less explored and the mechanisms controlling morphogenesis are poorly understood. We suspect that this under-representation as a model system is a consequence of the difficulties associated with finding, dissecting and culturing the LG. Thus, here we describe dissection techniques for harvesting embryonic and post-natal LG and methods for ex vivo culture of the tissue.

The lacrimal gland (LG) is a branching organ that produces the aqueous components of tears necessary for maintaining vision and ocular health. Here we describe murine LG dissection and ex vivo culture techniques to decipher signaling pathways involved in LG development.

التلاعب في الغدة الدمعية الفئران

The lacrimal gland (LG) secretes aqueous tears necessary for maintaining the structure and function of the cornea, a transparent tissue essential for ...

Luciferase Complementation Imaging Assay in Nicotiana benthamiana Leaves for Transiently Determining Protein-protein Interaction Dynamics

Protein-protein interactions are fundamental mechanisms for relaying signal transduction in most cellular processes; therefore, identification of novel protein-protein interaction pairs and monitoring protein interaction dynamics are of particular interest for revealing how plants respond to environmental factors and/or developmental signals. A plethora of approaches have been developed to examine protein-protein interactions, either in vitro or in vivo. Among them, the recently established luciferase complementation imaging (LCI) assay is the simplest and fastest method for demonstrating in vivo protein-protein interactions. In this assay, protein A or protein B is fused with the amino-terminal or carboxyl-terminal half of luciferase, respectively. When protein A interacts with protein B, the two halves of luciferase will be reconstituted to form a functional and active luciferase enzyme. Luciferase activity can be recorded with a luminometer or CCD-camera. Compared with other approaches, the LCI assay shows protein-protein interactions both qualitatively and quantitatively. Agrobacterium infiltration in Nicotiana benthamiana leaves is a widely used system for transient protein expression. With the combination of LCI and transient expression, these approaches show that the physical interaction between COP1 and SPA1 was gradually reduced after jasmonate treatment.

Luciferase Complementation Imaging Assay in Nicotiana benthamiana Leaves for Transiently Determining Protein-protein Interaction Dynamics

This manuscript describes an easy and rapid experimental procedure for determining protein-protein interactions based on the measurement of luciferase activity.

لوسيفراس "التكامل بالتصوير الإنزيم" في أوراق نيكوتيانا بينثاميانا "تحديد عابر ديناميات التفاعل" البروتين-بروتين

Protein-protein interactions are fundamental mechanisms for relaying signal transduction in most cellular processes; therefore, identification of novel ...

Visualization of DNA Repair Proteins Interaction by Immunofluorescence

Mammalian cells are constantly exposed to chemicals, radiations, and naturally occurring metabolic by-products, which create specific types of DNA insults. Genotoxic agents can damage the DNA backbone, break it, or modify the chemical nature of individual bases. Following DNA insult, DNA damage response (DDR) pathways are activated and proteins involved in the repair are recruited. A plethora of factors are involved in sensing the type of damage and activating the appropriate repair response. Failure to correctly activate and recruit DDR factors can lead to genomic instability, which underlies many human pathologies including cancer. Studies of DDR proteins can provide insights into genotoxic drug response and cellular mechanisms of drug resistance.
There are two major ways of visualizing&#160;proteins in vivo: direct observation, by tagging the protein of interest with a fluorescent protein and following it by live imaging, or indirect immunofluorescence on fixed samples. While visualization of fluorescently tagged proteins allows precise monitoring over time, direct tagging in N- or C-terminus can interfere with the protein localization or function. Observation of proteins in their unmodified, endogenous version is preferred. When DNA repair proteins are recruited to the DNA insult, their concentration increases locally and they form groups, or &#8220;foci&#8221;, that can be visualized by indirect immunofluorescence using specific antibodies.
Although detection of protein foci does not provide a definitive proof of direct interaction, co-localization of proteins in cells indicates that they regroup to the site of damage and can inform of the sequence of events required for complex formation. Careful analysis of foci spatial overlap in cells expressing wild type or mutant versions of a protein can provide precious clues on functional domains important for DNA repair function. Last, co-localization of proteins indicates possible direct interactions that can be verified by co-immunoprecipitation in cells, or direct pulldown using purified proteins.

Following DNA damage, human cells activate essential repair pathways to restore the integrity of their genome. Here, we describe the method of indirect immunofluorescence as a means to detect DNA repair proteins, analyze their spatial and temporal recruitment, and help interrogate protein-protein interaction at the sites of DNA damage.

التصور من الحمض النووي إصلاح البروتينات التفاعل من قبل immunofluorescence

Mammalian cells are constantly exposed to chemicals, radiations, and naturally occurring metabolic by-products, which create specific types of DNA ...

AirID-Based Proximity Labeling for Protein-Protein Interaction in Plants

In mammalian cells and plants, proximity labeling (PL) approaches using modified ascorbate peroxidase (APEX) or the Escherichia coli biotin ligase BirA (known as BioID) have proven successful in identifying protein-protein interactions (PPIs). APEX, BioID, and TurboID, a revised version of BioID have some restrictions in addition to being valuable technologies. The recently developed AirID, a novel version of BioID for proximity identification in protein-protein interactions, overcame these restrictions. Previously, AirID has been used in animal models, while the current study demonstrates the use of AirID in plants, and the results confirmed that AirID performs better in plant systems as compared to other PL enzymes such as BioID and TurboID for protein labeling that are proximal to the target proteins. Here is a step-by-step protocol for identifying protein interaction partners using AT4G18020 (APRR2) protein as a model. The methods describe the construction of vector, the transformation of construct through agroinfiltration, biotin transformation, extraction of proteins, and enrichment of biotin-labeled proteins through affinity purification technique. The results conclude that AirID is a novel and ideal enzyme for analyzing PPIs in plants. The method can be applied to study other proteins in plants.

Here, we present a step-by-step protocol for performing the proximity labeling (PL) experiment in cucumber (Cucumis sativus L.) using AT4G18020 (APRR2)-AirID protein as a model. The method describes the construction of a vector, the transformation of a construct through agroinfiltration, biotin infiltration, protein extraction, and purification of biotin-labeled proteins through affinity purification technique.

ملصقات القرب المستندة إلى AirID للتفاعل بين البروتين والبروتين في النباتات

In mammalian cells and plants, proximity labeling (PL) approaches using modified ascorbate peroxidase (APEX) or the Escherichia coli biotin ligase BirA ...

CorrelationCalculator: A Bioinformatics Tool for Building Single Interaction Metabolites Network Based on Expression Data

To begin, download a sample comma-delimited input file containing a list of metabolites with experimental measurements. Double click on the downloaded sample file to open it and verify that it contains labels for both the samples and the metabolites. Next, download the correlation calculator Java application, and double click on the downloaded JAR file to launch the application.On the input tab, click the browse button to upload the input file. Under specify file format, select samples in rows. Click on the next button from the bottom right of the window to move to the data normalization tab.Under select methods, check the box next to log to transform data and autoscale data. Under normalized data, click the run button. Once the normalization is complete, click the save button to save the new data file.Click on the next button to move to the data analysis tab and under Calculate Pearson's Correlation, click run to determine the best Pearson's correlation range for the data. Click on the view histogram button to review the frequency of the maximal Pearson's correlation scores per feature in the view heat map button to review the representation of Pearson's correlation matrix. Under Filter by Pearson's Correlations, leave the default numbers to filter by a range of 0.00 to 1.00.Then under Select Partial Correlation Method, select the desired method as DSPC method. And under Calculate Partial Correlations, click the run button. Click on the view CSV file to view the results, and click the save button to save the results.A representative network constructed from a subset of the KORA population study metabolomics data consisting of 151 metabolites across 240 subjects is shown. Consensus network clustering resulted in the identification of nine sub-networks or metabolic modules.

CorrelationCalculator: أداة المعلوماتية الحيوية لبناء شبكة مستقلبات تفاعل واحد بناء على بيانات التعبير

دراسات التفاعل الجزيئي الحيوي باستخدام تقنية الخميرة ثنائية الهجين 

Isolating Interaction-Null&#47;Impaired Mutants Using the Yeast Two-Hybrid Assay

Protein-protein interactions are one of the most basic processes that underlie biological phenomena. One of the simplest and best ways to understand the role(s) and function(s) of a specific protein-protein interaction is to compare the phenotype of the wild-type (with the relevant protein-protein interaction) and those of mutants that lack the relevant interaction. Therefore, if such mutants can be isolated, they will help to elucidate the related biological processes. The yeast two-hybrid (Y2H) procedure is a powerful approach not only to detect protein-protein interactions but also to isolate interaction-null/impaired mutants. In this article, a protocol is presented to isolate interaction-null/impaired mutants using Y2H technology. First, a mutation library is constructed by combining the polymerase chain reaction and efficient seamless cloning technology, which efficiently excludes the empty vector from the library. Second, interaction-null/impaired mutants are screened by the Y2H assay. Because of a trick in the Y2H vector, undesired mutants, such as those with frameshift and nonsense mutations, are efficiently eliminated from the screening process. This strategy is simple and can, therefore, be applied to any combination of proteins whose interaction can be detected by the two-hybrid system.

تسليط الضوء على المؤلف: تعزيز عزل الطفرات الفارغة للتفاعل في الخميرة

The interactions of biomolecules, such as protein-protein interactions, are the molecular basis of biological functions. If interaction-null/impaired mutants that specifically lack the relevant interaction can be isolated, they will greatly help to understand the function(s) of this interaction. This article presents an efficient way to isolate interaction-null/impaired mutants.

عزل الطفرات التفاعلية الفارغة / الضعيفة باستخدام مقايسة الخميرة ثنائية الهجين

Protein-protein interactions are one of the most basic processes that underlie biological phenomena. One of the simplest and best ways to understand the ...