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Single-cell qPCR Assay with Massively Parallel Microfluidic System

Authors: Marta Prieto-Vila, Takahiro Ochiya and Yusuke Yamamoto, date: 03/20/2020, view: 183, Q&A: 0

The single-cell transcriptome is the set of messenger RNA molecules expressed in one cell. It is extremely variable and changes according to external, physical and biochemical conditions. Due to sensitivity shortages, most of genetic studies use ...

High-resolution and Deep Phylogenetic Reconstruction of Ancestral States from Large Transcriptomic Data Sets

Authors: Sumanth Kumar Mutte and Dolf Weijers, date: 03/20/2020, view: 274, Q&A: 0

Phylogenetics is an important area of evolutionary biology that helps to understand the origin and divergence of genes, genomes and species. Building meaningful phylogenetic trees is needed for the accurate reconstruction of the past. To achieve a ...

In vitro Measurement of CMP-Sialic Acid Transporter Activity in Reconstituted Proteoliposomes

Authors: James Cahill, Shivani Ahuja and Matthew R. Whorton, date: 03/20/2020, view: 224, Q&A: 0

Nucleotide-sugar transporters (NSTs) facilitate eukaryotic cellular glycosylation by transporting nucleotide-sugar conjugates into the Golgi lumen and endoplasmic reticulum for use by glycosyltransferases, while also transferring nucleotide ...

Using Seed Chipping to Genotype Maize Kernels

Authors: Alison M. Mills, Lindy A. Allsman, Sareen Leon and Carolyn G. Rasmussen, date: 03/20/2020, view: 171, Q&A: 0

Zea mays (maize) is an important model organism for studying monocot growth and development. Genotyping maize in the greenhouse or field can be time consuming and costly. Here, we describe a method to remove or chip a small amount of the ...

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Single-cell qPCR Assay with Massively Parallel Microfluidic System

Authors: Marta Prieto-Vila, Takahiro Ochiya and Yusuke Yamamoto, date: 03/20/2020, view: 183, Q&A: 0

[Abstract] The single-cell transcriptome is the set of messenger RNA molecules expressed in one cell. It is extremely variable and changes according to external, physical and biochemical conditions. Due to sensitivity shortages, most of genetic studies use bulk samples, providing only the average gene expression. Single-cell technologies have provided a ...

High-resolution and Deep Phylogenetic Reconstruction of Ancestral States from Large Transcriptomic Data Sets

Authors: Sumanth Kumar Mutte and Dolf Weijers, date: 03/20/2020, view: 274, Q&A: 0

[Abstract] Phylogenetics is an important area of evolutionary biology that helps to understand the origin and divergence of genes, genomes and species. Building meaningful phylogenetic trees is needed for the accurate reconstruction of the past. To achieve a correct phylogenetic understanding of genes or proteins, reliable and robust methods are needed to ...

In vitro Measurement of CMP-Sialic Acid Transporter Activity in Reconstituted Proteoliposomes

Authors: James Cahill, Shivani Ahuja and Matthew R. Whorton, date: 03/20/2020, view: 224, Q&A: 0

[Abstract] Nucleotide-sugar transporters (NSTs) facilitate eukaryotic cellular glycosylation by transporting nucleotide-sugar conjugates into the Golgi lumen and endoplasmic reticulum for use by glycosyltransferases, while also transferring nucleotide monophosphate byproducts to the cytoplasm. Mutations in this family of proteins can cause a number of ...

Production, Purification and Characterization of Recombinant Biotinylated Phytochrome B for Extracellular Optogenetics

Authors: Maximilian Hörner, O. Sascha Yousefi, Wolfgang W. A. Schamel and Wilfried Weber, date: 03/05/2020, view: 412, Q&A: 0

[Abstract] In the field of extracellular optogenetics, photoreceptors are applied outside of cells to obtain systems with a desired functionality. Among the diverse applied photoreceptors, phytochromes are the only ones that can be actively and reversibly switched between the active and inactive photostate by the illumination with cell-compatible red and ...

mRNA Extraction from Gill Tissue for RNA-sequencing

Authors: Jukka-Pekka Verta and Felicity Jones, date: 03/05/2020, view: 298, Q&A: 0

[Abstract] Adaptation is thought to proceed in part through spatial and temporal changes in gene expression. Fish species such as the threespine stickleback are powerful vertebrate models to study the genetic architecture of adaptive changes in gene expression since divergent adaptation to different environments is common, they are abundant and easy to study ...

Assembly of Genetic Circuits with the Mammalian ToolKit

Authors: João P. Fonseca, Alain R Bonny, Jason Town and Hana El-Samad, date: 03/05/2020, view: 414, Q&A: 0

[Abstract] The ability to rapidly assemble and prototype cellular circuits is vital for biological research and its applications in biotechnology and medicine. The Mammalian ToolKit (MTK) is a Golden Gate-based cloning toolkit for fast, reproducible and versatile assembly of large DNA vectors and their implementation in mammalian models. The MTK consists of ...

Manganese Superoxide Dismutase Activity Assay in the Yeast Saccharomyces cerevisiae

Authors: Louise Thines and Pierre Morsomme, date: 03/05/2020, view: 393, Q&A: 0

[Abstract] Superoxide dismutases (SODs) act as a primary defence against reactive oxygen species (ROS) by converting superoxide anion radicals (O₂^-) into molecular oxygen (O₂) and hydrogen peroxide (H₂O₂). Members of this enzyme family include CuZnSODs, MnSODs, FeSODs, and NiSODs, depending on the nature ...

Cell-free Reconstitution of the Packaging of Cargo Proteins into Vesicles at the trans Golgi Network

Authors: Xiao Tang, Feng Yang and Yusong Guo, date: 03/05/2020, view: 301, Q&A: 0

[Abstract] Protein sorting at the trans Golgi network (TGN) plays important roles in targeting newly synthesized proteins to their specific destinations. The aim of this proposal is to reconstitute the packaging of non-Golgi resident cargo proteins into vesicles at the TGN, utilizing rat liver cytosol, semi-intact mammalian cells and nucleotides. ...

Super-resolution Microscopy-based Bimolecular Fluorescence Complementation to Study Protein Complex Assembly and Co-localization

Authors: Jingjing Chen, Zulin Yu, Jay R. Unruh, Brian D. Slaughter and Sue L. Jaspersen, date: 02/20/2020, view: 561, Q&A: 0

[Abstract] Numerous experimental approaches exist to study interactions between two subunits of a large macromolecular complex. However, most methods do not provide spatial and temporal information about binding, which are critical for dissecting the mechanism of assembly of nanosized complexes in vivo. While recent advances in super-resolution ...

Estimating Cellular Abundances of Halo-tagged Proteins in Live Mammalian Cells by Flow Cytometry

Authors: Claudia Cattoglio, Xavier Darzacq, Robert Tjian and Anders Sejr Hansen, date: 02/20/2020, view: 715, Q&A: 0

[Abstract] Accurate abundance measurements of cellular proteins are required to achieve a quantitative and predictive understanding of any biological process inside the cell. Existing methods to determine absolute protein abundances are labor-intensive and/or require sophisticated experimental and computational infrastructure (e.g., fluorescence ...

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