1,693 results match your criteria repertoire profiling

Stage- and sex-specific transcriptome analyses reveal distinctive sensory gene expression patterns in a butterfly.

BMC Genomics 2021 Aug 2;22(1):584. Epub 2021 Aug 2.

Department of Biological Sciences, University of Arkansas, 72701, Fayetteville, AR, USA.

Background: Animal behavior is largely driven by the information that animals are able to extract and process from their environment. However, the function and organization of sensory systems often change throughout ontogeny, particularly in animals that undergo indirect development. As an initial step toward investigating these ontogenetic changes at the molecular level, we characterized the sensory gene repertoire and examined the expression profiles of genes linked to vision and chemosensation in two life stages of an insect that goes through metamorphosis, the butterfly Bicyclus anynana. Read More

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Antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W.

Nat Commun 2021 07 29;12(1):4608. Epub 2021 Jul 29.

Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA.

The ubiquitin conjugating enzyme UBE2W catalyzes non-canonical ubiquitination on the N-termini of proteins, although its substrate repertoire remains unclear. To identify endogenous N-terminally-ubiquitinated substrates, we discover four monoclonal antibodies that selectively recognize tryptic peptides with an N-terminal diglycine remnant, corresponding to sites of N-terminal ubiquitination. Importantly, these antibodies do not recognize isopeptide-linked diglycine (ubiquitin) modifications on lysine. Read More

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Bacteria tolerant to colistin in coastal marine environment: Detection, microbiome diversity and antibiotic resistance genes' repertoire.

Chemosphere 2021 Oct 21;281:130945. Epub 2021 May 21.

Department of Biology, Faculty of Science, University of Split, Split, Croatia. Electronic address:

The global spread of mobilized colistin resistance (mcr) genes in clinical and natural environments dangerously diminishes the effectiveness of this last-resort antibiotic, becoming an urgent health threat. We used a multidisciplinary approach to detect mcr-1 gene and colistin (CL)-resistant bacteria in seawater from two Croatian public beaches. Illumina-based sequencing of metagenomic 16S rRNA was used to assess the taxonomic, functional, and antibiotic resistance genes (ARGs) profiling of the bacterial community tolerant to CL regarding different culture-based isolation methodologies. Read More

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October 2021

Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data.

Nat Commun 2021 07 19;12(1):4385. Epub 2021 Jul 19.

Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX, USA.

As the capacity for generating large-scale molecular profiling data continues to grow, the ability to extract meaningful biological knowledge from it remains a limitation. Here, we describe the development of a new fixed repertoire of transcriptional modules, BloodGen3, that is designed to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome data. The construction of this repertoire is based on co-clustering patterns observed across sixteen immunological and physiological states encompassing 985 blood transcriptome profiles. Read More

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Profiling the Genetic and Molecular Characteristics of Glanzmann Thrombasthenia: Can It Guide Current and Future Therapies?

Alan Nurden

J Blood Med 2021 8;12:581-599. Epub 2021 Jul 8.

Institut Hospitalo-Universitaire LIRYC, Pessac, France.

Glanzmann thrombasthenia (GT) is the most widely studied inherited disease of platelet function. Platelets fail to aggregate due to a defect in platelet-to-platelet attachment. The hemostatic plug fails to form and a moderate to severe bleeding diathesis results. Read More

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Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade.

Nat Med 2021 Jul 8. Epub 2021 Jul 8.

Department of Surgery, University of Rochester Medical Center, Rochester, NY, USA.

Treatment with combined immune checkpoint blockade (CICB) targeting CTLA-4 and PD-1 is associated with clinical benefit across tumor types, but also a high rate of immune-related adverse events. Insights into biomarkers and mechanisms of response and toxicity to CICB are needed. To address this, we profiled the blood, tumor and gut microbiome of 77 patients with advanced melanoma treated with CICB, with a high rate of any ≥grade 3 immune-related adverse events (49%) with parallel studies in pre-clinical models. Read More

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Clinical efficacy of T-cell therapy after short-term BRAF-inhibitor priming in patients with checkpoint inhibitor-resistant metastatic melanoma.

J Immunother Cancer 2021 Jul;9(7)

National Center for Cancer Immune Therapy, Department of Oncology, Herlev University Hospital, Herlev, Denmark

Purpose: Despite impressive response rates following adoptive transfer of autologous tumor-infiltrating lymphocytes (TILs) in patients with metastatic melanoma, improvement is needed to increase the efficacy and broaden the applicability of this treatment. We evaluated the use of vemurafenib, a small-molecule BRAF inhibitor with immunomodulatory properties, as priming before TIL harvest and adoptive T cell therapy in a phase I/II clinical trial.

Methods: 12 patients were treated with vemurafenib for 7 days before tumor excision and during the following weeks until TIL infusion. Read More

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A Rapid Pipeline for Pollen- and Anther-Specific Gene Discovery Based on Transcriptome Profiling Analysis of Maize Tissues.

Int J Mol Sci 2021 Jun 26;22(13). Epub 2021 Jun 26.

State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.

Recently, crop breeders have widely adopted a new biotechnology-based process, termed Seed Production Technology (SPT), to produce hybrid varieties. The SPT does not produce nuclear male-sterile lines, and instead utilizes transgenic SPT maintainer lines to pollinate male-sterile plants for propagation of nuclear-recessive male-sterile lines. A late-stage pollen-specific promoter is an essential component of the pollen-inactivating cassette used by the SPT maintainers. Read More

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The Fungal Effector Mlp37347 Alters Plasmodesmata Fluxes and Enhances Susceptibility to Pathogen.

Microorganisms 2021 Jun 6;9(6). Epub 2021 Jun 6.

Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC G8Z 4M3, Canada.

is a devastating pathogen of poplar trees, causing the defoliating poplar leaf rust disease. Genomic studies have revealed that possesses a repertoire of 1184 small secreted proteins (SSPs), some of them being characterized as candidate effectors. However, how they promote virulence is still unclear. Read More

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TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

Nucleic Acids Res 2021 Jul 1. Epub 2021 Jul 1.

Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.

Advances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Read More

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Profiling of T Cell Receptor β-Chain Complimentary Determining Regions 3 Repertoire in Subarachnoid Hemorrhage Patients Using High-Throughput Sequencing.

J Korean Neurosurg Soc 2021 Jul 29;64(4):505-513. Epub 2021 Jun 29.

Institute of New Frontier Stroke Research, Hallym University College of Medicine, Chuncheon, Korea.

Objective: The adaptive immune response following subarachnoid hemorrhage (SAH) is not well understood. We evaluated and compared the T cell receptor (TCR) immune repertoire of good-grade and poor-grade SAH patients to elucidate the T cell immunology after ictus.

Methods: Peripheral blood from six SAH patients was collected at two different times, admission and at the 7-day follow-up. Read More

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Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs.

Cell 2021 07 3;184(15):3962-3980.e17. Epub 2021 Jun 3.

Harvard Medical School, Boston, MA 02115, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.

T cell-mediated immunity plays an important role in controlling SARS-CoV-2 infection, but the repertoire of naturally processed and presented viral epitopes on class I human leukocyte antigen (HLA-I) remains uncharacterized. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two cell lines at different times post infection using mass spectrometry. We found HLA-I peptides derived not only from canonical open reading frames (ORFs) but also from internal out-of-frame ORFs in spike and nucleocapsid not captured by current vaccines. Read More

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Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum.

Nat Commun 2021 06 21;12(1):3820. Epub 2021 Jun 21.

Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.

Our current understanding of mitochondrial functioning is largely restricted to traditional model organisms, which only represent a fraction of eukaryotic diversity. The unusual mitochondrion of malaria parasites is a validated drug target but remains poorly understood. Here, we apply complexome profiling to map the inventory of protein complexes across the pathogenic asexual blood stages and the transmissible gametocyte stages of Plasmodium falciparum. Read More

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Cytokine Overproduction and Immune System Dysregulation in alloHSCT and COVID-19 Patients.

Front Immunol 2021;12:658896. Epub 2021 Jun 2.

Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland.

The COVID-19 pathomechanism depends on (i) the pathogenicity of the virus, (ii) ability of the immune system to respond to the cytopathic effect of the virus infection, (iii) co-morbidities. Inflammatory cytokine production constitutes a hallmark of COVID-19 that is facilitated by inability of adaptive immunity to control virus invasion. The effect of cytokine release syndrome is deleterious, but the severity of it depends on other confounding factors: age and comorbidities. Read More

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Long read transcript profiling of ion channel splice isoforms.

Methods Enzymol 2021 7;654:345-364. Epub 2021 Apr 7.

Department of Psychiatry, University of Oxford, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom. Electronic address:

Alternative splicing of RNA transcripts allows a single gene to generate multiple products and is a key means of generating functionally diverse voltage-gated ion channels. Splicing can be regulated according to cell type, cell state, and stage of development to produce a bespoke complement of protein isoforms. Characterizing the identities of full-length transcript isoforms is essential in order to fully understand a gene's expression and function. Read More

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Molecular Insights into the Role of Cysteine-Rich Peptides in Induced Resistance to Infection in Tomato Based on Transcriptome Profiling.

Int J Mol Sci 2021 May 27;22(11). Epub 2021 May 27.

Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General Genetics RAS, 119333 Moscow, Russia.

Cysteine-rich peptides (CRPs) play an important role in plant physiology. However, their role in resistance induced by biogenic elicitors remains poorly understood. Using whole-genome transcriptome sequencing and our CRP search algorithm, we analyzed the repertoire of CRPs in tomato L. Read More

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Interrelationship between miRNA and splicing factors in pancreatic ductal adenocarcinoma.

Epigenetics 2021 May 30:1-24. Epub 2021 May 30.

Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUMC), Amsterdam, The Netherlands.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers because of diagnosis at late stage and inherent/acquired chemoresistance. Recent advances in genomic profiling and biology of this disease have not yet been translated to a relevant improvement in terms of disease management and patient's survival. However, new possibilities for treatment may emerge from studies on key epigenetic factors. Read More

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Profiling T cell receptor β-chain in responders after immunization with recombinant hepatitis B vaccine.

J Gene Med 2021 May 28:e3367. Epub 2021 May 28.

State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.

Background: T cells with edited T cell receptor β-chain variable (TRBV) are involved in the immune response to recombinant hepatitis B surface antigen (rHBsAg) vaccine and the production of hepatitis B surface antibody (HBsAb). The immune repertoire (IR) profile and mechanism of vaccination positive responders (VPR) with rHBsAg are not fully understood.

Methods: The IR of six VPRs (HBsAb+, HbsAg-) with rHBsAg vaccination was established by the high throughput sequencing technique and bioinformatics analysis and compared with those in five vaccination negative responders (VNRs) (HbsAb-, HbsAg-) who were also inoculated with rHBsAg. Read More

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Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling.

Elife 2021 May 26;10. Epub 2021 May 26.

Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.

Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community's Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Read More

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Dissection of the anti-Candida albicans mannan immune response using synthetic oligomannosides reveals unique properties of β-1,2 mannotriose protective epitopes.

Sci Rep 2021 May 24;11(1):10825. Epub 2021 May 24.

INSERM U1285, Univ. Lille, CHU de Lille, UMR CNRS 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France.

Candida albicans mannan consists of a large repertoire of oligomannosides with different types of mannose linkages and chain lengths, which act as individual epitopes with more or less overlapping antibody specificities. Although anti-C. albicans mannan antibody levels are monitored for diagnostic purposes nothing is known about the qualitative distribution of these antibodies in terms of epitope specificity. Read More

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B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.

Cell 2021 06 24;184(12):3205-3221.e24. Epub 2021 Apr 24.

Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.

Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell sorting with single-cell VDJ and RNA sequencing (RNA-seq) and mAb structures to characterize B cell responses against SARS-CoV-2. We show that the SARS-CoV-2-specific B cell repertoire consists of transcriptionally distinct B cell populations with cells producing potently neutralizing antibodies (nAbs) localized in two clusters that resemble memory and activated B cells. Read More

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Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq.

Signal Transduct Target Ther 2021 05 17;6(1):195. Epub 2021 May 17.

School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China.

B cell response plays a critical role against SARS-CoV-2 infection. However, little is known about the diversity and frequency of the paired SARS-CoV-2 antigen-specific BCR repertoire after SARS-CoV-2 infection. Here, we performed single-cell RNA sequencing and VDJ sequencing using the memory and plasma B cells isolated from five convalescent COVID-19 patients, and analyzed the spectrum and transcriptional heterogeneity of antibody immune responses. Read More

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Comparative proteomics of is a useful toolbox for developing prophylactic interventions in a One-Health context.

One Health 2021 Dec 23;13:100253. Epub 2021 Apr 23.

Department of Health Sciences, University "Magna Græcia" of Catanzaro, viale Europa, 88100 Catanzaro, Italy.

Brucellosis caused by is a zoonosis frequently reported in the Mediterranean and Middle-East regions and responsible for important economic losses and reduced animal welfare. To date, current strategies applied to control or eradicate the disease relies on diagnostic tests that suffer from limited specificity in non-vaccinated animals; while prophylactic measures, when applied, use a live attenuated bacterial strain characterized by residual virulence on adult pregnant animals and difficulties in distinguishing vaccinated from infected animals. To overcome these issues, studies are desired to elucidate the bacterial biology and the pathogenetic mechanisms of both the vaccinal strain and the pathogenic strains. Read More

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December 2021

Transcriptome dynamics underlying elicitor-induced defense responses against Septoria leaf spot disease of tomato ( L.).

Physiol Mol Biol Plants 2021 Apr 31;27(4):873-888. Epub 2021 Mar 31.

Unit of Plant Pathology, Center for Advanced Studies in Botany, University of Madras, Tamil Nadu, Guindy Campus, Chennai, 600 025 India.

Elicitor-induced defense response against potential plant pathogens has been widely reported in several crop plants; however, transcriptome dynamics underlying such defense response remains elusive. Our previous study identified and characterized a novel elicitor, κ-carrageenan, from , a marine red seaweed. Our preliminary studies have shown that the elicitor-treatment enhances the tolerance of a susceptible tomato cultivar to (causative agent of leaf spot disease). Read More

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Single-Cell TCR Sequencing Reveals the Dynamics of T Cell Repertoire Profiling During Infection.

Front Microbiol 2021 20;12:637500. Epub 2021 Apr 20.

Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.

T cell responses play critical roles in host adaptive immunity against . However, the dynamics and diversity of the T cell immune repertoire in human immunodeficiency virus (HIV)-negative pneumonia (PCP) remains unclear. In this study, single-cell RNA and single-cell T cell receptor (TCR) sequencing were applied to cells sorted from lung tissues of mice infected with . Read More

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Profiling of T Cell Repertoire in SARS-CoV-2-Infected COVID-19 Patients Between Mild Disease and Pneumonia.

J Clin Immunol 2021 08 5;41(6):1131-1145. Epub 2021 May 5.

Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a public health emergency. The most common symptoms of COVID-19 are fever, cough, and fatigue. While most patients with COVID-19 present with mild illness, some patients develop pneumonia, an important risk factor for mortality, at early stage of viral infection, putting these patients at increased risk of death. Read More

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Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean.

ISME J 2021 May 3. Epub 2021 May 3.

CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France.

Marine microbes are major drivers of all elemental cycles. The processing of organic carbon by heterotrophic prokaryotes is tightly coupled to the availability of the trace element iron in large regions of the Southern Ocean. However, the functional diversity in iron and carbon metabolism within diverse communities remains a major unresolved issue. Read More

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CMV Status Drives Distinct Trajectories of CD4+ T Cell Differentiation.

Front Immunol 2021 15;12:620386. Epub 2021 Apr 15.

Emory Transplant Center, Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States.

Cytomegalovirus (CMV) is one of the most commonly recognized opportunistic pathogens and remains the most influential known parameter in shaping an individual's immune system. As such, T cells induced by CMV infection could have a long-term impact on subsequent immune responses. Accumulating evidence indicates that memory T cells developed during past bacterial and viral infection can cross-react with unrelated pathogens, including transplant antigens, and can alter responses to infections, vaccines, cancers, or rejection. Read More

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The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in .

Int J Mol Sci 2021 Apr 12;22(8). Epub 2021 Apr 12.

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.

is a facultative human pathogen, causing acute and chronic infections that are especially dangerous for immunocompromised patients. The eradication of is difficult due to its intrinsic antibiotic resistance mechanisms, high adaptability, and genetic plasticity. The bacterium possesses multilevel regulatory systems engaging a huge repertoire of transcriptional regulators (TRs). Read More

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Response to Hypomethylating Agents in Myelodysplastic Syndrome Is Associated With Emergence of Novel TCR Clonotypes.

Front Immunol 2021 12;12:659625. Epub 2021 Apr 12.

Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, United States.

Aberrant T-cell function is implicated in the pathogenesis of myelodysplastic syndrome (MDS). Monitoring the T-cell receptor (TCR) repertoire can provide insights into T-cell adaptive immunity. Previous studies found skewed TCR repertoires in MDS compared to healthy patients; however these studies that leverage mRNA-based spectratyping have limitations. Read More

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