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Genetics - GEG Tech top picks
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Erik Larsson and colleagues present an analysis pipeline for identifying likely transcription-altering noncoding somatic mutations in cancer using publicly available data from 505 tumor genomes across 14 cancer types. They find that TERT promoter mutations show strong associations to altered transcriptional levels and identify recurrent promoter mutations in DPH3 and PLEKHS1.
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David Jaffe and colleagues report a new algorithm, DISCOVAR, for variant calling and de novo genome assembly. They test the algorithm on a new reference variant call set and demonstrate improved variant calling, particularly in challenging regions of the genome.
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The authors report that stroke elicits a latent neurogenic program in striatal astrocytes in mice. Notch1 signaling is reduced in astrocytes after stroke, and attenuated Notch1 signaling is necessary for neurogenesis by striatal astrocytes. Blocking Notch signaling triggers astrocytes in the striatum and the medial cortex to enter a neurogenic program, even in the absence of stroke, resulting in 850 ± 210 (mean ± SEM) new neurons in a mouse striatum.
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The information that interprets the genetic code in a new embryo differs depending on whether it comes from the father or mother, researchers have found. This parent specific information is contained within modified histone proteins, also called 'epigenetic marks,' which influence the development plan of new embryos. The research opens up new avenues of study for scientists exploring the process of how genetic information is passed from parents to offspring.
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An obscure swatch of human DNA once thought to be nothing more than biological trash may actually offer a treasure trove of insight into complex genetic-related diseases such as cancer and diabetes, thanks to a novel sequencing technique developed by biologists.
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Structural and biochemical analyses of full-length human BRCA2 reveal how it facilitates RAD51-mediated homologous recombination to repair DNA double-strand breaks.
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A person's face is the first thing that others see, and much remains unknown about how it forms -- or malforms -- during early development. Recently, researchers have begun to unwind these mysteries.
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In a study published the authors describe how a mutation in a gene called TBX1 causes the facial and other deformities associated with DiGeorge syndrome.
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Holger Lerche, Camila Esguerra and colleagues report the identification of inactivating mutations in STX1B in individuals with various seizure-related disorders, including febrile seizures and epilepsy. Functional studies indicate that STX1B acts in the presynaptic release machinery.
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John Lis, Adam Siepel and colleagues map transcription start sites across the genome in two human cell lines using a nuclear run-on protocol called GRO-cap. They find a common architecture of initiation at both promoters and enhancers and that transcript elongation stability provides the strongest distinction between promoters and enhancers.
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Scientists studying birth defects in humans and purebred dogs have identified an association between cleft lip and cleft palate -- conditions that occur when the lip and mouth fail to form properly during pregnancy -- and a mutation in the ADAMTS20 gene.
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The bond between humans and dogs is strong and ancient. Dogs and people share many aspects of life. The relationship between the two species has been studied by psychologists, anthropologists, ethnologists and also by genetic and molecular biologists. In this sense, dogs are a great model for understanding the causes of human diseases, especially cancer. Unlike other mammals used in research, dogs develop cancer spontaneously as humans do and cancer is the most common cause of death in this spec
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Kristijan Ramadan and colleagues report the identification of three individuals from two families with biallelic inactivating mutations in SPRTN causing early onset hepatocellular carcinoma and defects in the DNA replication stress response. Functional studies confirmed critical roles for SPRTN in G2/M checkpoint response and DNA replication.
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Biochemists have developed a program that predicts the placement of chemical marks that control the activity of genes based on sequences of DNA. By comparing sequences with and without epigenomic modification, they identified DNA motifs associated with the changes. They call this novel analysis pipeline Epigram and have made both the program and the DNA motifs they identified openly available to other scientists.
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The structural features of HIV-1 Env characterized here provide grounds for a paradigm shift in loop exposure and epitope occlusion, while providing substantive rationale for epitope display required for elicitation of broadly neutralizing antibodies, as well as substantiating previous pertinent literature disregarded in recent reports.