Effects of genotypes of maitake (<Emphasis Type="Italic">Grifola frondosa</Emphasis>) on biological efficiency,quality and crop cycle time

Twenty-three genotypes of maitake (Grifola frondosa) from Asia, North America and Europe were compared for biological efficiency (BE), quality and crop cycle time. Significant differences among lines were found for BE and crop cycle time when mushrooms were produced on nutrient-supplemented (15% millet, 10% wheat bran and 0.2% gypsum) oak sawdust substrate. Four isolates (WC828, M036, M037, and M040) were found to have the most consistent and highest BEs (38.5%, 39.5%, 35.8%, and 38.9%, respectively) and quality ratings (1.2, 1.3, 1.4, and 1.2, respectively, where I is highest quality and 4 is lowest quality). A commercial line (M039) used in China had the shortest crop cycle time (8 weeks). Lines deemed to have the best commercial potential were of Asian origin.     

Neither agouti-related protein nor neuropeptide Y is critically required for the regulation of energy homeostasis in mice

Agouti-related protein (AgRP), a neuropeptide abundantly expressed in the arcuate nucleus of the hypothalamus, potently stimulates feeding and body weight gain in rodents. AgRP is believed to exert its effects through the blockade of signaling by alpha-melanocyte-stimulating hormone at central nervous system (CNS) melanocortin-3 receptor (Mc3r) and Mc4r. We generated AgRP-deficient (Agrp(-/-)) mice to examine the physiological role of AgRP. Agrp(-/-) mice are viable and exhibit normal locomotor activity, growth rates, body composition, and food intake. Additionally, Agrp(-/-) mice display normal responses to starvation, diet-induced obesity, and the administration of exogenous leptin or neuropeptide Y (NPY). In situ hybridization failed to detect altered CNS expression levels for proopiomelanocortin, Mc3r, Mc4r, or NPY mRNAs in Agrp(-/-) mice. As AgRP and the orexigenic peptide NPY are coexpressed in neurons of the arcuate nucleus, we generated AgRP and NPY double-knockout (Agrp(-/-);Npy(-/-)) mice to determine whether NPY or AgRP plays a compensatory role in Agrp(-/-) or NPY-deficient (Npy(-/-)) mice, respectively. Similarly to mice deficient in either AgRP or NPY, Agrp(-/-);Npy(-/-) mice suffer no obvious feeding or body weight deficits and maintain a normal response to starvation. Our results demonstrate that neither AgRP nor NPY is a critically required orexigenic factor, suggesting that other pathways capable of regulating energy homeostasis can compensate for the loss of both AgRP and NPY.     

Improved detection of small deletions in complex pools of DNA

About 40% of the genes in the nematode Caenorhabditis elegans have homologs in humans. Based on the history of this model system, it is clear that the application of genetic methods to the study of this set of genes would provide important clues to their function in humans. To facilitate such genetic studies, we are engaged in a project to derive deletion alleles in every gene in this set. Our standard methods make use of nested PCR to hunt for animals in mutagenized populations that carry deletions at a given locus. The deletion bearing animals exist initially in mixed populations where the majority of the animals are wild type at the target. Therefore, the production of the PCR fragment representing the deletion allele competes with the production of the wild type fragment. The size of the deletion fragment relative to wild type determines whether it can compete to a level where it can be detected above the background. Using our standard conditions, we have found that when the deletion is <600 bp, the deletion fragment does not compete effectively with the production of the wild type fragment in PCR. Therefore, although our standard methods work well to detect mutants with deletions >600 bp, they do not work well to detect mutants with smaller deletions. Here we report a new strategy to detect small deletion alleles in complex DNA pools. Our new strategy is a modification of our standard PCR based screens. In the first round of the nested PCR, we include a third PCR primer between the two external primers. The presence of this third primer leads to the production of three fragments from wild type DNA. We configure the system so that two of these three fragments cannot serve as a template in the second round of the nested PCR. The addition of this third primer, therefore, handicaps the amplification from wild type template. On the other hand, the amplification of mutant fragments where the binding site for the third primer is deleted is unabated. Overall, we see at least a 500-fold increase in the sensitivity for small deletion fragments using our new method. Using this new method, we report the recovery of new deletion alleles within 12 C.elegans genes.     

Involvement of actin-related proteins in ATP-dependent chromatin remodeling

Actin-related proteins (Arps) and conventional actin are enigmatic components of many chromatin-remodeling enzyme complexes. The yeast INO80 ATP-dependent chromatin-remodeling complex contains stoichiometric amounts of Arp4, Arp5, Arp8, and actin. Here we have revealed functions of Arp5 and Arp8 by analysis of mutants. arp5 Delta and arp8 Delta mutants display an ino80 Delta phenotype. Purification of INO80 complexes from arp5 Delta and arp8 Delta cells shows that protein complexes remain intact but are compromised for INO80 ATPase activity, DNA binding, and nucleosome mobilization. The INO80 (arp8 Delta) complex is strikingly deficient, not only for the Arp8 subunit, but also for Arp4 and actin, suggesting an ordered assembly of Arps. Binding of Arp8 to the INO80 complex requires an N-terminal region of Ino80 adjacent to the conserved ATPase domain. GST-Arp8 binds preferentially to histones H3 and H4 in vitro, suggesting a histone chaperone function. These findings show direct involvement of Arps in the chromatin-remodeling process.     

An XML message broker framework for exchange and integration of microarray data

MOTIVATION: Microarrays are an important research tool for the advancement of basic biological sciences. However this technology has yet to be integrated with clinical decision making. We have implemented an information framework based on the Microarray Gene Expression Markup Language (MAGE-ML) specification. We are using this framework to develop a test-bed integrated database application to identify genomic and imaging markers for diagnosis of breast cancer. RESULTS: We developed extensible software architecture for retrieving data from different microarray databases using MAGE-ML and for combining microarray data with breast cancer image analysis and clinical data for correlation studies. The framework we developed will provide the necessary data integration to move microarray research from basic biological sciences to clinical applications. AVAILABILITY: Open source software will be available from SourceForge (http://sourceforge.net/projects/microsoap/).     

RankViaContact: ranking and visualization of amino acid contacts

SUMMARY: RankViaContact is a web service for calculation of residue-residue contact energies in proteins based on a coarse-grained model, and for visualization of interactions. The service provides information about ranked contact energies of residues, coordination numbers and the relative solvent accessibility of selected residues, as well as sequence and structure information. The program can be used to design stabilizing mutations, to analyze residue-residue contacts and to study the consequences of mutations. AVAILABILITY: http://bioinf.uta.fi/Rank.htm.     

Chemical cytometry

Chemical cytometry refers to the use of high-sensitivity analytical tools to characterize single cells. These tools include mass spectrometry, electrochemistry and capillary separation methods. This review focuses on the use of capillary electrophoresis coupled with high-sensitivity detection to characterize single cells. In survey experiments, biogenic amines and proteins have been characterized in single cells. In directed experiments, fluorescent substrates are used to monitor the activity of sets of enzymes, either within a family or along an enzymatic cascade. When combined with classical cytometry tools, it is now possible to monitor several cellular components in single cells as a function of cell cycle, which provides insight into the evolution of cellular composition as cells prepare for division.     

Improved production of (<Emphasis Type="Italic">S</Emphasis>)-ketoprofen ester hydrolase by a mutant of<Emphasis Type="Italic"> Trichosporon brassicae</Emphasis> CGMCC 0574

An efficient screening method following UV mutagenesis yielded a high frequency of improved mutants of Trichosporon brassicae CGMCC 0574, a wild-type esterase-producer capable of enantioselectively hydrolyzing the ethyl ester of ketoprofen [2-(3-benzoylphenyl) propionic acid]. The mutant had an activity 1.8-fold higher than the wild type and was stable in its enzyme production for ten serial transfers. As the best single carbon source, isopropanol improved the specific activity of the enzyme 5-fold; and this did not result from the effect of cell permeabilization. An 18-h culture grown on a medium containing 0.5% glucose plus 0.5% isopropanol produced 3-fold as much esterase as a culture grown on 1% glucose.