Benzene containing polyhydroxyalkanoates homo- and copolymers synthesized by genome edited Pseudomonas entomophila

Microbial synthesis of functional polymers has become increasingly important for industrial biotechnology.For the first time,it became possible to synthesize controllable composition of poly(3-hydroxyalkanoate)(P3HA)consisting of 3-hydroxydodecanoate(3HDD)and phenyl group on the side-chain when chromosome of Pseudomonas entomophila was edited to weaken itsβ-oxidation.Cultured in the presence of 5-phenylvaleric acid(PVA),the edited P.entomophila produced only homopolymer poly(3-hydroxy-5-phenylvalerate)or P(3HPhV).While copolyesters P(3HPhV-co-3HDD)of 3-hydroxy-5-phenylvalerate(3HPhV)and 3-hydroxydodecanoate(3HDD)were synthesized when the strain was grown on mixtures of PVA and dodecanoic acid(DDA).Compositions of 3HPhV in P(3HPhV-co-3HDD)were controllable ranging from 3%to 32%depending on DDDA/PVA ratios.Nuclear magnetic resonance(NMR)spectra clearly indicated that the polymers were homopolymer of P(3HPhV)and random copolymers of 3HPhV and 3HDD.Their mechanical and thermal properties varied dramatically depending on the monomer ratios.Our results demonstrated the possibility to produce tailor-made,novel functional PHA using the chromosome edited P.entomophila.     

The Roles of p38 MAPK/MSK1 Signaling Pathway in the Neuroprotection of Hypoxic Postconditioning Against Transient Global Cerebral Ischemia in Adult Rats

Postconditioning has regenerated interest as a mechanical intervention against cerebral ischemia/reperfusion injury, but its molecular mechanisms remain unknown. We previously reported that hypoxic postconditioning (HPC) ameliorated neuronal death induced by transient global cerebral ischemia (tGCI) in hippocampal CA1 subregion of adult rats. This study tested the hypothesis that p38-mitogen-activated protein kinase (p38 MAPK)/mitogen- and stress-response kinase 1 (MSK1) signaling pathway plays a role in the HPC-induced neuroprotection. Male Wistar rats were subjected to 10 min ischemia induced by applying the four-vessel occlusion method. HPC with 120 min was applied at 24 h after reperfusion. Immunohistochemistry and Western blot were used to detect the expression of phosphorylation of p38 MAPK and MSK1, as well as cleaved caspase-3. We found that HPC induced a significant increase of phosphorylated p38 MAPK and MSK1 in neurons of hippocampal CA1 region and a significant decrease in glial cells after tGCI as well. Furthermore, HPC attenuated caspase-3 cleavation triggered by tGCI in CA1 region. Moreover, p38 MAPK inhibition by SB203580 significantly decreased the phosphorylation of MSK1, increased cleaved caspase-3 expression, and abolished the neuroprotection of HPC. These findings suggested that p38 MAPK/MSK1 signaling axis contributed to HPC-mediated neuroprotection against tGCI, at least in part, by regulating the activation of caspase-3.     

Sensitive and High Resolution Localization and Tracking of Membrane Proteins in Live Cells with BRET

Peripheral and integral membrane proteins can be located in several different subcellular compartments, and it is often necessary to determine the location of such proteins or to track their movement in living cells. Image‐based colocalization of labeled membrane proteins and compartment markers is frequently used for this purpose, but this method is limited in terms of throughput and resolution. Here we show that bioluminescence resonance energy transfer (BRET) between membrane proteins of interest and compartment‐targeted BRET partners can report subcellular location and movement of membrane proteins in live cells. The sensitivity of the method is sufficient to localize a few hundred protein copies per cell. The spatial resolution can be sufficient to determine membrane topology, and the temporal resolution is sufficient to track changes that occur in less than 1 second. BRET requires little user intervention, and is thus amenable to large‐scale experimental designs with standard instruments.     

SNP-SNP Interactions Discovered by Logic Regression Explain Crohn's Disease Genetics

In genome-wide association studies (GWAS), the association between each single nucleotide polymorphism (SNP) and a phenotype is assessed statistically. To further explore genetic associations in GWAS, we considered two specific forms of biologically plausible SNP-SNP interactions, ‘SNP intersection’ and ‘SNP union,’ and analyzed the Crohn''s Disease (CD) GWAS data of the Wellcome Trust Case Control Consortium for these interactions using a limited form of logic regression. We found strong evidence of CD-association for 195 genes, identifying novel susceptibility genes (e.g., ISX, SLCO6A1, TMEM183A) as well as confirming many previously identified susceptibility genes in CD GWAS (e.g., IL23R, NOD2, CYLD, NKX2-3, IL12RB2, ATG16L1). Notably, 37 of the 59 chromosomal locations indicated for CD-association by a meta-analysis of CD GWAS, involving over 22,000 cases and 29,000 controls, were represented in the 195 genes, as well as some chromosomal locations previously indicated only in linkage studies, but not in GWAS. We repeated the analysis with two smaller GWASs from the Database of Genotype and Phenotype (dbGaP): in spite of differences of populations and study power across the three datasets, we observed some consistencies across the three datasets. Notable examples included TMEM183A and SLCO6A1 which exhibited strong evidence consistently in our WTCCC and both of the dbGaP SNP-SNP interaction analyses. Examining these specific forms of SNP interactions could identify additional genetic associations from GWAS. R codes, data examples, and a ReadMe file are available for download from our website: http://www.ualberta.ca/~yyasui/homepage.html.     

C2ORF40 suppresses breast cancer cell proliferation and invasion through modulating expression of M phase cell cycle genes

Recently, it has been suggested that C2ORF40 is a candidate tumor suppressor gene in breast cancer. However, the mechanism for reduced expression of C2ORF40 and its functional role in breast cancers remain unclear. Here we show that C2ORF40 is frequently silenced in human primary breast cancers and cell lines through promoter hypermethylation. C2ORF40 mRNA level is significantly associated with patient disease-free survival and distant cancer metastasis. Overexpression of C2ORF40 inhibits breast cancer cell proliferation, migration and invasion. By contrast, silencing C2ORF40 expression promotes these biological phenotypes. Bioinformatics and FACS analysis reveal C2ORF40 functions at G2/M phase by downregulation of mitotic genes expression, including UBE2C. Our results suggest that C2ORF40 acts as a tumor suppressor gene in breast cancer pathogenesis and progression and is a candidate prognostic marker for this disease.