A probabilistic functional network of yeast genes

A conceptual framework for integrating diverse functional genomics data was developed by reinterpreting experiments to provide numerical likelihoods that genes are functionally linked. This allows direct comparison and integration of different classes of data. The resulting probabilistic gene network estimates the functional coupling between genes. Within this framework, we reconstructed an extensive, high-quality functional gene network for Saccharomyces cerevisiae, consisting of 4681 (approximately 81%) of the known yeast genes linked by approximately 34,000 probabilistic linkages comparable in accuracy to small-scale interaction assays. The integrated linkages distinguish true from false-positive interactions in earlier data sets; new interactions emerge from genes' network contexts, as shown for genes in chromatin modification and ribosome biogenesis.     

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

The high-resolution three-dimensional structure of a single immunoglobulin binding domain (B1, which comprises 56 residues including the NH2-terminal Met) of protein G from group G Streptococcus has been determined in solution by nuclear magnetic resonance spectroscopy on the basis of 1058 experimental restraints. The average atomic root-mean-square distribution about the mean coordinate positions is 0.27 angstrom (A) for the backbone atoms, 0.65 A for all atoms, and 0.39 A for atoms excluding disordered surface side chains. The structure has no disulfide bridges and is composed of a four-stranded beta sheet, on top of which lies a long helix. The central two strands (beta 1 and beta 4), comprising the NH2- and COOH-termini, are parallel, and the outer two strands (beta 2 and beta 3) are connected by the helix in a +3x crossover. This novel topology (-1, +3x, -1), coupled with an extensive hydrogen-bonding network and a tightly packed and buried hydrophobic core, is probably responsible for the extreme thermal stability of this small domain (reversible melting at 87 degrees C).     

Specific triiodothyronine binding sites in the anterior pituitary of the rat

Studies with L-[(125)l] triiodothyronine and L-[(125)l] thyroxine, and with equilibrium dialysis of plasma proteins indicate that rat pituitary binds L-triiodothyronine 9.8 times as strongly as it does L-thyroxine. Injection of even small doses of nonradioactive L-triiodothyronine reduces the pituitary/ plasma ratio of radioactive L-triiodothyronine, an indication of the existence of pituitary binding sites with a limited capacity for L-triiodothyronine. Limited capacity binding sites for L-thyroxine could not be demonstrated.     

Expression of the major surface antigen of Plasmodium knowlesi sporozoites in yeast

The circumsporozite protein, a surface antigen of the sporozoite stage of the monkey malarial parasite Plasmodium knowlesi, was expressed in the yeast Saccharomyces cerevisiae by using an expression vector containing the 5' regulatory region of the yeast alcohol dehydrogenase I gene. It was necessary to eliminate the entire 5' upstream region of the parasite DNA to obtain the expression of this protein. Only the circumsporozoite precursor was produced by the yeast transformants, as detected by immunoblotting. About 55 and 20 percent of the circumsporozoite protein produced in yeast was associated wtih the 25,000 g and 150,000 g particulate fractions, respectively. The protein could be solubilized in Triton X-100 and was stable in solubilized extracts.     

An opiate binding site in the rat brain is highly selective for 4,5-epoxymorphinans

In vitro binding studies have demonstrated the existence of multiple opiate receptor types. An additional site in the rat brain (termed the lambda site) is distinct from the established types by its selectivity for 4,5-epoxymorphinans (such as naloxone and morphine). While the lambda site displays a high affinity for naloxone in vivo and in vitro in fresh brain membrane homogenates, these sites rapidly convert in vitro to a state of low affinity. The regional distribution of the lambda site in the brain is strikingly different from that of the classic opiate receptor types.     

Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein

D-galactose-binding (or chemoreceptor) protein of Escherichia coli serves as an initial component for both chemotaxis towards galactose and glucose and high-affinity active transport of the two sugars. Well-refined x-ray structures of the liganded forms of the wild-type and a mutant protein isolated from a strain defective in chemotaxis but fully competent in transport have provided a molecular view of the sugar-binding site and of a site for interacting with the Trg transmembrane signal transducer. The geometry of the sugar-binding site, located in the cleft between the two lobes of the bilobate protein, is novel in that it is designed for tight binding and sequestering of either the alpha or beta anomer of the D-stereoisomer of the 4-epimers galactose and glucose. Binding specificity and affinity are conferred primarily by polar planar side-chain residues that form intricate networks of cooperative and bidentate hydrogen bonds with the sugar substrates, and secondarily by aromatic residues that sandwich the pyranose ring. Each of the pairs of anomeric hydroxyls and epimeric hydroxyls is recognized by a distinct Asp residue. The site for interaction with the transducer is about 18 A from the sugar-binding site. Mutation of Gly74 to Asp at this site, concomitant with considerable changes in the local ordered water structures, contributes to the lack of productive interaction with the transmembrane signal transducer.     

A gene-coexpression network for global discovery of conserved genetic modules

To elucidate gene function on a global scale, we identified pairs of genes that are coexpressed over 3182 DNA microarrays from humans, flies, worms, and yeast. We found 22,163 such coexpression relationships, each of which has been conserved across evolution. This conservation implies that the coexpression of these gene pairs confers a selective advantage and therefore that these genes are functionally related. Many of these relationships provide strong evidence for the involvement of new genes in core biological functions such as the cell cycle, secretion, and protein expression. We experimentally confirmed the predictions implied by some of these links and identified cell proliferation functions for several genes. By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules.     

Visualization of specific angiotensin II binding sites in the brain by fluorescent microscopy

The organum vasculosum of the lamina terminalis has been implicated as the site of receptors mediating central responses of angiotensin II. Up to now, this had been based on indirect evidence, but direct visualization of angiotensin II at its site of action has now been achieved by the use of a biologically active fluorescent angiotensin II agonist. The ventricular surface of the organum vasculosum lamina terminalis showed intense fluorescence, which was virtually eliminated by an excess of unlabeled angiotensin II.     

A general method for the chromosomal amplification of genes in yeast

The yeast retrotransposon Ty can be used to insert multiple copies of a gene at new sites in the genome. The gene of interest is inserted into a GALI-Ty fusion construct; the entire "amplification cassette" is then introduced into yeast on a high copy number plasmid vector. Transposition of the Ty element carrying the gene occurs at multiple sites in the genome. Two genes, a bacterial neomycin phosphotransferase gene and the yeast TRPl gene, were amplified in this way. Although the amplified genes were about 1 kilobase in length, they were amplified to about the same extent as a 40-base pair segment. The benefit of this "shotgun" approach is that amplification can be achieved in one set of manipulations.     

Novel sites of expression of functional angiotensin II receptors in the late gestation fetus

In the adult, the peptide hormone angiotensin II (AII) is primarily known as a regulator of circulatory homeostasis, but recent evidence also suggests a role in cell growth. This study of AII in late gestation rat fetuses revealed the unexpected presence of receptors in skeletal muscle and connective tissue, in addition to those in recognized adult target tissues. The AII receptors in this novel location decreased by 80 percent 1 day after birth and were almost undetectable in the adult. Studies in fetal skin fibroblasts showed that the receptors were coupled to phospholipid breakdown, with concomitant increases in inositol phosphate and cytosolic calcium. The abundance, timing of expression, and unique localization of functional AII receptors in the fetus suggest a role for AII in fetal development.     

A cell cycle phosphoproteome of the yeast centrosome

Centrosomes organize the bipolar mitotic spindle, and centrosomal defects cause chromosome instability. Protein phosphorylation modulates centrosome function, and we provide a comprehensive map of phosphorylation on intact yeast centrosomes (18 proteins). Mass spectrometry was used to identify 297 phosphorylation sites on centrosomes from different cell cycle stages. We observed different modes of phosphoregulation via specific protein kinases, phosphorylation site clustering, and conserved phosphorylated residues. Mutating all eight cyclin-dependent kinase (Cdk)-directed sites within the core component, Spc42, resulted in lethality and reduced centrosomal assembly. Alternatively, mutation of one conserved Cdk site within γ-tubulin (Tub4-S360D) caused mitotic delay and aberrant anaphase spindle elongation. Our work establishes the extent and complexity of this prominent posttranslational modification in centrosome biology and provides specific examples of phosphorylation control in centrosome function.     

Functional adaptation of BabA, the H. pylori ABO blood group antigen binding adhesin

Adherence by Helicobacter pylori increases the risk of gastric disease. Here, we report that more than 95% of strains that bind fucosylated blood group antigen bind A, B, and O antigens (generalists), whereas 60% of adherent South American Amerindian strains bind blood group O antigens best (specialists). This specialization coincides with the unique predominance of blood group O in these Amerindians. Strains differed about 1500-fold in binding affinities, and diversifying selection was evident in babA sequences. We propose that cycles of selection for increased and decreased bacterial adherence contribute to babA diversity and that these cycles have led to gradual replacement of generalist binding by specialist binding in blood group O-dominant human populations.     

A shorter 146Sm half-life measured and implications for 146Sm-142Nd chronology in the solar system

The extinct p-process nuclide (146)Sm serves as an astrophysical and geochemical chronometer through measurements of isotopic anomalies of its α-decay daughter (142)Nd. Based on analyses of (146)Sm/(147)Sm α-activity and atom ratios, we determined the half-life of (146)Sm to be 68 ± 7 (1σ) million years, which is shorter than the currently used value of 103 ± 5 million years. This half-life value implies a higher initial (146)Sm abundance in the early solar system, ((146)Sm/(144)Sm)(0) = 0.0094 ± 0.0005 (2σ), than previously estimated. Terrestrial, lunar, and martian planetary silicate mantle differentiation events dated with (146)Sm-(142)Nd converge to a shorter time span and in general to earlier times, due to the combined effect of the new (146)Sm half-life and ((146)Sm/(144)Sm)(0) values.     

木霉菌BTW41发酵条件的研究

木霉菌BTW4 1发酵条件的研究表明 :以糖分为培养基主要成分 ,pH值 5 1和 2 5℃的条件下最有利于木霉菌BTW4 1发酵产生分生孢子。在温、湿度两种条件中 ,温度是决定木霉菌BTW4 1产孢水平的关键因素     

新型功能性食品辅料———香蕉粉

香蕉营养全面,保健功能突出.我国香蕉资源丰富,但加工极其落后,因此香蕉深加工成为近年研究的热点.香蕉粉是一个极具前景的深加工产品.介绍了香蕉粉的分类与营养价值,提出了香蕉粉可以作为新型功能性食品辅料的可行性,综述了香蕉粉加工关键技术和应用的研究进展,为香蕉粉的进一步开发应用提供了技术支撑.