Systems Biology

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    Protocols in Current Issue
    Delayed Alternation Task for the Study of Spatial Working and Long Term Memory in Rats
    Authors:  Megi Hoxha and Marta Sabariego, date: 03/05/2020, view: 387, Q&A: 0
    [Abstract] Memory systems can hold previously presented information for several seconds, bridging gaps between discontinuous events. It has been previously demonstrated that the hippocampus and the medial entorhinal cortex (mEC) are necessary for memory retention over delay intervals in alternation tasks. Here we describe the delayed alternation task, a ...
    ChIP-Seq from Limited Starting Material of K562 Cells and Drosophila Neuroblasts Using Tagmentation Assisted Fragmentation Approach
    Authors:  Junaid Akhtar, Piyush More and Steffen Albrecht, date: 02/20/2020, view: 251, Q&A: 0
    [Abstract] Chromatin immunoprecipitation is extensively used to investigate the epigenetic profile and transcription factor binding sites in the genome. However, when the starting material is limited, the conventional ChIP-Seq approach cannot be implemented. This protocol describes a method that can be used to generate the chromatin profiles from as low as ...
    Probabilistic Models for Predicting Mutational Routes to New Adaptive Phenotypes
    Authors:  Eric Libby and Peter A. Lind, date: 10/20/2019, view: 881, Q&A: 0
    [Abstract] Understanding the translation of genetic variation to phenotypic variation is a fundamental problem in genetics and evolutionary biology. The introduction of new genetic variation through mutation can lead to new adaptive phenotypes, but the complexity of the genotype-to-phenotype map makes it challenging to predict the phenotypic effects of ...
    Genome-wide Estimation of Evolutionary Distance and Phylogenetic Analysis of Homologous Genes
    Authors:  Meixia Zhao, Biao Zhang, Jianxin Ma and Damon Lisch, date: 12/05/2018, view: 2773, Q&A: 0
    [Abstract] Homologous genes, including paralogs and orthologs, are genes that share sequence homologies within or between different species. Homologous genes originate from a common origin through speciation, genetic duplication or horizontal gene transfer. Estimation of the sequence divergence of homologous genes help us to understand divergence time, which ...
    Bacterial Microcolonies in Gel Beads for High-throughput Screening
    Author:  Yolanda Schaerli, date: 07/05/2018, view: 4204, Q&A: 0
    [Abstract] High-throughput screening of a DNA library expressed in a bacterial population for identifying potentially rare members displaying a property of interest is a crucial step for success in many experiments such as directed evolution of proteins and synthetic circuits and deep mutational scanning to identify gain- or loss-of-function mutants.
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    Extraction and 16S rRNA Sequence Analysis of Microbiomes Associated with Rice Roots
    Authors:  Joseph Edwards, Christian Santos-Medellín and Venkatesan Sundaresan, date: 06/20/2018, view: 7138, Q&A: 0
    [Abstract] Plant roots associate with a wide diversity of bacteria and archaea across the root-soil spectrum. The rhizosphere microbiota, the communities of microbes in the soil adjacent to the root, can contain up to 10 billion bacterial cells per gram of soil (Raynaud and Nunan, 2014) and can play important roles for the fitness of the host plant. Subsets ...
    Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9
    [Abstract] Genome modification in budding yeast has been extremely successful largely due to its highly efficient homology-directed DNA repair machinery. Several methods for modifying the yeast genome have previously been described, many of them involving at least two-steps: insertion of a selectable marker and substitution of that marker for the intended ...
    Extraction of DNA from Murine Fecal Pellets for Downstream Phylogenetic Microbiota Analysis by Next-generation Sequencing
    Authors:  Elien Eeckhout and Andy Wullaert, date: 02/05/2018, view: 6157, Q&A: 2
    [Abstract] Mouse models are widely used to evaluate the potential impact of the gut microbial composition on health and disease. Standardized protocols for sampling and storing murine feces, as well as for extracting DNA from these fecal pellets are needed to limit experimental variation between different studies. Both efficient lysis of the microbiota and ...
    Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data
    [Abstract] Next-generation sequencing (NGS) offers unparalleled resolution for untargeted organism detection and characterization. However, the majority of NGS analysis programs require users to be proficient in programming and command-line interfaces. EDGE bioinformatics was developed to offer scientists with little to no bioinformatics expertise a ...
    Validating Candidate Congenital Heart Disease Genes in Drosophila
    Authors:  Jun-yi Zhu, Yulong Fu, Adam Richman and Zhe Han, date: 06/20/2017, view: 5070, Q&A: 0
    [Abstract] Genomic sequencing efforts can implicate large numbers of genes and de novo mutations as potential disease risk factors. A high throughput in vivo model system to validate candidate gene association with pathology is therefore useful. We present such a system employing Drosophila to validate candidate congenital heart ...



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