1,086 results match your criteria representative transcripts

Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

iScience 2021 Jul 24;24(7):102782. Epub 2021 Jun 24.

Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.

We present Raptor, a system for approximately searching many queries such as next-generation sequencing reads or transcripts in large collections of nucleotide sequences. Raptor uses winnowing minimizers to define a set of representative -mers, an extension of the interleaved Bloom filters (IBFs) as a set membership data structure and probabilistic thresholding for minimizers. Our approach allows compression and partitioning of the IBF to enable the effective use of secondary memory. Read More

View Article and Full-Text PDF

Ranked Choice Voting for Representative Transcripts with TRaCE.

Bioinformatics 2021 Jul 23. Epub 2021 Jul 23.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11768, USA.

Summary: Genome sequencing projects annotate protein-coding gene models with multiple transcripts, aiming to represent all of the available transcript evidence. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical transcript. To choose canonical transcripts, TRaCE (Transcript Ranking and Canonical Election) holds an 'election' in which a set of RNA-seq samples rank transcripts by annotation edit distance. Read More

View Article and Full-Text PDF

Weathering the storm: A qualitative study of social prescribing in urban and rural Scotland during the COVID-19 pandemic.

SAGE Open Med 2021 30;9:20503121211029187. Epub 2021 Jun 30.

MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK.

Objectives: The non-clinical approach known as social prescribing aims to tackle multi-morbidity, reduce general practitioner (GP) workload and promote wellbeing by directing patients to community services. Usual in-person modes of delivery of social prescribing have been virtually impossible under social distancing rules. This study qualitatively examined and compared the responses of three social prescribing schemes in Scotland to the COVID-19 pandemic. Read More

View Article and Full-Text PDF

Accurate transcriptome assembly by Nanopore RNA sequencing reveals novel functional transcripts in hepatocellular carcinoma.

Cancer Sci 2021 Jul 13. Epub 2021 Jul 13.

The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.

The long reads of Nanopore sequencing permit accurate transcript assembly and ease in discovering novel transcripts with potentially important functions in cancers. The wide adoption of Nanopore sequencing for transcript quantification, however, is largely limited by high costs. To address this issue, we developed a bioinformatics software, NovelQuant, that can specifically quantify long-read-assembled novel transcripts with short-read sequencing data. Read More

View Article and Full-Text PDF

Molecular and evolutionary basis for survival, its failure, and virulence factors of the zoonotic nematode Anisakis pegreffii.

Genomics 2021 Jun 27;113(5):2891-2905. Epub 2021 Jun 27.

Laboratory of Functional Helminthology, Institute of Parasitology, Biology Centre of Czech Academy of Science, 37005 Ceske Budejovice, Czech Republic. Electronic address:

Parasitism is a highly successful life strategy and a driving force in genetic diversity that has evolved many times over. Accidental infections of non-targeted hosts represent an opportunity for lateral host switches and parasite niche expansion. However, if directed toward organisms that are phylogenetically distant from parasite's natural host, such as humans, it may present a dead-end environment where the parasite fails to mature or is even killed by host immunity. Read More

View Article and Full-Text PDF

Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes.

Clin Epigenetics 2021 Jun 28;13(1):132. Epub 2021 Jun 28.

Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.

Background: Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such techniques are used routinely in both rodent and human species. DNA methylation is a dynamic process that plays a role in epigenetic regulation of gametogenesis and development. Read More

View Article and Full-Text PDF

Pivoting in the pandemic: a qualitative study of child and adolescent psychiatrists in the times of COVID-19.

Child Adolesc Psychiatry Ment Health 2021 Jun 21;15(1):32. Epub 2021 Jun 21.

Child Study Center, Yale School of Medicine, New Haven, CT, USA.

Objectives: We examined the personal and professional impacts of the COVID-19 pandemic on the development, practice, and shifting values of child and adolescent psychiatrists (CAP), in order to inform how the field may move forward post-pandemic.

Methods: We conducted individual semi-structured interviews of child and adolescent psychiatrists (n = 24) practicing in the United States. Participants were selected as a diverse purposive sample of active members of the American Academy of Child and Adolescent Psychiatry (AACAP). Read More

View Article and Full-Text PDF

Detection of Gene Fusion Transcripts in Peripheral T-Cell Lymphoma Using a Multiplexed Targeted Sequencing Assay.

J Mol Diagn 2021 Aug 18;23(8):929-940. Epub 2021 Jun 18.

INSERM U955, Université Paris-Est, Créteil, France; Pathology Department, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France. Electronic address:

The genetic basis of peripheral T-cell lymphoma (PTCL) is complex and encompasses several recurrent fusion transcripts discovered over the past years by means of massive parallel sequencing. However, there is currently no affordable and rapid technology for their simultaneous detection in clinical samples. Herein, we developed a multiplex ligation-dependent RT-PCR-based assay, followed by high-throughput sequencing, to detect 33 known PTCL-associated fusion transcripts. Read More

View Article and Full-Text PDF

Assessment of a complete and classified platelet proteome from genome-wide transcripts of human platelets and megakaryocytes covering platelet functions.

Sci Rep 2021 Jun 11;11(1):12358. Epub 2021 Jun 11.

Department of Biochemistry, CARIM, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.

Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome-wide transcriptomes (57. Read More

View Article and Full-Text PDF

A Novel Minor Groove Binder as a Potential Therapeutic Agent for Myotonic Dystrophy Type 1.

ChemMedChem 2021 Jun 10. Epub 2021 Jun 10.

Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, 61801, Urbana, IL, USA.

Myotonic dystrophy type 1 (DM1) is a multisystemic neuromuscular disorder that is inherited in an autosomal dominant manner. DM1 originates in a (CTG⋅CAG) repeat expansion in the 3'-UTR of the dystrophia myotonic protein kinase (DMPK) gene on chromosome 19. One of the transcripts, r(CUG) , is toxic in various ways. Read More

View Article and Full-Text PDF

Measurable Residual Disease Detected by Multiparameter Flow Cytometry and Sequencing Improves Prediction of Relapse and Survival in Acute Myeloid Leukemia.

Front Oncol 2021 20;11:677833. Epub 2021 May 20.

Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.

The clinically ideal time point and optimal approach for the assessment of measurable residual disease (MRD) in patients with acute myeloid leukemia (AML) are still inconclusive. We investigated the clinical value of multiparameter flow cytometry-based MRD (MFC MRD) after induction (n = 492) and two cycles of consolidation (n = 421). The latter time point was proved as a superior indicator with independent prognostic significance for both relapse-free survival (RFS, HR = 3. Read More

View Article and Full-Text PDF

Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data.

Comput Struct Biotechnol J 2021 30;19:2708-2718. Epub 2021 Apr 30.

State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.

Bamboo, one of the most crucial nontimber forest resources worldwide, has the capacity for rapid growth. In recent years, the genome of moso bamboo () has been decoded, and a large amount of transcriptome data has been published. In this study, we generated the genome-wide profiles of the histone modification H3K4me3 in leaf, stem, and root tissues of bamboo. Read More

View Article and Full-Text PDF

Primary Care Physicians' Conceptualization of Quality in Medicare's Merit-Based Incentive Payment System.

J Am Board Fam Med 2021 May-Jun;34(3):590-601

From the Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA (CTB, TKN); Department of Emergency Medicine, Cedars-Sinai Medical Center, West Hollywood, CA (CTB); University of California, Los Angeles (UCLA) National Clinician Scholars Program (CTB, MCE); Department of Pediatrics, Cedars-Sinai Medical Center (MCE); Division of Neonatal Medicine, Department of Pediatrics, Los Angeles County and University of Southern California Medical Center (MCE); Kaiser Permanente School of Medicine, Pasadena, CA (GR); Department of Health Policy and Management, UCLA Fielding School of Public Health (JN).

Background: While administrators of pay-for-performance may have good intentions, physicians may be reluctant to participate for various reasons, including poor program alignment with realities of clinical practice. In this study, we sought to characterize how primary care physicians (PCPs) participating in Medicare's Merit-Based Incentive Payment System (MIPS) conceptualize the quality of health care to help inform future measurement strategies that physicians would understand and appreciate.

Methods: We performed semi-structured qualitative interviews with a nationwide sample of 20 PCPs in MIPS. Read More

View Article and Full-Text PDF
October 2020

AoATG5 plays pleiotropic roles in vegetative growth, cell nucleus development, conidiation, and virulence in the nematode-trapping fungus Arthrobotrys oligospora.

Sci China Life Sci 2021 May 17. Epub 2021 May 17.

State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, China.

Autophagy is an evolutionarily conserved process in eukaryotes, which is regulated by autophagy-related genes (ATGs). Arthrobotrys oligospora is a representative species of nematode-trapping (NT) fungi that can produce special traps for nematode predation. To elucidate the biological roles of autophagy in NT fungi, we characterized an orthologous Atg protein, AoAtg5, in A. Read More

View Article and Full-Text PDF

Transcriptome analyses of urine RNA reveal tumor markers for human bladder cancer: validated amplicons for RT-qPCR-based detection.

Oncotarget 2021 May 11;12(10):1011-1023. Epub 2021 May 11.

Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck D-23538, Germany.

Non-invasive clinical diagnostics of bladder cancer is feasible via a set of chemically distinct molecules including macromolecular tumor markers such as polypeptides and nucleic acids. In terms of tumor-related aberrant gene expression, RNA transcripts are the primary indicator of tumor-specific gene expression as for polypeptides and their metabolic products occur subsequently. Thus, in case of bladder cancer, urine RNA represents an early potentially useful diagnostic marker. Read More

View Article and Full-Text PDF

Primary care provider perspectives on screening mammography in older women: A qualitative study.

Prev Med Rep 2021 Jun 17;22:101380. Epub 2021 Apr 17.

Department of Radiology, Duke University School of Medicine, Durham, United States.

Objective: Guidelines informing screening mammography for older women are lacking. This study sought to characterize PCP perspectives on screening mammography for patients aged 75 and older.

Methods: This was an exploratory, qualitative study based on semi-structured, one-on-one interviews with PCPs from six clinics affiliated with a tertiary medical center. Read More

View Article and Full-Text PDF

Oral Health in Rheumatoid Arthritis: Listening to Patients.

JDR Clin Trans Res 2021 May 5:23800844211012678. Epub 2021 May 5.

Department of Internal Medicine, Max Rady School of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Canada.

Introduction: Rates of periodontal disease and tooth loss are increased in individuals with rheumatoid arthritis (RA). Understanding factors that contribute to the increased burden of periodontal disease in RA is critical to improving oral health and arthritis outcomes.

Objectives: To determine the perceptions held by people with RA relating to their oral health, to identify patient-centered priorities for oral health research, and to inform optimal strategies for delivering oral health knowledge. Read More

View Article and Full-Text PDF

Complexity of gene paralogues resolved in biosynthetic pathway of hepatoprotective iridoid glycosides in a medicinal herb, Picrorhiza kurroa through differential NGS transcriptomes.

Mol Genet Genomics 2021 Jul 25;296(4):863-876. Epub 2021 Apr 25.

Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, 201310, India.

Picrorhiza kurroa is a medicinal herb with diverse pharmacological applications due to the presence of iridoid glycosides, picroside-I (P-I), and picroside-II (P-II), among others. Any genetic improvement in this medicinal herb can only be undertaken if the biosynthetic pathway genes are correctly identified. Our previous studies have deciphered biosynthetic pathways for P-I and P-II, however, the occurrence of multiple copies of genes has been a stumbling block in their usage. Read More

View Article and Full-Text PDF

Multi-omics analysis provides insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600.

Biotechnol Biofuels 2021 Apr 17;14(1):96. Epub 2021 Apr 17.

Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.

Background: Wood-decay basidiomycetes are effective for the degradation of highly lignified and recalcitrant plant substrates. The degradation of lignocellulosic materials by brown-rot strains is carried out by carbohydrate-active enzymes and non-enzymatic Fenton mechanism. Differences in the lignocellulose catabolism among closely related brown rots are not completely understood. Read More

View Article and Full-Text PDF

Attitudes toward medical cannabis among family physicians practising in Ontario, Canada: a qualitative research study.

CMAJ Open 2021 Apr-Jun;9(2):E342-E348. Epub 2021 Apr 13.

Departments of Health Research Methods, Evidence and Impact (Ng, Gilotra, Usman, Chang, Busse) and Anesthesia (Busse), Faculty of Health Sciences, McMaster University; The Chronic Pain Centre of Excellence for Canadian Veterans (Busse); The Michael G. DeGroote Centre for Medicinal Cannabis Research (Busse), McMaster University, Hamilton, Ont.

Background: Medical cannabis has been legally available in Canada since 2001, but its benefits and harms remain uncertain. We explored attitudes toward medical cannabis among family physicians practising in Ontario.

Methods: Between January and October 2019, we conducted a qualitative study of Ontario family physicians using semistructured telephone interviews. Read More

View Article and Full-Text PDF

Comparative Analyses of Full-Length Transcriptomes Reveal e Stem Developmental Dynamics.

Front Genet 2021 25;12:615284. Epub 2021 Mar 25.

Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China.

Genus , of which the majority species are pantropical liana, have broad industrial uses including for string, nets, and paper production. Although numerous studies have investigated anatomical structures during stem development, the underlying molecular mechanisms that regulate this developmental trajectory in species remain poorly understood. A total of 12 full-length transcriptomes were generated from four stem developmental stages of an arborescent representative of this genus, , using Oxford Nanopore Technologies. Read More

View Article and Full-Text PDF

The RD2 Pathogenicity Island Modifies the Disease Potential of the Group A .

Infect Immun 2021 Jul 15;89(8):e0072220. Epub 2021 Jul 15.

Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.

Serotype M28 isolates of the group A (GAS; Streptococcus pyogenes) are nonrandomly associated with cases of puerperal sepsis, a potentially life-threatening infection that can occur in women following childbirth. Previously, we discovered that the 36.3-kb RD2 pathogenicity island, which is present in serotype M28 isolates but lacking from most other isolates, promotes the ability of M28 GAS to colonize the female reproductive tract. Read More

View Article and Full-Text PDF

The Impact of Spaceflight and Microgravity on the Human Islet-1+ Cardiovascular Progenitor Cell Transcriptome.

Int J Mol Sci 2021 Mar 30;22(7). Epub 2021 Mar 30.

Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA.

Understanding the transcriptomic impact of microgravity and the spaceflight environment is relevant for future missions in space and microgravity-based applications designed to benefit life on Earth. Here, we investigated the transcriptome of adult and neonatal cardiovascular progenitors following culture aboard the International Space Station for 30 days and compared it to the transcriptome of clonally identical cells cultured on Earth. Cardiovascular progenitors acquire a gene expression profile representative of an early-stage, dedifferentiated, stem-like state, regardless of age. Read More

View Article and Full-Text PDF

A mixed methods study to evaluate the impact of a student-run clinic on undergraduate medical education.

BMC Med Educ 2021 Mar 25;21(1):182. Epub 2021 Mar 25.

Division of Community Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.

Background: The purpose of this study was to evaluate the extent to which a longitudinal student-run clinic (SRC) is meeting its stated learning objectives, including providing critical community services and developing physicians who more fully appreciate the social factors affecting their patients' health.

Methods: This was a mixed methods program evaluation of an SRC at Mayo Clinic Alix School of Medicine (MCASOM). A survey was conducted of medical students who had participated in the clinic and seven interviews and three focus groups were conducted with SRC patients, students, faculty, staff, and board members. Read More

View Article and Full-Text PDF

Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage.

Genome Res 2021 Apr 15;31(4):732-744. Epub 2021 Mar 15.

Department of Animal Science, University of California, Davis, California 95616, USA.

Characterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was released; however, the functional annotation of the bovine genome lacks precise transcription start sites and contains a low number of transcripts in comparison to human and mouse. Read More

View Article and Full-Text PDF

Alternatively Splicing Interactomes Identify Novel Isoform-Specific Partners for NSD2.

Front Cell Dev Biol 2021 25;9:612019. Epub 2021 Feb 25.

Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.

() plays a fundamental role in the pathogenesis of Wolf-Hirschhorn Syndrome (WHS) and is overexpressed in multiple human myelomas, but its protein-protein interaction (PPI) patterns, particularly at the isoform/exon levels, are poorly understood. We explored the subcellular localizations of four representative transcripts with immunofluorescence microscopy. Next, we used label-free quantification to perform immunoprecipitation mass spectrometry (IP-MS) analyses of the transcripts. Read More

View Article and Full-Text PDF
February 2021

Development of RT-qPCR assays for the detection and quantification of three carlaviruses infecting hop.

J Virol Methods 2021 06 9;292:114124. Epub 2021 Mar 9.

Department of Plant Pathology, Washington State University, Prosser, WA 99350, United States.

American hop latent virus (AHLV), hop latent virus (HLV) and hop mosaic virus (HMV) infect members of the Humulus genus worldwide, but very little is known of the biology and etiology of these viruses. A better understanding of these viruses from the molecular level to their economic impact relies on efficient diagnostic assays. Therefore, in this study we developed reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays for the detection of AHLV, HLV, and HMV through an alignment of representative sequences from the National Center for Biotechnology Information (NCBI) database. Read More

View Article and Full-Text PDF

Pivoting in the pandemic: a qualitative study of child and adolescent psychiatrists in the times of COVID-19.

Res Sq 2021 Mar 4. Epub 2021 Mar 4.

Yale University School of Medicine.

Objectives We examined the personal and professional impacts of the COVID-19 pandemic on the development, practice, and shifting values of child and adolescent psychiatrists (CAP), in order to inform how the field may move forward post-pandemic. Methods We conducted individual semi-structured interviews of child and adolescent psychiatrists (n = 24) practicing in the US. Participants were selected as a diverse purposive sample of active members of the American Academy of Child and Adolescent Psychiatry (AACAP). Read More

View Article and Full-Text PDF

Delivering cognitive therapy for adolescent social anxiety disorder in NHS CAMHS: a qualitative analysis of the experiences of young people, their parents and clinicians-in-training.

Behav Cogn Psychother 2021 Mar 1:1-15. Epub 2021 Mar 1.

Department of Psychology, Aston Triangle, BirminghamB4 7ET, UK.

Background: Social anxiety disorder (SAD) is common. It usually starts in adolescence, and without treatment can disrupt key developmental milestones. Existing generic treatments are less effective for young people with SAD than with other anxiety disorders, but an adaptation of an effective adult therapy (CT-SAD-A) has shown promising results for adolescents. Read More

View Article and Full-Text PDF

The first Conus genome assembly reveals a primary genetic central dogma of conopeptides in C. betulinus.

Cell Discov 2021 Feb 23;7(1):11. Epub 2021 Feb 23.

Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, 518083, China.

Although there are various Conus species with publicly available transcriptome and proteome data, no genome assembly has been reported yet. Here, using Chinese tubular cone snail (C. betulinus) as a representative, we sequenced and assembled the first Conus genome with original identification of 133 genome-widely distributed conopeptide genes. Read More

View Article and Full-Text PDF
February 2021