Experimental Antiglomerular Basement Membrane GN Induced by a Peptide from Actinomyces.

BACKGROUND: Antiglomerular basement membrane (anti-GBM) disease is associated with HLA-DRB1*1501 (the major predisposing genetic factor in the disease), with α3127-148 as a nephritogenic T and B cell epitope. Although the cause of disease remains unclear, the association of infections with anti-GBM disease has been long suspected. METHODS: To investigate whether microbes might activate autoreactive T and B lymphocytes via molecular mimicry in anti-GBM disease, we used bioinformatic tools, including BLAST, SYFPEITHI, and ABCpred, for peptide searching and epitope prediction. We used sera from patients with anti-GBM disease to assess peptides recognized by antibodies, and immunized WKY rats and a humanized mouse model (HLA-DR15 transgenic mice) with each of the peptide candidates to assess pathogenicity. RESULTS: On the basis of the critical motif, the bioinformatic approach identified 36 microbial peptides that mimic human α3127-148. Circulating antibodies in sera from patients with anti-GBM recognized nine of them. One peptide, B7, derived from Actinomyces species, induced proteinuria, linear IgG deposition on the GBM, and crescent formation when injected into WKY rats. The antibodies to B7 also targeted human and rat α3127-148. B7 induced T cell activation from human α3127-148-immunized rats. T cell responses to B7 were detected in rats immunized by Actinomyces lysate proteins or recombinant proteins. We confirmed B7's pathogenicity in HLA-DR15 transgenic mice that developed kidney injury similar to that observed in α3135-145-immunized mice. CONCLUSIONS: Sera from patients with anti-GBM disease recognized microbial peptides identified through a bioinformatic approach, and a peptide from Actinomyces induced experimental anti-GBM GN by T and B cell crossreactivity. These studies demonstrate that anti-GBM disease may be initiated by immunization with a microbial peptide.

Gene-Focused Networks Underlying Phenotypic Convergence in a Systematically Phenotyped Cohort With Heterogeneous Intellectual Disability.

The broad spectrum of intellectual disability (ID) patients' clinical manifestations, the heterogeneity of ID genetic variation, and the diversity of the phenotypic variation represent major challenges for ID diagnosis. By exploiting a manually curated systematic phenotyping cohort of 3803 patients harboring ID, we identified 704 pathogenic genes, 3848 pathogenic sites, and 2075 standard phenotypes for underlying molecular perturbations and their phenotypic impact. We found the positive correlation between the number of phenotypes and that of patients that revealed their extreme heterogeneities, and the relative contribution of multiple determinants to the heterogeneity of ID phenotypes. Nevertheless, despite the extreme heterogeneity in phenotypes, the ID genes had a specific bias of mutation types, and the top 44 genes that ranked by the number of patients accounted for 39.9% of total patients. More interesting, enriched co-occurrent phenotypes and co-occurrent phenotype networks for each gene had the potential for prioritizing ID genes, further exhibited the convergences of ID phenotypes. Then we established a predictor called IDpred using machine learning methods for ID pathogenic genes prediction. Using10-fold cross-validation, our evaluation shows remarkable AUC values for IDpred (auc = 0.978), demonstrating the robustness and reliability of our tool. Besides, we built the most comprehensive database of ID phenotyped cohort to date: IDminer http://218.4.234.74:3100/IDminer/, which included the curated ID data and integrated IDpred tool for both clinical and experimental researchers. The IDminer serves as an important resource and user-friendly interface to help researchers investigate ID data, and provide important implications for the diagnosis and pathogenesis of developmental disorders of cognition.

Mapping the clinical outcomes and genetic evolution of Ebola virus in Sierra Leone.

Sierra Leone was the most severely affected country in Western Africa during the 2013-2016 outbreak of Ebola virus disease (EVD). Previous genome surveillance studies have revealed the origin, diversity, and evolutionary dynamics of the Ebola virus (EBOV); however, the information regarding EBOV sequences is insufficient, especially the clinical outcomes, given that the correlation between the clinical outcomes and the genetic evolution of EBOV is still not clear. Here, we collected and curated a comprehensive data set that includes 514 EBOV genome sequences from patients with confirmed EVD (including 60 sequences not previously studied), >87.5% of which have residence information and definitive clinical outcomes. Phylogenetic reconstruction revealed 11 lineages of EBOV in Sierra Leone. The median-joining haplotype network showed that haplotypes that are associated with lethal outcomes tend to contribute more to the spread of the EBOV in Sierra Leone than those with live outcomes. Analyses of the spatial-temporal distribution unraveled the lineage-distinctive distribution patterns. Different viral lineages have different case fatality rates (CFRs) during the same stage of the outbreak, implying that several lineages featuring SNPs may correlate with increased/decreased CFRs. This study provides invaluable data sets of EBOV infection and highlights the potential SNPs for further in-depth investigation.

Characterization of a novel reassortant influenza A virus (H2N2) from a domestic duck in Eastern China.

While H2N2 viruses have been sporadically isolated from wild and domestic birds, H2N2 viruses have not been detected among human populations since 1968. Should H2N2 viruses adapt to domestic poultry they may pose a risk of infection to people, as most anyone born after 1968 would likely be susceptible to their infection. We report the isolation of a novel influenza A virus (H2N2) cultured in 2013 from a healthy domestic duck at a live poultry market in Wuxi City, China. Sequence data revealed that the novel H2N2 virus was similar to Eurasian avian lineage avian influenza viruses, the virus had been circulating for ≥ two years among poultry, had an increase in α2,6 binding affinity, and was not highly pathogenic. Approximately 9% of 100 healthy chickens sampled from the same area had elevated antibodies against the H2 antigen. Fortunately, there was sparse serological evidence that the virus was infecting poultry workers or had adapted to infect other mammals. These findings suggest that a novel H2N2 virus has been circulating among domestic poultry in Wuxi City, China and has some has increased human receptor affinity. It seems wise to conduct better surveillance for novel influenza viruses at Chinese live bird markets.

The genetic basis of white tigers.

The white tiger, an elusive Bengal tiger (Panthera tigris tigris) variant with white fur and dark stripes, has fascinated humans for centuries ever since its discovery in the jungles of India. Many white tigers in captivity are inbred in order to maintain this autosomal recessive trait and consequently suffer some health problems, leading to the controversial speculation that the white tiger mutation is perhaps a genetic defect. However, the genetic basis of this phenotype remains unknown. Here, we conducted genome-wide association mapping with restriction-site-associated DNA sequencing (RAD-seq) in a pedigree of 16 captive tigers segregating at the putative white locus, followed by whole-genome sequencing (WGS) of the three parents. Validation in 130 unrelated tigers identified the causative mutation to be an amino acid change (A477V) in the transporter protein SLC45A2. Three-dimensional homology modeling suggests that the substitution may partially block the transporter channel cavity and thus affect melanogenesis. We demonstrate the feasibility of combining RAD-seq and WGS to rapidly map exotic variants in nonmodel organisms. Our results identify the basis of the longstanding white tiger mystery as the same gene underlying color variation in human, horse, and chicken and highlight its significance as part of the species' natural polymorphism that is viable in the wild.

A Novel Reaction Media for Horseradish Peroxidase (HRP) Catalysis in Organic Solvents.

It is important to select favorable reaction media for use of enzymes in organic synthesis. In the presence of PEG with a certain molecular weight, toluene was able to dissolve horseradish peroxidase and the latter maintained a high activity. The HRP reaction conditions, such as ratio of PEG/toluene, water content, pH, and substrate concentration were investigated. It was found that the activity of HRP increased when PEG concentration was low and water content was high. In such a system, the enzyme functioned best at pH 7.0,the concentration of H(2)O(2) and guaiacol being 20 mmol/L and 0.1 mol/L respectively. Under the same condition, no activity was detected in the PEG / ethanol and PEG / dioxane systems. However, in PEG / toluene system, HRP maintained a higher activity and the activity was ten-fold more than that in toluene alone.

PEG-Modified Horseradish Peroxidase and Its Properties in Nonaqueous Media.

Modification of enzymes can enhance their activities in organic solvents. Horseradish peroxidase (HRP) was modified with methoxy-PEG 5000 which was linked onto HRP peptidal free aminos or onto the aminos introduced through the oxidation of sugar side chains of HRP. It was found the enzyme with PEG linked to peptide chain expressed a nearly same activity as the native HRP in aqueous system. However, PEG modified HRP by oxidation of carbohydrate chains remained only about one third activity of the native HRP. The same results were observed in reversed micelles and in dioxane of less than 30%. Apparently, both PEG modified HRP had the higher activities in high concentration of dioxane. Especially, the activities of the modified HRP in toluene were both enhanced up to nearly 3 fold. When HRP was modified with PEG through the amino groups of peptide chain, it was more stable than the native enzyme in water, dioxane and toluene. However, the stability of PEG-modified HRP by carbohydrate chains was higher in water and lower in both dioxane and toluene in comparison with native HRP.

The Effect of Reversed Micelles on Horseradish Peroxidase (HRP) Structure and Function.

Effects of water content (W(0)) and surfactants on the activity of HRP in CTAB/isooctane-n-pentanol reversed micelles were investigated. Based on UV-Vis spectroanalysis and the activity of HRP at various W(0) and CTAB content, it was found that the active-site of HRP was mainly influenced by reversed micelles. However, CTAB had no effect on the active-site of HRP. In addition, the stabilities and Soret band of HRP-H(2)O(2) complexes in reversed micelles were compared to that in aqueous system. The complex HRP-II and HRP-III did disappear more rapidly in reversed micelles than in aqueous system. This demonstrated the enzyme molecules were destabilized in reversed micelles.