Tag: SILVA

Screen.seqs result varying – Commands in mothur

I have a data set of 2×150 reads of 54 pairs of 16S v4 metagenomic sequences from NCBI sra of gastritis patients. When I previously ran the sequences through mothur, the screen.seqs after silva alignment removed sufficient number of sequences. mothur > screen.seqs(fasta=current, count=current, start=2, end=13426)Using Ulcer_Donors\stability.trim.contigs.count_table as input file…

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Breast Reconstruction with Inferior Flap and Fat Transfer as Curative Treatment for BIA-ALCL

Araco A, Gravante G, Araco F, Delogu D, Cervelli V, Walgenbach K. A retrospective analysis of 3,000 primary aesthetic breast augmentations: postoperative complications and associated factors. Aesthet Plast Surg. 2007;31(5):532–9. doi.org/10.1007/s00266-007-0162-8. CAS  CrossRef  Google Scholar  Nahabedian MY, Patel K. Management of common and uncommon problems after primary breast augmentation. Clin…

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A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens

Gadde, U., Kim, W. H., Oh, S. T. & Lillehoj, H. S. Alternatives to antibiotics for maximizing growth performance and feed efficiency in poultry: a review. Animal Health Res. Rev. 18, 26–45 (2017). CAS  Google Scholar  Smits, C. H. M., Li, D., Patience, J. F. & den Hartog, L. A….

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Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Fricke, R., Eschmeyer, W. N. & van der Laan, R. (eds). Eschmeyer’s Catalog of Fishes: Genera, Species, Rererences. researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version, Accessed 15 October 2021. Nelson, J. S. Fishes of the World 4th edn, 372 (Wiley, 2006). Google Scholar  Chen, X. H., Lin, K. B. & Wang, X. W. Outbreaks…

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The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs

Avise, J. C., 2009. Phylogeography: Retrospect and prospect. Journal of Biogeography, 36: 3–15. Article  Google Scholar  Beheregaray, L. B., 2008. Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17: 3754–3774. Google Scholar  Clement, M., Posada, D., and Crandall, K. A.,…

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Predict Functional potential microbial communities

Predict Functional potential microbial communities – phyloseq Silva 0 Hi, Does anyone have good tutorials/resources on how to predict the metabolic potential from microbiome data. I have preprocessed using DADA2, resulting in a phyloseq object. I assigned taxonomy with SILVA database. I found this Tax4fun package in R implemented in…

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A core genome MLST (cgMLST) scheme for Mycobacterium abscessus complex subspecies

Dataset for manuscript “The use of comparative genomic analysis for the development of subspecies-specific PCR assays for the Mycobacterium abscessus complex” by Winifred Akwani et al. A core genome MLST scheme was developed for Mycobacterium abscessus complex (MABC) subspecies M. abscessus, M. bolletii and M. massiliense, using chewBBACA version 2.8.5…

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dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy

1. Dunbar, C. E. et al. Gene therapy comes of age. Science 359, eaan4672 (2018). PubMed Google Scholar  2. Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS PubMed PubMed Central Google Scholar  3. Eid, A.,…

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Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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18S gene not present in genome assembly?

18S gene not present in genome assembly? 0 I am designing PCR primers to amplify a region of the 18S rRNA gene of Penicillium expansum. As the template for primer design, I use the consensus sequence of a multiple sequence alignment of 18S sequences obtained from the SILVA database. When…

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Using reverse-complement or just complement of SILVA database to filter rRNA from metatranscriptomics

Using reverse-complement or just complement of SILVA database to filter rRNA from metatranscriptomics 0 I want to use SILVA database to filter rRNA from metatranscriptomics. The nucleobases in the SILVA fasta file are A, U, C and G. Therefore, before indexing the SILVA fasta file, should I get the reverse-complement…

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Running SortMeRNA on Multiple Files

Running SortMeRNA on Multiple Files 0 Hi all, I am VERY new to SortMeRNA (I’m a PhD student taking a bioinformatics class that has been very poorly taught). I have 27 paired samples for a total of 54 samples named like this: SRR13711719_1_val_1.fq SRR13711719_2_val_2.fq. So the format is _1_val_1.fq and…

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Is there a way to find the GWAS traits to a gene programmatically?

Is there a way to find the GWAS traits to a gene programmatically? 0 Hello folks, I would like to use a gene name (e.g. DOCK2) or its ENSEMBL ID as input, and get as output the reported GWAS traits to the respective gene. I did give a look into…

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BernardoGG/SARS-CoV-2_Genomic_lineages_Ecuador: Identification and analysis of the early transmission dynamics, importations and local circulation of SARS-CoV-2 in Ecuador inferred from genomic data.

Identification and analysis of the early transmission dynamics, importations and local circulation of SARS-CoV-2 in Ecuador inferred from genomic data. Bernardo Gutierrez1,2, Sully Márquez3, Belén Prado-Vivar3, Mónica Becerra-Wong3, Juan José Guadalupe4, Darlan da Silva Candido1, Juan Carlos Fernandez-Cadena5, Gabriel Morey-Leon6, Rubén Armas-Gonzalez7, Derly Madeleiny Andrade-Molina5, Alfredo Bruno8,9, Domenica de Mora8,…

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How to map SILVA taxa names to NCBI IDs (in R)?

How to map SILVA taxa names to NCBI IDs (in R)? 0 Hi, How to map taxonomy assigned using SILVA database to NCBI ID (preferably in R)? I’m using R Dada2 and SILVA database to assign taxonomy: Bacteria > Firmicutes > Bacilli > Lactobacillales > Enterococcaceae > Enterococcus I need…

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Future ‘Exceedingly Bright’ for Kidney Stone Prevention

Gene therapy, new therapeutics currently in clinical trials, and a promising dietary supplement are feeding the optimism of kidney stone expert Glenn Preminger, MD. Glenn Preminger “The future of kidney stones looks exceedingly bright,” said Preminger, professor of urology at Duke University in Durham, North Carolina, during his lecture at…

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Identification of immunodominant Bartonella bacilliformis proteins: a combined in-silico and serology approach

Introduction Carrión’s disease is a vector-borne biphasic illness restricted to the South American Andes, with Peru as the most affected country. 1 Gomes C Pons MJ Del Valle Mendoza J Ruiz J Carrion’s disease: an eradicable illness?. The causative agent, Bartonella bacilliformis, is transmitted to humans by sandflies (Lutzomyia spp)….

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

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Bioconductor – cageminer (development version)

DOI: 10.18129/B9.bioc.cageminer     This is the development version of cageminer; to use it, please install the devel version of Bioconductor. Candidate Gene Miner Bioconductor version: Development (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users…

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Plasmid-Encoded VIM-2-pProducing Pseudomonas stutzeri | IDR

Introduction Pseudomonas stutzeri is an aerobic, nonfermenting, active, Gram-negative oxidase-positive bacterium with unique colony morphology.1,2 Burri and Stutzer first described it in 1985,3 and the specific metabolic properties, such as denitrification, degradation of aromatic compounds, and nitrogen fixation, distinguish it from other pseudomonads species.2,4 Historically, P. stutzeri was not commonly…

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