نود أن نشكر أعضاء المجموعة بوتر لتقديم التعليقات بشأن البروتوكول لا تقدر بثمن. وقد تم تمويل هذا العمل من خلال التدريب زمالة بحثية سريرية من الأكاديمية الأميركية لعلم الأعصاب في مؤسسة CMH ، والزمالة من المعهد الوطني للعلوم الطبية العامة (NIGMS ؛ <a href="http://www.nigms.nih.gov/">http://www.nigms.nih.gov/</a> ) لJDR (GM08169 ) ، منحة من المعاهد القومية للصحة والمعهد الوطني للاضطرابات العصبية والسكتة الدماغية (NS054809) ، ولام روث القومي للبحوث لجائزة الخدمة كيرشتاين JDR (NS060392) ، وجبهة الخلاص الوطني منحة EFRI (0836017) ، ومؤسسة جائزة بحوث بالحركة كولتر ، و متعدية زمالات الأبحاث لJDR (NS007480).

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CMH ليس لديه ما يكشف.<br /وتدفع&gt; SMP JDR والاستشاريين لأكسيون النظم البيولوجية.<br /وقد تكرمت برعاية&gt; رسوم التقديم ورسوم معالجة الفيديو لهذه المادة ، والفيديو متعدد القنوات الأنظمة.

ويبين هذا البروتوكول على تعليمات حول كيفية الحفاظ على الثقافة والشبكات العصبية في الدقيقة الكهربائي صفائف فضلا عن مقدمة للتسجيل من وتحفيز شبكات الخلايا العصبية. كما تم بحث بعض من أكثر المشاكل شيوعا عند التسجيل من الاتفاقات في المقطع المشاكل MEA. هناك اختلافات في بعض الأحيان في البروتوكول كما نوقش في كثير من الأحيان في جميع أنحاء وتستخدم هذه التغييرات لتحسين الظروف المحددة التي تتطلبها بعض تصاميم تجريبية. على الرغم من أن يتألف منها نظام التسجيل وتحفيز المقدمة هنا من عادتنا صمم NeuroRighter 15 مع preamp MCS ، وهناك العديد من الأنظمة الأخرى التي يمكن أن توفر واجهة مع الشبكات العصبية. واختيار نمط معين يعتمد على احتياجات تجريبية محددة. وقدمت أمثلة تسجيل التبسيط والتحفيز في هذا البروتوكول ولكن يمكن استخدام هذه الثقافات على الاتفاقات البيئية المتعددة الأطراف لتقديم نظرة ثاقبة حول المسائل المعقدة نشاط الخلايا العصبية ومتشابك الاتصال بالشبكة. كما ذكر أعلاه ، هو العمل الجاري الاستفادة من هذه التكنولوجيا لدراسة العمليات مثل اللدونة الخلوية ، والتنمية ، وتنكس عصبي excitotoxicity. 60-10 وعلى سبيل المثال ، أظهرت نشرة صدرت مؤخرا من المختبر هدفنا تكرار توجيه التعلم في المختبر في الوقت الحقيقي مع التحفيز في حلقة مغلقة ردا على نشاط الشبكة العصبية الحالية 3. على الرغم من ثقافات الشرق الأوسط وأفريقيا غالبا ما صعب وحساس ، وذلك بفضل بساطتها وسهولة الوصول إليها (بالمقارنة مع الحيوانات سليمة) ، فإنها تقدم نموذجا قويا لدراسة نشاط الخلايا العصبية على مستوى الشبكة.

لوازم <ul style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> المتاح زجاجة التصفية العلوي (150ml ، حجم المسام 0.2μm ؛ Nalgene # 565-0020) </li><li style=";text-align:right;direction:rtl"> الجنينية يوم 18 توقيت الحامل الفئران الإناث </li><li style=";text-align:right;direction:rtl"> صفائف Microelectrode (انظر الوصف في البروتوكول ، B1) </li><li style=";text-align:right;direction:rtl"> مجموعة أغطية Microelectrode (انظر الوصف في البروتوكول ، B3) </li><li style=";text-align:right;direction:rtl"> النايلون مصفاة الخلية (40μm ، BD فالكون ، # 352340) </li><li style=";text-align:right;direction:rtl"> قوارير البولي بروبلين المخروطية (العقيمة ، 15ml) </li><li style=";text-align:right;direction:rtl"> البوليسترين أطباق بتري (العقيمة ، 35mm و100x15mm) </li><li style=";text-align:right;direction:rtl"> نصائح الماصة (العقيمة ، 20μl ، و200μl 1000μl) </li><li style=";text-align:right;direction:rtl"> المصلية pipets (5ml) </li></ul> المعدات : <ul style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> السلامة البيولوجية غطاء تدفق مجلس الوزراء / الصفحي </li><li style=";text-align:right;direction:rtl"> خلية مكافحة </li><li style=";text-align:right;direction:rtl"> الطرد المركزي </li><li style=";text-align:right;direction:rtl"> حاوية من الجليد </li><li style=";text-align:right;direction:rtl"> تشريح مقص وملقط (معقمة) </li><li style=";text-align:right;direction:rtl"> تشريح المجهر في التدفق الصفحي هود </li><li style=";text-align:right;direction:rtl"> محمول الكهربائية pipetman </li><li style=";text-align:right;direction:rtl"> عدادة الكريات </li><li style=";text-align:right;direction:rtl"> Isofluorane وغرفة الغاز </li><li style=";text-align:right;direction:rtl"> ضوء المجهر </li><li style=";text-align:right;direction:rtl"> محمول pipetman (P - 20 (20μl) ، P - 200 (200μl) ، P - 1000 (1000μl)) </li><li style=";text-align:right;direction:rtl"> MEA نظام تسجيل (انظر الوصف في D1 ، بروتوكول) </li><li style=";text-align:right;direction:rtl"> القوارض المقصلة </li><li style=";text-align:right;direction:rtl"> ثلاثي الغاز الحاضنة (انظر الوصف في البروتوكول ، B15) </li><li style=";text-align:right;direction:rtl"> قارورة فراغ المرفقة مع الشافطة في قلنسوة </li><li style=";text-align:right;direction:rtl"> دوامة </li><li style=";text-align:right;direction:rtl"> حمام الماء (35-37 درجة مئوية) </li></ul> حلول والكواشف : BSA الحل : جعل BSA 5 ٪ مخزنة (سيغما A - 9418) في الفوسفات 7.4 درجة الحموضة والملوحة في 0.2μm تصفيتها. يمكن تحضير هذا الحل في وقت مبكر وتخزينها في 4 درجات مئوية لعدة أشهر. خلية متوسطة : الجمع بين 90 مل Dulbecco لتعديل النسر المتوسطة (ايرفين العلمية 9024) ، و 10 مل حصان المصل (Gibco 16050) ، 1ml البيروفات الصوديوم (100mM ، Gibco 11360) ، و 250 GlutaMAX ميكرولتر (Gibco 35050) ، والانسولين (تركيز النهائي 2.5 ميكروغرام / لتر ، سيغما I - 5500) ثم تمرير من خلال الدافئة 0.2 ميكرومتر ويوازن filter.22 المتوسط ​​في الخلية الحاضنة قبل الاستخدام. حل تشريح لإعداد حل غراء : 23 <table border="1" style=";text-align:right;direction:rtl"><tr><td> حل تشريح (100ML الأسهم) </td><td> تجمع من أجل تصفية 0.22 ميكرون وتخزينها في 4 درجات مئوية. </td><td></td></tr><tr><td> مكون </td><td> حجم مل </td><td> التركيز النهائي (مم) </td></tr><tr><td> المزدوج الماء المقطر </td><td> 91.175 </td><td></td></tr><tr><td> 1 م 2 MgCl </td><td> 0.58 </td><td> 5.8 ملي </td></tr><tr><td> 1 م 2 CaCl </td><td> 0،025 </td><td> 0.25 ملم </td></tr><tr><td> 0.5 HEPES M </td><td> 0.32 </td><td> 1.6 ملم </td></tr><tr><td> أحمر الفينول 0.5 ٪ </td><td> 0.2 </td><td> (0.001 ٪) </td></tr><tr><td> هيدروكسيد الصوديوم 0.1 N </td><td> 0.2 </td><td> 0.2 ملم </td></tr><tr><td> 2 M Na2SO4 </td><td> 4.5 </td><td> 90 ملم </td></tr><tr><td> 1 م K2SO4 </td><td> 3.0 </td><td> 30 ملم </td></tr><tr><td> 0.1 M حمض Kynurenic </td><td> 1.0 </td><td> 1 ملم </td></tr><tr><td> 5 ملم APV </td><td> 1.0 </td><td> 0.05 ملم </td></tr></table> يمكن تحضير هذا الحل في وقت مبكر وتخزينها في 4 درجات مئوية لعدة أشهر. الدناز الأول : Invitrogen (# 18047019). وميض المجمدة aliquots 50μl وتخزينها على -80 درجة مئوية. هو إذابة وقسامة في التدفق الصفحي هود قبل البدء في عملية تفكك الخلية. هانك في محلول ملحي متوازن : سيغما (# 4891). ويتم إعداد حل 1X في الماء منزوع الأيونات ، العقيمة التي تمت تصفيتها في 0.2μm وتخزينها في 4 درجات مئوية. السبات الحل : يعد يوم من زراعة. الجمع بين 98 مل L - 15 متوسطة (Invitrogen 11415) مع 2 الملحق B - 27 مل (50X ، Invitrogen # 17504) ، وتصفية بنسبة 0.2 ميكرون. Laminin الحل : يعد يوم من زراعة. تمييع 20μl من laminin (1mg/ml ، سيغما L - 2020) في المتوسط ​​980 خلية ميكرولتر لتركيز 0.02mg/ml النهائي. يتم تخزين 20 aliquots ميكرولتر من laminin (1mg/ml) في -80 درجة مئوية ، وإذابة فقط قبل استخدامه. ذوبان يجب أن تحدث في أعلى المقعد وليس في الحمام المائي والسريع الذوبان يمكن أن يؤدي في بعض الأحيان إلى التبلور من laminin. غراء الحل : 23 10 مل من محلول دافئ تشريح (أعلاه) إلى 30-32 درجة مئوية. إضافة 200 وحدة غراء (سيغما P - 4762) و 1.6 ملغ L - السيستين (سيغما C - 7880). ضبط الرقم الهيدروجيني إلى 7.4 مع حوالي 14 ميكرولتر من هيدروكسيد الصوديوم N 0.1. احتضان لمدة حوالي 30 دقيقة حتى حل CLالأذنين ، وتصفية 0،2 ميكرون ، ومضة تجميد مع النيتروجين السائل في 2 مل aliquots في 15 مل قارورة المخروطية البولي بروبلين المعقمة وتخزينها في -80 درجة مئوية. ذوبان الجليد في قسامة an 35-37 درجة مئوية قبل البدء في البروتوكول. Polyethyleneimine (PEI) الحل : 13 غير المخفف 100 ميكرولتر من PEI (50 ٪ ث / ت ، ف سيغما 3143) في 100 مل من الصوديوم العازلة بورات (0.1 درجة الحموضة 8.4 M ، B - سيغما 9876) للتركيز النهائي من 0.05 ٪ ث / v. معقمة تصفية بنسبة 0.2 ميكرون. ويمكن إعداد هذا مسبقا وحفظها في 4 درجات مئوية لمدة شهور. عقيمة غير المتأينة المياه : الأوتوكلاف والسماح لتبرد إلى درجة حرارة الغرفة قبل الاستخدام. التربسين (0.25 ٪ مع EDTA ، Gibco 25200) : وميض المجمدة aliquots 1ml وتخزينها على -80 درجة مئوية. يتم إذابة Aliquots في الحمام 35-37 ° C المياه قبل استخدامها.

how to culture, record and stimulate neuronal networks on micro-electrode arrays (meas)

في القرن الماضي ، وقد كرس العديد من علماء الأعصاب في جميع أنحاء العالم حياتهم لفهم كيفية عمل الشبكات العصبية ، ولماذا توقفوا عن العمل في مختلف الأمراض. وشملت الدراسات neuropathological الملاحظة ، المجهر الفلورسنت مع العلامات الوراثية ، وتسجيلها في كل من الخلايا العصبية فصل والاستعدادات شريحة. يناقش هذا البروتوكول آخر التكنولوجيا ، والتي تنطوي على تنامي العصبية نأت على الثقافات الصغيرة مسرى صفائف (وتسمى أيضا متعدد القطب صفائف الاتفاقات البيئية المتعددة الأطراف). هناك مزايا عديدة لاستخدام هذا النظام أكثر من غيرها من التقنيات. ثقافات العصبية نأت على الاتفاقات تقديم نموذج مبسط يمكن من خلالها التلاعب نشاط شبكة الاتصال مع تسلسل التحفيز الكهربائي من خلال أقطاب الصفيف متعددة. لأن شبكة صغيرة ، ويقتصر أثر التحفيز إلى مناطق يمكن ملاحظتها ، والذي ليس هو الحال في الأعمال التحضيرية سليمة. الخلايا تنمو في المونولاير إجراء تغييرات في سهل التشكل لمراقبة بتقنيات التصوير المختلفة. أخيرا ، يمكن للثقافات على الاتفاقات البقاء على قيد الحياة لأكثر من سنة في المختبر الذي يزيل أية قيود زمنية واضحة متأصلة مع تقنيات زراعة أخرى. 1 مختبرنا وغيرها في جميع أنحاء العالم وتستخدم هذه التكنولوجيا لطرح أسئلة هامة حول الشبكات العصبية. الغرض من هذا البروتوكول هو توفير المعلومات اللازمة لإقامة ورعاية ، وتسجيل من الثقافات وتحفيز كهربائيا على الاتفاقات. شبكات الأنابيب وتوفر وسيلة لطرح الأسئلة ذات الصلة من الناحية الفسيولوجية في الشبكة الخلوية والمستويات مما يؤدي إلى فهم أفضل وظيفة الدماغ واختلال وظيفي.

Watch this Scientific Journal Video about How to Culture, Record and Stimulate Neuronal Networks on Micro-electrode Arrays MEAs at JoVE.com

How to Culture, Record and Stimulate Neuronal Networks on Micro-electrode Arrays MEAs

هذا البروتوكول يوفر المعلومات اللازمة لإقامة ورعاية ، وتسجيل من الثقافات وتحفيز كهربائيا على الاتفاقات.<em&gt; في المختبر</em&gt; شبكات توفير وسيلة لطرح الأسئلة ذات الصلة من الناحية الفسيولوجية في الشبكة الخلوية والمستويات مما يؤدي إلى فهم أفضل وظيفة الدماغ واختلال وظيفي.

كيفية تسجيل والثقافة والحث على الشبكات العصبية الصغيرة مسرى صالحة (الاتفاقات)

For the last century, many neuroscientists around the world have dedicated their lives to understanding how neuronal networks work and why they stop ...

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Biology

How to Culture, Record and Stimulate Neuronal Networks on Micro-electrode Arrays (MEAs)

54.3K Views.  Emory University School of Medicine. هذا البروتوكول يوفر المعلومات اللازمة لإقامة ورعاية ، وتسجيل من الثقافات وتحفيز كهربائيا على الاتفاقات. في المختبر شبكات توفير وسيلة لطرح الأسئلة ذات الصلة من الناحية الفسيولوجية في الشبكة الخلوية والمستويات مما يؤدي إلى فهم أفضل وظيفة الدماغ واختلال...

Video: How to Culture, Record and Stimulate Neuronal Networks on Micro-electrode Arrays MEAs

A Neuronal and Astrocyte Co-Culture Assay for High Content Analysis of Neurotoxicity

High Content Analysis (HCA) assays combine cells and detection reagents with automated imaging and powerful image analysis algorithms, allowing measurement of multiple cellular phenotypes within a single assay. In this study, we utilized HCA to develop a novel assay for neurotoxicity. Neurotoxicity assessment represents an important part of drug safety evaluation, as well as being a significant focus of environmental protection efforts. Additionally, neurotoxicity is also a well-accepted in vitro marker of the development of neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Recently, the application of HCA to neuronal screening has been reported. By labeling neuronal cells with &beta;III-tubulin, HCA assays can provide high-throughput, non-subjective, quantitative measurements of parameters such as neuronal number, neurite count and neurite length, all of which can indicate neurotoxic effects. However, the role of astrocytes remains unexplored in these models. Astrocytes have an integral role in the maintenance of central nervous system (CNS) homeostasis, and are associated with both neuroprotection and neurodegradation when they are activated in response to toxic substances or disease states. GFAP is an intermediate filament protein expressed predominantly in the astrocytes of the CNS. Astrocytic activation (gliosis) leads to the upregulation of GFAP, commonly accompanied by astrocyte proliferation and hypertrophy. This process of reactive gliosis has been proposed as an early marker of damage to the nervous system. The traditional method for GFAP quantitation is by immunoassay. This approach is limited by an inability to provide information on cellular localization, morphology and cell number. We determined that HCA could be used to overcome these limitations and to simultaneously measure multiple features associated with gliosis - changes in GFAP expression, astrocyte hypertrophy, and astrocyte proliferation - within a single assay. In co-culture studies, astrocytes have been shown to protect neurons against several types of toxic insult and to critically influence neuronal survival. Recent studies have suggested that the use of astrocytes in an in vitro neurotoxicity test system may prove more relevant to human CNS structure and function than neuronal cells alone. Accordingly, we have developed an HCA assay for co-culture of neurons and astrocytes, comprised of protocols and validated, target-specific detection reagents for profiling &beta;III-tubulin and glial fibrillary acidic protein (GFAP). This assay enables simultaneous analysis of neurotoxicity, neurite outgrowth, gliosis, neuronal and astrocytic morphology and neuronal and astrocytic development in a wide variety of cellular models, representing a novel, non-subjective, high-throughput assay for neurotoxicity assessment. The assay holds great potential for enhanced detection of neurotoxicity and improved productivity in neuroscience research and drug discovery.

This article describes a novel protocol and reagent set designed for sensitive measurement of neurotoxic effects of compounds and treatments on co-cultures of neurons and astrocytes using high content analysis. Results demonstrate that high content analysis represents an exciting novel technology for neurotoxicity assessment.

والخلايا العصبية ونجمية المشارك الثقافة الفحص لتحليل محتوى عال من العصبية

High Content Analysis (HCA) assays combine cells and detection reagents with automated imaging and powerful image analysis algorithms, allowing ...

Chick ex ovo Culture and ex ovo CAM Assay: How it Really Works

Chicken eggs in the early phase of breeding are between in vitro and in vivo systems and provide a vascular test environment not only to study angiogenesis but also to study tumorigenesis. After the chick chorioallantoic membrane (CAM) has developed, its blood vessel network can be easily accessed, manipulated and observed and therefore provides an optimal setting for angiogenesis assays. Since the lymphoid system is not fully developed until late stages of incubation, the chick embryo serves as a naturally immunodeficient host capable of sustaining grafted tissues and cells without species-specific restrictions. In addition to nurturing developing allo- and xenografts, the CAM blood vessel network provides a uniquely supportive environment for tumor cell intravasation, dissemination, and vascular arrest and a repository where arrested cells extravasate to form micro metastatic foci.
For experimental purposes, in most of the recent studies the CAM was exposed by cutting a window through the egg shell and experiments were carried out in ovo, resulting in significant limitations in the accessibility of the CAM and possibilities for observation and photo documentation of effects. When shell-less cultures of the chick embryo were used1-4, no experimental details were provided and, if published at all, the survival rates of these cultures were low. We refined the method of ex ovo culture of chick embryos significantly by introducing a rationally controlled extrusion of the egg content. These ex ovo cultures enhance the accessibility of the CAM and chick embryo, enabling easy in vivo documentation of effects and facilitating experimental manipulation of the embryo. This allows the successful application to a large number of scientific questions: (1) As an improved angiogenesis assay5,6, (2) an experimental set up for facilitated injections in the vitreous of the chick embryo eye7-9, (3) as a test environment for dissemination and intravasation of dispersed tumor cells from established cell lines inoculated on the CAM10-12, (4) as an improved sustaining system for successful transplantation and culture of limb buds of chicken and mice13 as well as (5) for grafting, propagation, and re-grafting of solid primary tumor tissue obtained from biopsies on the surface of the CAM14.
In this video article we describe the establishment of a refined chick ex ovo culture and CAM assay with survival rates over 50%. Besides we provide a step by step demonstration of the successful application of the ex ovo culture for a large number of scientific applications. 
Daniel S. Dohle, Susanne D. Pasa, and Sebastian Gustmann contributed equally to this study.

Chick ex ovo Culture and ex ovo CAM Assay: How it Really Works

The chick chorioallantoic membrane (CAM) is a unique, naturally immunodeficient supportive culture environment to study angiogenesis and tumorigenesis. This video article demonstrates the different steps in chick ex ovo culture, application of potentially angiogenic substances and successful inoculation of tumor cells and tissues on the surface of the CAM.

كتكوت البيضة السابقين الثقافة و البيضة السابقين CAM الفحص : كيف يعمل حقا

Chicken eggs in the early phase of breeding are between in vitro and in vivo systems and provide a vascular test environment not only to study ...

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Phenotypes are determined by a complex series of physical (e.g. protein-protein) and functional (e.g. gene-gene or genetic) interactions (GI)1. While physical interactions can indicate which bacterial proteins are associated as complexes, they do not necessarily reveal pathway-level functional relationships1. GI screens, in which the growth of double mutants bearing two deleted or inactivated genes is measured and compared to the corresponding single mutants, can illuminate epistatic dependencies between loci and hence provide a means to query and discover novel functional relationships2. Large-scale GI maps have been reported for eukaryotic organisms like yeast3-7, but GI information remains sparse for prokaryotes8, which hinders the functional annotation of bacterial genomes. To this end, we and others have developed high-throughput quantitative bacterial GI screening methods9, 10.
Here, we present the key steps required to perform quantitative E. coli Synthetic Genetic Array (eSGA) screening procedure on a genome-scale9, using natural bacterial conjugation and homologous recombination to systemically generate and measure the fitness of large numbers of double mutants in a colony array format. Briefly, a robot is used to transfer, through conjugation, chloramphenicol (Cm) - marked mutant alleles from engineered Hfr (High frequency of recombination) 'donor strains' into an ordered array of kanamycin (Kan) - marked F- recipient strains. Typically, we use loss-of-function single mutants bearing non-essential gene deletions (e.g. the 'Keio' collection11) and essential gene hypomorphic mutations (i.e. alleles conferring reduced protein expression, stability, or activity9, 12, 13) to query the functional associations of non-essential and essential genes, respectively. After conjugation and ensuing genetic exchange mediated by homologous recombination, the resulting double mutants are selected on solid medium containing both antibiotics. After outgrowth, the plates are digitally imaged and colony sizes are quantitatively scored using an in-house automated image processing system14. GIs are revealed when the growth rate of a double mutant is either significantly better or worse than expected9. Aggravating (or negative) GIs often result between loss-of-function mutations in pairs of genes from compensatory pathways that impinge on the same essential process2. Here, the loss of a single gene is buffered, such that either single mutant is viable. However, the loss of both pathways is deleterious and results in synthetic lethality or sickness (i.e. slow growth). Conversely, alleviating (or positive) interactions can occur between genes in the same pathway or protein complex2 as the deletion of either gene alone is often sufficient to perturb the normal function of the pathway or complex such that additional perturbations do not reduce activity, and hence growth, further. Overall, systematically identifying and analyzing GI networks can provide unbiased, global maps of the functional relationships between large numbers of genes, from which pathway-level information missed by other approaches can be inferred9.

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Systematic, large-scale synthetic genetic (gene-gene or epistasis) interaction screens can be used to explore genetic redundancy and pathway cross-talk. Here, we describe a high-throughput quantitative synthetic genetic array screening technology, termed eSGA that we developed for elucidating epistatic relationships and exploring genetic interaction networks in Escherichia coli.

رسم خرائط الشبكات الوظيفية البكتيرية والممرات في<em&gt; كولاي</em&gt; استخدام المصفوفات الوراثية الاصطناعية

Phenotypes  are determined by a complex series of physical (e.g. protein-protein) and  functional (e.g. gene-gene or genetic) interactions (GI)1. While ...

Design and Use of Multiplexed Chemostat Arrays

Chemostats are continuous culture systems in which cells are grown in a tightly controlled, chemically constant environment where culture density is constrained by limiting specific nutrients.1,2 Data from chemostats are highly reproducible for the measurement of quantitative phenotypes as they provide a constant growth rate and environment at steady state. For these reasons, chemostats have become useful tools for fine-scale characterization of physiology through analysis of gene expression3-6 and other characteristics of cultures at steady-state equilibrium.7 Long-term experiments in chemostats can highlight specific trajectories that microbial populations adopt during adaptive evolution in a controlled environment. In fact, chemostats have been used for experimental evolution since their invention.8 A common result in evolution experiments is for each biological replicate to acquire a unique repertoire of mutations.9-13 This diversity suggests that there is much left to be discovered by performing evolution experiments with far greater throughput. 
We present here the design and operation of a relatively simple, low cost array of miniature chemostats&mdash;or ministats&mdash;and validate their use in determination of physiology and in evolution experiments with yeast. This approach entails growth of tens of chemostats run off a single multiplexed peristaltic pump. The cultures are maintained at a 20 ml working volume, which is practical for a variety of applications. It is our hope that increasing throughput, decreasing expense, and providing detailed building and operation instructions may also motivate research and industrial application of this design as a general platform for functionally characterizing large numbers of strains, species, and growth parameters, as well as genetic or drug libraries.

We developed and validated a small-footprint array of miniature chemostats built from readily available parts for low cost. Physiological and experimental evolution results were similar to larger volume chemostats. The ministat array provides a compact, inexpensive, and accessible platform for traditional chemostat experiments, functional genomics, and chemical screening applications.

تصميم واستخدام المصفوفات ناظم كيميائي تعدد في الإرسال

Chemostats are continuous culture systems in which cells are grown in a tightly controlled, chemically constant environment where culture density is ...

Using an Automated 3D-tracking System to Record Individual and Shoals of Adult Zebrafish

Like many aquatic animals, zebrafish (Danio rerio) moves in a 3D space. It is thus preferable to use a 3D recording system to study its behavior. The presented automatic video tracking system accomplishes this by using a mirror system and a calibration procedure that corrects for the considerable error introduced by the transition of light from water to air. With this system it is possible to record both single and groups of adult zebrafish. Before use, the system has to be calibrated. The system consists of three modules: Recording, Path Reconstruction, and Data Processing. The step-by-step protocols for calibration and using the three modules are presented. Depending on the experimental setup, the system can be used for testing neophobia, white aversion, social cohesion, motor impairments, novel object exploration etc. It is especially promising as a first-step tool to study the effects of drugs or mutations on basic behavioral patterns. The system provides information about vertical and horizontal distribution of the zebrafish, about the xyz-components of kinematic parameters (such as locomotion, velocity, acceleration, and turning angle) and it provides the data necessary to calculate parameters for social cohesions when testing shoals.

The use of a 3D automatic video system that can track individual and groups of zebrafish is described. As application example we explore the effects of the NMDA-receptor antagonist MK-801 on shoals of zebrafish.

باستخدام نظام 3D تتبع الآلي لتسجيل الفردية وشولز من اسماك الزرد الكبار

Like many aquatic animals, zebrafish (Danio rerio) moves in a 3D space. It is thus preferable to use a 3D recording system to study its behavior. The ...

Measurement and Analysis of Extracellular Acid Production to Determine Glycolytic Rate

Extracellular measurement of oxygen consumption and acid production is a simple and powerful way to monitor rates of respiration and glycolysis1. Both mitochondrial (respiration) and non-mitochondrial (other redox) reactions consume oxygen, but these reactions can be easily distinguished by chemical inhibition of mitochondrial respiration. However, while mitochondrial oxygen consumption is an unambiguous and direct measurement of respiration rate2, the same is not true for extracellular acid production and its relationship to glycolytic rate 3-6. Extracellular acid produced by cells is derived from both lactate, produced by anaerobic glycolysis, and CO2, produced in the citric acid cycle during respiration. For glycolysis, the conversion of glucose to lactate- + H+ and the export of products into the assay medium is the source of glycolytic acidification. For respiration, the export of CO2, hydration to H2CO3 and dissociation to HCO3- + H+ is the source of respiratory acidification. The proportions of glycolytic and respiratory acidification depend on the experimental conditions, including cell type and substrate(s) provided, and can range from nearly 100% glycolytic acidification to nearly 100% respiratory acidification 6. Here, we demonstrate the data collection and calculation methods needed to determine respiratory and glycolytic contributions to total extracellular acidification by whole cells in culture using C2C12 myoblast cells as a model.

Glycolysis is a defining metabolic marker in multiple biological systems. Monitoring glycolysis by measuring the extracellular flux of H+ is common, but requires correction to be quantitative and unambiguous. Here, we demonstrate how to gather and correct extracellular flux data to distinguish between respiratory and glycolytic sources of extracellular acidification.

قياس وتحليل حمض خارج الخلية الإنتاج لتحديد معدل حال السكر

Extracellular measurement of oxygen consumption and acid production is a simple and powerful way to monitor rates of respiration and glycolysis1. Both ...

Techniques to Induce and Quantify Cellular Senescence

In response to cellular stress or damage, proliferating cells can induce a specific program that initiates a state of long-term cell-cycle arrest, termed cellular senescence. Accumulation of senescent cells occurs with organismal aging and through continual culturing in vitro. Senescent cells influence many biological processes, including embryonic development, tissue repair and regeneration, tumor suppression, and aging. Hallmarks of senescent cells include, but are not limited to, increased senescence-associated &#946;-galactosidase activity (SA-&#946;-gal); p16INK4A, p53, and p21 levels; higher levels of DNA damage, including &#947;-H2AX; the formation of Senescence-associated Heterochromatin Foci (SAHF); and the acquisition of a Senescence-associated Secretory Phenotype (SASP), a phenomenon characterized by the secretion of a number of pro-inflammatory cytokines and signaling molecules. Here, we describe protocols for both replicative and DNA damage-induced senescence in cultured cells. In addition, we highlight techniques to monitor the senescent phenotype using several senescence-associated markers, including SA-&#946;-gal, &#947;-H2AX and SAHF staining, and to quantify protein and mRNA levels of cell cycle regulators and SASP factors. These methods can be applied to the assessment of senescence in various models and tissues.

Cellular senescence, the irreversible state of cell-cycle arrest, can be induced by various cellular stresses. Here, we describe protocols to induce cellular senescence and methods to assess markers of senescence.

تقنيات للحث وتحديد الخلوي الشيخوخة

In response to cellular stress or damage, proliferating cells can induce a specific program that initiates a state of long-term cell-cycle arrest, termed ...

An Adipocyte Cell Culture Model to Study the Impact of Protein and Micro-RNA Modulation on Adipocyte Function

Alteration of adipocyte function contributes to the pathogenesis of metabolic diseases including Type 2 diabetes and insulin resistance. This highlights the need to better understand the molecular mechanism involved in adipocyte dysfunction to develop new therapies against obesity-related diseases. Modulating the expression of proteins and micro-RNAs in adipocytes remains highly challenging. This paper describes a protocol to differentiate murine fibroblasts into mature adipocytes and to modulate the expression of proteins and micro-RNAs in mature adipocytes through reverse-transfection using small-interfering RNA (siRNA) and micro-RNA mimicking (miR mimic) oligonucleotides. This reverse-transfection protocol involves the incubation of the transfection reagent and the oligonucleotides to form a complex in the cell culture plate to which the mature adipocytes are added. The adipocytes are then allowed to reattach to the adherent plate surface in the presence of the oligonucleotides/transfection reagent complex. Functional analyses such as the study of insulin signaling, glucose uptake, lipogenesis, and lipolysis can be performed on the transfected 3T3-L1 mature adipocytes to study the impact of protein or micro-RNA manipulation on adipocyte function.

Presented here is a protocol to deliver oligonucleotides such as small-interfering RNA (siRNA), micro-RNA mimics (miRs), or anti-micro-RNA (anti-miR) into mature adipocytes to modulate protein and micro-RNA expression.

نموذج ثقافة الخلية Adipocyte لدراسة تأثير البروتين وتعديل الحمض النووي الريبي الدقيق على وظيفة Adipocyte

Alteration of adipocyte function contributes to the pathogenesis of metabolic diseases including Type 2 diabetes and insulin resistance. This highlights ...

Isolation of High Quality Murine Atrial and Ventricular Myocytes for Simultaneous Measurements of Ca2+ Transients and L-Type Calcium Current

Mouse models play a crucial role in arrhythmia research and allow studying key mechanisms of arrhythmogenesis including altered ion channel function and calcium handling. For this purpose, atrial or ventricular cardiomyocytes of high quality are necessary to perform patch-clamp measurements or to explore calcium handling abnormalities. However, the limited yield of high-quality cardiomyocytes obtained by current isolation protocols does not allow both measurements in the same mouse. This article describes a method to isolate high-quality murine atrial and ventricular myocytes via retrograde enzyme-based Langendorff perfusion, for subsequent simultaneous measurements of calcium transients and L-type calcium current from one animal. Mouse hearts are obtained, and the aorta is rapidly cannulated to remove blood. Hearts are then initially perfused with a calcium-free solution (37 &#176;C) to dissociate the tissue at the level of intercalated discs and afterwards with an enzyme solution containing little calcium to disrupt extracellular matrix (37 &#176;C). The digested heart is subsequently dissected into atria and ventricles. Tissue samples are chopped into small pieces and dissolved by carefully pipetting up and down. The enzymatic digestion is stopped, and cells are stepwise reintroduced to physiologic calcium concentrations. After loading with a fluorescent Ca2+-indicator, isolated cardiomyocytes are prepared for simultaneous measurement of calcium currents and transients. Additionally, isolation pitfalls are discussed and patch-clamp protocols and representative traces of L-type calcium currents with simultaneous calcium transient measurements in atrial and ventricular murine myocytes isolated as described above are provided.

Isolation of High Quality Murine Atrial and Ventricular Myocytes for Simultaneous Measurements of Ca2+ Transients and L-Type Calcium Current

Mouse models allow studying key mechanisms of arrhythmogenesis. For this purpose, high quality cardiomyocytes are necessary to perform patch-clamp measurements. Here, a method to isolate murine atrial and ventricular myocytes via retrograde enzyme-based Langendorff perfusion, which allows simultaneous measurements of calcium-transients and L-type calcium current, is described.

عزل الخلايا العضلية الأذينية والبطينية عالية الجودة للقياسات المتزامنة لتيار الكالسيوم2+ العابر وتيار الكالسيوم من النوع L

Mouse models play a crucial role in arrhythmia research and allow studying key mechanisms of arrhythmogenesis including altered ion channel function and ...

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

The root microbiome plays an important role in plant growth and environmental adaptation. Network analysis is an important tool for studying communities, which can effectively explore the interaction relationship or co-occurrence model of different microbial species in different environments. The purpose of this manuscript is to provide details on how to use the weighted correlation network algorithm to analyze different co-occurrence networks that may occur in microbial communities due to different ecological environments. All analysis of the experiment is performed in the WGCNA package. WGCNA is an R package for weighted correlation network analysis. The experimental data used to demonstrate these methods were microbial community data from the NCBI (National Center for Biotechnology Information) database for three niches of the rice (Oryza sativa) root system. We used the weighted correlation network algorithm to construct co-abundance networks of microbial community in each of the three niches. Then, differential co-abundance networks among endosphere, rhizoplane and rhizosphere soil were identified. In addition, the core genera in network were obtained by the "WGCNA" package, which plays an important regulated role in network functions. These methods enable researchers to analyze the response of microbial network to environmental disturbance and verify different microbial ecological response theories. The results of these methods show that the significant differential microbial networks identified in the endosphere, rhizoplane and rhizosphere soil of rice.

Network analysis was applied to evaluate the association of various ecological microbial communities, such as soil, water and rhizosphere. Presented here is a protocol on how to use the WGCNA algorithm to analyze different co-occurrence networks that may occur in the microbial communities due to different ecological environments.

اختلاف ميكروبيوتا الجذر في الموائل المختلفة على أساس شبكات الارتباط المرجح

The root microbiome plays an important role in plant growth and environmental adaptation. Network analysis is an important tool for studying communities, ...