B cell receptor repertoire analysis in primary Sjogren's syndrome salivary glands identifies repertoire features associated with clinical activity.

Background: Primary Sjogren's syndrome (pSS) is a complex autoimmune disease featuring damage to salivary and lacrimal glands, with the possibility of manifestations across multiple organs. Antibody-producing B cells have long been appreciated to play a significant role in pSS pathogenesis, with a number of autoreactive antibody species having been identified to be elevated in pSS patients. While several studies have attempted to characterize the BCR repertoires of peripheral blood B cells in pSS patients, much remains unknown about the repertoire characteristics of gland-infiltrating B cells.

Screening single-cell trajectories via continuity assessments for cell transition potential.

Advances in single-cell sequencing and data analysis have made it possible to infer biological trajectories spanning heterogeneous cell populations based on transcriptome variation. These trajectories yield a wealth of novel insights into dynamic processes such as development and differentiation. However, trajectory analysis relies on an assumption of trajectory continuity, and experimental limitations preclude some real-world scenarios from meeting this condition.

Single-cell clonal tracing of glandular and circulating T cells identifies a population of CD9+ CD8+ T cells in primary Sjogren's syndrome.

Primary Sjogren's syndrome (pSS) is a complex chronic autoimmune disease in which local tissue damage in exocrine glands is combined with broader systemic involvement across the body in tissues including the skin. These combined manifestations negatively impact patient health and quality of life. While studies have previously reported differences in immune cell composition in the peripheral blood of pSS patients relative to healthy control subjects, a detailed immune cell landscape of the damaged exocrine glands of these patients remains lacking.

Highly diastereoselective synthesis of benzothiazolo[3,2-]pyridines [4 + 2] annulation reaction of 2-vinylbenzothiazoles and azlactones.

An efficient AgOTf-catalyzed [4 + 2] annulation reaction of 2-vinylbenzothiazoles and azlactones was successfully performed under mild reaction conditions. With this approach, a series of novel benzothiazolo[3,2-]pyridine derivatives was readily obtained in good to excellent yields (68-96%), with high diastereoselectivities and tolerating quite a broad scope of substituents. By using chiral phosphoric acid catalyst, the desired products were obtained in high enantioselectivities, up to -94%.

Mapping the spatial distribution of T cells in repertoire dimension.

T cells mediate adaptive immunity in diverse anatomic compartments through recognition of specific antigens via unique T cell receptor (TCR) structures. However, little is known about the spatial distribution of an organism's TCR repertoire. Here, using high-throughput TCR sequencing (TCRseq), we investigated the TCR repertoires of sixteen tissues in healthy C57B/L6 mice.

TIPS: trajectory inference of pathway significance through pseudotime comparison for functional assessment of single-cell RNAseq data.

Recent advances in bioinformatics analyses have led to the development of novel tools enabling the capture and trajectory mapping of single-cell RNA sequencing (scRNAseq) data. However, there is a lack of methods to assess the contributions of biological pathways and transcription factors to an overall developmental trajectory mapped from scRNAseq data. In this manuscript, we present a simplified approach for trajectory inference of pathway significance (TIPS) that leverages existing knowledgebases of functional pathways and other gene lists to provide further mechanistic insights into a biological process.

MiR-26a targets EphA2 to resist intracellular Listeria monocytogenes in macrophages.

At infection sites, macrophages are sentinels that resist and destroy various pathogens, through direct phagocytosis. In macrophages, microRNAs play a variety of crucial roles, the most striking of which is the regulation of the ability of the host cell to resist infection. However, the underlying mechanisms associated with the anti-infection effects mediated by microRNAs remain largely unknown.

VisTCR: An Interactive Software for T Cell Repertoire Sequencing Data Analysis.

Recent progress in high throughput sequencing technologies has provided an opportunity to probe T cell receptor (TCR) repertoire, bringing about an explosion of TCR sequencing data and analysis tools. For easier and more heuristic analysis TCR sequencing data, we developed a client-based HTML program (VisTCR). It has a data storage module and a data analysis module that integrate multiple cutting-edge analysis algorithms in a hierarchical fashion.

Conversion of effector CD4 T cells to a CD8 MHC II-recognizing lineage.

CD4 and CD8 T cells are dichotomous lineages in adaptive immunity. While conventionally viewed as distinct fates that are fixed after thymic development, accumulating evidence indicates that these two populations can exhibit significant lineage plasticity, particularly upon TCR-mediated activation. We define a novel CD4CD8αβ MHC II-recognizing population generated by lineage conversion from effector CD4 T cells.

TCR repertoire and CDR3 motif analyses depict the role of αβ T cells in Ankylosing spondylitis.

Background: Ankylosing spondylitis (AS) is a chronic inflammatory disease with worldwide high prevalence. Although AS is strongly associated with HLA-B27 MHC-I antigen presentation, the role played by αβ T cells in AS remains elusive.

Methods: Utilizing TCRβ repertoire sequencing and bioinformatics tools developed in house, we analyzed overall TCR repertoire structures and antigen-recognizing CDR3 motifs in AS patients with different disease activities.

Comparative analysis and characterization of Enterobacteria phage SSL-2009a and 'HK578likevirus' bacteriophages.

Enterobacteria phage SSL-2009a is a virulent bacteriophage with strong and abroad lytic ability against lots of engineering E. coli strains. In this study, we re-sequenced its whole genome and made a detail analysis on its genomic and proteomic characteristics according to the updated genomic sequence.

Rab32-related antimicrobial pathway is involved in the progression of dextran sodium sulfate-induced colitis.

Inflammatory bowel disease (IBD) is a multifactorial disease involving defective immune responses against invasive microbiota. Genes associated with innate immune responses to microbes have been highlighted in the pathogenesis of IBD. To determine the role of Rab32 in the pathogenesis of IBD, we administered dextran sodium sulfate (DSS) to CD11c cell-specific Rab32 knockout (-CreRab32) mice to induce colitis.

Transcriptomic and Metabolomic Analysis Revealed Multifaceted Effects of Phage Protein Gp70.1 on .

The impact of phage infection on the host cell is severe. In order to take over the cellular machinery, some phage proteins were produced to shut off the host biosynthesis early in the phage infection. The discovery and identification of these phage-derived inhibitors have a significant prospect of application in antibacterial treatment.

Glimpse of natural selection of long-lived T-cell clones in healthy life.

Homeostatic maintenance of T cells with broad clonal diversity is influenced by both continuing output of young T cells from the thymus and ongoing turnover of preexisting clones in the periphery. In the absence of infection, self and commensal antigens are thought to play important roles in selection and homeostatic maintenance of the T-cell pool. Most naïve T cells are short-lived due to lack of antigen encounter, whereas antigen-experienced T cells may survive and persist as long-lived clones.

Analysis of the Rab GTPase Interactome in Dendritic Cells Reveals Anti-microbial Functions of the Rab32 Complex in Bacterial Containment.

Dendritic cells (DCs) orchestrate complex membrane trafficking through an interconnected transportation network linked together by Rab GTPases. Through a tandem affinity purification strategy and mass spectrometry, we depicted an interactomic landscape of major members of the mammalian Rab GTPase family. When complemented with imaging tools, this proteomic analysis provided a global view of intracellular membrane organization.

Association of CD8(+) T lymphocyte repertoire spreading with the severity of DRESS syndrome.

T-cell receptor (TCR)-mediated cross-recognition is a major mechanism in the pathogenesis of drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome. However, the characteristics of the TCR repertoire and the clinical significance of repertoire reformation throughout the course of DRESS are unknown. Here, we isolated CD4(+) and CD8(+) T-cells from peripheral blood of 8 DRESS patients at 10-day intervals and, sequenced CDR3-regions of the TCRB chain by high-throughput sequencing to analyze the dynamic reformation in the T-cell repertoire hierarchy.

Factor XIII-A Val34Leu polymorphism might beassociated with myocardial infarction risk: an updated meta-analysis.

Although many epidemiologic studies have investigated the FXIII-A Val34Leu polymorphism and their associations with myocardial infarction (MI), definite conclusions can't be drawn. To clarify the effects of FXIII-A Val34Leu polymorphism on the risk of MI, a meta-analysis was performed. Related studies were identified from PubMed, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure (CNKI), and Chinese Biology Medicine (CBM) till 10 August 2014.

Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity.

Background: Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1.

Modulation, bioinformatic screening, and assessment of small molecular peptides targeting the vascular endothelial growth factor receptor.

Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) are important factors in tumor growth and metastasis. Molecular probes or drugs designed to target VEGF/VEGFR interactions are crucial in tumor molecular imaging and targeted therapy. Bioinformatic methods enable molecular design based on the structure of bio-macromolecules and their interactions.

Accurate discrimination of outer membrane proteins using secondary structure element alignment and support vector machine.

Outer membrane proteins (OMPs) play critical roles in many cellular processes and discriminating OMPs from other types of proteins is very important for OMPs identification in bacterial genomic proteins. In this study, a method SSEA_SVM is developed using secondary structure element alignment and support vector machine. Moreover, a novel kernel function is designed to utilize secondary structure information in the support vector machine classifier.

Dependence of the impact response of polyvinylidene fluoride sensors on their supporting materials' elasticity.

Polyvinylidene fluoride (PVDF) is popular sensing material because of its unique piezoelectric characteristics. In this work an impact sensor was prepared from a sandwiched structure PVDF film, and the related detection circuits were presented. The dependence of the PVDF sensors' response on the elasticity of the supporting materials was examined and discussed.

Effect of the quality of the interaction data on predicting protein function from protein-protein interactions.

Protein function prediction is an important issue in the post-genomic era. When protein function is deduced from protein interaction data, the traditional methods treat each interaction sample equally, where the qualities of the interaction samples are seldom taken into account. In this paper, we investigate the effect of the quality of protein-protein interaction data on predicting protein function.

A novel algorithm for finding interspersed repeat regions.

The analysis of repeats in the DNA sequences is an important subject in bioinformatics. In this paper, we propose a novel projection-assemble algorithm to find unknown interspersed repeats in DNA sequences. The algorithm employs random projection algorithm to obtain a candidate fragment set, and exhaustive search algorithm to search each pair of fragments from the candidate fragment set to find potential linkage, and then assemble them together.