Detergent-Induced Changes in the Protein Constituents of Various Cell Types of Opercular Epidermis of Rita rita

Fish (Rita rita) were exposed to an anionic detergent, dodecylbenzene sodium sulfonate, at a concentration of 6.9mg/liter (96-hr LC_(50) of the detergent).A series of histochemical techniques, used in this study for the demonstration of various protein constituents, indicated a gradual decrease in the intensity of staining reactions of the cytoplasmic material, suggesting a loss of protein moieties from the club cells and the epithelial cells of the opercular epidermis as a result of detergent exposure. 1990 Academic Press.Inc.

Cell Type Specific Expression of CD80 （B7-1） Gene in Murine

The CD80 （B7-1） costimulatory molecule is expressed on the surface of B cells and its expression is transcriptionally upregulated upon stimuli. To identify the region of murine CD80 promoter that direct cell type specific gene expression, four promoters construct of CD80 gene were generated with DNA fragments fused to the GFP reporter gene. In the present study, significant promoter activity was detected with all four promoter constructs only in the murine B lymphocyte. Further, the CD80 promoter region extending from -3,005 bp to ＋273 bp in relation to the previously reported transcription start site, was identified as tissue specific region. Interestingly, the shortest 700 bp （-427/＋273） of promoter fragment was sufficient to direct the CD80 gene expression. The level of CD80 expression was also found to be modulated by exogenous stimuli in B lymphocyte. Additionally, it was demonstrated that the CD80 gene expression is regulated at the level of transcription where the inducible CD80 gene transcript was detected in B lymphocyte with increasing time.

Toxic Effects of an Anionic Detergent on the Lipid Constituents of Various Cell Types of the Gill Epithelium of Rita rita:A Histochemical Investigation

Rita rita exposed to a concentration of 6.9 mg per liter(96-h LC_(50)of an anionic detergent, dodecylbenzene sodium sulfonate)exhibited a gradual decrease in the lipid moieties of the epi- thelial cells,club cells,and goblet mucous cells lining the gill arch and gill filament epithelium. However,in time,no reaction of any of the lipid moieties could be observed,indicating the absence of the same,using various histochemical techniques.The results are discussed in light of the mechanistic understanding of detergent action.1989 Academic Press,Inc.

Presentation of signet ring cell type at carcinoma ventriculi of the patient aged 20 years old

Introduction: Diffuse variant of GC is composed of gastric-type mucous cells, which generally do not form glands, but rather permit the mucosa and wall as scattered individual cells or small clusters in an “infiltrative” growth pattern. These cells appear to arise from the middle layer of the mucosa, and the presence of intestinal metaplasia is not a prerequisite. In this version, mucin formation expands the malignant cells and pushes the nucleus to the periphery, creating a “signet ring” conformation. If the signetring cells are more than 50% of the tumor, the tumor is classified as signetring cell carcinoma [1]. This case is important for reporting because we encountered for the first time such a carcinoma type, due to the new age and its atypical presentation. Case Presentation: We report a case of a 20 years Albanian old patient with Signet Ring Cell Type of Gastric CA. The patient was brought at the urgency with severe abdominal pain, nausea and peritoneal irritation. Clinical examination has been made in emergency, where we conclude the signs of peritoneal irritation, from native Ro no signs of pneumoperitoneum, while laboratory tests found a slight anemia (erythrocytes 3.36, HCT 25, HGB 8.6). Two hours later we repeated the native RTG and there were present the signs of pneumoperitoneum. It was indicated urgent surgical in-tervention. Intraoperatively, we found Ulcer duodenal perforation and?undertook the operation procedures by Roscoe Graham technique. Conclusions: At this age, it is rare, and it is difficult to detect in its early stages, because the signs and symptoms are often non-existent, non-specific, or mimic as an ulcer. The most common symptoms are early heartburn indigestion, abdominal pain or discomfort, vomiting, constipation, diarrhea or to feel of filling after a small meal, loss of appetite, weakness and fatigue. Less common symptoms are anemia and weight loss.

Accurate cell type annotation for single-cell chromatin accessibility data via contrastive learning and reference guidance

Recent advances in single-cell chromatin accessibility sequencing(scCAS)technologies have resulted in new insights into the characterization of epigenomic heterogeneity and have increased the need for automatic cell type annotation.However,existing automatic annotation methods for scCAS data fail to incorporate the reference data and neglect novel cell types,which only exist in a test set.Here,we propose RAINBOW,a reference-guided automatic annotation method based on the contrastive learning framework,which is capable of effectively identifying novel cell types in a test set.By utilizing contrastive learning and incorporating reference data,RAINBOW can effectively characterize the heterogeneity of cell types,thereby facilitating more accurate annotation.With extensive experiments on multiple scCAS datasets,we show the advantages of RAINBOW over state-of-the-art methods in known and novel cell type annotation.We also verify the effectiveness of incorporating reference data during the training process.In addition,we demonstrate the robustness of RAINBOW to data sparsity and number of cell types.Furthermore,RAINBOW provides superior performance in newly sequenced data and can reveal biological implication in downstream analyses.All the results demonstrate the superior performance of RAINBOW in cell type annotation for scCAS data.We anticipate that RAINBOW will offer essential guidance and great assistance in scCAS data analysis.The source codes are available at the GitHub website(BioX-NKU/RAINBOW).

Identification of susceptibility loci and relevant cell type for IgA nephropathy in Han Chinese by integrative genome-wide analysis

Although many susceptibility loci for IgA nephropathy(IgAN)have been identified,they only account for 11.0%of the overall IgAN variance.We performed a large genome-wide meta-analysis of IgAN in Han Chinese with 3616 cases and 10417 controls to identify additional genetic loci of IgAN.Considering that inflammatory bowel disease(IBD)and asthma might share an etiology of dysregulated mucosal immunity with IgAN,we performed cross-trait integrative analysis by leveraging functional annotations of relevant cell type and the pleiotropic information from IBD and asthma.Among 8669456 imputed variants,we identified a novel locus at 4p14 containing the long noncoding RNA LOC101060498.Cell type enrichment analysis based on annotations suggested that PMA-I-stimulated CD4+CD25–IL17+Th17 cell was the most relevant cell type for IgAN,which highlights the essential role of Th17 pathway in the pathogenesis of IgAN.Furthermore,we identified six more novel loci associated with IgAN,which included three loci showing pleiotropic effects with IBD or asthma(2q35/PNKD,6q25.2/SCAF8,and 22q11.21/UBE2L3)and three loci specific to IgAN(14q32.32/TRAF3,16q22.2/TXNL4B,and 21q21.3/LINC00113)in the pleiotropic analysis.Our findings support the involvement of mucosal immunity,especially T cell immune response and IL-17 signal pathway,in the development of IgAN and shed light on further investigation of IgAN.

deCS:A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues

Single-cell RNA sequencing(scRNA-seq)is revolutionizing the study of complex and dynamic cellular mechanisms.However,cell type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation,which is cumbersome and subjective.The increasing number of scRNA-seq datasets,as well as numerous published genetic studies,has motivated us to build a comprehensive human cell type reference atlas.Here,we present decoding Cell type Specificity(deCS),an automatic cell type annotation method augmented by a comprehensive collection of human cell type expression profiles and marker genes.We used deCS to annotate scRNAseq data from various tissue types and systematically evaluated the annotation accuracy under different conditions,including reference panels,sequencing depth,and feature selection strategies.Our results demonstrate that expanding the references is critical for improving annotation accuracy.Compared to many existing state-of-the-art annotation tools,deCS significantly reduced computation time and increased accuracy.deCS can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation.Finally,we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits,providing deep insights into the cellular mechanisms underlying disease pathogenesis.

The Effect of Tuberculosis Infection on Pancreatic Beta-Cell Function in Patients with Type 2 Diabetes Mellitus

Objective: The aim of this study is to investigate how individuals with type 2 diabetes mellitus’ pancreatic β-cell function index and insulin resistance index are affected by tuberculosis infection. Methods: The study group consisted of 89 patients with type 2 diabetes mellitus and tuberculosis infection who were admitted to Jingzhou Chest Hospital between March 2019 and March 2021. Gender and duration of diabetes were matching conditions. The control group was made up of 89 patients with type 2 diabetes who were admitted to Jingzhou Central Hospital’s endocrinology department during the same period. The two patient groups provided general information such as gender, age, length of diabetes, and blood biochemical indexes such as glycosylated hemoglobin (HbA1c), fasting glucose (FPG), and fasting C-peptide (FC-P). The HOMA calculator was used to calculate the HOMA-β and the HOMA-IR, and intergroup comparisons and correlation analyses were carried out. Results: Regarding gender, age, disease duration, FC-P, and HbA1c, the differences between the two groups were not statistically significant (P > 0.05). However, BMI, FPG, HOMA-β, and HOMA-IR showed statistically significant differences (P < 0.05). In comparison to the control group, the study group’s HOMA-β was lower and its HOMA-IR was greater. According to Spearman’s correlation analysis, HOMA-β had a negative association (P th FPG, HbA1c, and the length of the disease, and a positive correlation with BMI and FC-P. A positive correlation was found between HOMA-IR and BMI, FPG, and FC-P (P < 0.01), as well as a correlation with the length of the disease (P > 0.05) and HbA1c. Conclusions: In type 2 diabetes mellitus combined with tuberculosis infection, the patients had higher FPG levels and lower FC-P levels, the secretory function of pancreatic β-cells was more severely impaired, and insulin resistance was more obvious.

A cell marker-based clustering strategy(cmCluster)for precise cell type identification of scRNA-seq data

Background:The precise and efficient analysis of single-cell transcriptome data provides powerful support for studying the diversity of cell functions at the single-cell level.The most important and challenging steps are cell clustering and recognition of cell populations.While the precision of clustering and annotation are considered separately in most current studies,it is worth attempting to develop an extensive and flexible strategy to balance clustering accuracy and biological explanation comprehensively.Methods:The cell marker-based clustering strategy(cmCluster),which is a modified Louvain clustering method,aims to search the optimal clusters through genetic algorithm(GA)and grid search based on the cell type annotation results.Results:By applying cmCluster on a set of single-cell transcriptome data,the results showed that it was beneficial for the recognition of cell populations and explanation of biological function even on the occasion of incomplete cell type information or multiple data resources.In addition,cmCluster also produced clear boundaries and appropriate subtypes with potential marker genes.The relevant code is available in GitHub website(huangyuwei301/cmCluster).Conclusions:We speculate that cmCluster provides researchers effective screening strategies to improve the accuracy of subsequent biological analysis,reduce artificial bias,and facilitate the comparison and analysis of multiple studies.

Primary Ovarian Small Cell Carcinoma of Pulmonary Type: Analysis of 6 Cases and Review of 31 Cases in the Literatures

Objective Primary ovarian small cell carcinoma of pulmonary type(SCCOPT)is a rare ovarian tumor with a poor prognosis.The platinum-based chemotherapy is the standard treatment.However,there is little research on the clinical characteristics of SCCOPT and the potential benefits of other treatments due to its low incidence.The study aims to investigate clinicopathological characteristics and treatment of SCCOPT.Methods We summarized the clinical,imaging,laboratorical and pathological characteristics of 37 SCCOPT cases,in which 6 cases were admitted to the Gansu Provincial Hospital from the year of 2008 to 2022 and 31 cases reported in 17 English and 3 Chinese literatures.Results The median age of the studied SCCOPT cases(n=37)was 56.00(range,22-80)years.Almost 80%of them had a stageⅢorⅣtumor.All patients underwent an operation and postoperative chemotherapy.Nevertheless,all cases had a poor prognosis,with a median overall survival time of 12 months.Immunohistochemical y,the SCCOPT of all patients showed positive expressions of epithelial markers,such as CD56 and sex-determining region of Y chromosome-related high-mobility-group box 2(SOX-2),and negative expressions of estrogen receptor,progesterone receptor,vimentin,Leu-7,and somatostatin receptor 2.The tumor of above 80%cases expressed synaptophysin.Only a few cases expressed neuron-specific enolase,chromogranin A,and thyroid transcription factor-1.Conclusions SCCOPT had a poor prognosis.SOX-2 could be a biomarker to be used to diagnose SCCOPT.

A rare case of Castleman＇s disease of plasma cell type within kidney

Castleman＇s disease （CD）, also known as angiofollicular lymph node hyperplasia, giant lymph node hyperplasia, and angiomatous lymphoid hyperplasia, was first described by Castleman in 1954.1 It is an uncommon disorder characterized by benign proliferation of lymphoid tissue. The etiology of CD is unclear, although its origins have been explored in various perspectives, such as immuno-depressed states, chronic inflammation or infection, and autoimmune processes.

Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq

Annotating cell types is a critical step in single-cell RNA sequencing(scRNA-seq)data analysis.Some supervised or semi-supervised classification methods have recently emerged to enable automated cell type identification.However,comprehensive evaluations of these methods are lacking.Moreover,it is not clear whether some classification methods originally designed for analyzing other bulk omics data are adaptable to scRNA-seq analysis.In this study,we evaluated ten cell type annotation methods publicly available as R packages.Eight of them are popular methods developed specifically for single-cell research,including Seurat,scmap,SingleR,CHETAH,SingleCellNet,scID,Garnett,and SCINA.The other two methods were repurposed from deconvoluting DNA methylation data,i.e.,linear constrained projection(CP)and robust partial correlations(RPC).We conducted systematic comparisons on a wide variety of public scRNA-seq datasets as well as simulation data.We assessed the accuracy through intra-dataset and inter-dataset predictions;the robustness over practical challenges such as gene filtering,high similarity among cell types,and increased cell type classes;as well as the detection of rare and unknown cell types.Overall,methods such as Seurat,SingleR,CP,RPC,and SingleCellNet performed well,with Seurat being the best at annotating major cell types.Additionally,Seurat,SingleR,CP,and RPC were more robust against downsampling.However,Seurat did have a major drawback at predicting rare cell populations,and it was suboptimal at differentiating cell types highly similar to each other,compared to SingleR and RPC.All the code and data are available from https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark.

Localized Castleman disease of plasma cell type in the abdomen

Castleman disease is a relatively rare entity, with the hyaline-vascular type the predominant form. Although the plasma cell type is uncommon, it still comprises approximately 10% of cases of localized diseases. In addition, the abdomen is a rare site for involvement and localized Castleman disease of the plasma cell type in the abdomen is rare. The radiologic features of localized plasma cell type in the abdomen are mostly limited to case reports. In addition to the conventional imaging findings, we present some new imaging findings of localized plasma cell type in the abdomen.

SSRE:Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement

Accurate identification of cell types from single-cell RNA sequencing(scRNA-seq)data plays a critical role in a variety of scRNA-seq analysis studies.This task corresponds to solving an unsupervised clustering problem,in which the similarity measurement between cells affects the result significantly.Although many approaches for cell type identification have been proposed,the accuracy still needs to be improved.In this study,we proposed a novel single-cell clustering framework based on similarity learning,called SSRE.SSRE models the relationships between cells based on subspace assumption,and generates a sparse representation of the cell-to-cell similarity.The sparse representation retains the most similar neighbors for each cell.Besides,three classical pairwise similarities are incorporated with a gene selection and enhancement strategy to further improve the effectiveness of SSRE.Tested on ten real scRNA-seq datasets and five simulated datasets,SSRE achieved the superior performance in most cases compared to several state-of-the-art single-cell clustering methods.In addition,SSRE can be extended to visualization of scRNA-seq data and identification of differentially expressed genes.The matlab and python implementations of SSRE are available at https://github.com/CSUBioGroup/SSRE.

Single-cell transcriptomics reveals cell type diversity of human prostate

Extensive studies have been performed to describe the phenotypic changes occurring during malignant transformation of the prostate.However,the cell types and associated changes that contribute to the development of prostate diseases and cancer remain elusive,largely due to the heterogeneous composition of prostatic tissues.Here,we conduct a comprehensive evaluation of four human prostate tissues by singlecell RNA sequencing(sc RNA-seq)to analyze their cellular compositions.We identify 18 clusters of cell types,each with distinct gene expression profiles and unique features;of these,one cluster of epithelial cells(Ep)is found to be associated with immune function.In addition,we characterize a special cluster of fibroblasts and aberrant signaling changes associated with prostate cancer(PCa).Moreover,we provide insights into the epithelial changes that occur during the cellular senescence and aging.These results expand our understanding of the unique functional associations between the diverse prostatic cell types and the contributions of specific cell clusters to the malignant transformation of prostate tissues and PCa development.

Cell type specificity of signaling:view from membrane receptors distribution and their downstream transduction networks

Studies on cell signaling pay more attention to spatial dynamics and how such diverse organization can relate to high order of cellular capabilities.To overview the specificity of cell signaling,we integrated human receptome data with proteome spatial expression profiles to systematically investigate the specificity of receptors and receptor-triggered transduction networks across 62 normal cell types and 14 cancer types.Six percent receptors showed cell-type-specific expression,and 4% signaling networks presented enriched cell-specific proteins induced by the receptors.We introduced a concept of“response context”to annotate the cell-type dependent signaling networks.We found that most cells respond similarly to the same stimulus,as the“response contexts”presented high functional similarity.Despite this,the subtle spatial diversity can be observed from the difference in network architectures.The architecture of the signaling networks in nerve cells displayed less completeness than that in glandular cells,which indicated cellular-context dependent signaling patterns are elaborately spatially organized.Likewise,in cancer cells most signaling networks were generally dysfunctional and less complete than that in normal cells.However,glioma emerged hyper-activated transduction mechanism in malignant state.Receptor ATP6AP2 and TNFRSF21 induced rennin-angiotensin and apoptosis signaling were found likely to explain the glioma-specific mechanism.This work represents an effort to decipher context-specific signaling network from spatial dimension.Our results indicated that although a majority of cells engage general signaling response with subtle differences,the spatial dynamics of cell signaling can not only deepen our insights into different signaling mechanisms,but also help understand cell signaling in disease.

Advances in plant cell type-specific genome-wide studies of gene expression

Cell is the functional unit of life.To study the complex interactions of systems of biological molecules,it is crucial to dissect these molecules at the cell level.In recent years,major progresses have been made by plant biologists to profile gene expression in specific cell types at the genome-wide level.Approaches based on the isolation of cells,polysomes or nuclei have been developed and successfully used for studying the cell types from distinct organs of several plant species.These cell-level data sets revealed previously unrecognized cellular properties,such as cell-specific gene expression modules and hormone response centers,and should serve as essential resources for functional genomic analyses.Newly developed technologies are more affordable to many laboratories and should help to provide new insights at the cellular resolution in the near future.

ISOFLURANE REDUCES THE SYNTHESIS OF SURFACTANT-RELATED PROTEIN A OF ALVEOLAR TYPE II CELLS INJURED BY H_2O_2

Objective To explore the influence of isoflurane(Iso) on the synthesis of surfactant-related protein(SP-A) of alveolar type II cells(AT II cells) cultured in primary and injured by hydrogen peroxide(H2O2).Methods AT II cells were isolated from adult SD rats and used for experiments after 32h in primary culture and randomized into six groups: control group,0.28 mM Iso group,2.8mM Iso group,75 μM H2O2 group,75 μM H2O2 +0.28 mM Iso group and 75 μM H2O2 +2.8 mM Iso group. Each group was continuously incubated for 3 h after administration of Iso or/and H2O2. The intracellular SP-A and the SP-A of cultured medium were measured with an enzyme-linked immunosorbent assay(ELISA).Results Iso significantly decreased SP-A content of cultured medium and the intracellular,and aggravated the decrease of SP-A content induced by H2O2 in a dose-dependent manner.Conclusion Iso itself may decrease SP-A synthesis of AT II cells in vitro,and aggravate the damage of AT II cells especially under peroxidation condition.

Effect of Amygdalin on the Proliferation of Hyperoxia-exposed Type Ⅱ Alveolar Epithelial Cells Isolated from Premature Rat

Summary: The pathogenesis of hyperoxia lung injury and the mechanism of amygdalin on type 2 alveolar epithelial cells (AEC2) isolated from premature rat lungs in vitro were investigated. AEC2 were obtained by primary culture from 20-days fetal rat lung and hyperoxia-exposed cell model was established. Cell proliferating viability was examined by MTT assay after treatment of amygdalin at various concentrations. DNA content and the proliferating cell nuclear antigen (PCNA) protein expression of AEC2 were measured by using flow cytometry and immunocytochemistry respectively after 24 h of hyperoxia exposure or amygdalin treatment. The results showed that hyperoxia inhibited the proliferation and decreased PCNA protein expression in AEC2 of premature rat in vitro. Amygdalin at the concentration range of 50-200 μmol/L stimulated the proliferation of AEC2 in a dose-dependent manner, however, 400 μmol/L amygdalin inhibited the proliferation of AEC2. Amygdalin at the concentration of 200 μmol/L played its best role in facilitating proliferation of AEC2s in vitro and could partially ameliorated the changes of proliferation in hyperoxia exposed AEC2 of premature rat. It has been suggested that hyperoxia inhibited the proliferation of AEC2s of premature rat, which may contribute to hyperoxia lung injury. Amygdalin may play partial protective role in hyperoxia-induced lung injury.