Tag: SILVA

Antimicrobial potential of Streptomyces coeruleofuscus SCJ isolated from microbiologically unexplored garden soil in Northwest Morocco

Zaman, S. B. et al. A review on antibiotic resistance: Alarm bells are ringing. Cureus doi.org/10.7759/cureus.1403 (2017). Article  PubMed  PubMed Central  Google Scholar  Peterson, E. & Kaur, P. Antibiotic resistance mechanisms in bacteria: Relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front. Microbiol. 9, 2928 (2018)….

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Bioconductor – BioNERO

DOI: 10.18129/B9.bioc.BioNERO     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioNERO. Biological Network Reconstruction Omnibus Bioconductor version: 3.15 BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses…

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N6-methyladenosine modification positively regulate Japanese encephalitis virus replication | Virology Journal

Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Targeting the m6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes Dev. 2021;35:1005–19. Article  CAS  PubMed  PubMed Central  Google Scholar  Chambers…

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How did a man born 2,000 years ago in Russia end up dead in the U.K.? DNA solves the mystery.

A man born 2,000 years ago in Russia ended up buried in England — and researchers think they’ve finally figured out how, thanks to DNA. Scientists from London’s Francis Crick Institute, Durham University in England, and MOLA Headland Infrastructure, a consortium of two U.K. archaeology companies, worked together to determine…

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Research reveals man born thousands of miles to the east traveled to Cambridgeshire 2,000 years ago

Archaeologists excavate the Offord Cluny 203645 burial. Credit: MOLA Headland Infrastructure Scientists from the Francis Crick Institute, Durham University, and MOLA Headland Infrastructure have discovered that a man who lived between AD 126–228 during the Roman period did not originally come from a rural farmstead near where he was buried,…

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Sacramento bee obituaries for today

Sacramento,CA Obituaries. The Dignity Memorial® online obituary search tool gives you access to obituaries from thousands of locations across North America. You can search by first or last name, state and publication date. Once you find the obituary you are looking for, you can get important information about upcoming services,…

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Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout

FAO. The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation (FAO, 2022). Google Scholar  Hua, K. et al. The future of aquatic protein: Implications for protein sources in aquaculture diets. One Earth 3, 316–329 (2019). Article  Google Scholar  Hardy, R. W. Utilization of plant proteins in fish diets:…

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Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach

Bacterial profile variations in mock communities at the genus level While 16S rRNA metabarcoding only identified bacteria and archaea, Saccharomyces cerevisiae and Cryptosporidium were only identified by a shotgun metagenomics approach. Only three metabarcoding partners (P1, P4, and P5), out of six, detected all eight bacterial species present in the…

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Analysis of biomarkers in speculative CNS-enriched extracellular vesicles for parkinsonian disorders: a comprehensive systematic review and diagnostic meta-analysis

44. Zurück zum Zitat Thery C, Witwer KW, Aikawa E, Alcaraz MJ, Anderson JD, Andriantsitohaina R, Antoniou A, Arab T, Archer F, Atkin-Smith GK, Ayre DC, Bach JM, Bachurski D, Baharvand H, Balaj L, Baldacchino S, Bauer NN, Baxter AA, Bebawy M, Beckham C, Bedina Zavec A, Benmoussa A, Berardi…

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Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein | Parasites & Vectors

Akhoundi M, Downing T, Votypka J, Kuhls K, Lukes J, Cannet A, et al. Leishmania infections: molecular targets and diagnosis. Mol Aspects Med. 2017;57:1–29. Article  PubMed  Google Scholar  Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. A historical overview of the classification, evolution, and…

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MIMt: A curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification

Abstract Motivation: Accurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly used 16S rRNA reference databases, which either contain a lot of redundancy, or a high…

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Tree size diversity is the major driver of aboveground carbon storage in dryland agroforestry parklands

Albrecht, A. & Kandji, S. T. Carbon sequestration in tropical agroforestry systems. Agric. Ecosyst. Environ. 1–3, 15–27 (2003). Article  Google Scholar  Nair, P. K. R. Agroforestry systems and environmental quality: Introduction. J. Environ. Qual. 40, 784–790 (2011). Article  CAS  PubMed  Google Scholar  Schroth, G. & McNeely, J. A. Biodiversity conservation,…

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ENPICOM and Carterra Advance Antibody Screening

14 December 2023 Science Salt Lake City, Utah, USA and Hertogenbosch, Netherlands – December 11, 2023 – Life Science Newswire – Carterra Inc., the world leader in label-free high-throughput antibody discovery and development, and ENPICOM B.V., an innovative bioinformatics software solutions provider, announced today a collaboration to streamline the analysis…

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Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes

Abstract For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. The 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique…

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The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases

Annesley SJ, Fisher PR (2019) Mitochondria in health and disease. Cells 8(7). doi.org/10.3390/cells8070680 Cannino G, Ferruggia E, Luparello C, Rinaldi AM (2009) Cadmium and mitochondria. Mitochondrion 9(6):377–384. doi.org/10.1016/j.mito.2009.08.009 Article  CAS  PubMed  Google Scholar  Bonora M, Missiroli S, Perrone M, Fiorica F, Pinton P, Giorgi C (2021) Mitochondrial control of genomic…

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Characterizing viral species in mosquitoes (Culicidae) in the Colombian Orinoco: insights from a preliminary metagenomic study

Kraemer, M. U. et al. The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus. Elife 4, e08347. doi.org/10.7554/eLife.08347 (2015). Article  PubMed  PubMed Central  Google Scholar  Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504–507. doi.org/10.1038/nature12060 (2013). Article  ADS  CAS  PubMed  PubMed Central …

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A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery

Flemming, H.-C. & Wuertz, S. Bacteria and archaea on earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). Article  CAS  PubMed  Google Scholar  Flemming, H.-C., Neu, T. R. & Wozniak, D. J. The EPS matrix: The “house of biofilm cells”. J. Bacteriol. 189, 7945–7947 (2007). Article  CAS …

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Wide bovine tick-borne pathogen spectrum: Predominancy of Theileria annulata and the first molecular detection of Ehrlichia minasensis in Turkey

Agina OA, Shaari MS, Isa NMM, Ajat M, Zamri-Saad M, Hamzah H (2020) Clinical pathology, immunopathology and advanced vaccine technology in bovine theileriosis: A review. Pathogens 9:697. doi.org/10.3390/pathogens9090697 Article  PubMed  PubMed Central  CAS  Google Scholar  Aktas M (2014) A survey of ixodid tick species and molecular identification of tick-borne pathogens….

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Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome

doi: 10.1128/msphere.00470-23. Online ahead of print. Affiliations Expand Affiliation 1 Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. Item in Clipboard Vinícius da Silva Duarte et al. mSphere. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1128/msphere.00470-23. Online ahead of print. Affiliation 1…

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Advanced Emerging Techniques for Forensic DNA Analysis: STRs, SNPs, and mtDNA Analysis

Alshehhi A, Almarzooqi A, Alhammadi K, Werghi N, Tay GK, Alsafar H (2023) Advancement in human face prediction using DNA. Genes (Basel) 14:136. doi.org/10.3390/genes14010136 CrossRef  CAS  PubMed  Google Scholar  Amorim A, Fernandes T, Taveira N (2019) Mitochondrial DNA in human identification: a review. PeerJ 7:e7314. doi.org/10.7717/peerj.7314 CrossRef  PubMed Central  PubMed …

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Applications of NGS Technology in Forensic DNA Analysis

Caratti S, Turrina S, Ferrian M et al (August 2015) MiSeq FGx sequencing system: a new platform for forensic genetics. Forensic Sci Int Genet Suppl Ser 5:e98–e100. doi.org/10.1016/j.fsigss.2015.09.040 Elkins KM, Garloff AT, Zeller CB (2023) Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen…

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Integrating extracellular vesicle and circulating cell-free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients

doi: 10.1002/jex2.108. Epub 2023 Sep 25. Vera Mugoni  1 , Yari Ciani  1 , Orsetta Quaini  1 , Simone Tomasini  1 , Michela Notarangelo  1 , Federico Vannuccini  1 , Alessia Marinelli  1 , Elena Leonardi  2 , Stefano Pontalti  3 , Angela Martinelli  1 , Daniele Rossetto  1 , Isabella Pesce  1 , Sheref S Mansy  1 , Mattia Barbareschi  2 , Antonella…

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Borrelia puertoricensis in opossums (Didelphis marsupialis) from Colombia | Parasites & Vectors

Oppler Z, Keeffe K, McCoy K, Brisson D. Evolutionary genetics of Borrelia. Curr Issues Mol Biol. 2021;42:97–112. doi.org/10.21775/cimb.042.097.2. Article  PubMed  Google Scholar  Margos G, Fingerle V, Cutler S, Gofton A, Stevenson B, Estrada-Peña A. Controversies in bacterial taxonomy: the example of the genus Borrelia. Ticks Tick Borne Dis. 2020;11:101335. doi.org/10.1016/j.ttbdis.2019.101335….

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Lower-limb ulcers in participants with leprosy sequelae

Introduction Leprosy is a disabling infectious disease that predominantly occurs in the skin and peripheral nerves and is transmitted by contact with pathogenic bacteria through the respiratory tract and broken skin. Leprosy is attributed to infection with Mycobacterium leprae (M. leprae)1 and the more recently discovered Mycobacterium lepromatosis.2 In addition,…

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File mismatch detected after align.seqs or screen.seqs – Commands in mothur

Hello, I’ve seen the topic of file mismatch opened on this forum multiple times, but have not seen a solution to my issue. I have V4 region 16S sequences, and I’m using the silva v148.1 reference alignment. After cleaning up my sequences (using the SOP until the alignment point), and…

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The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism

Al-Dosari MS, Al-Jenoobi FI, Alkharfy KM, Alghamdi AM, Bagulb KM, Parvez MK, Al-Mohizea AM, Al-Muhsen S, Halwani R (2013) High prevalence of CYP2D6*41 (G2988A) allele in Saudi Arabians. Environ Toxicol Pharmacol 36:1063–1067. doi.org/10.1016/j.etap.2013.09.008 Article  PubMed  CAS  Google Scholar  Almandil NB, Alkuroud DN, AbdulAzeez S, AlSulaiman A, Elaissari A, Borgio JF…

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Direct Detection of Fluoroquinolone Resistance in Sputum Samples from Tuberculosis Patients by High Resolution Melt Curve Analysis

WHO (2022) Global Tuberculosis Report. WHO (2022) WHO consolidated guidelines on tuberculosis, Module 4: Treatment- Drug-resistant tuberculosis treatment: 2022 update. WHO (2020) Meeting report of the WHO expert consultation on the definition of extensively drug-resistant tuberculosis. Jabeen K, Shakoor S, Hasan R (2015) Fluoroquinolone-resistant tuberculosis: implications in settings with weak…

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Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

Tsudzuki, M. Mutations of Japanese quail (Coturnix japonica) and recent advances of molecular genetics for this species. J. Poult. Sci. 45, 159–179 (2008). CAS  Google Scholar  Recoquillay, J. et al. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genom. 16, 10 (2015)….

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Scientists unearth secrets of the world’s smallest porcupine species

Scientists conducted the first investigation in 22 years into the Roosmalen’s dwarf porcupine, an elusive forest porcupine in Brazil. With the fresh tissue of a new specimen, the scientists used the porcupine’s DNA sequence and physical traits to better trace its relationship to other species. Their discovery shows the porcupines…

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Beginner questions: Working step for organism identification

Kanapol November 30, 2023, 9:57am 1 Hello everyone, I am the beginner for this area of study, and I have no one to ask these simple questions. I want to identify organism using NGS sequencing. I read from tutorial and I known that I have to make contigs and filter…

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EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023 | Nucleic Acids Research

Abstract The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe’s only intergovernmental life sciences organisation. This…

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High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ

Zmora, N., Suez, J. & Elinav, E. You are what you eat: diet, health and the gut microbiota. Nat. Rev. Gastroenterol. Hepatol. 16, 35–56 (2019). Article  CAS  PubMed  Google Scholar  Lamont, R. J., Koo, H. & Hajishengallis, G. The oral microbiota: dynamic communities and host interactions. Nat. Rev. Microbiol. 16,…

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Adipose cDC1s contribute to obesity-associated inflammation through STING-dependent IL-12 production

Ward, Z. J. et al. Projected U.S. state-level prevalence of adult obesity and severe obesity. N. Engl. J. Med. 381, 2440–2450 (2019). Article  PubMed  Google Scholar  Khaodhiar, L., McCowen, K. C. & Blackburn, G. L. Obesity and its comorbid conditions. Clin. Cornerstone 2, 17–31 (1999). Article  CAS  PubMed  Google Scholar …

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Development and evaluation of specific polymerase chain reaction assays for detecting Theileria equi genotypes | Parasites & Vectors

Knowles DP, Kappmeyer LS, Stiller D, Hennager SG, Perryman LE. Antibody to a recombinant merozoite protein epitope identifies horses infected with Babesia equi. J Clin Microbiol. 1992;30:3122–6. CAS  PubMed  PubMed Central  Google Scholar  Ueti MW, Palmer GH, Kappmeyer LS, Statdfield M, Scoles GA, Knowles DP. Ability of the vector tick…

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Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article  Google Scholar  Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…

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Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

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Molecular epidemiology and characteristics of respiratory syncytial virus among hospitalized children in Guangzhou, China | Virology Journal

Falsey AR, Walsh EE. Respiratory syncytial virus infection in adults. Clin Microbiol Rev. 2000;13(3):371–84. Article  CAS  PubMed  PubMed Central  Google Scholar  Walker CLF, Rudan I, Liu L, Nair H, Theodoratou E, Bhutta ZA, O’Brien KL, Campbell H, Black RE. Global burden of childhood pneumonia and diarrhoea. Lancet (London, England). 2013;381(9875):1405–16….

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Improving Species Level-taxonomic Assignment from 16S rRNA Sequencing Technologies

Affiliations Expand Affiliations 1 Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain. 2 ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain. 3 Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute…

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Association between mitochondrial DNA levels and depression: a systematic review and meta-analysis | BMC Psychiatry

Tartt AN, Mariani MB, Hen R, Mann JJ, Boldrini M. Dysregulation of adult hippocampal neuroplasticity in major depression: pathogenesis and therapeutic implications. Mol Psychiatry. 2022;27(6):2689–99. doi.org/10.1038/s41380-022-01520-y Article  CAS  PubMed  PubMed Central  Google Scholar  Friedrich MJ. Depression is the leading cause of disability around the World. JAMA. 2017;317(15):1517. doi.org/10.1001/jama.2017.3826 Article  PubMed …

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Molecular detection and whole genome sequencing of Pectobacterium and Dickeya, the casual agents of soft rot disease in lettuce

Azadmanesh S, Marefat A (2013) and Kayhan Azadmanesh. Detection of Pectobacteria causal agents of potato soft rot in north-western provinces of Iran. J Plant Pathol Microbiol 4(1) Babadoost M (1990) Bacterial soft rot of vegetables, fruits and ornamentals. Rep Plant Dis 943:7 Google Scholar  Ben Fekih I, Zhang C, Li…

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The analysis of the genotype of Sapovirus outbreaks in Zhejiang Province | Virology Journal

Leblanc D, Inglis GD, Boras VF, Brassard J, Houde A. The prevalence of enteric RNA viruses in stools from diarrheic and non-diarrheic people in southwestern Alberta, Canada. Arch Virol. 2017;162(1):117–28. Article  CAS  PubMed  Google Scholar  Becker-Dreps S, González F, Bucardo F. Sapovirus: an emerging cause of childhood diarrhea. Curr Opin…

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Multiple micronutrient deficiencies in early life cause multi-kingdom alterations in the gut microbiome and intrinsic antibiotic resistance genes in mice

Han, X., Ding, S., Lu, J. & Li, Y. Global, regional, and national burdens of common micronutrient deficiencies from 1990 to 2019: a secondary trend analysis based on the Global Burden of Disease 2019 study. eClinicalMedicine 44, 101299 (2022). Article  PubMed  PubMed Central  Google Scholar  Bailey, R. L., West, K….

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Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….

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Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article  CAS  PubMed  Google Scholar  Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…

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Bioconductor – TCGAbiolinks

DOI: 10.18129/B9.bioc.TCGAbiolinks     TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data Bioconductor version: Release (3.5) The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses…

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In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data | BMC Genomics

Bentes B, Martinelli J, Souza L, Cavalcante D, Almeida M, Isaac V. Spatial distribution of the amazon river prawn Macrobrachium Amazonicum (Heller, 1862) (Decapoda, Caridea, Palaemonidae) in two perennial creeks of an estuary on the northern coast of Brazil (Guajará Bay, Belém, Pará). Brazilian J Biol. 2011;71:925–35. Article  Google Scholar …

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Genome interpretation in a federated learning context allows the multi-center exome-based risk prediction of Crohn’s disease patients

Goodwin, S., McPherson, J. D. & Richard McCombie, W. Coming of age: Ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17(6), 333–351 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Van Dijk, E. L., Auger, H., Jaszczyszyn, Y. & Thermes, C. Ten years of next-generation sequencing technology. Trends Genet….

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Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges

Aizawa M, Yoshimaru H, Saito H, Katsuki T, Kawahara T, Kitamura K et al. (2009) Range‐wide genetic structure in a north‐east Asian spruce (Picea jezoensis) determined using nuclear microsatellite markers. J Biogeogr 36(5):996–1007 Article  Google Scholar  Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated…

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Leukaemia Foundation, HSANZ Fund Future Clinicians to Boost Aussie Survival Rates

The Leukaemia Foundation and Haematology Society of Australia and New Zealand (HSANZ) have again partnered to award three of Australia’s brightest blood cancer researchers and clinicians with PhD scholarships. The 2023 recipients were announced last night at the annual Blood conference in Melbourne and include Dr Helen Cashman, Dr Eric…

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The correlation between gut microbiome and atrial fibrillation: pathophysiology and therapeutic perspectives | Military Medical Research

Kim JE, Li B, Fei L, Horne R, Lee D, Loe AK, et al. Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal development. Immunity. 2022;55(12):2300-17.e6. Article  CAS  PubMed  Google Scholar  Xiao W, Su J, Gao X, Yang H, Weng R, Ni W, et al….

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The evolutionary innovation of root suberin lamellae contributed to the rise of seed plants

Fich, E. A., Segerson, N. A. & Rose, J. K. C. The plant polyester cutin: biosynthesis, structure, and biological roles. Annu. Rev. Plant Biol. 67, 207–233 (2016). Article  CAS  PubMed  Google Scholar  Geldner, N. The endodermis. Annu. Rev. Plant Biol. 64, 531–558 (2013). Article  CAS  PubMed  Google Scholar  Calvo-Polanco, M….

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Molecular diagnosis, phylogenetic analysis, and antifungal susceptibility profiles of Candida species isolated from neutropenic oncological patients | BMC Infectious Diseases

Eissa S, Khedr R, Romeih M, Halaby L, Elanany M, Madney Y. Clinical characteristics and outcome of invasive fungal sinusitis in children with hematological malignancies. Med Mycol. 2022;60(4):myac010. Article  PubMed  Google Scholar  Lin G-L, Chang H-H, Lu C-Y, Chen C-M, Lu M-Y, Lee P-I, Jou S-T, Yang Y-L, Huang L-M,…

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Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection

Shreiner, A. B., Kao, J. Y. & Young, V. B. The gut microbiome in health and in disease. Curr. Opin. Gastroenterol. 31, 69–75. doi.org/10.1097/Mog.0000000000000139 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Selber-Hnatiw, S. et al. Human gut microbiota: Toward an ecology of disease. Front. Microbiol. 8, 1265. doi.org/10.3389/fmicb.2017.017E5 (2017)….

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Metagenomic analysis of the microbial community in kefir grains from different milk sources

Bengoa AA, Iraporda C, Garrote GL, Abraham AG. 2019. Kefir micro?organisms: their role in grain assembly and health properties of fermented milk. Journal of applied microbiology 126:686-700.doi.org/10.1111/jam.14107. Biçer Y, Telli AE, Sönmez G, Turkal G, Telli N, Uçar G. 2021. Comparison of commercial and traditional kefir microbiota using metagenomic analysis….

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DNA damage response(DDR): a link between cellular senescence and human cytomegalovirus | Virology Journal

Hayflick L, Moorhead PS. The serial cultivation of human diploid cell strains. Exp Cell Res. 1961;25:585–621. Article  CAS  PubMed  Google Scholar  Hayflick L. THE LIMITED IN VITRO LIFETIME OF HUMAN DIPLOID CELL STRAINS. Exp Cell Res. 1965;37:614–36. Article  CAS  PubMed  Google Scholar  Schmitt CA, Tchkonia T, Niedernhofer LJ, Robbins PD,…

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Exploratory Data Analysis and Prediction of Human Genetic Disorder and Species Using DNA Sequencing

Sanders, S.J.: First glimpses of the neurobiology of autism spectrum disorder. Curr. Opin. Genet. Dev. 33, 80–92 (2015) CrossRef  Google Scholar  Schizophrenia working group of the psychiatric genomics consortium: biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014) Google Scholar  Jamie, P., et al.: Global, regional, and national…

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IL-1R8 expression in DLBCL regulates NK cell recruitment and influences patient prognosis

Al-Mterin MA, Murshed K, Elkord E (2022) PD-1 expression, among other immune checkpoints, on tumor-infiltrating NK and NKT cells is associated with longer disease-free survival in treatment-naive CRC patients. [Journal Article]. Cancer Immunol Immunother. doi.org/10.1007/s00262-022-03337-8 Baecklund E, Smedby KE, Sutton LA, Askling J, Rosenquist R (2014) Lymphoma development in patients…

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Human remains ID’d 50 years after found in CA bay, cops say

Arminda Grangeia Rodrigues da Silva Ribeiro’s remains were found by fishermen June 13, 1973, in the San Diego Bay in California. DNA testing identified her remains 50 years later. Fishermen found a woman’s dismembered remains in an orange suitcase in a California bay 50 years ago, police said. DNA testing…

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The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum

Ethics approval and consent to participate The study was approved by the Human Research Ethics Committees of the Children’s Hospital of Soochow University (Reference 2020CS017). All specimens were collected according to the guidelines set by the Children’s Hospital of Soochow University. All authors confirm that all methods were performed in…

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Decoding Life’s Secrets: Researchers Solve Protein Mystery

Proteins in human cells commonly undergo N-terminal acetylation, a modification by the enzyme group N-terminal acetyltransferases (NATs), the function of which has been largely mysterious. Recent research using CRISPR-Cas9 technology and collaborative studies in fruit flies reveal that this modification protects proteins from degradation, playing a crucial role in longevity…

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Higher abundance of Campylobacter in the oral microbiome of Japanese patients with moyamoya disease

A flow diagram of the study is shown in Fig. 3. Figure 3 Flow diagram of the study. Ethical approval and consent to participant This study was approved by the Institutional Review Board of the Nagoya University Graduate School of Medicine (approval number 2022-0084; approval date, June 3, 2022). Written informed…

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Seasonal dynamics of Amblyomma cajennense (Fabricius, 1787) sensu stricto in a degraded area of the Amazon biome, with notes on Rickettsia amblyommatis infection | Parasites & Vectors

Szabó MPJ, Pinter A, Labruna MB. Ecology, biology and distribution of spotted-fever tick vectors in Brazil. Front Cell Infect Microbiol. 2013;3:27. Article  PubMed  PubMed Central  Google Scholar  Luz HR, Costa FB, Benatti HR, Ramos VN, Serpa A, Martins MC, et al. Epidemiology of capybara-associated Brazilian spotted fever. PLoS Neg Trop…

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Researchers Uncover the Answer to Protein Mystery

Register for free to listen to this article Thank you. Listen to this article using the player above. ✖ Want to listen to this article for FREE? Complete the form below to unlock access to ALL audio articles. Proteins are key to all processes in our cells…

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Mitochondrial DNA copy number is associated with incident chronic kidney disease and proteinuria in the AIDS linked to the intravenous experience cohort

Chronic Kidney Disease in the United States, 2021. www.cdc.gov/kidneydisease/publications-resources/ckd-national-facts.html. Saran, R. et al. US renal data system 2019 annual data report: Epidemiology of kidney disease in the United States. Am. J. Kidney Dis. 75, A6–A7 (2020). Article  PubMed  Google Scholar  Matsushita, K. et al. Epidemiology and risk of cardiovascular disease…

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Leishmania genetic exchange is mediated by IgM natural antibodies

Rapaka, R. R. et al. Conserved natural IgM antibodies mediate innate and adaptive immunity against the opportunistic fungus Pneumocystis murina. J. Exp. Med. 207, 2907–2919 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Boehm, T., Iwanami, N. & Hess, I. Evolution of the immune system in the lower vertebrates. Annu….

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Age and severity-dependent gut microbiota alterations in Tunisian children with autism spectrum disorder

Hodges, H., Fealko, C. & Soares, N. Autism spectrum disorder: definition, epidemiology, causes, and clinical evaluation. Transl. Pediatr. 9, 55–65 (2020). Article  Google Scholar  Fombonne, E., MacFarlane, H. & Salem, A. C. Epidemiological surveys of ASD: Advances and remaining challenges. J. Autism Dev. Disord. 51, 4271–4290 (2021). Article  PubMed  Google…

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Safety and Immunogenicity of an In Vivo Muscle Electroporation Delivery System for DNA-hsp65 Tuberculosis Vaccine in Cynomolgus Monkeys[v1]

Cite MDPI and ACS Style Lima, M.R.D.; Leandro, A.C.C.; Souza, A.L.; Barradas, M.M.; Roma, E.H.; Fernandes, A.T.G.; Galdino-Silva, G.; Carvalho, J.K.M.R.; Marchevisky, R.S.; Coelho, J.M.C.O.; Gonçalves, E.D.C.; VandeBerg, J.L.; Silva, C.L.; Bonecini-Almeida, M.D.G. Safety and Immunogenicity of an In Vivo Muscle Electroporation Delivery System for DNA-hsp65 Tuberculosis Vaccine in Cynomolgus…

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Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica)

Aguilera F, McDougall C, Degnan BM (2017) Co-option and de novo gene evolution underlie molluscan shell diversity. Mol Biol Evol 34(4):779–792 CAS  PubMed  PubMed Central  Google Scholar  Alexa A, Rahnenfuhrer J (2020) topGO: Enrichment analysis for gene ontology. R package version 2.40.0 Google Scholar  Arivalagan J, Yarra T, Marie B,…

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Macrophage polarization and metabolism in atherosclerosis

Organization WH the top 10 causes of death. www.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death, 2019. Rana JS, Khan SS, Lloyd-Jones DM, Sidney S. Changes in mortality in Top 10 causes of death from 2011 to 2018. J Gen Intern Med. 2021;36:2517–8. Article  PubMed  Google Scholar  Libby P. The changing landscape of atherosclerosis. Nature. 2021;592:524–33. Article …

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After 50 years, Coast Guard Jane Doe is Identified

Summary In June 1973, at approximately 11:20 a.m., fishermen found the body of an unidentified female in the San Diego Bay between Laurel Street and the US Coast Guard Station. The woman’s body had been dismembered and placed into an orange suitcase and several plastic bags. An autopsy revealed the…

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Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing

Phuangkum, P., Lair, R. C. & Angkawanith, T. Elephant Care Manual for Mahouts and Camp Managers (FAO Regional Office for Asia and the Pacific, 2005). Google Scholar  Sukumar, R. The Asian Elephant: Ecology and Management (Cambridge University Press, 1992). Google Scholar  Bansiddhi, P., Brown, J. L., Thitaram, C., Punyapornwithaya, V….

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Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers | Parasites & Vectors

Machado-Ferreira E, Vizzoni VF, Balsemao-Pires E, Moerbeck L, Gazeta GS, Piesman J, et al. Coxiella symbionts are widespread into hard ticks. Parasitol Res. 2016;115:4691–9. doi.org/10.1007/s00436-016-5230-z. Article  PubMed  Google Scholar  Jung M, Kho JW, Lee WG, Roh JY, Lee DH. Seasonal occurrence of Haemaphysalis longicornis (Acari: Ixodidae) and Haemaphysalis flava, vectors…

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Cingulate to Host CNS Key Opinion Leader Panel in New York City

KANSAS CITY, Kan., Oct. 17, 2023 (GLOBE NEWSWIRE) — Cingulate Inc. (NASDAQ: CING) , a biopharmaceutical company utilizing its proprietary Precision Timed Release™ (PTR™) drug delivery platform technology to build and advance a pipeline of next-generation pharmaceutical products, announced today that it will be hosting a key opinion leader event…

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Distinct non-synonymous mutations in cytochrome b highly correlate with decoquinate resistance in apicomplexan parasite Eimeria tenella | Parasites & Vectors

Chapman HD, Rathinam T. Focused review: the role of drug combinations for the control of coccidiosis in commercially reared chickens. Int J Parasitol Drugs Drug Resist. 2022;18:32–42. PubMed  PubMed Central  Google Scholar  Peek HW, Landman WJM. Coccidiosis in poultry: anticoccidial products, vaccines and other prevention strategies. Vet Q. 2011;31:143–61. CAS …

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XRCC1 R194W and R399Q Polymorphisms and Colorectal Cancer Risk in a Northeastern Mexican Population

. 2023 Oct 4:2023:5565646. doi: 10.1155/2023/5565646. eCollection 2023. Affiliations Expand Affiliations 1 Facultad de Medicina e Ingeniería en Sistemas Computacionales de Matamoros, Universidad Autónoma de Tamaulipas, Sendero Nacional km 3, CP 87349, Col. San José, Matamoros, Tamaulipas, Mexico. 2 Centro Universitario del Sur, Universidad de Guadalajara, Av. Enrique Arreola Silva…

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HK2 contributes to the proliferation, migration, and invasion of diffuse large B-cell lymphoma cells by enhancing the ERK1/2 signaling pathway

References [1] Thandra KC, Barsouk A, Saginala K, Padala SA, Barsouk A, Rawla P. Epidemiology of Non-Hodgkin’s Lymphoma. Med Sci (Basel). 2021 Jan 30;9(1):5.10.3390/medsci9010005Search in Google Scholar PubMed PubMed Central [2] Mafra A, Laversanne M, Gospodarowicz M, Klinger P, De Paula Silva N, Piñeros M, et al. Global patterns of…

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Bacterial networks in Atlantic salmon with Piscirickettsiosis

Verschuere, L., Rombaut, G., Sorgeloos, P. & Verstraete, W. Probiotic bacteria as biological control agents in aquaculture. Microbiol. Mol. Biol. Rev. 64(4), 655–671 (2000). Article  CAS  PubMed  PubMed Central  Google Scholar  Gomez, G. D. & Balczar, J. L. A review on the interactions between gut microbiota and innate immunity of…

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Ardelyx to Present Data Updates for XPHOZAH (tenapanor) for Hyperphosphatemia at Kidney Week 2023 November 1-5 in Philadelphia, PA

Ardelyx, Inc. WALTHAM, Mass., Oct. 13, 2023 (GLOBE NEWSWIRE) — Ardelyx, Inc. (Nasdaq: ARDX), a biopharmaceutical company founded with a mission to discover, develop and commercialize innovative, first-in-class medicines that meet significant unmet medical needs, today announced upcoming data presentations for tenapanor for hyperphosphatemia at the American Society of Nephrology…

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The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection | Genome Biology

Dawson SJ, Tsui DWY, Murtaza M, Biggs H, Rueda OM, Chin SF, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013;368:1199–209. Massachusetts Medical Society. Article  CAS  PubMed  Google Scholar  van der Pol Y, Mouliere F. Toward the early detection of cancer by…

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Mitochondrial SOS: how mtDNA may act as a stress signal in Alzheimer’s disease

Review doi: 10.1186/s13195-023-01322-6. Affiliations Expand Affiliations 1 Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA. 2 Department of Family Medicine, Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA. 3…

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Mitochondrial SOS: how mtDNA may act as a stress signal in Alzheimer’s disease | Alzheimer’s Research & Therapy

2021 Alzheimer’s disease facts and figures – 2021 – Alzheimer’s & Dementia – Wiley Online Library. Available from: alz-journals.onlinelibrary.wiley.com/doi/doi.org/10.1002/alz.12328. [Cited 2022 Nov 13]. Jack CR, Bennett DA, Blennow K, Carrillo MC, Dunn B, Haeberlein SB, et al. NIA-AA research framework: toward a biological definition of Alzheimer’s disease. Alzheimers Dement J…

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Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Anderson, P. K. et al. Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19, 535–544. doi.org/10.1016/j.tree.2004.07.021 (2004). Article  PubMed  Google Scholar  Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012). Article  ADS  CAS  PubMed …

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Diabetic Foot Ulcer and the Bacterial Colony of the Skin

Introduction Diabetes is a growing public health problem with increasing prevalence and mortality that threatens the health of people globally.1 In 2021, the global prevalence of diabetes in adults aged 20 to 79 years was estimated at 537 million, mainly caused by type 2 diabetes, and the number is expected…

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Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium

Rabus, R., Hansen, T. A. & Widdel, F. In Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes. The Prokaryotes: Prokaryotic Physiology and Biochemistry, Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., and Thompson F. at (2013). Rabus, R. et al. Chapter Two—A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing…

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feature-classifier not producing an output – Technical Support

Hello, I have a problem with the feature classifier.So I tried this on multiple computers (with intel and AMD chips) and with multiple versions of QIIME2 (QIIME2 2023.5 and 2023.7)So I have a dual boot on my computer with Windows and Linux Ubuntu, newest release. It has 16 GB of…

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Qiime2 unable to perform ADONIS on multiple variable – Technical Support

Hello,I’ve previously used fragment-insertion plugin without any issues. However, recently as I’m trying generate the tree using rep_seq file generated from vsearch open-reference clustering. I’m getting the following error from the this plugin. And the log file says- Removing /tmp/tmp.etXzw1y7jQ/sepp-tmp-CaHDDnOVOTTraceback (most recent call last):File “/home/turtle/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py”, line 352, in callresults =…

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The recovery of the microbial community after plaque removal depends on periodontal health status

Jin, L. & Group, E. Initiator paper. Interprofessional education and multidisciplinary teamwork for prevention and effective management of periodontal disease. J. Int. Acad. Periodontol. 17, 74–79 (2015). PubMed  Google Scholar  Kassebaum, N. J. et al. Global burden of severe periodontitis in 1990–2010: a systematic review and meta-regression. J. Dent. Res….

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Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

Review doi: 10.1111/omi.12434. Online ahead of print. Affiliations Expand Affiliation 1 Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain. Item in…

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Polymorphisms of DNA repair genes XRCC1 and XRCC3, interaction with environmental exposure and risk of chronic gastritis and gastric cancer

The server is under maintenance between 08:00 to 12:00 (GMT+08:00), and please visit later. We apologize for any inconvenience caused Polymorphisms of DNA repair genes XRCC1 and XRCC3, interaction with environmental exposure and risk of chronic gastritis and gastric cancer Author(s): Márcia Cristina Duarte, Jucimara Colombo,…

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The Therapeutic Effects of MUC1-C shRNA@Fe3O4 Magnetic Nanoparticles i

Introduction Breast cancer (BC) is a malignant tumor originating from the epithelial tissue of the breast and is the most common malignancy in women.1 It is estimated that by 2040, there will be 3,000,000 new cases of BC and 100,000 deaths worldwide. Triple-negative breast cancer (TNBC), which accounts for 15–20%…

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First-tier detection of intragenomic 16S rRNA gene variation in…

Abstract Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria…

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Kraken2 is falsely assigning Klebsiella

Kraken2 is falsely assigning Klebsiella 1 Hi everyone! I’ve been running Kraken on a couple of clinical related samples (metagenomes) using Kraken2/Bracken using the silva Database. As a sanity check I run the same workflow on a mock community (SRR8073716) using different confidence values (0.1, 0.3 and 0.5). The classification…

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Protistan predation selects for antibiotic resistance in soil bacterial communities

Courtenay M, Castro-Sanchez E, Fitzpatrick M, Gallagher R, Lim R, Morris G. Tackling antimicrobial resistance 2019-2024–the UK’s five-year national action plan. J Hosp Infect. 2019;101:426–7. Article  CAS  PubMed  Google Scholar  D’Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, et al. Antibiotic resistance is ancient. Nature. 2011;477:457–61….

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Identification of eQTL from porcine muscle and liver mRNA sequencing

Master’s Dissertation DOI doi.org/10.11606/D.11.2023.tde-02102023-151405 Document Author Freitas, Felipe André Oliveira (Catálogo USP) Full name Felipe André Oliveira Freitas E-mail Institute/School/College Escola Superior de Agricultura Luiz de Queiroz Knowledge Area Animal Science and Pastures Date of Defense Published Piracicaba, 2023 Supervisor Cesar, Aline Silva Mello (Catálogo USP) Committee Cesar, Aline Silva…

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18S taxonomy assignment SILVA database formatting

Hi Bioinformatic community, I would like to classify 18S data (V7) of Fungi with assignTaxonomy from dada2. For that I downloaded SILVA_132_SSURef_tax_silva.fasta.gz from the SILVA website and need to format it, what I do with some Linux command line oneliner. But some species in the database have a different number…

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Study on mysterious Amazon porcupine can help its protection

Credit: Menezes et al. Porcupines of the genus Coendou are arboreal, herbivorous, nocturnal rodents distributed in tropical and subtropical regions of the Americas. Most of what we currently know on them is restricted to species that occur near urban areas, and we still have a lot to learn about these…

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Construction & assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data

Abstract Background & objectives: For bacterial community analysis, 16S rRNA sequences are subjected to taxonomic classification through comparison with one of the three commonly used databases [Greengenes, SILVA and Ribosomal Database Project (RDP)]. It was hypothesized that a unified database containing fully annotated, non-redundant sequences from all the three databases,…

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Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing

Soil incubation and cell extraction Approximately 3 kg of unmanaged marginal soil (pH 8) was collected from the Pacific Northwest National Laboratory field site in Prosser, Washington (46° 15′ 04″ N and 119° 43′ 43″ W) [23], homogenized, sieved (4 mm mesh size), and stored at 4 °C until further processing. Probe specific…

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Molecular classification of hormone receptor-positive HER2-negative breast cancer

Siegel, R. L., Miller, K. D. & Jemal, A. Cancer statistics, 2020. CA Cancer J. Clin. 70, 7–30 (2020). Article  PubMed  Google Scholar  Huppert, L. A., Gumusay, O., Idossa, D. & Rugo, H. S. Systemic therapy for hormone receptor-positive/human epidermal growth factor receptor 2-negative early stage and metastatic breast cancer….

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Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats

Jayanthi, S., McCoy, M. T. & Cadet, J. L. Epigenetic Regulatory Dynamics in Models of Methamphetamine-Use Disorder. Genes 12, 1614 (2021). Article  CAS  Google Scholar  Meredith, C. W., Jaffe, C., Ang-Lee, K. & Saxon, A. J. Implications of chronic methamphetamine use: a literature review. Harv. Rev. Psychiatry 13, 141–154 (2005)….

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