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10.1093/bioinformatics/btaa1002 http://scihub22266oqcxt.onion/10.1093/bioinformatics/btaa1002 33244583!7717134!33244583     free     free     free Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 231.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Bioinformatics 2021 ; 36 (24): 5571-5581 Nephropedia Template TP {{tp|p=33244583|t=2021. Novel SARS-CoV-2 encoded small RNAs in the passage to humans |pdf=|usr=}}{{33244583}} gab.com Text Novel SARS-CoV-2 encoded small RNAs in the passage to humans JO: Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=33244583 #FOAvip MOTIVATION: The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease 2019. This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. RESULTS: We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprograming of the new host upon infection. AVAILABILITY AND IMPLEMENTATION: https://github.com/sinc-lab/sarscov2-mirna-discovery. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Twit Text FOAVip Novel SARS-CoV-2 encoded small RNAs in the passage to humans ????Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=33244583 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33244583 #FOAvip English Wikipedia <ref>{{Cite pmid|33244583}}</ref> Novel SARS-CoV-2 encoded small RNAs in the passage to humans #MMPMID33244583 Merino GA; Raad J; Bugnon LA; Yones C; Kamenetzky L; Claus J; Ariel F; Milone DH; Stegmayer G Bioinformatics 2021[Apr]; 36 (24): 5571-5581 PMID33244583show ga MOTIVATION: The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease 2019. This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. RESULTS: We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprograming of the new host upon infection. AVAILABILITY AND IMPLEMENTATION: https://github.com/sinc-lab/sarscov2-mirna-discovery. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |*COVID-19[MESH] |*Coronavirus/genetics[MESH] |Animals[MESH] |Betacoronavirus[MESH] |Genome, Viral[MESH] |Humans[MESH] |Pandemics[MESH]Novel SARS-CoV-2 encoded small RNAs in the passage to humans (epmc).pdf DeepDyve Pubget Overpricing