Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)

BACKGROUND: The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level. RESULTS: Here, we build an integrative platform, the Encyclopedia of Hepatocellular Carcinoma genes Online, dubbed EHCO , to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (~25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs. CONCLUSION: This architectural map may represent the first step toward the attempt to decipher the hepatocarcinogenesis at the systems level. Targeting hubs and/or disruption of the network formation might reveal novel strategy for HCC treatment

Applications of Nanomaterials in Electrogenerated Chemiluminescence Biosensors

Electrogenerated chemiluminescence (also called electrochemiluminescence and abbreviated ECL) involves the generation of species at electrode surfaces that then undergo electron-transfer reactions to form excited states that emit light. ECL biosensor, combining advantages offered by the selectivity of the biological recognition elements and the sensitivity of ECL technique, is a powerful device for ultrasensitive biomolecule detection and quantification. Nanomaterials are of considerable interest in the biosensor field owing to their unique physical and chemical properties, which have led to novel biosensors that have exhibited high sensitivity and stability. Nanomaterials including nanoparticles and nanotubes, prepared from metals, semiconductor, carbon or polymeric species, have been widely investigated for their ability to enhance the efficiencies of ECL biosensors, such as taking as modification electrode materials, or as carrier of ECL labels and ECL-emitting species. Particularly useful application of nanomaterials in ECL biosensors with emphasis on the years 2004-2008 is reviewed. Remarks on application of nanomaterials in ECL biosensors are also surveyed

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Different Roles Of Class-I And Class-II Clostridium-histolyticum Collagenase In Rat Pancreatic-islet Isolation

Crude Clostridium histolyticum collagenase was purified by gel filtration and fractionated by anion exchange chromatography into class I with high collagen digestion activity (CDA) and low FALGPA (2-furanacryloyl-L-leucylglycyl-L-prolyI-L-alanine )hydrolysis activity (FHA), class II with low CDA and high FHA, and a fraction called class I/II with intermediate activities. The roles of these collagenase classes in rat pancreatic islet isolation were investigated. Dissociations were carried out with 360 mg of pancreatic tissue in 10 mi of buffer containing 10% (wt/vol) albumin to suppress endogenous proteolytic activity, 100 U of C. histolyticum neutral protease, and one or two purified collagenase(s). For purified nonfractionated (PNF) collagenase, 2.6 mg of enzyme containing 2.4 U CDA and 38.0 U FHA was used, and for the separate classes, comparable amounts of activity were added. PNF collagenase dissociated the tissue completely in 32 min and yielded 5.0 +/- 0.4 mu l islet tissue/g pancreas. Class I collagenase alone dissociated pancreatic tissue extremely slowly and incompletely; only a few islets were released (0.7 +/- 0.2 mu l/g pancreas). Class II collagenase alone dissociated the tissue adequately in 50 min, and a high islet yield of 5.7 +/- 0.6 mu l/g was obtained. With class I/II, a similar dissociation time (47 min) and islet yield (5.5 +/- 0.3 mu/g) were obtained. Combining class I and class II collagenase resulted in a more rapid dissociation (32 min) and a higher islet yield (7.1 +/- 0.8 mu l/g) than that obtained with PNF collagenase (P <0.05). Similar results were obtained when purified class I collagenase was replaced by recombinant class I collagenase (32 min, islet yield 6.1 +/- 0.3 mu l/g). We conclude that class II collagenase plays a major role in pancreas dissociation and islet isolation and that class I collagenase acts synergistically with class II collagenase

DESIGN OF A VIRTUAL LABORATORY FOR ANALYZING NANOSCALE MAGNETIC MATERIALS

ABSTRAC

POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome

One possible path towards understanding the biological function of a target protein is through the discovery of how it interfaces within protein-protein interaction networks. The goal of this study was to create a virtual protein-protein interaction model using the concepts of orthologous conservation (or interologs) to elucidate the interacting networks of a particular target protein. POINT (the prediction of interactome database) is a functional database for the prediction of the human protein-protein interactome based on available orthologous interactome datasets. POINT integrates several publicly accessible databases, with emphasis placed on the extraction of a large quantity of mouse, fruit fly, worm and yeast protein-protein interactions datasets from the Database of Interacting Proteins (DIP), followed by conversion of them into a predicted human interactome. In addition, protein-protein interactions require both temporal synchronicity and precise spatial proximity. POINT therefore also incorporates correlated mRNA expression clusters obtained from cell cycle microarray databases and subcellular localization from Gene Ontology to further pinpoint the likelihood of biological relevance of each predicted interacting sets of protein partners

Polymeric Carbon Nitride with Localized Aluminum Coordination Sites as a Durable and Efficient Photocatalyst for Visible Light Utilization

The development of efficient and yet economic photocatalysts that can utilize solar light is crucial for the sustainable future. We report a simple approach to introduce a bidentate type of metal coordination site in polymeric carbon nitride (PCN) by an <i>in situ</i> keto–enol cyclization route of acetylacetone and urea to incorporate a metal chelating pyrimidine derivative into the molecular framework of PCN. The resulting new metal coordination sites provide both N- and O-complexing ligands unlike the unmodified PCN that has N-ligands only. As a proof-of-concept experiment, we introduced Al³⁺ ions into these coordination sites, which induced significant enhancements in visible light photocatalytic activities for organic pollutant degradation and H₂ evolution as compared to those of bulk PCN and the conventional “nitrogen pot” metal-coordinated PCN. The optimized Al loading was as low as 0.32 wt %. The photocatalytic activities <i>sensitively</i> depended on the Al incorporation, and the Al-incorporated sample demonstrated an excellent stability in water with showing little sign of metal leaching. While the aluminum ions complexed in the nitrogen pot little influenced the photocatalytic activity, Al³⁺ ions complexed by both N and O ligands in the alternative coordination sites significantly enhanced the photocatalytic activity of PCN. This study demonstrates a facile and scalable synthesis of PCN with alternative metal coordination sites for efficient solar energy conversion

Modulatory impact of cardiac rehabilitation on hyperhomocysteinemia in patients with coronary artery disease and "normal" lipid levels

Despite these limitations, this study suggests that cardiac rehabilitation and exercise training may significantly reduce homocysteine levels in normolipidemic patients with CAD and hyperhomocysteinemia. This 12% reduction in homocysteine levels noted in our study would be expected to produce 20% to 30% reductions in CAD risk. Further larger studies are needed to confirm our findings on the additional beneficial effect of exercise training in patients with CAD