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      Profilin is involved in G1 to S phase progression and mitotic spindle orientation during Leishmania donovani cell division cycle

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          Abstract

          Profilin is a multi-ligand binding protein, which is a key regulator of actin dynamics and involved in regulating several cellular functions. It is present in all eukaryotes, including trypanosomatids such as Leishmania. However, not much is known about its functions in these organisms. Our earlier studies have shown that Leishmania parasites express a single homologue of profilin (LdPfn) that binds actin, phosphoinositides and poly- L- proline motives, and depletion of its intracellular pool to 50%of normal levels affects the cell growth and intracellular trafficking. Here, we show, employing affinity pull-down and mass spectroscopy, that LdPfn interacted with a large number of proteins, including those involved in mRNA processing and protein translation initiation, such as eIF4A1. Further, we reveal, using mRNA Seq analysis, that depletion of LdPfn in Leishmania cells (LdPfn +/-) resulted in significantly reduced expression of genes which encode proteins involved in cell cycle regulation, mRNA translation initiation, nucleosides and amino acids transport. In addition, we show that in LdPfn +/- cells, cellular levels of eIF4A1 protein were significantly decreased, and during their cell division cycle, G1-to-S phase progression was delayed and orientation of mitotic spindle altered. These changes were, however, reversed to normal by episomal expression of GFP-LdPfn in LdPfn +/- cells. Taken together, our results indicate that profilin is involved in regulation of G1-to-S phase progression and mitotic spindle orientation in Leishmania cell cycle, perhaps through its interaction with elF4A1 protein.

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            HTSeq—a Python framework to work with high-throughput sequencing data

            Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. Contact: sanders@fs.tum.de
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              Differential expression analysis for sequence count data

              High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.
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                Author and article information

                Contributors
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: Writing – original draft
                Role: Formal analysisRole: SoftwareRole: Visualization
                Role: Funding acquisitionRole: Project administrationRole: Supervision
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                22 March 2022
                2022
                : 17
                : 3
                : e0265692
                Affiliations
                [1 ] Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
                [2 ] Manipal Academy of Higher Education, Manipal, Karnataka, India
                Centre de Recherche en Biologie cellulaire de Montpellier, FRANCE
                Author notes

                Competing Interests: The authors of this manuscript have no conflicts of interest to declare.

                [¤]

                Current address: The Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India

                Author information
                https://orcid.org/0000-0002-7290-627X
                Article
                PONE-D-21-38894
                10.1371/journal.pone.0265692
                8939790
                35316283
                1174c587-320e-4bbc-89a3-e394cebbe696
                © 2022 Ambaru et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 17 December 2021
                : 4 March 2022
                Page count
                Figures: 6, Tables: 2, Pages: 28
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100007296, Infosys Foundation;
                Funded by: funder-id http://dx.doi.org/10.13039/501100001409, Department of Science and Technology, Ministry of Science and Technology;
                Award ID: SR/WOS-A/LS-352/2017
                Award Recipient :
                This study was supported by a Corpus grant by Infosys Foundation to IBAB and by the Department of IT, BT, and S&T, Government of Karnataka. BA is the recipient of the Women Scientist Grant by DST, GOI (No: SR/WOS-A/LS-352/2017 (G)). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Cell Biology
                Cell Processes
                Cell Cycle and Cell Division
                Biology and Life Sciences
                Organisms
                Eukaryota
                Protozoans
                Parasitic Protozoans
                Leishmania
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Biochemistry
                Bioenergetics
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Energy-Producing Organelles
                Mitochondria
                Biology and life sciences
                Biochemistry
                Proteins
                DNA-binding proteins
                Biology and life sciences
                Biochemistry
                Nucleic acids
                RNA
                Messenger RNA
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Cell Membranes
                Membrane Proteins
                Outer Membrane Proteins
                Biology and Life Sciences
                Cell Biology
                Cell Processes
                Cell Cycle and Cell Division
                Synthesis Phase
                Custom metadata
                The proteomics data have been deposited to the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [ 63] with the dataset identifier PXD026036. RNA-sequencing data has been deposited online and can be accessed through NCBI GEO series accession number “GSE173907” at the following URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE173907.

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                Uncategorized

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