18 Works

De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability

Wen-Xiong Chen, Bin Liu, Lijie Zhou, Xiaoli Xiong, Jie Fu, Zhi-Fang Huang, Ting Tan, Mingxi Tang, Jun Wang & Ya-Ping Tang
Abstract Background Autism spectrum disorder (ASD) is often accompanied by intellectual disability (ID). Despite extensive studies, however, the genetic basis for this comorbidity is still not clear. In this study, we tried to develop an analyzing pipeline for de novo mutations and possible pathways related to ID phenotype in ASD. Whole-exome sequencing (WES) was performed to screen de novo mutations and candidate genes in 79 ASD children together with their parents (trios). The de novo...

Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level

Jens Michaelis, Anna Sefer, Eleni Kallis, Tobias Eilert, Carlheinz Röcker, Olga Kolesnikova, David Neuhaus & Sebastian Eustermann
Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1’s multi-domain organization. Here, we directly probe this fundamental yet poorly understood process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1’s N-terminal zinc fingers convert DNA SSBs...

A single-cell transcriptomic atlas of complete insect nervous systems across multiple life stages

Marc Corrales, Benjamin T. Cocanougher, Andrea B. Kohn, Jason D. Wittenbach, Xi S. Long, Andrew Lemire, Albert Cardona, Robert H. Singer, Leonid L. Moroz & Marta Zlatic
Abstract Molecular profiles of neurons influence neural development and function but bridging the gap between genes, circuits, and behavior has been very difficult. Here we used single cell RNAseq to generate a complete gene expression atlas of the Drosophila larval central nervous system composed of 131,077 single cells across three developmental stages (1 h, 24 h and 48 h after hatching). We identify 67 distinct cell clusters based on the patterns of gene expression. These...

Imaging the onset of oscillatory signaling dynamics during mouse embryo gastrulation

Henning J Falk, Takehito Tomita, Gregor Moenke, Katie McDole & Alexander Aulehla
A fundamental requirement for embryonic development is the coordination of signaling activities in space and time. A notable example in vertebrate embryos is found during somitogenesis, where gene expression oscillations linked to the segmentation clock are synchronized across cells in the presomitic mesoderm (PSM) and result in tissue-level wave patterns. To examine their onset during mouse embryo development, we studied the dynamics of the segmentation clock gene Lfng during gastrulation. To this end, we established...

Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes

Evan Janzen, Yuning Shen, Alberto Vazquez-Salazar, Ziwei Liu, Celia Blanco, Josh Kenchel & Irene Chen
The emergence of the genetic code was a major transition in the evolution from a prebiotic RNA world to the earliest modern cells. A prominent feature of the standard genetic code is error minimization, or the tendency of mutations to be unusually conservative in preserving biophysical features of the amino acid. While error minimization is often assumed to result from natural selection, it has also been speculated that error minimization may be a by-product of...

Data from: Neuropeptide signalling shapes feeding and reproductive behaviours in male C. elegans

Matthew Gadenne, Iris Hardege, Eviatar Yemini, Djordji Suleski, Paris Jaggers, Isabel Beets, William Schafer & Yee Lian Chew
Sexual dimorphism occurs where different sexes of the same species display differences in characteristics not limited to reproduction. For the nematode Caenorhabditis elegans, in which the complete neuroanatomy has been solved for both hermaphrodites and males, sexually dimorphic features have been observed both in terms of the number of neurons and in synaptic connectivity. In addition, male behaviours, such as food-leaving to prioritise searching for mates, have been attributed to neuropeptides released from sex-shared or...

Additional file 1 of A single-cell transcriptomic atlas of complete insect nervous systems across multiple life stages

Marc Corrales, Benjamin T. Cocanougher, Andrea B. Kohn, Jason D. Wittenbach, Xi S. Long, Andrew Lemire, Albert Cardona, Robert H. Singer, Leonid L. Moroz & Marta Zlatic
Additional file 1: Supplementary Spreadsheets and Figures. All spreadsheets for marker genes contain the following columns: p-value (pval), average log2 fold-change (avg_log2FC), percent of cells in the cluster expressing the marker (pct.1), percent of cells outside the cluster expressing the marker (pct.2), the multiple test corrected p-value (p_val_adj), the cluster number (cluster), the gene name (gene), the flybase id (Fbgn_ID), gene long name (GeneName), datestamp of flybase snapshot inclusion (datestamp) and the Flybase gene snapshot...

Shared IGHV1-69-encoded neutralizing antibodies contribute to the emergence of L452R substitution in SARS-CoV-2 variants

Qihong Yan, Ruitian Hou, Xiaohan Huang, Yanjun Zhang, Ping He, Yudi Zhang, Banghui Liu, Qian Wang, Haiyue Rao, Xianying Chen, Xinwei Zhao, Xuefeng Niu, Jincun Zhao, Xiaoli Xiong & Ling Chen
SARS-CoV-2 variants continue to emerge facing established herd immunity. L452R, previously featured in the Delta variant, quickly emerged in Omicron subvariants, including BA.4/BA.5, implying a continued selection pressure on this residue. The underlying links between spike mutations and their selective pressures remain incompletely understood. Here, by analyzing 221 structurally characterized antibodies, we found that IGHV1-69-encoded antibodies preferentially contact L452 using germline-encoded hydrophobic residues at the tip of HCDR2 loop. Whereas somatic hypermutations or VDJ rearrangements...

Data supplement to: Quality control of image sensors using gaseous tritium light sources

David McFadden, Brad Amos & Rainer Heintzmann
In the article “Quality Control of Image Sensors using Gaseous Tritium Light Sources” (https://doi.org/10.1098/rsta.2021.0130) we propose a practical method for radiometrically calibrating cameras using widely available gaseous tritium light sources (betalights). This dataset includes all the recorded data along with the scripts necessary to reproduce the results and figures.

Additional file 2 of De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability

Wen-Xiong Chen, Bin Liu, Lijie Zhou, Xiaoli Xiong, Jie Fu, Zhi-Fang Huang, Ting Tan, Mingxi Tang, Jun Wang & Ya-Ping Tang
Additional file 2. Table S2: De novo mutations confirmed in 79 probands and their 2 siblings (Excel file) (dataset1). Table S6: De novo altering genes that involved in protein synthesis, pressure, energy metabolism, development, and amino acid metabolism (Excel file) (dataset2).

Additional file 1 of De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability

Wen-Xiong Chen, Bin Liu, Lijie Zhou, Xiaoli Xiong, Jie Fu, Zhi-Fang Huang, Ting Tan, Mingxi Tang, Jun Wang & Ya-Ping Tang
Additional file 1. Figure S1: Mendelian error rate of all families. Figure S2: The number of de novo mutations in probands and siblings followed Poisson distribution. Figure S3: Gene (protein synthesis) expression in different brain regions at various periods. Figure S4: Gene (energy) expression in different brain regions at various periods. Figure S5: Gene (pressure) expression in different brain regions at various periods. Figure S6: Gene (amino acid) expression in different brain regions at various...

De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability

Wen-Xiong Chen, Bin Liu, Lijie Zhou, Xiaoli Xiong, Jie Fu, Zhi-Fang Huang, Ting Tan, Mingxi Tang, Jun Wang & Ya-Ping Tang
Abstract Background Autism spectrum disorder (ASD) is often accompanied by intellectual disability (ID). Despite extensive studies, however, the genetic basis for this comorbidity is still not clear. In this study, we tried to develop an analyzing pipeline for de novo mutations and possible pathways related to ID phenotype in ASD. Whole-exome sequencing (WES) was performed to screen de novo mutations and candidate genes in 79 ASD children together with their parents (trios). The de novo...

Deep sequencing data for document titled: Rolling circle RNA synthesis catalysed by RNA

Emil L. Kristoffersen
RNA-catalysed RNA replication is widely considered a key step in the emergence of life’s first genetic system. However, RNA replication can be impeded by the extraordinary stability of duplex RNA products, which must be dissociated for re-initiation of the next replication cycle. Here we have explored rolling circle synthesis (RCS) as a potential solution to this strand separation problem. RCS on small circular RNAs - as indicated by molecular dynamics simulations - induces a progressive...

Additional file 1 of A single-cell transcriptomic atlas of complete insect nervous systems across multiple life stages

Marc Corrales, Benjamin T. Cocanougher, Andrea B. Kohn, Jason D. Wittenbach, Xi S. Long, Andrew Lemire, Albert Cardona, Robert H. Singer, Leonid L. Moroz & Marta Zlatic
Additional file 1: Supplementary Spreadsheets and Figures. All spreadsheets for marker genes contain the following columns: p-value (pval), average log2 fold-change (avg_log2FC), percent of cells in the cluster expressing the marker (pct.1), percent of cells outside the cluster expressing the marker (pct.2), the multiple test corrected p-value (p_val_adj), the cluster number (cluster), the gene name (gene), the flybase id (Fbgn_ID), gene long name (GeneName), datestamp of flybase snapshot inclusion (datestamp) and the Flybase gene snapshot...

A single-cell transcriptomic atlas of complete insect nervous systems across multiple life stages

Marc Corrales, Benjamin T. Cocanougher, Andrea B. Kohn, Jason D. Wittenbach, Xi S. Long, Andrew Lemire, Albert Cardona, Robert H. Singer, Leonid L. Moroz & Marta Zlatic
Abstract Molecular profiles of neurons influence neural development and function but bridging the gap between genes, circuits, and behavior has been very difficult. Here we used single cell RNAseq to generate a complete gene expression atlas of the Drosophila larval central nervous system composed of 131,077 single cells across three developmental stages (1 h, 24 h and 48 h after hatching). We identify 67 distinct cell clusters based on the patterns of gene expression. These...

Additional file 1 of De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability

Wen-Xiong Chen, Bin Liu, Lijie Zhou, Xiaoli Xiong, Jie Fu, Zhi-Fang Huang, Ting Tan, Mingxi Tang, Jun Wang & Ya-Ping Tang
Additional file 1. Figure S1: Mendelian error rate of all families. Figure S2: The number of de novo mutations in probands and siblings followed Poisson distribution. Figure S3: Gene (protein synthesis) expression in different brain regions at various periods. Figure S4: Gene (energy) expression in different brain regions at various periods. Figure S5: Gene (pressure) expression in different brain regions at various periods. Figure S6: Gene (amino acid) expression in different brain regions at various...

Additional file 2 of De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability

Wen-Xiong Chen, Bin Liu, Lijie Zhou, Xiaoli Xiong, Jie Fu, Zhi-Fang Huang, Ting Tan, Mingxi Tang, Jun Wang & Ya-Ping Tang
Additional file 2. Table S2: De novo mutations confirmed in 79 probands and their 2 siblings (Excel file) (dataset1). Table S6: De novo altering genes that involved in protein synthesis, pressure, energy metabolism, development, and amino acid metabolism (Excel file) (dataset2).

Shared IGHV1-69-encoded neutralizing antibodies contribute to the emergence of L452R substitution in SARS-CoV-2 variants

Qihong Yan, Ruitian Hou, Xiaohan Huang, Yanjun Zhang, Ping He, Yudi Zhang, Banghui Liu, Qian Wang, Haiyue Rao, Xianying Chen, Xinwei Zhao, Xuefeng Niu, Jincun Zhao, Xiaoli Xiong & Ling Chen
SARS-CoV-2 variants continue to emerge facing established herd immunity. L452R, previously featured in the Delta variant, quickly emerged in Omicron subvariants, including BA.4/BA.5, implying a continued selection pressure on this residue. The underlying links between spike mutations and their selective pressures remain incompletely understood. Here, by analyzing 221 structurally characterized antibodies, we found that IGHV1-69-encoded antibodies preferentially contact L452 using germline-encoded hydrophobic residues at the tip of HCDR2 loop. Whereas somatic hypermutations or VDJ rearrangements...

Registration Year

  • 2022
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Affiliations

  • MRC Laboratory of Molecular Biology
    18
  • Zhejiang University
    8
  • Guangzhou Medical University
    8
  • Lanzhou University
    7
  • Helmholtz Centre for Environmental Research
    6
  • Affiliated Hospital of Southwest Medical University
    6
  • Beijing Tian Tan Hospital
    6
  • Tianjin Medical University General Hospital
    6
  • North West Agriculture and Forestry University
    6
  • Sun Yat-sen University
    6