Tag: GBS

Cao, C. et al. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet. 17(2), e1009405 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  De Camargo, G. M. F. et al. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 1–14 (2015). Article  Google Scholar  El-Halawany, N….

Abstract High-throughput sequencing technologies have increasingly led to discovery of disease-causing genetic variants, primarily in postnatal multi-cell DNA samples. However, applying these technologies to preimplantation genetic testing (PGT) in nuclear or mitochondrial DNA from single or few-cells biopsied from in vitro fertilised (IVF) embryos is challenging. PGT aims to select…

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)….

The PacBio RS II sequencer has been effectively utilized to generate a 1.27 Gb genome assembly of Dendrobium officinale [70]. By utilizing advanced sequencing technologies such as Illumina HiSeq, Nanopore, PacBio, and Hi-C, the results have revealed remarkable N50 values of 44 Mb and 65.35 Mb for Gardenia jasminoides and…

SciCheck Digest The mRNA COVID-19 vaccines — like many other vaccines — can contain small amounts of DNA left over from the manufacturing process. There’s no evidence this residual DNA causes “turbo cancer,” or very aggressive cancer. Nor did Moderna admit that “mRNA Jabs Cause Turbo-Cancer,” contrary to an online…

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…

Abebe TD, Naz AA, Léon J (2015) Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L.). Front Plant Sci 6:813 Article  PubMed  PubMed Central  Google Scholar  Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 Article  CAS  PubMed …

Instruments MISEQ ILLUMINA NGS sequencing platform that allows to generate up to 25 million reads from 25 to 300 nucleotides in paired end mode (PE 2X300)  MinION ONT Portable real time device for DNA and RNA sequencing by nanopore technology 3730xl GENETIC ANALYZER Capillary electrophoresis platform for high throughput genetic…

Biologic License Application submission expected for 2025  LUND, Sweden, Oct. 11, 2023 /PRNewswire/ — Hansa Biopharma, “Hansa” (Nasdaq Stockholm: HNSA), a pioneer in enzyme technology for rare immunological conditions, today announced randomization for the US ConfIdeS trial is expected to conclude in mid-2024. The ConfIdeS trial is an open-label, controlled, randomized…

AnaptysBio, Inc. announced positive top-line results from its global Phase 3 GEMINI-1 trial evaluating the safetyAnaptysBio, Inc. and efficacy of imsidolimab (IL-36R mAb) in patients with generalized pustular psoriasis (GPP) flares. Investigational imsidolimab met its primary endpoint in the study population achieving rapid clearance of pustulation, erythema and scaling through…

53.3% of patients who received a single dose of 750mg IV imsidolimab achieved GPPPGA 0/1 (clear or almost clear) at Week 4 (primary endpoint), compared to 13.3% of patients on placebo (p=0.0131) Demonstrated favorable safety and tolerability with no SAEs, low incidence and no increase of infections vs….

Dear all, there are still a few seats available for the upcoming RADseq data analysis course! Dates: online October 30th – November 3rd Website: www.physalia-courses.org/courses-workshops/course16/ Our course will introduce you to various approaches for obtaining reduced representation genome sequencing data, with a special focus on data analysis using Stacks. We’ll…

Moderna Expands the Field of mRNA Medicine with Positive Clinical Results Across Cancer, Rare Disease, and Infectious Disease Company’s flu vaccine, mRNA-1010, met its primary endpoint in Phase 3 trial; separate Phase 1/2 data demonstrated higher HAI titers than Fluzone HD Vaccine pipeline advancing rapidly with Company announcing the completion…

Our research fuls all relevant ethical requirements and was conducted in accordance with the Declaration of Helsinki. The parent study and the mNGS testing amendment was approved by the Human Research Ethics Committee of the University of the Witwatersrand (HREC reference number 150215). The parents of decedents had provided written…

A simple blood test based on patterns of gene expression could radically improve and speed up the diagnosis of febrile childhood diseases, say researchers. Proof-of-concept work by an international team has shown it is possible to detect and distinguish between 18 infections or inflammatory diseases, such as group B Streptococcus…

To recognize International Group B Strep Awareness Month in July, we had a conversation with MinervaX CEO, Per Fischer.  MinervaX is a privately-held Danish biotechnology company developing a novel prophylactic vaccine against Group B streptococcus (GBS), with two phase II clinical trials ongoing in pregnant women and a phase I clinical trial…

Abdi, H. (2007). Discriminant correspondence analysis. In N. J. Salkind (Ed.), Encyclopedia of measurement and statistic (pp. 270–275). Sage. Google Scholar  Ando, K., Carr, K. M., & Grumet, R. (2012). Transcriptome analyses of early cucumber fruit growth identifies distinct gene modules associated with phases of development. BMC Genomics, 13, 518….

CRISPR-Cas12a RNA-guided complexes have been developed to facilitate the rapid and sensitive detection of nucleic acids. However, they are limited by the complexity of the operation, risk of carry-over contamination, and degradation of CRISPR RNA (crRNA). In this study, a Cas12a-based single-stranded DNA (ssDNA)-modified crRNA (mD-crRNA)-mediated one-step diagnostic method (CasDOS)…

Tools for SNP imputation 0 Hello, I am working with polyploid plant species (tetraploid, hexaploid, octaploid). I have genotype by sequencing (GBS) SNP data from different sequencing platforms like Affymetrix and SeqSNP. Now, I want to perform SNP imputation for some species and increase the number of SNPs and also…

Adams MD, Kelley JM, Gocayne JD et al (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252(5013):1651–1656 CrossRef  CAS  PubMed  Google Scholar  Alipour H, Bihamta MR, Mohammadi V, Peyghambari SA, Bai G, Zhang G (2017) Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and…

Varshney, R. K. et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31, 240–246 (2013). Article  CAS  PubMed  Google Scholar  Li, Y. et al. Investigating drought tolerance in chickpea using genome-wide association mapping and genomic selection based on whole-genome resequencing data. Front….

Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387. doi.org/10.1111/2041-210x.12158 Article  Google Scholar  Aguirre-Liguori JA, Ramírez-Barahona S, Gaut BS (2021) The evolutionary genomics of species’ responses to climate change. Nat Ecol Evol 5:1350–60. doi.org/10.1038/s41559-021-01526-9 Article  PubMed  Google Scholar  Ahrens CW, Rymer PD,…

Amino acid sequence comparisons between GAS and GBS Cas9 identify orthologous active sites Relationships between the amino acid sequence of GBS Cas9 endonuclease and its molecular functions can be deduced from detailed studies of its GAS ortholog, SpyCas9 (Supplementary Fig. 1). As a first step in locating DNA complementary to a…

A prospective study of pregnant women We established a prospective cohort of 2313 pregnant women with the goal of studying the vaginal microbiota, its community composition and the presence of pathogenic bacteria in the peripartum period. Inclusions and data collection were performed in accordance with applicable laws and ethical standards. Ethical…

Hello! I’m trying to get the gradient values of my quantum circuit to do a Barren Plateaus analysis. I am following the following tutorial: Barren plateaus in quantum neural networks — PennyLane documentation. However, I am using the torch interface, and I am running into a TypeError when I just…

Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…

Liu, L. et al. Identification of quantitative trait loci for growth-related traits in the swimming crab Portunus trituberculatus. Aquacult. Res. 46, 850–860 (2015). Article  CAS  Google Scholar  Sun, Q. F. et al. Astaxanthin: The ubiquitous and abundant carotenoid as a pivotal interior factor of anti-oxidation and immune for the moulting…

Experimental design. Sows were maintained in an enriched (a) or barren environment (b). Sows kept in the barren environment were subdivided into two groups (c) depending on whether they expressed (BS) or did not express stereotypy (BN). Piglets from different prenatal environments were kept in the same conditions after weaning,…

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

Abstract A waxing variety of “genotype-by-sequencing” (GBS) methods use restriction enzymes and high throughput DNA ordering to generation data for a set of genomic loci, allowing the simultaneous discovery press genotyping of thousands of polymorphisms in a set of multiplexed samples. We evaluated a “double-digest” restriction-site associated DNA sequencing (ddRAD-seq)…

First quarter 2023 revenues of $1.9 billion; GAAP net income of $79 million and GAAP diluted EPS of $0.19 Company in negotiations for new orders for fall of 2023 in U.S., Japan, and EU, in addition to reiterating 2023 minimum sales expectations of approximately $5.0 billion from previously announced COVID-19…

Barcoding and demultiplexing in high-throughput sequencing experiments Barcoding, or indexing, is a widely used strategy in high-throughput sequencing experiments. This method enables the multiplexing of numerous samples in a single sequencing run by adding a unique DNA sequence to each sample before sequencing. During sequencing, the barcodes are read along…

Two new Tepidiforma species expand on a small number of cultivated Dehalococcoidia Two bacterial strains were isolated from terrestrial geothermal springs by plating benthic mat and sediment slurries onto R2A medium and were identified by 16S rRNA gene sequencing as members of the recently described genus Tepidiforma [27]. Strain YIM…

Next-generation, refrigerator-stable COVID-19 vaccine candidate, mRNA-1283, has dosed first participant in its Phase 3 trial Company expects to file for approval of its investigational RSV vaccine candidate, mRNA-1345, this quarter Company’s first influenza candidate, mRNA-1010, did not accrue sufficient cases at the interim efficacy analysis to declare early success in…

zh-CN Chinese (China) 无乳链球菌 rRNA:存在情况或阈值:时间点:XXX:序数型:DNA探针Synonyms: B 族链球菌 rRNA B 族链球菌;B 组链球菌;B 群链球菌;GBS B 组链球菌 rRNA B 群链球菌 rRNA 不明的;其他;将在相应消息内其他部分之中加以详细说明;未作详细说明的;未作说明的;未做说明的标本;未加规定的;未加说明的标本;杂项 依次型;分类顺序型;定性的;序数型（或称等级型）;性质上的;有序型;有序性分类应答;有序性分类结果;秩次型;等级型;筛查;顺序型 存在情况;存在;存在与否;是否存在;阈值;界值;界限;阀值;临界值;存在情况（存在、存在与否、是否存在）或阈值（界值、界限、阀值、临界值） 微生物学;微生物学试验;微生物学试验（培养、DNA、抗原及抗体） 时刻;随机;随意;瞬间 核糖体核糖核酸;核糖核酸 RNA 核蛋白体 RNA 核蛋白体 RNA（Ribosomal RNA，RRNA） 核蛋白体核糖核酸 核醣体 RNA 脱氧核糖核酸探针 es-AR Spanish (Argentina) ARNr de Streptococcus agalactiae:concentración arbitraria:punto en el tiempo:XXX:ordinal:sonda fr-CA French (Canada) Streptococcus agalactiae…

MultiQC output: opposing output 1 Hi, I’m working with RAD genomic data (produced through genotype-by-sequencing). Two panels in my MultiQC document seem to contradict one another, the “Trimmed Sequence Lengths (3′)” and the “Sequence Length Distribution” panels. I expect a lot of duplication because of the GBS protocol. In the…

Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article  Google Scholar  Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…

Principal findings of the study In this re-analysis of fifteen placental microbiota studies, of the ASVs which were ranked in the top five ASVs for relative abundance in any one study, Lactobacillus ASVs were clearly the most prevalent across studies. Yet, Lactobacillus ASV prevalence was explained by background DNA contamination,…

Kaggle is a platform for sharing ideas, getting inspired, competing against other data scientists and learning new information and coding tricks. Kaggle is free and open to the entire online community, featuring machine learning contests and data challenges as well as notebooks and datasets. Getting Started Kaggle is an ideal…

Today, the Vaccines and Related Biological Products Advisory Committee (VRBPAC) voted in favor of the safety and efficacy of Pfizer’s respiratory syncytial virus (RSV) vaccine candidate. If the US Food and Drug Administration (FDA) and Centers for Disease Control and Prevention (CDC) abide by this recommendation, the vaccine, Abrysvo (RSVpreF),…

CNN — Two people who received Pfizer’s respiratory syncytial virus (RSV) vaccine during a clinical trial were later diagnosed with Guillain-Barre syndrome, and the US Food and Drug Administration has asked Pfizer to conduct a safety study if the shot is approved, according to agency documents released Friday. The cases…

Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756. doi.org/10.1093/genetics/124.3.743 CrossRef  CAS  Google Scholar  Rafalski JA, Tingey SV (1993) Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends Genet 9:275–280. doi.org/10.1016/0168-9525(93)90013-8 CrossRef  CAS  Google Scholar  Ragot M, Hoisington DA (1993) Molecular…

I’m trying to identify SNP outliers on my GBS (genotype-by-sequencing) SNP dataset. I found “Arlequin” and have installed it successfully. Furthermore, I’ve converted my “VCF” file into “arp” which is the format needed for Arlequin. When I load my data into Arlequin and choose “Detecting loci under selection” and press…

Biogeography of Culexarchaeia. Sites from where Culexarchaeia MAGs were recovered and where 16S rRNA gene sequences have been detected. A full list of samples and associated metadata can be found in Supplementary File 8. Yellowstone map modified from (97), GBS picture modified from (18), and JZ picture modified from (25)….

Background: Streptococcus agalactiae or group B Streptococcus (GBS) is a leading infectious cause of neonatal morbidity and mortality. It is essential to establish a robust method for the rapid and ultra-sensitive detection of GBS in pregnant women with premature rupture of membrane (PROM). Methods: This study developed a CRISPR-GBS assay…

Company Description Eurofins Scientific is an international life sciences company, providing a unique range of analytical testing services to clients across multiple industries, to make life and our environment safer, healthier and more sustainable. From the food you eat, to the water you drink, to the medicines you rely on,…

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

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…

H20 interview questions and answers 1) What is AutoML in H2O? H2O’s Automatic Machine Learning (AutoML) H2O is a fully open-source, distributed in-memory machine learning platform with linear scalability. … H2O AutoML can be used for automating the machine learning workflow, which includes automatic training and tuning of many models…

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

Filter criteria for variants based on GBS data 0 Are there recommended filter criteria for variants based on GBS data? I currently use this filter formula that is used in bcbio for WGS based variants soft-filtering bcftools –soft-filter GATKCutoffSNP -e TYPE=”snp” && (MQRankSum < -12.5 || ReadPosRankSum < -8.0 ||…

Hey everyone, I’m having some trouble with the imputation step in my GBS pipeline. I’m following the FastGBS pipeline basically as written up until this point. Before running Beagle, i’ve performed a filtering step using vcftools (though I get the same error whether or not I do this; I just…