Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome

The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR) mediated by low-copy repeats (LCRs). Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ~1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs) from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH) chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR-mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease.     

A Two-Antibody Pan-Ebolavirus Cocktail Confers Broad Therapeutic Protection in Ferrets and Nonhuman Primates

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Morphological Changes in the Midgut of Aedes aegypti L. (Diptera: Culicidae) Larvae Following Exposure to an Annona coriacea (Magnoliales: Annonaceae) Extract

Bioinsecticides are important in the control of disease vectors, but data regarding their physiological effects on target insects are incomplete. This study describes morphological changes that occur in the midgut of third instar Aedes aegypti L. (Diptera: Culicidae) following treatment with a methanolic extract of Annona coriacea (Magnoliales: Annonaceae). Dissected midguts were subdivided into anterior and posterior regions and analyzed by light and scanning electron microscopy. Insects exposed to the extract displayed intense, destructive cytoplasmic vacuolization in columnar and regenerative midgut cells. The apical surfaces of columnar cells exhibited cytoplasmic protrusions oriented toward the lumen, suggesting that these cells could be involved in apocrine secretory processes and/or apoptosis. We report that A. coriacea extracts induced morphological alterations in the midgut of A. aegypti midgut larvae, supporting the use of plant extracts for control of the dengue vector.     

Vaccinia virus DNA ligase recruits cellular topoisomerase II to sites of viral replication and assembly

Vaccinia virus replication is inhibited by etoposide and mitoxantrone even though poxviruses do not encode the type II topoisomerases that are the specific targets of these drugs. Furthermore, one can isolate drug-resistant virus carrying mutations in the viral DNA ligase and yet the ligase is not known to exhibit sensitivity to these drugs. A yeast two-hybrid screen was used to search for proteins binding to vaccinia ligase, and one of the nine proteins identified comprised a portion (residue 901 to end) of human topoisomerase IIbeta. One can prevent the interaction by introducing a C(11)-to-Y substitution mutation into the N terminus of the ligase bait protein, which is one of the mutations conferring etoposide and mitoxantrone resistance. Coimmunoprecipitation methods showed that the native ligase and a Flag-tagged recombinant protein form complexes with human topoisomerase IIalpha/beta in infected cells and that this interaction can also be disrupted by mutations in the A50R (ligase) gene. Immunofluorescence microscopy showed that both topoisomerase IIalpha and IIbeta antigens are recruited to cytoplasmic sites of virus replication and that less topoisomerase was recruited to these sites in cells infected with mutant virus than in cells infected with wild-type virus. Immunoelectron microscopy confirmed the presence of topoisomerases IIalpha/beta in virosomes, but the enzyme could not be detected in mature virus particles. We propose that the genetics of etoposide and mitoxantrone resistance can be explained by vaccinia ligase binding to cellular topoisomerase II and recruiting this nuclear enzyme to sites of virus biogenesis. Although other nuclear DNA binding proteins have been detected in virosomes, this appears to be the first demonstration of an enzyme being selectively recruited to sites of poxvirus DNA synthesis and assembly.     

Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in the Pseudomonas syringae species complex

The Pseudomonas syringae species complex is composed of several closely related species of bacterial plant pathogens. Here, we used in silico methods to assess 16 PCR primer sets designed for broad identification of isolates throughout the species complex. We evaluated their in silico amplification rate in 2161 publicly available genomes, the correlation between pairwise amplicon sequence distance and whole genome average nucleotide identity, and trained naive Bayes classification models to quantify classification resolution. Furthermore, we show the potential for using single amplicon sequence data to predict type III effector protein repertoires, which are important determinants of host specificity and range.     

Association between sexually selected traits and allelic distance in two unlinked MHC II loci in white-tailed deer (Odocoileus virginianus)

Evolutionary Ecology - Body size and secondary sexual characteristics are drivers of male reproductive success among polygynous species. A gene complex found to be associated with morphology in...     

The association of Amyloid P-Component (AP) With The Amyloid Fibril: An updated Method for Amyloid Fibril Protein Isolation

Abstract

An amyloid fibril isolation procedure is proposed which uses citrate as well as saline washes to dissociate the calcium dependent linkage of amyloid P-component (AP) from the amyloid fibril. In two amyloid rich tissues, the amount of AP was quantitated in each saline and citrate wash and totalled 13.8% and 20.8% of the amyloid fibrils isolated. The amount of AP removed from these and 22 additional amyloid rich tissues was greater than had previously been recognized.

AP protein was present in tissue only when amyloid fibrils were present. It could not be found in normal non-amyloidotic tissue, nor could it be found in tissue sediment after the fibrils were removed.     

Loss Mechanisms in Thick‐Film Low‐Bandgap Polymer Solar Cells

Polymer bulk heterojunction solar cells based on low bandgap polymer:fullerene blends are promising for next generation low‐cost photovoltaics. While these solution‐processed solar cells are compatible with large‐scale roll‐to‐roll processing, active layers used for typical laboratory‐scale devices are too thin to ensure high manufacturing yields. Furthermore, due to the limited light absorption and optical interference within the thin active layer, the external quantum efficiencies (EQEs) of bulk heterojunction polymer solar cells are severely limited. In order to produce polymer solar cells with high yields, efficient solar cells with a thick active layer must be demonstrated. In this work, the performance of thick‐film solar cells employing the low‐bandgap polymer poly(dithienogermole‐thienopyrrolodione) (PDTG‐TPD) was demonstrated. Power conversion efficiencies over 8.0% were obtained for devices with an active layer thickness of 200 nm, illustrating the potential of this polymer for large‐scale manufacturing. Although an average EQE > 65% was obtained for devices with active layer thicknesses > 200 nm, the cell performance could not be maintained due to a reduction in fill factor. By comparing our results for PDTG‐TPD solar cells with similar P3HT‐based devices, we investigated the loss mechanisms associated with the limited device performance observed for thick‐film low‐bandgap polymer solar cells.