Pre-TCR signaling and CD8 gene bivalent chromatin resolution during thymocyte development

The CD8 gene is silent in CD4(-)CD8(-) double-negative thymocytes, expressed in CD4(+)CD8(+) double-positive cells, and silenced in cells committing to the CD4(+) single-positive (SP) lineage, remaining active in the CD8(+) SP lineage. In this study, we show that the chromatin of the CD8 locus is remodeled in C57BL/6 and B6/J Rag1(-/-) MOM double-negative thymocytes as indicated by DNaseI hypersensitivity and widespread bivalent chromatin marks. Pre-TCR signaling coincides with chromatin bivalency resolution into monovalent activating modifications in double-positive and CD8 SP cells. Shortly after commitment to CD4 SP cell lineage, monovalent repressive characteristics and chromatin inaccessibility are established. Differential binding of Ikaros, NuRD, and heterochromatin protein 1α on the locus during these processes may participate in the complex regulation of CD8.     

New tools for gene manipulation in chicken embryos

Genomics has changed the pace by which genes are analyzed. Rather than looking at genes one by one, gene expression today is studied at the genome level. Unfortunately, the data we get from microarray analysis do not give us any clues about the function of these genes. Functional analyses are still refractory to large-scale, high-throughput studies, particularly in vertebrates. With the development of in ovo RNAi as a tool for specific gene silencing, the chicken embryo has become an efficient in vivo system to study gene function during development. A major advantage of in ovo RNAi is the fact that the knowledge of a cDNA fragment of the gene of interest is sufficient to get loss-of-function phenotypes. Thus, this new approach is a valuable tool for functional genomics.     

Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1

Background

The inability of aspirin (ASA) to adequately suppress platelet aggregation is associated with future risk of coronary artery disease (CAD). Heritability studies of agonist-induced platelet function phenotypes suggest that genetic variation may be responsible for ASA responsiveness. In this study, we leverage independent information from genome-wide linkage and association data to determine loci controlling platelet phenotypes before and after treatment with ASA.

Methods

Clinical data on 37 agonist-induced platelet function phenotypes were evaluated before and after a 2-week trial of ASA (81 mg/day) in 1231 European American and 846 African American healthy subjects with a family history of premature CAD. Principal component analysis was performed to minimize the number of independent factors underlying the covariance of these various phenotypes. Multi-point sib-pair based linkage analysis was performed using a microsatellite marker set, and single-SNP association tests were performed using markers from the Illumina 1 M genotyping chip from deCODE Genetics, Inc. All analyses were performed separately within each ethnic group.

Results

Several genomic regions appear to be linked to ASA response factors: a 10 cM region in African Americans on chromosome 5q11.2 had several STRs with suggestive (p-value < 7 × 10^-4) and significant (p-value < 2 × 10^-5) linkage to post aspirin platelet response to ADP, and ten additional factors had suggestive evidence for linkage (p-value < 7 × 10^-4) to thirteen genomic regions. All but one of these factors were aspirin response variables. While the strength of genome-wide SNP association signals for factors showing evidence for linkage is limited, especially at the strict thresholds of genome-wide criteria (N = 9 SNPs for 11 factors), more signals were considered significant when the association signal was weighted by evidence for linkage (N = 30 SNPs).

Conclusions

Our study supports the hypothesis that platelet phenotypes in response to ASA likely have genetic control and the combined approach of linkage and association offers an alternative approach to prioritizing regions of interest for subsequent follow-up.     

Hidden diversity and productivity patterns in mixed Mediterranean grasslands

A detailed study of the variation in productivity across a diversity gradient in an experimental Mediterranean grassland examines the effects of a dominant perennial grass species upon the overall diversity–productivity relationship. The experiment took place at the Greek site of the European-wide BIODEPTH programme. The experimental design is characterized by the use of a number of communities containing annuals and perennials within the total set of manipulated plots. The main results are: 1) a log-linear relationship between diversity and productivity exists in Mediterranean grasslands synthesized by annuals only, 2) in mixed communities where multiple growth forms coexist, the performance of a dominant or keystone species may reverse or hide the diversity–productivity pattern of a functional or growth form group of species taken separately, and 3) the introduction of the dominant grass in the low-diversity mixtures creates an 'inverted' sampling effect which can produce as an artefact a constant productivity response across the diversity gradient.     

A novel sensor of NADH/NAD+ redox poise in Streptomyces coelicolor A3(2)

We describe the identification of Rex, a novel redox-sensing repressor that appears to be widespread among Gram-positive bacteria. In Streptomyces coelicolor Rex binds to operator (ROP) sites located upstream of several respiratory genes, including the cydABCD and rex-hemACD operons. The DNA-binding activity of Rex appears to be controlled by the redox poise of the NADH/NAD+ pool. Using electromobility shift and surface plasmon resonance assays we show that NADH, but not NAD+, inhibits the DNA-binding activity of Rex. However, NAD+ competes with NADH for Rex binding, allowing Rex to sense redox poise over a range of NAD(H) concentrations. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved. In support of this, the central glycine in the signature motif (GlyXGlyXXGly) is shown to be essential for redox sensing. Rex homologues exist in most Gram-positive bacteria, including human pathogens such as Staphylococcus aureus, Listeria monocytogenes and Streptococcus pneumoniae.     

858. PAEONIA PARNASSICA

Paeonia parnassica is illustrated, its habitat is shown and suggestions for its successful cultivation are given.     

Isolation of detergent-resistant membranes (DRMs) from Escherichia coli

Lipid rafts or membrane microdomains have been proposed to compartmentalize cellular processes by spatially organizing diverse molecules/proteins in eukaryotic cells. Such membrane microdomains were recently reported to also exist in a few bacterial species. In this work, we report the development of a procedure for membrane microdomain isolation from Escherichia coli plasma membranes as well as a method to purify the latter. The method here reported could easily be adapted to other gram-negative bacteria, wherein the isolation of this kind of sub-membrane preparation imposes special difficulties. The analysis of isolated membrane microdomains might provide important information on the nature and function of these bacterial structures and permit their comparison with the ones of eukaryotic cells.     

Propensity of lignin to associate: light scattering photometry study with native lignins

Many studies of lignins in solution invoke association and aggregation phenomena to explain their solution behavior (e.g., reprecipitation onto pulp fibers, condensation, etc.). Following their colloidal (apparent) molecular weights in solution as a function of time allows us to explore observable dissociation phenomena. These measurements were carried out using multiple angle laser light scattering (MALLS) photometry in the static mode. The challenges and opportunities of measuring the specific refractive index increment (dn/dC) of lignin solutions and determining the kinetics of the dissociation process were thus investigated. Hardwood and softwood representative lignins were isolated, and method for their full dissolution in THF was further developed, which then lead to accurate dn/dC values being obtained as a function of time. When coupled to additional work using light scattering static measurements and Zimm plots for the same solutions, this effort offers insight into the aggregation and ensuing dissociative events that operate within the lignin macromolecules.