MPIC: Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation.

Prognostic biomarkers are vital in the management of progressive chronic diseases such as liver cirrhosis, affecting 1-2% of the global population and causing over 1 million deaths every year. Despite numerous candidate biomarkers in literature, the costly and lengthy process of validation hampers their clinical translation. Existing omics databases are not suitable for in silico validation due to the ignorance of critical factors, i.e., study design, clinical context of biomarker application, and statistical power. To address the unmet need, we have developed the Molecular Prognostic Indicators in Cirrhosis (MPIC) database as a representative example of an omics database tailored for prognostic biomarker validation. MPIC consists of (i) a molecular and clinical database structured by defined disease context and specific clinical outcome and annotated with employed study design and anticipated statistical power by disease domain experts, (ii) a bioinformatics analysis engine for user-provided gene-signature- or gene-based prognostic prediction, and (iii) a user interface for interactive exploration of relevant clinical cohort/scenario and assessment of significance and reliability of the result for prognostic prediction. MPIC assists cost-effective prognostic biomarker development by facilitating the process of validation, and will transform the care of chronic diseases such as cirrhosis. MPIC is freely available at www.mpic-app.org. The website is implemented in Java, Apache, and MySQL with all major browsers supported.

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data.

Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. With scRNA-seq, highly variable gene (HVG) discovery allows the detection of genes that contribute strongly to cell-to-cell variation within a homogeneous cell population, such as a population of embryonic stem cells. This analysis is implemented in many software packages. In this study, we compare seven HVG methods from six software packages, including BASiCS, Brennecke, scLVM, scran, scVEGs and Seurat. Our results demonstrate that reproducibility in HVG analysis requires a larger sample size than DEG analysis. Discrepancies between methods and potential issues in these tools are discussed and recommendations are made.

Linnorm: improved statistical analysis for single cell RNA-seq expression data.

Linnorm is a novel normalization and transformation method for the analysis of single cell RNA sequencing (scRNA-seq) data. Linnorm is developed to remove technical noises and simultaneously preserve biological variations in scRNA-seq data, such that existing statistical methods can be improved. Using real scRNA-seq data, we compared Linnorm with existing normalization methods, including NODES, SAMstrt, SCnorm, scran, DESeq and TMM. Linnorm shows advantages in speed, technical noise removal and preservation of cell heterogeneity, which can improve existing methods in the discovery of novel subtypes, pseudo-temporal ordering of cells, clustering analysis, etc. Linnorm also performs better than existing DEG analysis methods, including BASiCS, NODES, SAMstrt, Seurat and DESeq2, in false positive rate control and accuracy.

Functional networks of aging markers in the glomeruli of IgA nephropathy: a new therapeutic opportunity.

IgA nephropathy(IgAN) is the most common primary glomerular disease in China. Primary infections always occur before IgAN. However, the pathology of IgAN is still unclear. Previously we found that LL37, a protein secreted by senescent cells, was specific for the progression of IgAN, and also played a role in the neutrophil function. So we hypothesized that the infiltration of neutrophils, inflammation factors, and aging markers , which were modulated by functional networks, induced the immune response and renal injury. RNA-Sequencing (RNA-seq) can be used to study the whole transcriptome and detect splicing variants that are expressed in a specific cell type or tissue. We separate glomerulus from the renal biopsy tissues. After RNA extraction, the sequences were analyzed with Illumina HiSeq 2000/2500. 381 genes with differential expression between the IgAN patients and the healthy controls were identified. Only PLAU, JUN, and FOS were related to DNA damage, telomere dysfunction-induced aging markers, neutrophil function and IgA nephropathy. The networks showed the possibility of these genes being connected. We conclude that DNA damage and telomere dysfunction could play important roles in IgA nephropathy. In addition, neutrophils are also important factors in this disease. The networks of these markers showed the mechanism pathways that are involved in the duration of the occurrence and progression of IgA nephropathy and might be a new therapeutic opportunity for disease treatment.

Identification of differentially expressed genes in early stages of Eimeria tenella by suppression subtractive hybridization and cDNA microarray.

Avian coccidiosis, a major parasitic disease of poultry, is caused by Eimeria spp. infection. It inflicts severe economic losses on the poultry industry worldwide. To further understand the molecular basis of sporulation and invasion of Eimeria spp., suppression subtractive hybridization and microarray approaches were combined to identify novel and important genes involved in the development and invasion of the early stages of Eimeria tenella . Three subtractive cDNA libraries were constructed for 3 stages of E. tenella including unsporulated oocysts, sporulated oocysts, and sporozoites. A subset of clones was selected from the 3 subtractive libraries to construct cDNA microarrays. Microarray analysis was used to assay expression changes of these clones. A total of 657 valid expressed sequence tags (ESTs) was obtained, including 119 unique sequences, 31 from sporulated oocysts and 88 from sporozoites. Homology searches of the public sequence databases showed that, among the 119 ESTs, 32 genes encoded proteins homologous with previously reported proteins including microneme proteins and surface antigen proteins of E. tenella , small heat shock proteins, rhoptry proteins of Toxoplasma gondii , and calcium-dependent protein kinase of Plasmodium spp. Thus, the remaining 87 ESTs have not previously been reported. Further characterization of these differentially expressed genes will be useful in understanding those responsible for sporulation, invasion, growth, and development of E. tenella .

Hexavalent chromium reduction by Pannonibacter phragmitetus BB isolated from soil under chromium-containing slag heap.

The objective of this study was to find an indigenous Cr(VI)-reducing bacterium that can effectively be used for Cr(VI) remediation in the contaminated soils. The results showed that one isolate from soil under a chromium-containing slag heap at a steel-alloy factory in China had a strong ability of reducing Cr(VI). It can completely reduce 500 mg L(-1) Cr (VI) within 24 h. Based on 16S rRNA gene sequence and similarity analysis, this isolate was identified as Pannonibacter phragmitetus and assigned as strain BB. Images of scanning electron microscopy (SEM) indicated that the cell surface of P. phragmitetus BB remained intact without cell rupture under 500 mg L(-1) Cr (VI) stress. The transmission electron microscopy (TEM) patterns showed that the Cr(VI) reduction products were both bound to the outer surface of the cells and dispersed in the culture medium, thereby suggesting that the reduction of Cr (VI) occurred extracellularly. Elemental analysis by energy dispersive X-ray (EDX) revealed that Cr was the major element comprising the reduction product. Furthermore, X-ray photoelectron spectroscope (XPS) verified that the Cr(VI) reduction product was Cr(III) compounds.

[The MN typing of whole blood and bloodstains by the method of one-step sandwich ELISA].

The samples of whole blood and bloodstain were MN-typed by the method of one-step sandwich ELISA, monoclonal antibodies include anti-M, N and glycern-protein. The lowest sample amount in this study is: for whole blood is 0.065 microliter, for bloodstain about 10 to 50 ng. 455 cases of fresh blood and 200 cases of fresh bloodstain are correctly typed. For 58 cases of old bloodstains, the success rate is 96.6%.

Ultrasonically guided inferior vena cava stent placement: experience in 83 cases.

PURPOSE: Traditionally, inferior vena cava (IVC) stent placement is performed with fluoroscopic guidance. The object of this study was to evaluate use of ultrasound (US) as guidance for IVC stent placement for the management of Budd-Chiari syndrome. MATERIALS AND METHODS: Eighty-three patients with IVC membranous stenosis (n = 30), membranous occlusion (n = 19), segmental stenosis (n = 21), or segmental occlusion (n = 13) underwent IVC recanalization, balloon dilation, and stent placement under US guidance. Among the 83 patients, 67 had at least one patent hepatic vein, while 16 patients had three occluded hepatic veins. RESULTS: IVC stents were successfully placed in 79 of 83 patients, with a success rate of 95%. After the procedure, the symptoms and signs of IVC obstruction disappeared or markedly improved in all patients, and the blockage of hepatic outflow was alleviated in 67 patients. Pericardial effusion, complete atrial ventricular block, and stent migration into the right atrium occurred, respectively, in one patient. During 1-46-month follow-up, stent restenosis occurred in one patient; the other stents remained open and functioned effectively. CONCLUSION: Because of the absence of nonionizing radiation and iodinated contrast material, and its low cost, US is well suited and often preferred for guidance of IVC stent placement.