The interaction of beta-amyloid protein with cellular membranes stimulates its own production

Gradual changes in steady-state levels of beta amyloid peptides (Aβ) in brain are considered an initial step in the amyloid cascade hypothesis of Alzheimer's disease. Aβ is a product of the secretase cleavage of amyloid precursor protein (APP). There is evidence that the membrane lipid environment may modulate secretase activity and alters its function. Cleavage of APP strongly depends on membrane properties. Since Aβ perturbs cell membrane fluidity, the cell membrane may be the location where the neurotoxic cascade of Aβ is initiated. Therefore, we tested effects of oligomeric Aβ on membrane fluidity of whole living cells, the impact of exogenous and cellular Aβ on the processing of APP and the role of GM-1 ganglioside. We present evidence that oligoAβ_(1-40) stimulates the amyloidogenic processing of APP by reducing membrane fluidity and complexing with GM-1 ganglioside. This dynamic action of Aβ may start a vicious circle, where endogenous Aβ stimulates its own production. Based on our novel findings, we propose that oligoAβ_(1-40) accelerates the proteolytic cleavage of APP by decreasing membrane fluidity.     

A combinatorial approach to hybrid enzymes independent of DNA homology

We present a methodology, termed incremental truncation for the creation of hybrid enzymes (ITCHY), that creates combinatorial fusion libraries between genes in a manner that is independent of DNA homology. We compared the ability of ITCHY and DNA shuffling to create interspecies fusion libraries between fragments of the Escherichia coli and human glycinamide ribonucleotide transformylase genes, which have only 50% identity on the DNA level. Sequencing of several randomly selected positives from each library illustrated that ITCHY identified a more diverse set of active fusion points including those in regions of nonhomology and those with crossover points that diverged from the sequence alignment. Furthermore, some of the hybrids found by ITCHY that were fused at nonhomologous locations had activities that were greater than or equal to the activity of the hybrids found by DNA shuffling.     

Calcium Signaling Controls Pathogenic Th17 Cell-Mediated Inflammation by Regulating Mitochondrial Function

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Spatial variability in structural and functional aspects of macrofauna communities and their environmental parameters in the Jade Bay (Wadden Sea Lower Saxony, southern North Sea)

Spatial distribution and functional structure of intertidal benthic macrofauna in relation to environmental variables in the Jade Bay (southern North Sea) were studied and compared with other intertidal areas of the Wadden Sea. A total of 128 stations covering the whole Jade Bay were sampled in summer 2009. A total of 114 taxa were found. Highest species numbers occurred in the subtidal areas, whereas highest mean abundances were found in the upper intertidal areas. Based on species abundance data, six significantly distinct macrofauna communities in the Jade Bay were identified and evaluated with multivariate statistics, univariate correlations and canonical correspondence analysis. Differences in these community patterns were caused by the response of the dominant species (Hydrobia ulvae, Tubificoides benedii, Pygospio elegans, Caulleriella killariensis, Scoloplos armiger, Urothoe poseidonis, Microprotopus maculatus) to prevailing environmental conditions along the gradient from the lower and exposed sandy intertidal areas via intermediate mixed sediments to the upper mudflat areas. Distribution patterns in relation to tidal zonation were best explained by variability in submergence time, Chlorophyll a (chl a) content and sediment composition (mud content), which are proxies for hydrodynamic conditions and food availability. Species inventory and species richness were comparable with other intertidal areas of the Wadden Sea, but the Jade Bay differs from these areas regarding dominant species. Differences in sediment composition and morphological characteristics (macrotidal versus mesotidal Wadden Sea areas) are discussed for comparison of regional differences.     

The Vinculin-ΔIn20/21 Mouse: Characteristics of a Constitutive,Actin-Binding Deficient Splice Variant of Vinculin

Background

The cytoskeletal adaptor protein vinculin plays a fundamental role in cell contact regulation and affects central aspects of cell motility, which are essential to both embryonal development and tissue homeostasis. Functional regulation of this evolutionarily conserved and ubiquitously expressed protein is dominated by a high-affinity, autoinhibitory head-to-tail interaction that spatially restricts ligand interactions to cell adhesion sites and, furthermore, limits the residency time of vinculin at these sites. To date, no mutants of the vinculin protein have been characterized in animal models.

Methodology/Principal Findings

Here, we investigate vinculin-ΔEx20, a splice variant of the protein lacking the 68 amino acids encoded by exon 20 of the vinculin gene VCL. Vinculin-ΔEx20 was found to be expressed alongside with wild type protein in a knock-in mouse model with a deletion of introns 20 and 21 (VCL-ΔIn20/21 allele) and shows defective head-to-tail interaction. Homozygous VCL-ΔIn20/21 embryos die around embryonal day E12.5 showing cranial neural tube defects and exencephaly. In mouse embryonic fibroblasts and upon ectopic expression, vinculin-ΔEx20 reveals characteristics of constitutive head binding activity. Interestingly, the impact of vinculin-ΔEx20 on cell contact induction and stabilization, a hallmark of the vinculin head domain, is only moderate, thus allowing invasion and motility of cells in three-dimensional collagen matrices. Lacking both F-actin interaction sites of the tail, the vinculin-ΔEx20 variant unveils vinculin''s dynamic binding to cell adhesions independent of a cytoskeletal association, and thus differs from head-to-tail binding deficient mutants such as vinculin-T12, in which activated F-actin binding locks the protein variant to cell contact sites.

Conclusions/Significance

Vinculin-ΔEx20 is an active variant supporting adhesion site stabilization without an enhanced mechanical coupling. Its presence in a transgenic animal reveals the potential of splice variants in the vinculin gene to alter vinculin function in vivo. Correct control of vinculin is necessary for embryonic development.     

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

Background

Copy number variants (CNVs), including deletions, amplifications, and other rearrangements, are common in human and cancer genomes. Copy number data from array comparative genome hybridization (aCGH) and next-generation DNA sequencing is widely used to measure copy number variants. Comparison of copy number data from multiple individuals reveals recurrent variants. Typically, the interior of a recurrent CNV is examined for genes or other loci associated with a phenotype. However, in some cases, such as gene truncations and fusion genes, the target of variant lies at the boundary of the variant.

Results

We introduce Neighborhood Breakpoint Conservation (NBC), an algorithm for identifying rearrangement breakpoints that are highly conserved at the same locus in multiple individuals. NBC detects recurrent breakpoints at varying levels of resolution, including breakpoints whose location is exactly conserved and breakpoints whose location varies within a gene. NBC also identifies pairs of recurrent breakpoints such as those that result from fusion genes. We apply NBC to aCGH data from 36 primary prostate tumors and identify 12 novel rearrangements, one of which is the well-known TMPRSS2-ERG fusion gene. We also apply NBC to 227 glioblastoma tumors and predict 93 novel rearrangements which we further classify as gene truncations, germline structural variants, and fusion genes. A number of these variants involve the protein phosphatase PTPN12 suggesting that deregulation of PTPN12, via a variety of rearrangements, is common in glioblastoma.

Conclusions

We demonstrate that NBC is useful for detection of recurrent breakpoints resulting from copy number variants or other structural variants, and in particular identifies recurrent breakpoints that result in gene truncations or fusion genes. Software is available at http://http.//cs.brown.edu/people/braphael/software.html.     

Downstream processing of serinol from a glycerol‐based fermentation broth and transfer to other amine containing molecules

A possible application of glycerol, which is produced in large amounts as a by‐product from the biodiesel industry, is its fermentation to serinol (2‐amino‐1,3‐propanediol), a glycerol derivative. The downstream processing of this glycerol‐based fermentation broth was investigated. The challenge of the isolation of serinol was the complex media and the solubility of the desired substance in aqueous media. In this study, the isolation of serinol was investigated by an appropriate reversible derivatization method. Serinol was isolated by protecting the amino group with diethyl ethoxymethylenemalonate directly in the aqueous phase, followed by extraction of the 2,2‐bis(ethoxycarbonyl)vinyl‐serinol (BECV‐serinol) with ethyl acetate resulting in an isolated yield of 63%. We demonstrate the possibility of isolation of a hydroscopic amino alcohol from the fermentation broth and the comparison of the products in water as well as the cleavage of the 2,2‐bis(ethoxycarbonyl)vinyl group (BECV group). The procedure can also be used for other amino group containing molecules, such as serine, glucosamine, hexylamine and amino methyl laureate.