Tag: GC

Allikmets, R. et al. A photoreceptor cell-specific ATP-binding transporter gene (ABCR) is mutated in recessive Stargardt macular dystrophy. Nat. Genet. 15, 236–246 (1997). Article  CAS  PubMed  Google Scholar  Tanna, P., Strauss, R. W., Fujinami, K. & Michaelides, M. Stargardt disease: Clinical features, molecular genetics, animal models and therapeutic options. Br….

Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…

WHO. World malaria report 2021. Geneva: World Health Organization; 2021. Google Scholar  CDC, Global. COVID-19: centres for disease control and prevention; 2021. www.cdc.gov/coronavirus/2019-ncov/global-covid-19/index.html. Accessed 14 Dec 2021. Sidhu ABS, Valderramos SG, Fidock DA. Pfmdr1 mutations contribute to quinine resistance and enhance mefloquine and artemisinin sensitivity in Plasmodium falciparum. Mol Microbiol. 2005;57:913–26. Article …

Cell culture and cell line construction Cells were cultured at 37 °C in 5% CO2 atmosphere with 100% humidity. Telomerase-immortalized RPE-1 retinal pigment epithelium cells (CRL-4000, American Type Culture Collection), U2OS osteosarcoma cells (HTB-96, American Type Culture Collection) and derivative cell lines were grown in DMEM/F12 (1:1) medium without phenol red…

Intel Xeon E5-2666 v4 testing with a Supermicro X10DRL-CT v0123456789 (3.2 BIOS) and NVIDIA GeForce GTX 1080 Ti 11GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2306074-NE-E52666V4X88 Intel Xeon E5-2666…

Cold Spring Harb Mol Case Stud. 2023 Apr; 9(2): a006256. ,1,2 ,1,2 ,1,2 ,2,3 ,4 and 1,2 Mahvish Q. Rahim 1Pediatric Hematology Oncology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA; 2Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana, USA; April Rahrig 1Pediatric Hematology Oncology,…

Avise J (2008) Clonality: the genetics, ecology, and evolution of sexual abstinence in vertebrate animals. Oxford University Press, USA Book  Google Scholar  Avise JC (2015) Evolutionary perspectives on clonal reproduction in vertebrate animals. Proc Natl Acad Sci USA 112(29):8867–8873 Article  CAS  PubMed  PubMed Central  Google Scholar  Andrews S (2010) FastQC:…

PRESS RELEASE Published June 6, 2023 [130 Pages] The Contact-Tracing App Market Report 2023 provides a comprehensive analysis of the industry with a focus on business strategies, major trends, and regional segments. It also includes valuable insights into the value chain analysis of key players – Apple, Oracle Corporation, ServiceNow,…

General structure, organization, and composition of mitogenomes The gene order and arrangement characteristics of the twelve mitogenomes in the present study (Chironomus kiiensis, Chironomus nipponensis, Chironomus plumosus, Dicrotendipes pelochloris, Dicrotendipes sp., Einfeldia sp., Glyptotendipes tokunagai, Limnophyes sp., Nilodorum tainanus, Polypedilum nubifer, Smittia aterrima, and Tanytarsus formosanus) were similar to those…

  The following is an excerpt from an E-book that Twist developed for Genetic Engineering News: The Changing Landscape of CRISPR Screening: A guidebook to the latest CRISPR screening methodologies and technologies. You can download the full E-book here.   Even for seasoned researchers, designing an sgRNA library can be…

Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…

KEGG ORTHOLOGY: K16564     ORTHOLOGY: K16564 Help Entry K16564                      KO                                      Symbol exoU Name succinoglycan biosynthesis protein ExoU [EC:2.4.-.-] Pathway map00543   Exopolysaccharide biosynthesis Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00543 Exopolysaccharide biosynthesis    K16564  exoU; succinoglycan biosynthesis protein ExoU 09180 Brite Hierarchies  09181 Protein families: metabolism   01003 Glycosyltransferases    K16564  exoU; succinoglycan biosynthesis protein ExoUEnzymes [BR:ko01000] 2. Transferases  2.4  Glycosyltransferases   2.4.-    2.4.-.-     K16564  exoU; succinoglycan…

Wasti S, Sah N, Mishra B. Impact of heat stress on poultry health and performances, and potential mitigation strategies. Animals. 2020;10:1266. doi.org/10.3390/ani10081266. Article  PubMed  PubMed Central  Google Scholar  Lara LJ, Rostagno MH. Impact of heat stress on poultry production. Animals. 2013;3:356–69. Article  PubMed  PubMed Central  Google Scholar  Al-Saffar AA, Rose…

Introduction Escherichia coli, a member of the Enterobacterales family, is a common opportunistic pathogen that can cause various infectious illnesses, including urinary tract infections (UTIs) and other infections acquired in the community.1,2 The presence of carbapenemases in E. coli poses a serious threat to public health. These carbapenemase genes may…

Low mapping percentage 0 Hello, biostars. What are the steps that you do when you get a mapping percentage below 70% with STAR software while mapping with a human reference genome? I want an overall instruction that works for most human samples. Based on my searches, I propose the following…

Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…

Davison AJ. Herpesvirus systematics. Vet. Microbiol. 2010;143:52–69. doi.org/10.1016/j.vetmic.2010.02.014 Article  CAS  Google Scholar  Mettenleiter TC, Ehlers B, Müller T, Yoon K, Teifke JP. Herpesviruses. In: Zimmerman, J., Karriker, L. A., Ramirez, A., Schwartz, K. J., Stevenson. G. W., editor. Diseases of Swine: John Wiley & Sons, Inc. Published 2012 by John…

Introduction Although globalization has provided opportunities for consumers to enjoy a wide range of products and expanded global food trade, the complexity of the international food supply has contributed to an increase in foodborne outbreaks (Quested et al., 2010; Hussain and Dawson, 2013). Worldwide efforts have ensured food safety by…

I’ll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I’ll then polish my assembly and pare it down to the targeted contigs (eg. those annotated as bacteria/viruses/your genome of interest/etc.) then I like to use quast/metaquast to evaluate…

Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11:697–709. doi.org/10.1038/nrg2844 Article  CAS  PubMed  Google Scholar  Beheregaray LB, Caccone A (2007) Cryptic biodiversity in a changing world. J Biol. doi.org/10.1186/jbiol60 Article  PubMed  PubMed Central  Google Scholar  Bickford D, Lohman DJ, Sodhi NS…

Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…

Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…

Introduction The reptilian order Crocodylia is comprised of alligators, caimans, crocodiles, and gharials. These animals live in North and South America, Africa, India, Southeast Asia, and northern Australia. Crocodylia includes the families Alligatoridae, Crocodylidae, and Gavialidae. The latter two families belong to the clade Longirostres, since they…

Over the past year I have started having occasional performance issues with RStudio that make it run increasingly slow/sluggish: whenever called, the RStudio console (and eventually, the entire GUI) gets stuck for at most 10-15 min as if awaiting a connection, similar to what is described here. If it returns…

1. Introduction Tuberculosis (TB) is a significant global burden and is widely reported to be a major public health and economic problem, costing the world $617 billion between 2000 and 2015 and projected to cost $1 trillion between 2015 and 2030 (1). It is the second leading cause of death…

Abstract Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein…

Occurrence of prophage sequences in L. casei group genomes The first stage of the analysis involved the identification of prophage-like sequences in 439 genomic sequences of bacterial strains belonging to the following 5 species: L. casei (27), L. paracasei (200), L. rhamnosus (204), L. zeae (6) and L. chiayiensis (2)….

ExomeDepth error in getBamCounts when adding a fasta reference 1 Whenever I try to add a reference fasta file for computing the GC content in the GetBamCounts function: my.countsV6 <- getBamCounts(bed.frame =AgilentV6, bam.files = BAMFiles, include.chr = TRUE, referenceFasta = “data/hg19.fa” ) I get an error like this: Reference fasta…

The infant and maternal gut microbiota are defined by different Bifidobacterium species The samples analysed in this study were collected during the MicrobeMom study (ISRCTN5302301420,21), these included samples from the maternal stool, vagina, oral cavity, and breast milk in addition to infant stool (Table 1; Fig. 1a). From the 160 participants recruited,…

Picard’s CollectGcBiasMetrics gc-bias plot- help with interpretation 0 Hi all, Setup I ran picard’s CollectGcBiasMetrics tool for my WES sample, with the intention of assessing the performance of the Exome capture panel in terms of the uniformity of read coverage at various %GC windows. I obtained the gc bias plot…

Agnes Stephanie Harahap,1– 3 Imam Subekti,4 Sonar Soni Panigoro,5 Asmarinah,6 Lisnawati,1 Retno Asti Werdhani,7 Hasrayati Agustina,8 Dina Khoirunnisa,1 Mutiah Mutmainnah,1 Salinah,1 Alvita Dewi Siswoyo,9 Maria Francisca Ham1,2 1Department of Anatomical Pathology, Faculty of Medicine Universitas Indonesia/Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia; 2Human Cancer Research Center-Indonesian Medical Education and Research Institute,…

1Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China; 2Department of Clinical Laboratory, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China Correspondence: Qian Chen, Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China, Tel +8618951768213, Email [email protected]…

Wozniakowski G, Samorek-Salamonowicz E: Animal herpesviruses and their zoonotic potential for cross-species infection. Ann Agric Environ Med 2015, 22:191–194. Article  CAS  PubMed  Google Scholar  He W, Auclert LZ, Zhai X, Wong G, Zhang C, Zhu H, Xing G, Wang S, He W, Li K, et al: Interspecies Transmission, genetic diversity,…

Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article  Google Scholar  Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article  Google Scholar  Erickson AB. The…

I have multiple bed files (master_gr.bed, gr_2.bed, gr_3.bed) and want to find complete overlaps/intersection but seem to be getting results with at least 1 overlap Here, i simulated data set with R and highlighted the spurious results. line ‘chr1 2 2’ is represented by only 1 file hence should not…

Stability: RNA molecules are inherently unstable and prone to degradation by nucleases. Protecting RNA from degradation during synthesis, purification, and storage is crucial to maintain its integrity and functionality. Purity: Contaminants, such as residual DNA, chemicals, or other impurities, can affect the quality and activity of synthesized RNA. Thorough purification…

1. Introduction Diffuse large B-cell lymphoma (DLBCL) represents an aggressive subtype of Non-Hodgkin’s lymphomas (NHL) that accounts for approximately 40% of such tumours [1]. DLBCL is a highly heterogeneous disease that has an estimated 5-year survival of 69% in some studies [2]. The treatment is generally centred around the CHOP…

Introduction Microalgae encompass a large number of organisms with both prokaryotic and eukaryotic nature, making them an archetypal platform for recombinant technology (Malla et al., 2021). The nutraceutical significance of microalgae is characterized by their rich natural biomolecules and high amount of protein, vitamins, and lipid substances (Potvin and Zhang, 2010;…

Samples used in this observational cohort study (tumor tissue and matched healthy colon tissue, AC-ICAM cohort) are from patients with colon cancer diagnosed at Leiden University Medical Center, the Netherlands, from 2001 to 2015 that did not object for future use of human tissues for scientific research and that were…

Phthalates (PAEs) are commonly utilized as plasticizers within the plastic industry to enhance the flexibility, transparency, durability, and lifespan of plastics [1]. However, these phthalate-based plasticizers have a tendency to leach into the environment rather than forming a covalent bond with the resin [2]. Due to their extensive use, plasticizer…

 This article explores sequencing coverage fundamentals. Uncover key concepts and discover how highly accurate long-read sequencing provides a comprehensive view of the genome, at any coverage level.  What is sequencing coverage? Genomics professionals use the terms “sequencing coverage” or “sequencing depth” to describe the number of unique sequencing reads that…

Life Science Instrumentation Market The global life science instrumentation market is projected to reach USD 73.9 billion by 2028 from USD54.9 billion in 2023, at a CAGR of 6.1% from 2023 to 2028.Factors such as increasing funding and grants supporting research and development, rising proteomics research, and increasing prevalence of…

FastQC Function AMPERE quality control tool for elevated throughput sequence data. Your Java What A match Java Runtime Ecology This Picard BAM/SAM Libraries (included in download) Code Maturation Robust. Mature code, but feedback exists comprehended. Code Released No, under GPL v3 or later. Initial Contact Simon Andrews Download Now Views…

PRESS RELEASE Published May 17, 2023 The breast implants market has experienced significant growth and evolution over the years, driven by factors such as increasing aesthetic consciousness, advancements in implant technology, and a rising number of breast reconstruction procedures. Breast implants are medical devices used to enhance breast size and…

Cells 2023, 12(10), 1415; doi.org/10.3390/cells12101415 (registering DOI) Cells 2023, 12(10), 1415; doi.org/10.3390/cells12101415 (registering DOI) Received: 22 March 2023 / Revised: 28 April 2023 / Accepted: 15 May 2023 / Published: 17 May 2023 Round 1 Reviewer 1 Report this is an interesting paper on the role of FBXW7, a protein that regulates…

Topic participation The examine protocol was accredited by the ethics committees of Osaka College and associated medical establishments in addition to the Translational Well being Science and Know-how Institute (Faridabad). Japanese people (n = 343) for whom intestine metagenome shotgun sequencing had been carried out in earlier research had been included on…

Polymerase chain reaction (PCR) has revolutionized the field of molecular biology and genomics since its invention in the 1980s. This versatile technique enables the amplification of specific DNA sequences from minute samples, generating multiple copies for further analysis. As an indispensable tool in modern research, PCR plays a critical role…

Mitogenome features Nine new mitogenomes were assembled and annotated. Their circular maps were similar, thus only the map of Abraximorpha esta is shown (Fig. 1, Supplementary Fig. S1). The length of the mitogenomes ranged from the shortest, 15,284 bp (Coladenia maeniata) to the longest, 15,853 bp (Lotongus saralus chinensis and Trapezites iacchus). Each…

The M5 Competition, hosted on Kaggle, has recently drawn attention to the effectiveness of gradient-boosting methods for volume forecasts of retail products. In this article, we will focus on the accuracy track of the competition and tackle a time series problem. By replicating one of the top-ranking, yet simplest and…

Metabolites 2023, 13(5), 661; doi.org/10.3390/metabo13050661 (registering DOI) Metabolites 2023, 13(5), 661; doi.org/10.3390/metabo13050661 (registering DOI) Received: 5 April 2023 / Revised: 11 May 2023 / Accepted: 13 May 2023 / Published: 16 May 2023 Round 1 Reviewer 1 Report The manuscript titled “The evaluation of CYP2D6, CYP2C9, CYP2C19 and CYP2B6 phenoconversion in post-mortem…

Subject participation The study protocol was approved by the ethics committees of Osaka University and related medical institutions as well as the Translational Health Science and Technology Institute (Faridabad). Japanese individuals (n = 343) for whom gut metagenome shotgun sequencing were performed in previous studies were included in this study46,47,48. Among these…

Background: Over the past years, sequencing technologies have expanded our ability to examine novel microbial metabolisms and diversity previously obscured by isolation approaches. Long-read sequencing promises to revolutionize the metagenomic field and recover less fragmented genomes from environmental samples. Nonetheless, how to best benefit from long-read sequencing and whether long-read…

  Post Hoc Analyses of Phase 2 Study of Crinecerfont in Adults with CAH Demonstrate Androgen Reduction Across a Broad Range of Glucocorticoid Doses Post Hoc Analyses of Phase 3 Study Demonstrate EFMODY® (hydrocortisone modified-release hard capsules) Reduced Androgen Levels Compared to Immediate-Release Hydrocortisone in…

At rstudio::conf(2022) our workshops featured hands-on exercises, discussions, and Q&A forums. This was an opportunity to meet, share, and collaborate with …In July, we wrapped up rstudio::conf(2022). Throughout the conference, we had an exciting array of workshops, an inspiring lineup of speakers, Birds of a …We are delighted to announce the rstudio::conf…

Transcript: Andre H. Goy, MD: Generally speaking, how has the treatment paradigm of large cell lymphoma shifted in recent years? In particular, how many patients develop relapsed/refractory disease? Andrew Ip, MD: It’s probably easier to answer the second question. There are already great statistics from the post-rituximab era from the…

Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq? 1 Or “Everything You Always Wanted to Know About RNA-Seq (But Were Afraid to Ask) Part 2” In RNA-Seq, it is common practice to compare the abundance of transcripts within the same sample after some form of…

NEW YORK − An international team of researchers has come up with an updated version of the human reference genome — a pangenome — that combines phased diploid assemblies from 47 individuals of diverse ancestries. The new reference is more inclusive and provides a more complete image of the human genome than…

Transcribed image text: 3c. You isolate all of the bacterial species present in your favorite local environment. After you sequence all of the 16S rRNA sequences present in this environment, how would creation of your phylogenetic tree be affected by this particular environment being highly mutagenic? How would this phylogenetic…

GC content of WES cohort 0 Hello, I know a lot of questions have been asked before about GC content, but I just wanted to see if anyone had experience with WES GC content. I have 134 WES (not all the same exome panel or from the same sequencing company)….

In this article, we present a description of the genome sequencing data and the draft genome of L. plantarum FCa3L. Genome sequencing was performed using the Illumina MiSeq platform and a total of 40 Mb raw data was obtained. The genome sequence of L. plantarum FCa3L at 30× coverage was…

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)…

Enter a project name for your analyze runner. This name will help you identify insert final in case yours do manifold runs in a brawl. Provision of an email site exists optional, but desires rented you safely close the browser during the analysis and receive a notification following verwirklichung. Upload…

According to Glaukos, the Prescription Drug User Fee Act goal date for the completion of the FDA’s review of the iDose TR NDA is set for December 22, 2023. (Image courtesy of Adobe Stock) Glaukos Corp. today announced it has received the “Day 74” notification from the FDA acknowledging its…

Whole genome sequencing of viruses is playing an increasingly important role in clinical practice. On the one hand, analyzing the drug resistance information of the virus can assist in more accurate clinical diagnosis, treatment, and disease course management; On the other hand, through the establishment of molecular epidemiology of the…

We present a method for culturing and gene editing primary rhesus macaque B cells using CRISPR/Cas9 and recombinant adeno-associated virus serotype 6 for the study of B cell therapies. The method is relatively simple and allows efficient gene editing of rhesus macaque B cells. The method allows the testing of…

1. Introduction Melioidosis is a tropical disease caused by the aerobic, Gram-negative motile bacillus which is classified as a category B biological agent by the Centers for Disease Control and Prevention (CDC) of America (1, 2). It is a highly pathogenic endemic zoonotic disease in many tropical countries, particularly in…

Hi, I am optimizing pipeline for CNV analysis of WES data. I was getting quite strange output out of CNVkit, so I tried to run the same data as both, tumor (sample) and control (from which the reference is build). To my surprise the output contained quite a variable bins…

1. Introduction Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella, which affects domestic livestock and a wide range of wild mammals (Ducrotoy et al., 2017). The disease is amongst the most common zoonotic infections globally, with an estimated 500,000 human cases annually (Pappas et al., 2006),…

1. Introduction Pyropia is a representative genus in the rhodophyte order Bangiales. It is of fundamental commercial and social importance as the edible seaweed “nori” [1]. Pyropia species, particularly Pyropia yezoensis (also referred to as Neopyropia yezoensis) and Pyropia haitanensis (also referred to as Neoporphyra haitanensis), are widely cultivated in…

Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: A Resource for fungal biology and biotechnology. Abstract Agaricus subrufescens, also known as the “mushroom of the sun,” has significant nutritional and medicinal value. However, its short shelf life due to the browning process results in post-harvest losses unless it’s quickly…

Ethics statement All animal experimental procedures were approved by the Biomedical Ethics Committee of Qufu Normal University (approval number: 2022001). Sampling and sequening The experimental sample is a wounded male duck found during the wild bird survey in Jiangsu, China, which died unexpectedly during rescue. We dissected the sample and…

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Allis CD, Jenuwein T. The molecular hallmarks of epigenetic control. Nat Rev Genet. 2016;17:487–500. Article  CAS  PubMed  Google Scholar  Boccaletto P, Stefaniak F, Ray A, Cappannini A, Mukherjee S, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 2022;50:D231–D235. Article  CAS  PubMed  Google…

Agreement evaluates induced pluripotent stem cell-derived feeder cells to improve NK manufacturing NEWARK, N.J. and SEATTLE, May 2, 2023 /PRNewswire/ — BioCentriq, Inc. and panCELLa, a Pluristyx Company, announced that they have signed a research agreement designed to evaluate the ability of panCELLa’s genetically-engineered, induced Pluripotent Stem Cell (iPSC)-derived, feeder…

Three samples of S. 4,[5],12:i:-, all isolated in 2010, harbored mcr-3.1. Two were from human stool and the other was from ready-to-eat frozen food. Phenotypic characterization confirmed that all three isolates were resistant to colistin, all with MIC and MBC of 8 µg/ml. WGS of H1-012, H1-014 and H1-120 were analyzed…

Study design The objective of the study was to evaluate the influence of long-term WD intake on intestinal inflammation and investigate possible mechanisms by which WD intake could affect IBD development. To this end, mice were fed normal diet (ND) or WD for 10 weeks, and bowel inflammation was evaluated through…

Tissue collection and crypt isolation A small piece of colon is collected from individuals who have undergone surgery to remove part of the colon under the standard of care at either Keck Hospital of USC or Children’s Hospital Los Angeles through the Norris Comprehensive Cancer Center Translational Pathology Core. A…

CircRNA expression profiles in GC progression plus bioinformatics prediction analysis High-throughput individual circRNA microarray was conducted using plasma sample free 10 GC patients, containing 5 patients with T1-3N0M0 (case1) and the other 5 sufferers with T3 N1-3 M0 (case2), and 5 normal individuals (control) up judgment circRNA expressing profiles in GC progression….

Introduction The worldwide dissemination of carbapenem-resistant Enterobacteriaceae (CRE), particularly carbapenem-resistant K. pneumoniae (CRKP), poses a significant risk to public health. CRKP can cause various infections, such as urinary tract infections, bloodstream infections, and pneumonia, leading to high morbidity and mortality.1 Prevention and control of K. pneumoniae infection are becoming more…

Typhoid GBD, Paratyphoid C. The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Infect Dis. 2019;19(4):369–81. Article  Google Scholar  Arndt MB, Mosites EM, Tian M, Forouzanfar MH, Mokhdad AH, Meller M, Ochiai RL, Walson JL. Estimating the burden of…

The Ribosome: historical monolith – evolutionary chameleon The ribosome is generally considered a highly conserved ribonucleoprotein complex translating messenger RNA (mRNA) into proteins, a function that makes it essential across all species and domains of life. Composed of ribosomal RNAs (rRNAs) and proteins (r-proteins), and assembled from a small and…

Expression of PPP2R3B/ppp2r3b in human foetuses and zebrafish To begin to investigate the requirement for PR70 in vertebrates, we looked for expression of PPP2R3B in human foetuses. The orientation of tissue sections used is given in Supplementary Fig. 1. Using in situ hybridisation, we noted some locations of PPP2R3B expression that…

Saudi Arabia Laboratories Market to reach USD 1.46 Billion by 2030 : Growth Driven by Rising Demand for High Quality Healthcare Services and Technological Advancements. Ohio, Cleveland, April 25, 2023 (GLOBE NEWSWIRE) — Market Overview: In Saudi Arabia, laboratories are vital for preserving the public’s health, fostering creativity, and advancing…

Feldhaar H. Bacterial symbionts as mediators of ecologically important traits of insect hosts. Ecol Entomol. 2011;36:533–43. Article  Google Scholar  Douglas AE. Symbiosis as a general principle in eukaryotic evolution. Cold Spring Harb Perspect Biol. 2014;6:a016113–a016113. Article  PubMed  PubMed Central  Google Scholar  Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive…

BeiGene Announces Positive Phase 3 Tislelizumab Trial in Advanced Gastric or Gastroesophageal Junction Adenocarcinoma Details Category: Antibodies Published on Friday, 21 April 2023 11:28 Hits: 161 Superior overall survival for tislelizumab plus chemotherapy versus chemotherapy in first-line treatment setting BASEL, Switzerland & BEIJING, China & CAMBRIDGE, MA, USA I…

AMD Ryzen Threadripper 1950X 16-Core testing with a ASUS PRIME X399-A (1203 BIOS) and llvmpipe on Linuxmint 20.3 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2304201-NE-VAILAMMPS89 Threadripper 1950X lammps Processor: AMD Ryzen Threadripper…

     Seq2science ChIP-seq hub ChIP-seqhidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 updated Fix Patcheshidedensesquishpackfull p14 updated Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow Problematic Regionshidedensesquishpackfull new Recomb…

State-of-the-art phylogenomic pipelines require many steps, which can be both time consuming and error prone (Fig. 1a). With Read2Tree, we directly process raw sequencing reads and reconstruct sequence alignments for conventional tree inference methods (Fig. 1b and Supplementary Fig. 1). We start by aligning raw reads to nucleotide sequences derived…

As depicted below, a kubernetes API server is at the heart of any kyma/k8s cluster. The API server exposes an HTTP API for pretty much every single k8s cluster object Whether using kubectl command line interface or a kubernetes client library, the communication is passing through the kubernetes API server…

YONGIN, South Korea, April 18, 2023 /PRNewswire/ — GC Genome Corporation, a leading diagnostics company, today announced that the company will present data showcasing the deep learning algorithm that detects and classifies multi-cancer using methylation information and genomic data at the American Association for Cancer Research (AACR) Annual Meeting 2023…

Lisa Ximena Rodriguez-Rojas,1,2 Estephania Candelo,3,4 Harry Pachajoa,1,2,4 Juan Esteban Garcia-Robledo,3 Jose Antonio Nastasi-Catanese,1,2 Jorge Andres Olave-Rodriguez,2 Angela R Zambrano5 1Department of Human Genetics, Fundación Valle del Lili, Cali, Colombia; 2Faculty of Health Sciences, Universidad Icesi, Cali, Colombia; 3Fundación Valle del Lili, Centro de Investigaciones Clínicas, Cali, Colombia; 4Centro de Investigaciones…

[London, 05 April 2023] — PCR Biosystems has launched a new proofreading polymerase mix for NGS library preparation workflows. VeriFi™ Library Amplification Mix combines the powerful and robust performance of VeriFi™ Hot Start Polymerase with greatly reduced GC-dependent bias to push the limits of NGS data. Guaranteeing quality when sequencing…

Molecular identification and phylogenetic relationship of Bangladeshi pufferfish based on mitochondrial COI and 16S rRNA genes Abstract Pufferfish is common in marine, brackish and freshwater habitats in Bangladesh. Pufferfish poisoning sporadically occurs due to the consumptions of toxic pufferfish throughout the country. A study was conducted for molecular characterization and…

Akoya Biosciences PhenoCode Discovery Panels and Enable Cloud Platform Akoya Biosciences has launched PhenoCode Discovery Panels to simplify spatial biology workflows on the company’s PhenoCycler-Fusion platform. The ready-to-use, modular panels include biomarkers that can answer key biological questions related to immune profiling, lymphocyte profiling, tissue architecture, and immune activation and proliferation,…

At rstudio::conf(2023) our workshops featured hands-on exercises, discussions, and Q&A forums. This was an opportunity to meet, share, and collaborate with …In July, we wrapped up rstudio::conf(2023). Throughout the conference, we had an exciting array of workshops, an inspiring lineup of speakers, Birds of a …We are delighted to announce the rstudio::conf…

Back to Bioinformatics Main Menu Evaluation FastQC GCATemplates available: grace terra module spider FastQC After running FastQC via the command line, you can ssh to an HPRC cluster enabling X11 forwarding by using the -X option and view the images using the eog tool. From your desktop: ssh -X username@grace.hprc.tamu.edu From your FastQC working…

Agency for Toxic Substances and Disease Registry (ATSDR) (2002) Toxicological profile for copper. Atlanta, GA: Centers for Disease Control Ahemad M (2012) Implications of bacterial resistance against heavy metals in bioremediation: A review. IIOAB J 3:39–46 CAS  Google Scholar  Alcamán-Arias ME, Pedrós-Alió C, Tamames J, Fernández C, Pérez-Pantoja D, Vásquez M,…

Introduction Ovarian cancer is one of the most common gynecologic malignancies with high morbidity.1 Due to its relatively asymptomatic nature, about 70% of patients are diagnosed at an advanced stage and have poor prognosis, leading to high mortality rates.2,3 The clinical treatment of ovarian cancer mainly relies on chemotherapy after…

The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…

PCR Biosystems has launched a new proofreading polymerase mix for NGS library preparation workflows. VeriFi Library Amplification Mix combines the powerful and robust performance of VeriFi Hot Start Polymerase with greatly reduced GC-dependent bias to push the limits of NGS data. Guaranteeing quality when sequencing long and complex targets, VeriFi Library Amplification Mix…