Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data

We present two complementary approaches for the interpretation of clusters of co-regulated genes, such as those obtained from DNA chips and related methods. Starting from a cluster of genes with similar expression profiles, two basic questions can be asked: 1. Which mechanism is responsible for the coordinated transcriptional response of the genes? This question is approached by extracting motifs that are shared between the upstream sequences of these genes. The motifs extracted are putative cis-acting regulatory elements. 2. What is the physiological meaning for the cell to express together these genes? One way to answer the question is to search for potential metabolic pathways that could be catalyzed by the products of the genes. This can be done by selecting the genes from the cluster that code for enzymes, and trying to assemble the catalyzed reactions to form metabolic pathways. We present tools to answer these two questions, and we illustrate their use with selected examples in the yeast Saccharomyces cerevisiae. The tools are available on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/; http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/)

Carbon clusters near the crossover to fullerene stability

The thermodynamic stability of structural isomers of $\mathrm{C}_{24}$, $\mathrm{C}_{26}$, $\mathrm{C}_{28}$ and $\mathrm{C}_{32}$, including fullerenes, is studied using density functional and quantum Monte Carlo methods. The energetic ordering of the different isomers depends sensitively on the treatment of electron correlation. Fixed-node diffusion quantum Monte Carlo calculations predict that a $\mathrm{C}_{24}$ isomer is the smallest stable graphitic fragment and that the smallest stable fullerenes are the $\mathrm{C}_{26}$ and $\mathrm{C}_{28}$ clusters with $\mathrm{C}_{2v}$ and $\mathrm{T}_{d}$ symmetry, respectively. These results support proposals that a $\mathrm{C}_{28}$ solid could be synthesized by cluster deposition.Comment: 4 pages, includes 4 figures. For additional graphics, online paper and related information see http://www.tcm.phy.cam.ac.uk/~prck

Human-iPSC-Derived Cardiac Stromal Cells Enhance Maturation in 3D Cardiac Microtissues and Reveal Non-cardiomyocyte Contributions to Heart Disease

Cardiomyocytes (CMs) from human induced pluripotent stem cells (hiPSCs) are functionally immature, but this is improved by incorporation into engineered tissues or forced contraction. Here, we showed that tri-cellular combinations of hiPSC-derived CMs, cardiac fibroblasts (CFs), and cardiac endothelial cells also enhance maturation in easily constructed, scaffold-free, three-dimensional microtissues (MTs). hiPSC-CMs in MTs with CFs showed improved sarcomeric structures with T-tubules, enhanced contractility, and mitochondrial respiration and were electrophysiologically more mature than MTs without CFs. Interactions mediating maturation included coupling between hiPSC-CMs and CFs through connexin 43 (CX43) gap junctions and increased intracellular cyclic AMP (cAMP). Scaled production of thousands of hiPSC-MTs was highly reproducible across lines and differentiated cell batches. MTs containing healthy-control hiPSC-CMs but hiPSC-CFs from patients with arrhythmogenic cardiomyopathy strikingly recapitulated features of the disease. Our MT model is thus a simple and versatile platform for modeling multicellular cardiac diseases that will facilitate industry and academic engagement in high-throughput molecular screening

Overwintering, migration and migratory morphs of Sitobion avenae (F.)

SIGLEAvailable from British Library Document Supply Centre- DSC:DX179753 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Urban biodiversity: comparison of insect assemblages on native and non-native trees

Trees are thought to be important for supporting urban biodiversity. However tree species differ considerably in the numbers of invertebrates they support, with potential consequences for higher trophic groups such as birds. In this study the influence of native and non-native trees on the abundance of insects (Hemiptera) and the incidence of insectivorous birds (Paridae) were investigated in the southern English town of Bracknell. The number and species of tree were recorded from each of 17 roundabout and parkland sites. Tree beating was used to sample arboreal Hemiptera and Paridae were recorded either with point counts and transect walks, depending on the size of the site. Due to the great variation between tree species, there was no overall significant difference in species richness or abundance of Hemiptera between native and non-native tree species. However, individual native trees had more species and individuals than non-natives. The proportion of native trees at Bracknell sites was positively related to the abundance of both Hemiptera and the number of Paridae observed. The consequences of vegetation type for insect abundance indicates that in order to sustain and enhance urban biodiversity, careful consideration needs to be given to species of trees present in urban areas

Structural alterations in chromatin during myogenesis in the chicken

[No abstract available]Articl

Improved method for the routine identification of toxigenic Escherichia coli by DNA amplification of a conserved region of the heat-labile toxin A subunit

This report describes a DNA amplification procedure for routine identification of heat-labile-toxin-producing Escherichia coli. Two oligonucleotide primers were used in a polymerase chain reaction procedure to amplify a highly conserved region of the A subunit of the heat-labile enterotoxin gene. Amplifications were done directly on E. coli colonies from plates when Salmonella, Shigella, or parasite infections were excluded as agents of the severe diarrhea in the patients. The conditions for the polymerase chain reaction method were empirically determined, and the procedure is inexpensive, sensitive, and specific. Positive results can be obtained over a wide variation in bacterial numbers, with no inhibition of Thermus aquaticus DNA polymerase. Detection of the amplified product can be done by agarose gel electrophoresis, which is specific and sensitive enough for routine diagnosis of this pathogen in clinical isolates. If greater sensitivity and specificity are required, hybridization with 32P- or alkaline phosphatase-labeled oligonucleotide probes can be used. Our results suggest that heat-labile-toxin-producing E. coli is responsible for about 9% of nondiagnosed diarrhea cases in Tygerberg Hospital, Tygerberg, Republic of South Africa.Articl

Hydration and dehydration of sorption materials: experiments in a small-scale reactor

No abstract