Categories
Tag: relatedness
Different relatedness estimates by PLINK and VCFTOOLS despite same method
According to the vcftools manual, specifying the “–relatedness2” flag allows calculating relatedness statistics using the method by Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559). That is, based on KING. According to the PLINK manual, PLINK uses the same method to calculate relatedness when specifying the flag “–make-king-table”. So, although both PLINK…
Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing | Antimicrobial Resistance & Infection Control
Isolate characteristics From June 2020 to October 2021, our analysis included a total of 28 isolates from patient and environmental samples, all subjected to Whole Genome Sequencing (WGS) (refer to Table 1). To ensure robustness and minimize the influence of sequencing errors on our findings, all 28 WGS datasets maintained a…
Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population
Kershaw, F. et al. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conserv. Sci. Pract. 4, e12635 (2022). Article Google Scholar Waits, L. P. & Paetkau, D. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations…
Whole Genome Sequencing (WGS) Program
Whole genome sequencing (WGS) is a cutting-edge technology that FDA has put to a novel and public health-promoting use. FDA is laying the foundation for the use of whole genome sequencing to protect consumers from foodborne illness in countries all over the world. On this page: Introduction Whole genome sequencing…
Relatedness and GWAS False Signals
Relatedness and GWAS False Signals 1 I have just realized that a GWAS that I ran sadly included related individuals (the flagged samples file that came with the dataset did not include relatedness). As relatedness is expected to increase false positives, is it reasonable to solely rerun the GWAS on…
A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Animals All experimental procedures were performed in compliance with animal protocols approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol no. 20-05-4165 R). Mice were provided with food and water ad libitum, housed on a 12-hour light/dark schedule (7 a.m.–7 p.m. light period) with no more than five mice…
Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis
Whole genome sequencing and analysis To understand the mechanisms underlying the biological control capability of bacterial pathogens, the complete genome of MEP218 was sequenced, assembled, and deposited in the GenBank database under the accession number CP042864.2. The genome of MEP218 consists of a single circular chromosome of 3,944,892 bp with a…
Indigenous Australian genomes show deep structure and rich novel variation
Inclusion and ethics The DNA samples analysed in this project form part of a collection of biospecimens, including historically collected samples, maintained under Indigenous governance by the NCIG11 at the John Curtin School of Medical Research at the Australian National University (ANU). NCIG, a statutory body within ANU, was founded…
MAPS PBC Announces Submission of New Drug Application to the FDA for MDMA-Assisted Therapy for PTSD
Filing marks first NDA submission for any psychedelic-assisted therapy Submission represents 30 plus years of clinical research into potential use of MDMA-assisted therapy for PTSD NDA includes two Phase 3 trials (MAPP1 and MAPP2) that both met primary and secondary endpoints …
An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes | BMC Infectious Diseases
When compared to the genomes of other RNA viruses, coronaviruses have been found to possess largest genome sizes. They are capable of establishing reservoirs in both human and zoonotic populations, enabling their transmission and circulation among a range of animal hosts, including bats, pangolins, civets, cats, mice, pigs, whales, dogs,…
Genetic architecture of cardiac dynamic flow volumes
Virani, S. S. et al. Heart disease and stroke statistics-2021 update: a report from the American Heart Association. Circulation 143, e254–e743 (2021). Article PubMed Google Scholar Nauffal, V. et al. Genetics of myocardial interstitial fibrosis in the human heart and association with disease. Nat. Genet. 55, 777–786 (2023). Article CAS …
Multiple host colonization and differential expansion of multidrug-resistant ST25-Acinetobacter baumannii clades
Features of animal and human isolates of this study On average, sequencing of isolates of this study generated 2.36 M of reads per genome, with an estimated genome size of 4.2 M bases, with a coverage depth of 204X (Table S1). Animal isolates included in this study (n = 33) were found mostly in…
Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath
Bacterial strains We used P. putida strains S12, DOT-T1E, F1 (kindly gifted by Grant Rybnicky), ATCC 12633 (purchased from ATCC), JUb85 (kindly provided by Samuel Buck), EM383 (kindly gifted by Huseyin Tas), p106 (kindly provided by Carey-Ann Burnham), and KT2440 (obtained from lab stocks). An overnight culture of each P….
Relatedness of human races – RELATEDNESS OF HUMAN RACES Mikayla Buchanan 12. BIOL 2610L INTRODUCTION
Preview text RELATEDNESS OF HUMAN RACES Mikayla Buchanan 12. BIOL 2610L INTRODUCTION Within a species, there can be subspecies that are of the same species but are genetically different enough not to be the same. For example, Chimpanzees have subspecies that differ by the region they live in and the…
How much is 1% of your DNA?
How much is 1% of your DNA? DNA, or deoxyribonucleic acid, is the genetic material that carries the instructions for the development and functioning of all living organisms. It is composed of four chemical bases: adenine (A), cytosine (C), guanine (G), and thymine (T). These bases form pairs, creating the…
Solved You are given a list of seven 16S rRNA gene sequences
You are given a list of seven 16S rRNA gene sequences (below) from unknown organisms. Based on the instructions below go to Genbank and identify them. Then Google or go to the original publication that describe the organism to find out what each is famous for (for example “fixes nitrogen”,…
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)….
Music compensates for altered gene expression in age-related cognitive disorders
Global impact of music on the human transcriptome We first aimed at quantifying the global effect of music on the transcriptomes of the two groups of donors separately. ACD patients exposed to music showed 2.3 times more DEGs (n = 2605) than controls (n = 1148); Table 2. Moreover, while the proportion up-regulated/down-regulated DEGs…
What is the advantage of having multiple copies of the 16S rRNA gene in bacteria?
Is the 16S rRNA gene the only sporulating gene in human microbiome?5 answersThe 16S rRNA gene is not the only sporulating gene in the human microbiome. The abstracts do not mention anything about the presence or absence of sporulating genes in the human microbiome. How long is the 16s rRNA…
Why rRNA is used for identification?
Why is strain identification for labeling accuracy of probiotic products important?5 answersStrain identification for labeling accuracy of probiotic products is important because probiotic health benefits are strain-specific. Different strains of probiotics have different effects on human health, and therefore it is crucial to include the correct strains in probiotic products…
Bioconductor Code: SNPRelate
SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ==== ![GPLv3](http://www.gnu.org/graphics/gplv3-88×31.png) [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![R](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml/badge.svg)](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…
Investigation of antimicrobial susceptibility and genetic diversity among Staphylococcus pseudintermedius isolated from dogs in Rio de Janeiro
Devriese, L. A. et al. Staphylococcus pseudintermedius sp. nov., a coagulase-positive species from animals. Int. J. Syst. Evol. Microbiol. 1569–1573. doi.org/10.1099/ijs.0.63413-0 (2005). Gharsa, H. et al. Antimicrobial resistance, virulence genes, and genetic lineages of Staphylococcus pseudintermedius in healthy dogs in Tunisia. Microb. Ecol. 66, 363–368 (2013). Article CAS PubMed Google…
Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus
Bacteriophage isolation Streptomyces phages Vanseggelen and Verabelle were isolated from a soil sample obtained from the National Park Zuid-Kennemerland in the Netherlands (N52° 23′ 31″, E4° 34′ 49″) using Streptomyces coelicolor as the host. Details on isolation procedures are reported previously in detail12. The collected phage stock solutions were stored…
Global perspective of environmental distribution and diversity of Perkinsea (Alveolata) explored by a meta-analysis of eDNA surveys
Phylogenetic classification of environmental Perkinsea sequences Using a phylogenetic approach, we investigated the diversity and community structure of Perkinsea ASV sequences retrieved from the published EukBank dataset37. We first conducted a phylogenetic analysis using a reference tree derived from an alignment of 1790 characters, which included representative alveolate groups and…
Mitochondrial DNA and human mitochondrial diseases – Mitochondrial DNA and human mitochondrial
Mitochondrial DNA and human mitochondrial diseases Mitochondria are organelles found in nearly all eukaryotic cells that are responsible for producing energy in the form of ATP through oxidative phosphorylation. Mitochondrial DNA (mtDNA) is a small, circular genome that is located within the mitochondria and is inherited maternally. Mutations in mtDNA…
Which Career Combines DNA Technology And Agriculture
The Importance of DNA Technology in Agriculture DNA technology has revolutionized the agricultural industry by providing innovative solutions to increase crop productivity, improve livestock health, and enhance overall agricultural sustainability. This powerful tool allows scientists to gain a deeper understanding of the genetic makeup of plants and animals, enabling targeted…
Why is it difficult to distinguish streptomyces species using 16S rRNA gene sequencing?
The 16S rRNA gene sequencing is insufficient to distinguish closely related Streptomyces species due to the large size of the Streptomyces genus. Strains with identical 16S rRNA gene sequences can have markedly different properties and be classified as different species. Multilocus sequence analysis (MLSA) based on atpD, gyrB, recA, rpoB,…
Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance
De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…
Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders
Kessler, R. C. et al. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Arch. Gen. Psychiatry 62, 593–602 (2005). Article PubMed Google Scholar Kessler, R. C. et al. Prevalence, persistence, and sociodemographic correlates of DSM-IV disorders in the National Comorbidity Survey Replication Adolescent Supplement….
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…
Fonsecaea monophora causing cerebral phaeohyphomycosis
Introduction Phaeohyphomycosis (PHM) is a group of superficial and deep mycoses, including central nervous system (CNS) infections, pulmonary infections, cutaneous and subcutaneous infections, associated with high mortality and caused by dematiaceous fungi that have brown-pigmented cell walls due to the formation of melanin.1,2 Previously, fungal brain infections generally occurred in…
Mutational spectra are associated with bacterial niche
Bacteria exhibit diverse mutational spectra Using a specifically-developed open-source bioinformatic tool, MutTui (github.com/chrisruis/MutTui), we analysed whole genome sequence alignments and phylogenetic trees to reconstruct single base substitution (SBS) mutational spectra of 84 phylogenetic clades from 31 diverse bacterial species representing a broad range of phylogenetic diversity and replication sites (Figs. S1…
Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing
Study population We included 67,390 participants from 19 TOPMed studies: Genetics of Cardiometabolic Health in the Amish (n = 1,109) (ref. 32), Atherosclerosis Risk in Communities Study (n = 3,780) (ref. 33), Barbados Genetics Asthma Study (n = 980), Mount Sinai BioMe Biobank (n = 9,392) (ref. 34), Coronary Artery Risk Development in Young Adults (n = 3,293) (ref. 35),…
Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock
A total of 178 samples were collected from livestock production systems and were screened for Enterococcus using bile esculin azide agar selective media. Based on the phenotypic colony morphology of brown and a black halo shape, 24 isolates (13.5%) were presumptively identified as Enterococcus spp. The isolates were identified using…
[Solved] How is genomic fingerprinting similar to rRNA sequence analysis – Microbiology (MICB01)
Genomic Fingerprinting vs rRNA Sequence Analysis Genomic fingerprinting and rRNA sequence analysis are both molecular techniques used in the field of genetics to study and compare organisms. While they have similarities, they also have distinct differences. Similarities Both genomic fingerprinting and rRNA sequence analysis are used to determine the genetic…
Genomic Characteristics of Carbapenem-Resistant Klebsiella pneumoniae
Introduction Klebsiella pneumoniae (K. pneumoniae), which belongs to the family Enterobacteriaceae, is a common nosocomial pathogen that causes a variety of human infections, including bloodstream infection, respiratory tract infection, urinary tract infection, and abdominal infection.1,2 Carbapenems are generally considered to be a last choice for the treatment of multi-drug resistant…
Genes | Free Full-Text | Phylogenomic Analysis of Cytochrome P450 Gene Superfamily and Their Association with Flavonoids Biosynthesis in Peanut (Arachis hypogaea L.)
4.1. The Evolution of AhCYP Superfamily: Diversity and Expansion The CYP gene superfamily, one of the largest in plants, plays a pivotal role in catalyzing a diverse range of reactions involved in growth, development, and secondary metabolite biosynthetic pathways. Systematic identification and study of the CYP gene superfamily are paramount….
Mexican Biobank advances population and medical genomics of diverse ancestries
Encuesta Nacional de Salud 2000 Since 1988, Mexico has established periodical National Health Surveys (Encuesta Nacional de Salud (ENSA), originally conceived as National Nutrition Surveys) for surveillance of Mexican population-based nutrition and health metrics. In this study, we use data and samples collected from the survey carried out in 2000,…
A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters
doi: 10.1128/jcm.00558-23. Online ahead of print. Affiliations Expand Affiliation 1 Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Item in Clipboard Myrthe M A Toorop et al. J Clin Microbiol. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1128/jcm.00558-23. Online ahead of print. Affiliation 1 Department…
Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex
Adams RV, Burg TM (2015) Gene flow of a forest-dependent bird across a fragmented landscape. PLoS One 10:1–22 Article Google Scholar Aguillon S, Rohwer V (2022) Revisiting a classic hybrid zone: movement of the northern flicker hybrid zone in contemporary times. Evolution 76:1082–1090 Article PubMed Google Scholar Aktas C (2020)…
Incorporation of long-read 16s rRNA sequences into QIIME2 and ASV generation – Technical Support
Hi all, I am trying to incorporate some complete/near complete 16s rRNA sequences that I have extracted from annotated genomes following some PacBio HiFi metagenomic sequencing I have done. The aim here is to compare these sequences against a V1-V2 16s rRNA sequencing dataset, generating a phylogenetic tree to see…
Solved Why is the 16S rRNA portion of bacterial and archaeal
Transcribed image text: Why is the 16 S rRNA portion of bacterial and archaeal genomes used to evaluate their evolutionary relatedness? It is the shortest section of DNA available to sequence. Its function and sequence is highly conserved across these organisms. Its function and sequence show large differences between closely related…
IJMS | Free Full-Text | Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761
1. Introduction The alarming decline of biodiversity worldwide necessitates urgent conservation measures, particularly for wild, endangered, and understudied species. According to the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species, of the 5973 mammal species assessed, 1340 were classified as threatened with extinction, including 233 critically…
Genetics lab report – Natalia Wood Genomic DNA Analysis through PCR and RFLP using Gel
Natalia Wood Genomic DNA Analysis through PCR and RFLP using Gel Electrophoresis April 11, 2022 Dr. Heidari Abstract: This course aimed to explore ancestral relatedness through the use of PCR and RFLP using gel electrophoresis, and a series of experiments were conducted to gain further insight on this topic. Initially,…
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen
V. cholerae in Yemen in 2018 and 2019 The National Centre of Public Health Laboratories (NCPHL) in Sana’a, the capital city of Yemen, received 6,311 and 3,225 clinical samples from suspected cholera patients in 2018 and 2019, respectively (Supplementary Table 1). Of these, 2,204 (35%) and 2,171 (67%) were confirmed…
Viruses | Free Full-Text | Optimizing the Conditions for Whole-Genome Sequencing of Avian Reoviruses
1. Introduction Avian orthoreoviruses (avian reoviruses, ARVs) are a persistent challenge to poultry producers in the United States and globally. Infection with ARVs has been associated with a variety of symptoms and syndromes in commercial poultry, including tenosynovitis/viral arthritis, enteric symptoms such as watery diarrhea, respiratory symptoms, myocarditis, viral hepatitis,…
MAPS PBC Announces Publication of Results from Confirmatory Phase 3 “MAPP2” Trial of MDMA-Assisted Therapy for PTSD in Nature Medicine
Study met primary and secondary endpoints confirming first Phase 3 study findings MAPP2 population reflects PTSD demographic with approximately half of study participants identifying as racially or ethnically diverse Company on track for NDA filing in 2023 SAN JOSE, Calif. , Sept. 14, 2023 /PRNewswire/ — MAPS Public Benefit Corporation…
MDMA-assisted therapy for moderate to severe PTSD: a randomized, placebo-controlled phase 3 trial
Study design and oversight This multi-site, randomized, double-blind, placebo-controlled study assessed the efficacy and safety of MDMA-AT versus placebo with therapy in participants diagnosed with moderate or severe PTSD (NCT04077437). Thirteen study sites (11 in the United States and two in Israel, both institutional and private) participated. The trial was…
Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress
Bacterial isolation from Antarctic soil Soil samples were collected from the Cape Burk area (1: 74° 45′ 19.6″ S, 136° 48′ 44.6″ W)51. The soil (1 g) was inoculated in a Reasoner’s 2A (R2A) liquid (composed of 0.5% proteose peptone, 0.05% casamino acid, 0.05% yeast extract, 0.05% dextrose, 0.05% soluble starch,…
The Chromosomal Virulence D | IDR
Introduction The clinical symptoms and signs of pulmonary disease caused by nontuberculous mycobacteria (NTM) are very similar to tuberculosis, so differentiating the two becomes extremely challenging. Both diseases manifest cough, expectoration, hemoptysis, chest pain, and other respiratory symptoms, as well as systemic symptoms, such as fatigue and anorexia.1–3 Furthermore, NTM…
Genome analysis of ST1 Bartonella henselae
Introduction Infective endocarditis (IE), as a disease first recognized in 1885, is defined by infection of a native or prosthetic heart valve, the endocardial surface, or an indwelling cardiac device.1–3 Despite advances in diagnostic capabilities and treatment options, IE remains a rare condition but with high associated mortality. And epidemiological…
Panoramic analysis of coronaviruses carried by representative bat species in Southern China to better understand the coronavirus sphere
Bat sample collection From August 2016 to July 2021, a total of 13,064 oral and anal swabs were collected from bats in 14 provinces across China. Of these, 4755 samples were collected following the COVID-19 outbreak. Sampling sites covered the hotspots of bats carrying Alpha-CoV and Beta-CoV in China9,29(Supplementary Data 1…
The Biostar Herald for Wednesday, September 06, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Characterisation and comparative genomics of three new Varanus-associated Borrelia spp. from Indonesia and Australia | Parasites & Vectors
The following results clearly demonstrate that the Borrelia spp. identified in ticks collected from V. salvator, V. varius, and V. giganteus are distinct species. Therefore, for clarity, we herein refer to these Borrelia spp. by their proposed names: Borrelia salvatorii (from V. salvator), ‘Ca. Borrelia undatumii’ (from V. varius), and…
Biology 1040 Chapter 15 – Be able to correctly label in-groups and branch-points.(s17, s19)
– Be able to correctly label in-groups and branch-points.(s17, s19) outgroup: frog because all examples have 4 limbs Ingroup: iguana, duck-billed platypus, kangaroo, and beaver Branch point: green; derived character: gestation – Define, describe, and evaluate how mtDNA and rRNA are used to infer relatedness. Know-apply when to use each…
Functional conservation of microbial communities determines composition predictability in anaerobic digestion
Lin Q, De Vrieze J, Li C, Li J, Li J, Yao M, et al. Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process. Water Res. 2017;123:134–43. Article CAS PubMed Google Scholar Coban O, De Deyn GB, van der Ploeg M. Soil microbiota as game-changers…
Effects of host species on microbiota composition in Phlebotomus and Lutzomyia sand flies | Parasites & Vectors
Maroli M, Feliciangeli MD, Bichaud L, Charrel RN, Gradoni L. Phlebotomine sandflies and the spreading of leishmaniases and other diseases of public health concern. Med Vet Entomol. 2013;27:123–47. CAS PubMed Google Scholar Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. Historical overview of the…
Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland
Growth conditions and identification The growth of the strain W-6 was measured at different temperatures of 4, 10, 15, 20, 25, 30, and 37 °C. It can be seen that strain W-6 could grow at the range from 4 to 30 °C with the optimal growth temperature 15 °C. Then, the growth curve of…
Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments
Core genomes of Listeria species strongly differ between natural and food-associated environments and can accurately predict isolation sources at a lineage level To assess the relationship between the core genome of L. monocytogenes (which entails genomes of all three L. monocytogenes lineages identified in this study – lineage I, II,…
Multidrug-resistant Providencia rettgeri strain YQ150713.
Introduction Providencia rettgeri is a Gram-negative opportunistic human pathogenic bacterium that belongs to the Proteae bacteria. It is a pathogen commonly found in the hospitals that mainly cause urinary tract infections, pneumonia, bacteremia, neonatal sepsis, eye infections, meningitis, endocarditis, and diarrhea.1–3 The pathogen Providencia rettgeri demonstrates inherent resistance to numerous…
Reassessing Stephanofilaria stilesi dermatitis in cattle, with characterization of molecular markers for confirming diagnosis | Parasites & Vectors
Although a common dermatitis of cattle in North America, much remains undescribed about the histological features of S. stilesi, and very little is known about aspects of its evolutionary biology and taxonomic classification. This can be partly attributed to the dated literature on stephanofilariasis in North American cattle [17]. However,…
Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica
Genome assembly, annotation, and overview We assembled a chromosome-scale genome of a GS E. indica plant using PacBio Sequel II and long-range interaction (Hi-C) datasets. The assembly consists of nine chromosomes spanning 509,878,742 base pairs estimated to be ~97.8% complete by Benchmarking Universal Single-Copy Orthologs (BUSCO)28 analysis with an LTR…
Molecular characterization of emerging chicken and turkey parvovirus variants and novel strains in Guangxi, China
PCR confirmation of Guangxi ChPV and TuPV strains The nonstructural (NS) and VP genes of the positive samples were amplified by PCR using primers targeting the conserved 561-bp NS1 region and 249-bp VP1/VP2 region, respectively. The epidemiological survey results are shown in Table 1. Table 1 shows that the total…
Meningococcal reference unit: user manual
Executive summary This document contains information on reference services for: Neisseria meningitidis (meningococcal) isolate characterisation Capsular polysaccharide antigen detection (serogrouping) Porin B (PorB) serotyping Porin A (PorA) serosubtyping Antimicrobial susceptibility testing meningococcal (and Streptococcus pneumoniae) DNA detection and meningococcal capsular grouping by real-time polymerase chain reaction (PCR) meningococcal serology including…
Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants
Klepzig KD, Adams AS, Handelsman J, Raffa KF. Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans. Environ Entomol. 2009;38:67–77. CAS PubMed Google Scholar Dale C, Moran NA. Molecular interactions between bacterial symbionts and their hosts. Cell. 2006;126:453–65. CAS PubMed Google Scholar Salem…
Historical DNA study connects living people t
image: Site of Catoctin Furnace in Cunningham Falls State Park, Maryland. view more Credit: Aneta Kaluzna At a glance: DNA analysis of African Americans buried at an early U.S. iron forge reveals locations of their African and European ancestors and finds more than 40,000 living U.S. relatives. The study is the…
Bioinformatics Research Scientist, Division of Infectious Diseases and International Health – Charlottesville
The Division of Infectious Diseases and International Health is seeking a talented and passionate Bioinformatics Research Scientist to support ongoing bioinformatics analysis needs. The individual will integrate their knowledge and experience into current research and clinical efforts undertaken by two investigators, especially in analyzing large-scale genomic data with a focus…
Historical DNA Study Connects Living People to Enslaved and Free African Americans at Early Ironworks
Answers in ancient DNA The new method — developed by a team led by Reich and first author Éadaoin Harney, a population geneticist at 23andMe, for the study — analyzes DNA segments that are shared by two or more people because they were inherited from a recent common ancestor. For…
Plotting relatedness2 output in R
Plotting relatedness2 output in R 0 OK, I have a question that I feel has a quite simple solution, but my brain has just hit a wall… I would like to plot the output from : vcftools -relatedness2 into a plot where the samples are nodes and the axes show…
Close-kin mark-recapture informs critically endangered terrestrial mammal status
Sampling and tissue collection Christmas Island is a territory of Australia located in the Indian Ocean approximately 380 km south of Java, Indonesia, and 1500 km west of the Australian mainland. It is a small 135 km2 island composed of tertiary limestone overlying volcanic andesite and basalt and its topography consists of…
Microorganisms | Free Full-Text | Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin
1. Introduction Staphylococcus aureus is an important pathogen in healthcare and community settings that can cause a broad spectrum of diseases, ranging from skin and soft-tissue infections to invasive diseases such as pneumonia, septicemia, and endocarditis [1]. In the 1960s [2], soon after the introduction of methicillin into the healthcare…
Forensic Genetic Genealogy Searches: What Defense Attorneys Need to Know
Contents IntroductionI. How Genetic Genealogy Searches WorkII. Law Enforcement Use of Genetic Genealogy Services A. Comparing Genetic Genealogy Searches with Traditional Criminal DNA Searches B. How Forensic Genetic Genealogy (FGG) Searches WorkIII. Regulation is MinimalIV. FGG Can Both Misidentify Suspects and Exonerate Wrongfully Convicted PeopleV. Discovery and Building a Record…
Extensive pedigrees reveal the social organization of a Neolithic community
Fox, R. Kinship and Marriage: An Anthropological Perspective (Cambridge Univ. Press, 1983). Morgan, L. H. Ancient Society: Or, Researches in the Lines of Human progress from Savagery, Through Barbarism to Civilization (C. H. Kerr, 1877). Lévi-Strauss, C. The Elementary Structures of Kinship (Beacon Press, 1971). Schneider, D. M. A Critique…
Ancient DNA Study Points to Societal Patterns in Neolithic Europe
NEW YORK – A genetic analysis on samples going back thousands of years from a site in France has provided new insights into societal and population patterns present there during the Neolithic period. For a paper appearing in Nature on Wednesday, researchers at the University of Bordeaux, the Max Planck…
Consumer Genomics Global Market Report 2023
ReportLinker Major players in the consumer genomics market are 23andMe Inc., Gene By Gene Ltd., Mapmygenome Ltd., Ancestry.com LLC, Color Genomics Inc., Futura Genetics, Pathway Genomics, Helix OpCo LLC, Positive Biosciences Ltd. New York, July 25, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Consumer Genomics Global…
Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs | BMC Genomics
Wähner M, Brüssow K. Biological potential of fecundity of sows. Biotechnol Anim Husb. 2009;25(5–6–1):523–33. Article Google Scholar Argente MJ. Chap. 4 Major Components in Limiting Litter Size. In: 2018; 2018. Malopolska MM, Tuz R, Schwarz T, Ekanayake LD, D’Ambrosio J, Ahmadi B, Nowicki J, Tomaszewska E, Grzesiak M, Bartlewski PM….
A Guideline of Genetic Map Construction for Different Populations
What is Genetic Map? Genetic map construction for different populations is a fundamental process in plant genetics research, allowing us to gain insights into the arrangement and linkage of genes on chromosomes. Also referred to as a genetic linkage map, it is built by analyzing the connections between genetic markers…
Bioinformatics Research Scientist, Division of Infectious Diseases and International Health job with Virginia Jobs
The Division of Infectious Diseases and International Health is seeking a talented and passionate Bioinformatics Research Scientist to support ongoing bioinformatics analysis needs. The individual will integrate their knowledge and experience into current research and clinical efforts undertaken by two investigators, especially in analyzing large-scale genomic data with a focus…
Organization of the human intestine at single-cell resolution
Tissue collection and processing This study complies with all relevant ethical regulations and was approved by the Washington University Institutional Review Board and the Stanford University Institutional Review Board. Human bowel tissues were procured from deceased organ donors. Written informed consent was obtained from the next-of-kin for all donor participants….
Mathematics | Free Full-Text | A Study on Graph Centrality Measures of Different Diseases Due to DNA Sequencing
2.1. The Literature of Disease Network To begin, a broad range of phenotypes are associated with uncommon illness events, from those that are extremely cell-type or organ-specific to those that are more generalized, such as those related to heterogeneous syndromic disorders. Very little is known about how a genetic aberration…
Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella
A common ancestor of pathogenic Kingella species acquired the RTX toxin Consistent with existing literature, when the five Kingella species were assessed for β-hemolysis on BHI plates supplemented with 10% sheep blood, only K. kingae and K. negevensis were hemolytic (Fig. 1A), suggesting that the two pathogenic Kingella species produce the…
Study links endogamy to persistence of harmful genetic variants in India
In 2009, a study in Nature Genetics by the group of Kumarasamy Thangaraj, at the Centre for Cellular and Molecular Biology, Hyderabad, reported a fascinating finding on why a small group of Indians were prone to cardiac failure at relatively young ages. They found that the DNA of such individuals…
Evaluating cpn60 for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis
Mammalian host swab sample selection To investigate mammalian skin microbial communities using the cpn60 gene, 95 representative skin swab samples, already extracted for genomic DNA and sequenced from a previous project [8], were selected for additional amplification and sequencing of the cpn60 gene. This cpn60 gene amplicon dataset contained samples…
Development of microsatellite markers for the invasive mosquito Aedes koreicus | Parasites & Vectors
Invasive Aedes mosquitoes represent a global concern for public health due to their role as vectors of several pathogens and their ability to colonise new territories [1, 2]. Their dispersal in non-native regions is mainly associated with climate change, and the increasing movement of people and goods (e.g. used tires,…
Bioinformatics Research Scientist, Division of Infectious Diseases and International Health job with University of Virginia
The Division of Infectious Diseases and International Health is seeking a talented and passionate Bioinformatics Research Scientist to support ongoing bioinformatics analysis needs. The individual will integrate their knowledge and experience into current research and clinical efforts undertaken by two investigators, especially in analyzing large-scale genomic data with a focus…
Consumer Genomics Market Size Will Rise to USD 17.51 by
Ottawa, July 03, 2023 (GLOBE NEWSWIRE) — The global consumer genomics market size will reach USD 12.2 billion in 2030. The Direct-to-Consumer (DTC) testing business, which has seen a massive rise in recent years as a result of rising consumer and medical professional interest in personalized genetic analysis, is the…
Illinois Study Unveils Genetic Secrets of America’s Favorite Snack
In its simplest form, popcorn is pretty uncomplicated. Most supermarket varieties offer the choice of two kernel colors, yellow or white, and two kernel shapes, pointed or pearl. When popped, the flake typically expands into one of two shapes: mushroom or butterfly. But there’s more to popcorn than meets the…
Whole strains vs MGEs in short and longterm transmission of ESBL genes between healthcare and community settings in Uganda
ESBL carriage Of the 1556 samples analyzed, 81.9% (1275) yielded suspected ESBL producing bacteria. The antimicrobial susceptibility testing of the obtained isolates showed that many of the strains were resistant to critical cephalosporin and carbapenem antimicrobials such as Cefepime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem and Imipenem in both healthcare and community…
Logistic Regression In R including related individuals
Logistic Regression In R including related individuals 0 Dear all, I am currently trying to perform a logistic regression to assess the association between a disease and measurement. The measurement is computed through genetic data, thus I should exclude genetic related individuals. However, I am losing a significant number of…
A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
Grimont PAD, W. F. X. Antigenic formulae of the Salmonella serovars, 9th ed. (World health organization collaborating center for reference and research on Salmonella, Insitut Pasteur, 2007). Gal-Mor, O., Boyle, E. C. & Grassl, G. A. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ….
Natera Announces Data from the
Natera%2C+Inc. (NASDAQ: NTRA), a global leader in cell-free DNA testing, today announced new data on its Prospera test being presented at the American Transplant Congress (ATC) 2023 taking place June 3-7, 2023. The presentations include several interim analyses from ProActive, a prospective donor-derived cell-free DNA (dd-cfDNA) study evaluating Natera’s Prospera…
Discrimination of monozygotic twins using mtDNA heteroplasmy through probe capture enrichment and massively parallel sequencing
Oosthuizen T, Howes LM (2022) The development of forensic DNA analysis: new debates on the issue of fundamental human rights. Forensic Sci Int Genet 56:102606 Article CAS PubMed Google Scholar Nwawuba Stanley U et al (2020) Forensic DNA profiling: autosomal short tandem repeat as a prominent marker in crime investigation….
Why Aren’t The Three Rrna Genes Of Corn One Anothers Closest Relatives?
Ribosomal RNA (rRNA) genes play a crucial role in the process of protein synthesis and are essential components of the ribosome, the cellular machinery responsible for translating genetic information into functional proteins. In many organisms, these genes are found as multiple copies within their genomes, with each copy exhibiting varying…
How Do DNA And mtDNA Differ?
The field of genetics has experienced significant advancements in recent years, shedding light on the complex molecular mechanisms that govern inheritance and the expression of genetic traits. Central to this understanding is the distinction between two distinct types of genetic material, namely deoxyribonucleic acid (DNA) and mitochondrial DNA (mtDNA). While…
Polygenic prediction of preeclampsia and gestational hypertension
Burton, G. J., Redman, C. W., Roberts, J. M. & Moffett, A. Pre-eclampsia: pathophysiology and clinical implications. BMJ 366, l2381 (2019). Article PubMed Google Scholar Jiang, L. et al. A global view of hypertensive disorders and diabetes mellitus during pregnancy. Nat. Rev. Endocrinol. 18, 760–775 (2022). Article PubMed PubMed Central …
Ex vivo RSA and pfkelch13 targeted-amplicon deep sequencing reveal parasites susceptibility to artemisinin in Senegal, 2017 | Malaria Journal
WHO. Guidelines for malaria. WHO/UCN/GMP/2022.01 Rev. 2. Geneva. World Health Organization; 2022. Nzoumbou-Boko R, Panté-Wockama CBG, Ngoagoni C, Petiot N, Legrand E, Vickos U, et al. Molecular assessment of kelch13 non-synonymous mutations in Plasmodium falciparum isolates from central African Republic (2017–2019). Malar J. 2020;19:191. Article CAS PubMed PubMed Central Google…
The impact of rare protein coding genetic variation on adult cognitive function
The UKB is approved by the North West Multi-centre Research Ethics Committee (www.ukbiobank.ac.uk/learn-more-about-uk-biobank/about-us/ethics). The current study was conducted under UKB application no. 26041. The data in the UKB were collected after written informed consent was obtained from all participants. The Human Research Committee of the MGB approved the Biobank research…
Ribosomal RNA – Study Achievement
Ribosomal RNA Definition Ribosomal ribonucleic acid (rRNA) is the RNA component of ribosomes, the molecular machines that catalyze protein synthesis. Ribosomal RNA constitute over sixty percent of the ribosome by weight and are crucial for all its functions – from binding to mRNA and recruiting tRNA to catalyzing the formation…
Genome data sheds light on how Homo sapiens arose in Africa
Our species arose in Africa more than 300,000 years ago, with the oldest-known Homo sapiens fossils discovered at a site in Morocco called Jebel Irhoud, located between Marrakech and the Atlantic coast. But the scarcity of Homo sapiens fossils from early in our evolutionary history and the geographical spread of…
Genetic Origins of Ancient Pict Warriors in Britain
Genetic analysis has uncovered the mysterious origin of the Picts, a people group that lived in many parts of northern Britain roughly 1,500 years ago. Research reveals that the ethnic group, which many thought might have come from Eastern Europe, had a local origin similar to other British Celtic groups….