1) Coleta Egg Zebrafish <ol><li> Na tarde anterior ao dia da tela químicos, criado 10-20 tanques de criação de peixe-zebra. Encher cada tanque com água do sistema de aquicultura. Usando uma rede de pesca, a transferência de um adulto do sexo masculino e 1-2 fêmeas adultas para recipiente interno em cada tanque de criação. Separar os peixes machos e fêmeas do outro com uma divisória. Rótulo as gaiolas e colocar uma tampa em cima deles. </li><li> Na manhã da tela, remover os divisores de tanques de criação e permitir zebrafish para acasalar. Ao longo de 1 hora seguinte, permitem ovos fertilizados para cair através de grade no fundo de cada recipiente interior. </li><li> Depois de uma hora, o retorno zebrafish adulto de volta para os tanques de armazenamento permanente, remova o recipiente interior e recolher os ovos por esforço da água em cada tanque de criação através de um coador de chá de plástico. </li><li> Inverter o filtro mais de uma placa de Petri e lavar o filtro com cuidado para lavar os ovos na placa de Petri, usando um frasco de lavagem contendo o meio E3. </li><li> Todos os ovos não fertilizados, que aparecem opaco, deve ser removido com uma pipeta de plástico descartáveis. Cada cruz de acasalamento deve render cerca de 200 embriões. </li></ol> 2) arraying embriões em placas de 96 poços <ol><li> Transferência de cerca de 5 embriões em meio E3 em cada poço de uma placa de 96 poços usando um copo Pasteur pipeta. </li><li> Uma vez que os embriões são dispostos sobre a placa de 96 poços, remover o máximo do meio E3 possível fora dos poços usando um de 12 canais (3-30 mL) pipeta, tomando cuidado para não perfurar o embrião. Usando a pipeta de 12 canais, entregar 250 L de meio contendo canamicina E3 0.5μg/ml a cada poço o mais rapidamente possível de modo a não permitir que os embriões a secar. </li><li> Coloque as placas de 96 poços em 28,5 ° C incubadora até atingir o estágio desejado quando os compostos a serem adicionados. </li></ol> 3) Transferência da Biblioteca pequena molécula Enquanto a transferência de composto pode ser automatizada com métodos de transferência de robótica, vamos descrever o método de transferência manual. <ol><li> Bibliotecas de moléculas pequenas são normalmente fornecidos em um formato de 96 poços, com cada composto armazenados em DMSO como um estoque de 10 mm. Cerca de 60 minutos antes de os embriões atingem o estágio quando os compostos estão a ser adicionado, descongelar um número desejado de placas de 96 poços contendo alíquotas de pequenas moléculas (placa fonte). Tome nota do número de identificação de série ou outra das placas fonte. Para minimizar a condensação nas placas, o descongelamento pode ocorrer em uma câmara de dessecação contendo Drierite (WA HAMMOND DRIERITE CO, Xenia, OH). </li><li> Brevemente girar os pratos em uma centrífuga de mesa equipados com multi-bem adaptador placa. </li><li> Remova a fita de vedação de alumínio da placa fonte. Com uma pipeta de 12 canais, diluir os compostos na placa fonte para a concentração de 0,5 mM (por exemplo, se iniciar com 250 nL alíquotas de estoque 10mM, adicionar 4,75 mL de DMSO a cada poço). </li><li> Quando os embriões na placa de 96 poços (placa destinatário) alcançar o estágio desejado, use uma de 12 canais (20-20 mL) pipeta para transferir 2.5μL de compostos (0,5 mm) das placas de origem para as placas contendo o destinatário embriões. </li><li> Registre o número de identificação das placas de fonte nas placas embrião destinatário. Cobrir as placas destinatário agora contendo os embriões e os compostos com tampas, misture delicadamente as placas rodando suavemente, e colocá-los em uma incubadora de 28,5 ° C. </li><li> Cubra cada prato de origem que contém pequenas moléculas não utilizados (0,5 mM), com uma fita de vedação de alumínio e coloque em um freezer -80 ° C para armazenamento de longo prazo. </li></ol> 4) Triagem para efeitos de pequenas moléculas por Inspeção Visual de fenótipos <ol><li> Antes de executar a tela, formular um critério específico para o que constituiria um &quot;hit&quot;. </li><li> Às vezes desejado em desenvolvimento, remover as placas de 96 poços contendo compostos tratados com embriões de incubadora e analisar cada um bem sob um estereomicroscópio. Para melhor visualização de mudanças sutis, tais como mudanças no padrão circulatório, um microscópio de contraste de fase invertido pode ser usado. Microscopia fluorescente pode ser usado para examinar perturbação da expressão de GFP ou proteínas DsRed sob um promotor de tecidos específicos. </li><li> Digitalizar rapidamente as placas de 96 poços para qualquer bem em que pelo menos 3 de 5 embriões apresentam o prescrito &quot;hit&quot; fenótipo. Registo da identidade da placa ea localização de cada bem hit em potencial. </li><li> Reconfirmar um hit em potencial por novos testes dos efeitos do composto em diversas doses (1 uM, 5 uM, 10 mM e 50 mM). Para cada dose, 10 embriões são testados em 0,5 mL de mídia E3 em um formato de placa 48 poços. O momento da adição de compostos de um novo ensaio deve ser idêntica à do exame original. Um hit é confirmado quando o fenótipo é reproduzido em provocou a reavaliação do compound </li><li> Identificar o composto hit do banco de dados de pequenas moléculas na biblioteca química. </li></ol>

<ol>
	<li>Bayliss, P. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemical+modulation+of+receptor+signaling+inhibits+regenerative+angiogenesis+in+adult+zebrafish.">Chemical modulation of receptor signaling inhibits regenerative angiogenesis in adult zebrafish.</a> Nature chemical biology. 2, 265-273 (2006).</li><li>Burns, C. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+assay+for+small+molecules+that+modulate+zebrafish+embryonic+heart+rate.">High-throughput assay for small molecules that modulate zebrafish embryonic heart rate.</a> Nature chemical biology. 1, 263-264 (2005).</li><li>Hao, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+structure-activity+relationship+study+of+dorsomorphin+analogues+identifies+selective+VEGF+and+BMP+inhibitors.">In vivo structure-activity relationship study of dorsomorphin analogues identifies selective VEGF and BMP inhibitors.</a> ACS chemical biology. 5, 245-253 (2010).</li><li>Hong, C. C., Peterson, Q. P., Hong, J. Y., Peterson, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Artery/vein+specification+is+governed+by+opposing+phosphatidylinositol-3+kinase+and+MAP+kinase/ERK+signaling.">Artery/vein specification is governed by opposing phosphatidylinositol-3 kinase and MAP kinase/ERK signaling.</a> Curr Biol. 16, 1366-1372 (2006).</li><li>Milan, D. J., Peterson, T. A., Ruskin, J. N., Peterson, R. T., MacRae, C. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drugs+that+induce+repolarization+abnormalities+cause+bradycardia+in+zebrafish.">Drugs that induce repolarization abnormalities cause bradycardia in zebrafish.</a> Circulation. 107, 1355-1358 (2003).</li><li>Peterson, R. T., Link, B. A., Dowling, J. E., Schreiber, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+molecule+developmental+screens+reveal+the+logic+and+timing+of+vertebrate+development.">Small molecule developmental screens reveal the logic and timing of vertebrate development.</a> Proceedings of the National Academy of Sciences of the United States of America. 97, 12965-12969 (2000).</li><li>Yu, P. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dorsomorphin+inhibits+BMP+signals+required+for+embryogenesis+and+iron+metabolism.">Dorsomorphin inhibits BMP signals required for embryogenesis and iron metabolism.</a> Nature chemical biology. 4, 33-41 (2008).</li><li>Zon, L. I., Peterson, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+drug+discovery+in+the+zebrafish.">In vivo drug discovery in the zebrafish.</a> Nature reviews. 4, 35-44 (2005).</li><li>Stern, H. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+molecules+that+delay+S+phase+suppress+a+zebrafish+bmyb+mutant.">Small molecules that delay S phase suppress a zebrafish bmyb mutant.</a> Nature chemical biology. 1, 366-370 (2005).</li><li>Peterson, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemical+suppression+of+a+genetic+mutation+in+a+zebrafish+model+of+aortic+coarctation.">Chemical suppression of a genetic mutation in a zebrafish model of aortic coarctation.</a> Nature biotechnology. 22, 595-599 (2004).</li></ol>

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Ao planejar uma tela químicos baseados em zebrafish, atenção especial deve ser dada a robustez do fenótipo em questão e da taxa de fundo de fenótipo tal. Isto é particularmente importante para as telas de supressores químicos de um fenótipo induzido. Por exemplo, para um fenótipo causado por choque térmico a indução de um transgene, a condição que induz o fenótipo reproducibly deve ser precisamente traçada antes de iniciar a tela para evitar inaceitavelmente elevado as taxas de falsos positivos. Com um ...

<ol><li> Mínimo de 20 pares de peixe-zebra adulto do genótipo desejado. </li><li> Redes de peixes, tanques de criação, com recipiente interno removível e divisores (Habitats Aquáticos). </li><li> Placas de Petri (10 cm). </li><li> Coador de chá de plástico. </li><li> Lavar garrafa de água embrião containg. </li><li> Pipetas de transferência descartável de polietileno. </li><li> Poliestireno de 96 poços de fundo redondo de placas de ensaio (Corning COSTAR; Lowell, MA). </li><li> Pasteur de vidro pipeta (Fisher Scientific). </li><li> Manual da bomba de pipeta, 10 mL (Bel-Art Products, Pequannock, NJ). </li><li> Médio embrião E3: 5 mM NaCl, 0,17 mM KCl, 0,33 mM CaCl 2, 0,33 mM MgSO 4, contendo 0,003% PTU (feniltio-carbamida, Sigma, St. Louis, MO). PTU pode ser preparado como uma solução 10x dissolvendo 0,3 g-PTU em 1 L de mídia embrião E3. Soluções contendo PTU deve ser protegido da luz, cobrindo com papel alumínio. </li><li> 12 canais pipetas, 20-20 mL (Eppendorf). </li><li> 12 canais pipetas, 300-300 mL (Eppendorf). </li><li> Descartáveis ​​de poliestireno pipeta bacia, 50 mL (Fisher Scientific). </li><li> Biblioteca pequena molécula de compostos estruturalmente diversos, dispostos em um formato de 96 wll menos 10 ações mM em DMSO. Cada prato principal é aliquotado em placas de 96 poços de armazenamento de polipropileno (Corning), e armazenadas a -80 ° C até o uso. </li><li> Vedação de alumínio fita para placas de 96 poços (Nunc, Rochester, NY). </li><li> DMSO (Sigma, St. Louis, MO). </li><li> Básicos incubadora, 28,5 ° C (Fisher Scientific). </li><li> Estereomicroscópio com base de luz transmitida (Leica Microsystems, Bannockburn, IL). </li></ol>

large scale zebrafish-based in vivo small molecule screen

Dado o seu tamanho pequeno embrião, o rápido desenvolvimento, a transparência, a fecundidade, e numerosas semelhanças moleculares, morfológicas e fisiológicas para os mamíferos, peixe-zebra tem emergido como uma poderosa<em&gt; In vivo</em&gt; Plataforma para telas baseadas em fenótipo de drogas e análise química genética. Aqui, nós demonstramos um método simples e prática em larga escala de triagem de pequenas moléculas usando embriões zebrafish.

Watch this Scientific Journal Video about Large Scale Zebrafish-Based In vivo Small Molecule Screen at JoVE.com

Large Scale Zebrafish-Based In vivo Small Molecule Screen

Peixe-zebra tem emergido como uma poderosa<em&gt; In vivo</em&gt; Plataforma para telas baseadas em fenótipo de drogas e análise química genética. Aqui, nós demonstramos um método simples e prática em larga escala de triagem de pequenas moléculas usando embriões zebrafish.

Grande Escala Zebrafish-Based In vivo Tela pequena molécula

Given their small embryo size, rapid development, transparency, fecundity, and numerous molecular, morphological and physiological similarities to ...

large-scale-zebrafish-based-in-vivo-small-molecule-screen

Research

JoVE Journal

Biology

Large Scale Zebrafish-Based In vivo Small Molecule Screen

13.4K visualizações.  Vanderbilt University School of Medicine. Peixe-zebra tem emergido como uma poderosa In vivo Plataforma para telas baseadas em fenótipo de drogas e análise química genética. Aqui, nós demonstramos um método simples e prática em larga escala de triagem de pequenas moléculas usando embriões zebrafish.

Vídeo: Large Scale Zebrafish-Based In vivo Small Molecule Screen

Large-Scale Screens of Metagenomic Libraries

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation. Generating a streamlined procedure for creating and screening metagenomic libraries is therefore useful for efficient high-throughput investigations into the genetic and metabolic properties of uncultured microbial assemblages. Here, key protocols are presented on video, which we propose is the most useful format for accurately describing a long process that alternately depends on robotic instrumentation and (human) manual interventions. First, we employed robotics to spot library clones onto high-density macroarray membranes, each of which can contain duplicate colonies from twenty-four 384-well library plates. Automation is essential for this procedure not only for accuracy and speed, but also due to the miniaturization of scale required to fit the large number of library clones into highly dense spatial arrangements. Once generated, we next demonstrated how the macroarray membranes can be screened for genes of interest using modified versions of standard protocols for probe labeling, membrane hybridization, and signal detection. We complemented the visual demonstration of these procedures with detailed written descriptions of the steps involved and the materials required, all of which are available online alongside the video.

Grande Escala Telas de Bibliotecas metagenomic

Metagenomic libraries archive large fragments of contiguous genomic sequences from microorganisms without requiring prior cultivation.  Generating a ...

Biologia

Batch Immunostaining for Large-Scale Protein Detection in the Whole Monkey Brain

Immunohistochemistry (IHC) is one of the most widely used laboratory techniques for the detection of target proteins in situ. Questions concerning the expression pattern of a target protein across the entire brain are relatively easy to answer when using IHC in small brains, such as those of rodents. However, answering the same questions in large and convoluted brains, such as those of primates presents a number of challenges. Here we present a systematic approach for immunodetection of target proteins in an adult monkey brain. This approach relies on the tissue embedding and sectioning methodology of NeuroScience Associates (NSA) as well as tools developed specifically for batch-staining of free-floating sections. It results in uniform staining of a set of sections which, at a particular interval, represents the entire brain. The resulting stained sections can be subjected to a wide variety of analytical procedures in order to measure protein levels, the population of neurons expressing a certain protein.

Large-scale immunodetection of target proteins across the entire primate brain is possible by employing novel tissue embedding and sectioning methods combined with the use of creative apparatus for batch staining of multiple free-floating sections at a given time.

A imunocoloração lote de Grande Escala da detecção de proteínas no cérebro do macaco inteiro

Immunohistochemistry (IHC) is one of the most widely used laboratory techniques for the detection of target proteins in situ. Questions concerning the ...

Small-scale Nuclear Extracts for Functional Assays of Gene-expression Machineries

A great deal of progress in understanding gene expression has been made using in vitro systems. For most studies, functional assays are carried out using extracts that are prepared in bulk from 10-50 or more liters of cells grown in suspension. However, these large-scale preparations are not amenable to rapidly testing in vitro effects that result from a variety of in vivo cellular treatments or conditions. This journal video article shows a method for preparing functional small-scale nuclear extracts, using HeLa cells as an example. This method is carried out using as few as three 150 mm plates of cells grown as adherent monolayers. To illustrate the efficiency of the small-scale extracts, we show that they are as active as bulk nuclear extracts for coupled RNA Polymerase II transcription/splicing reactions. To demonstrate the utility of the extract protocol, we show that splicing is abolished in extracts prepared from HeLa cells treated with the splicing inhibitor drug E7107. The small-scale protocol should be generally applicable to any process or cell type that can be investigated in vitro using cellular extracts. These include patient cells that are only available in limited quantities or cells exposed to numerous agents such as drugs, DNA damaging agents, RNAi, or transfection, which require the use of small cell populations. In addition, small amounts of freshly grown cells are convenient and/or required for some applications.

A protocol for preparation of robust, small-scale HeLa nuclear extracts is described. This protocol is valuable for assays that require use of small populations of cells, such as cells treated with drugs or RNAi. The method should be applicable to a wide variety of gene expression assays and other cell types, including patient cells.

Os pequenos extratos nucleares para ensaios funcionais da expressão gênica Machineries

A great deal of progress in understanding gene expression has been made using in vitro systems.  For most studies, functional assays are carried out using ...

Infinium Assay for Large-scale SNP Genotyping Applications

Genotyping variants in the human genome has proven to be an efficient method to identify genetic associations with phenotypes. The distribution of variants within families or populations can facilitate identification of the genetic factors of disease. Illumina&#39;s panel of genotyping BeadChips allows investigators to genotype thousands or millions of single nucleotide polymorphisms (SNPs) or to analyze other genomic variants, such as copy number, across a large number of DNA samples. These SNPs can be spread throughout the genome or targeted in specific regions in order to maximize potential discovery. The Infinium assay has been optimized to yield high-quality, accurate results quickly. With proper setup, a single technician can process from a few hundred to over a thousand DNA samples per week, depending on the type of array. This assay guides users through every step, starting with genomic DNA and ending with the scanning of the array. Using propriety reagents, samples are amplified, fragmented, precipitated, resuspended, hybridized to the chip, extended by a single base, stained, and scanned on either an iScan or Hi Scan high-resolution optical imaging system. One overnight step is required to amplify the DNA. The DNA is denatured and isothermally amplified by whole-genome amplification; therefore, no PCR is required. Samples are hybridized to the arrays during a second overnight step. By the third day, the samples are ready to be scanned and analyzed. Amplified DNA may be stockpiled in large quantities, allowing bead arrays to be processed every day of the week, thereby maximizing throughput.

A protocol is described that uses Illumina&#39;s Infinium assays to perform large-scale genotyping. These assays can reliably genotype millions of SNPs across hundreds of individual DNA samples in three days. Once generated, these genotypes can be used to check for associations with a variety of different diseases or phenotypes.

Infinium Ensaio para a grande escala Applications genotipagem

Genotyping variants in the human genome has proven to be an efficient method to identify genetic associations with phenotypes. The distribution of ...

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, intensive method optimization for each metabolite, and the inability to measure both positively and negatively charged ions in single experiments. Therefore, a novel metabolomics protocol could advance metabolomics studies. Amide-based hydrophilic chromatography enables polar metabolite analysis without any chemical derivatization. High resolution MS using the Q-Exactive (QE-MS) has improved ion optics, increased scan speeds (256 msec at resolution 70,000), and has the capability of carrying out positive/negative switching. Using a cold methanol extraction strategy, and coupling an amide column with QE-MS enables robust detection of 168 targeted polar metabolites and thousands of additional features simultaneously.&#160; Data processing is carried out with commercially available software in a highly efficient way, and unknown features extracted from the mass spectra can be queried in databases.

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. Utilizing normal-phased liquid chromatography coupled to high-resolution mass spectrometry with polarity switching and a rapid duty cycle, we describe a protocol to analyze the polar metabolic composition of biological material with high sensitivity, accuracy, and resolution.

Uma estratégia para sensíveis, Large Scale quantitativos Metabolomics

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting ...

A Manual Small Molecule Screen Approaching High-throughput Using Zebrafish Embryos

Zebrafish have become a widely used model organism to investigate the mechanisms that underlie developmental biology and to study human disease pathology due to their considerable degree of genetic conservation with humans. Chemical genetics entails testing the effect that small molecules have on a biological process and is becoming a popular translational research method to identify therapeutic compounds. Zebrafish are specifically appealing to use for chemical genetics because of their ability to produce large clutches of transparent embryos, which are externally fertilized. Furthermore, zebrafish embryos can be easily drug treated by the simple addition of a compound to the embryo media. Using whole-mount in situ hybridization (WISH), mRNA expression can be clearly visualized within zebrafish embryos. Together, using chemical genetics and WISH, the zebrafish becomes a potent whole organism context in which to determine the cellular and physiological effects of small molecules. Innovative advances have been made in technologies that utilize machine-based screening procedures, however for many labs such options are not accessible or remain cost-prohibitive. The protocol described here explains how to execute a manual high-throughput chemical genetic screen that requires basic resources and can be accomplished by a single individual or small team in an efficient period of time. Thus, this protocol provides a feasible strategy that can be implemented by research groups to perform chemical genetics in zebrafish, which can be useful for gaining fundamental insights into developmental processes, disease mechanisms, and to identify novel compounds and signaling pathways that have medically relevant applications.

The zebrafish is an excellent experimental organism to study vertebrate developmental processes and model human disease. Here, we describe a protocol on how to perform a manual high-throughput chemical screen in zebrafish embryos with a whole-mount in situ hybridization (WISH) read-out.

Um manual de tela pequena molécula Aproximando de alta capacidade Usando embriões Zebrafish

Zebrafish have become a widely used model organism to investigate the mechanisms that underlie developmental biology and to study human disease pathology ...

Novel Production Protocol for Small-scale Manufacture of Probiotic Fermented Foods

A novel dried bacterial consortium of Lactobacillus rhamnosus yoba 2012 and Streptococcus thermophilus C106 is cultured in 1 L of milk. This fresh starter can be used for the production of fermented milk and other fermented foods either at home or at small-scale in rural settings. For the fresh starter, 1 L of milk is pasteurized in a pan that fits into a larger pan containing water, placed on a source of heat. In this water bath, the milk is heated and incubated at 85 &#176;C for 30 min. Thereafter, the milk is cooled down to 45 &#176;C, transferred to a vacuum flask, inoculated with the dried bacteria and left for at least 16 hr between 30 &#176;C and 45 &#176;C. For the purpose of frequent home production, the fresh starter is frozen into ice cubes, which can be used for the production of small volumes of up to 2 L of fermented milk. For the purpose of small-scale production in resource-poor countries, pasteurization of up to 100 L of milk is conducted in milk cans that are placed in a large sauce pan filled with water and heated on a fire at 85 &#176;C for 30 min, and subsequently cooled to 45 &#176;C. Next, the 100 L batch is inoculated with the 1 L freshly prepared starter mentioned before. To assure an effective fermentation at a temperature between 30 and 45 &#176;C, the milk can is covered with a blanket for 12 hr. For the production of non-dairy fermented foods, the fresh starter is left in a cheese cloth for 12 hr, and the drained-off whey can be subsequently used for the inoculation of a wide range of food raw materials, including vegetables and cereal-based foods.

A production protocol is described for the small-scale production of probiotic fermented dairy drink with the aid of a novel bacterial starter culture.

Protocolo de Produção da novela para em pequena escala Fabricação de alimentos fermentados probióticos

A novel dried bacterial consortium of Lactobacillus rhamnosus yoba 2012 and Streptococcus thermophilus C106 is cultured in 1 L of milk. This fresh starter ...

ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth

Growth phenotypes of microorganisms are a strong indicator of their underlying genetic fitness and can be segregated into 3 growth regimes: lag-phase, log-phase, and stationary-phase. Each growth phase can reveal different aspects of fitness that are related to various environmental and genetic conditions. High-resolution and quantitative measurements of all 3 phases of growth are generally difficult to obtain. Here we present a detailed method to characterize all 3 growth phases on solid media using an assay called One-cell Doubling Evaluation of Living Arrays of Yeast (ODELAY). ODELAY quantifies growth phenotypes of individual cells growing into colonies on solid media using time-lapse microscopy. This method can directly observe population heterogeneity with each growth parameter in genetically identical cells growing into colonies. This population heterogeneity offers a unique perspective for understanding genetic and epigenetic regulation, and responses to genetic and environmental perturbations. While the ODELAY method is demonstrated using yeast, it can be utilized on any colony forming microorganism that is visible by bright field microscopy.

We present a method for quantifying growth phenotypes of individual yeast cells as they grow into colonies on solid media using time-lapse microscopy termed, One-cell Doubling Evaluation of Living Arrays of Yeast (ODELAY). Population heterogeneity of genetically identical cells growing into colonies can be directly observed and quantified.

ODELAY: um método em larga escala para a quantificação multiparamétrica do crescimento de fermento

Growth phenotypes of microorganisms are a strong indicator of their underlying genetic fitness and can be segregated into 3 growth regimes: lag-phase, ...

Identification of Novel Regulators of Plant Transpiration by Large-Scale Thermal Imaging Screening in Helianthus Annuus

Plant adaptation to biotic and abiotic stresses is governed by a variety of factors, among which the regulation of stomatal aperture in response to water deficit or pathogens plays a crucial role. Identifying small molecules that regulate stomatal movement can therefore contribute to understanding the physiological basis by which plants adapt to their environment. Large-scale screening approaches that have been used to identify regulators of stomatal movement have potential limitations: some rely heavily on the abscisic acid (ABA) hormone signaling pathway, therefore excluding ABA-independent mechanisms, while others rely on the observation of indirect, long-term physiological effects such as plant growth and development. The screening method presented here allows the large-scale treatment of plants with a library of chemicals coupled with a direct quantification of their transpiration by thermal imaging. Since evaporation of water through transpiration results in leaf surface cooling, thermal imaging provides a non-invasive approach to investigate changes in stomatal conductance over time. In this protocol, Helianthus annuus seedlings are grown hydroponically and then treated by root feeding, in which the primary root is cut and dipped into the chemical being tested. Thermal imaging followed by statistical analysis of cotyledonary temperature changes over time allows for the identification of bioactive molecules modulating stomatal aperture. Our proof-of-concept experiments demonstrate that a chemical can be carried from the cut root to the cotyledon of the sunflower seedling within 10 minutes. In addition, when plants are treated with ABA as a positive control, an increase in leaf surface temperature can be detected within minutes. Our method thus allows the efficient and rapid identification of novel molecules regulating stomatal aperture.

Identification of Novel Regulators of Plant Transpiration by Large-Scale Thermal Imaging Screening in Helianthus Annuus

We provide a method for identifying modulators of foliar transpiration by large-scale screening of a compound library.

Identificação de novos reguladores de transpiração vegetal por triagem de imagens térmicas em larga escala em Helianthus Annuus

Plant adaptation to biotic and abiotic stresses is governed by a variety of factors, among which the regulation of stomatal aperture in response to water ...

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is a powerful and widely used approach to profile chromatin DNA associated with specific histone modifications, such as H3K27ac, to help identify cis-regulatory DNA elements. The manual process to complete a ChIP-Seq is labor intensive, technically challenging, and often requires large-cell numbers (&#62;100,000 cells). The method described here helps to overcome those challenges. A complete semiautomated, microscaled H3K27ac ChIP-Seq procedure including cell fixation, chromatin shearing, immunoprecipitation, and sequencing library preparation, for batch of 48 samples for cell number inputs less than 100,000 cells is described in detail. The semiautonomous platform reduces technical variability, improves signal-to-noise ratios, and drastically reduces labor. The system can thereby reduce costs by allowing for reduced reaction volumes, limiting the number of expensive reagents such as enzymes, magnetic beads, antibodies, and hands-on time required. These improvements to the ChIP-Seq method suit perfectly for large-scale epigenetic studies of clinical samples with limited cell numbers in a highly reproducible manner.

This paper describes a semiautomated, microscaled ChIP-Seq protocol of DNA regions associated with a specific histone modification (H3K27ac) using a ChIP liquid-handler platform, followed by library preparation using tagmentation. The procedure includes control assessment for quality and quantity purposes and can be adopted to other histone modifications or transcription factors.

Um procedimento de ChIP-Seq semiautônomo para estudos epigenéticos em larga escala

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is a powerful and widely used approach to profile chromatin DNA associated with specific ...