Regioselective oxidation of steroids by a manganese porphyrin carrying metal coordinating groups

A manganese porphyrin having four 2,2'-bipyridyl groups on its meso positions was synthesized. In the presence of Cu2+ ions it catalyzes the regioselective oxidation of steroid substrates carrying auxiliary metal coordinating groups.     

DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation

Rare variants affecting phenotype pose a unique challenge for human genetics. Although genome-wide association studies have successfully detected many common causal variants, they are underpowered in identifying disease variants that are too rare or population-specific to be imputed from a general reference panel and thus are poorly represented on commercial SNP arrays. We set out to overcome these challenges and detect association between disease and rare alleles using SNP arrays by relying on long stretches of genomic sharing that are identical by descent. We have developed an algorithm, DASH, which builds upon pairwise identical-by-descent shared segments to infer clusters of individuals likely to be sharing a single haplotype. DASH constructs a graph with nodes representing individuals and links on the basis of such segments spanning a locus and uses an iterative minimum cut algorithm to identify densely connected components. We have applied DASH to simulated data and diverse GWAS data sets by constructing haplotype clusters and testing them for association. In simulations we show this approach to be significantly more powerful than single-marker testing in an isolated population that is from Kosrae, Federated States of Micronesia and has abundant IBD, and we provide orthogonal information for rare, recent variants in the outbred Wellcome Trust Case-Control Consortium (WTCCC) data. In both cohorts, we identified a number of haplotype associations, five such loci in the WTCCC data and ten in the isolated, that were conditionally significant beyond any individual nearby markers. We have replicated one of these loci in an independent European cohort and identified putative structural changes in low-pass whole-genome sequence of the cluster carriers.     

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome

Functional genomic studies in Saccharomyces cerevisiae have contributed enormously to our understanding of cellular processes. Their full potential, however, has been hampered by the limited availability of reagents to systematically study essential genes and the inability to quantify the small effects of most gene deletions on growth. Here we describe the construction of a library of hypomorphic alleles of essential genes and a high-throughput growth competition assay to measure fitness with unprecedented sensitivity. These tools dramatically increase the breadth and precision with which quantitative genetic analysis can be performed in yeast. We illustrate the value of these approaches by using genetic interactions to reveal new relationships between chromatin-modifying factors and to create a functional map of the proteasome. Finally, by measuring the fitness of strains in the yeast deletion library, we addressed an enigma regarding the apparent prevalence of gene dispensability and found that most genes do contribute to growth.     

Structures of an unliganded neurophysin and its vasopressin complex: implications for binding and allosteric mechanisms

The structures of des 1-6 bovine neurophysin-II in the unliganded state and as its complex with lysine vasopressin were determined crystallographically at resolutions of 2.4 A and 2.3 A, respectively. The structure of the protein component of the vasopressin complex was, with some local differences, similar to that determined earlier of the full-length protein complexed with oxytocin, but relatively large differences, probably intrinsic to the hormones, were observed between the structures of bound oxytocin and bound vasopressin at Gln 4. The structure of the unliganded protein is the first structure of an unliganded neurophysin. Comparison with the liganded state indicated significant binding-induced conformational changes that were the largest in the loop region comprising residues 50-58 and in the 7-10 region. A subtle binding-induced tightening of the subunit interface of the dimer also was shown, consistent with a role for interface changes in neurophysin allosteric mechanism, but one that is probably not predominant. Interface changes are suggested to be communicated from the binding site through the strands of beta-sheet that connect these two regions, in part with mediation by Gly 23. Comparison of unliganded and liganded states additionally reveals that the binding site for the hormone alpha-amino group is largely preformed and accessible in the unliganded state, suggesting that it represents the initial site of hormone protein recognition. The potential molecular basis for its thermodynamic contribution to binding is discussed.     

Methylation patterns of the human apoA-I/C-III/A-IV gene cluster in adult and embryonic tissues suggest dynamic changes in methylation during development.

We describe here a detailed analysis of the methylation patterns of the apoC-III and apoA-IV genes in adult and embryonic tissues. Together with previously reported data on the human apoA-I gene (4), the results presented here constitute a comprehensive study on the methylation pattern of the apoA-I/C-III/A-IV gene cluster. The two genes (apoC-III and apoA-IV) display tissue-specific methylation patterns that correlate with their activity. This gene-specific methylation pattern indicates that the apoA-I/C-III/A-IV gene cluster is not one entity with respect to methylation. The cluster is almost entirely methylated in tissues that do not express any of the genes; however, individual gene regions are unmethylated in the tissue of expression. A comparison of the observed methylation patterns in adult tissues with those in embryonic tissues suggests that the mature tissue-specific methylation patterns are a result of an interplay between demethylation and de novo methylation events in the embryo. These changes in DNA methylation include demethylation in the early embryo followed by de novo methylation at later stages. A second round of tissue-specific demethylation and methylation de novo occurs in the late embryo as well. Evidence presented here supports the idea that CpG islands are protected in general from methylation de novo by a built-in signal and not by CpG density per se.     

Apolipoprotein C-III0 lacks carbohydrate residues: use of mass spectrometry to study apolipoprotein structure

Apolipoprotein C-III (apo C-III) is a 79 amino acid glycoprotein. The sugar moiety of apoC-III is attached to amino acid residue 74 and is thought to consist of 1 mole of galactose, 1 mole of N-acetyl-galactosamine, and either 0, 1, or 2 moles of sialic acid. This results in three isoproteins called C-III0, C-III1, and C-III2 designated by the number of sialic acid residues. It has been assumed, although not experimentally tested, that apoC-III0 lacks sialic acid residues but possesses the D-galactosyl-(1-3)-N-acetyl-D-galactosamine sugar backbone. To verify the structure of the three apoC-III isoproteins, we applied the method of 252Cf plasma desorption mass spectrometry to measure the exact molecular weight (Mr) of each of the isoproteins. Our data confirmed the proposed structure of apoC-III1 and apoC-III2. However, the difference in mass between apoC-III1 (9420.6, 9420.0, 9422.2 daltons) and apoC-III0 (8763.9, 8764.9, 8765.5 daltons, respectively, in three subjects) suggests that the latter is missing not just sialic acid but the entire sugar moiety. This finding may have important implications for the metabolism of apoC-III. The accuracy and reproducibility of Mr measurements described in this paper suggest that this technique holds promise for the detection of apolipoprotein amino acid substitutions or modifications undetected by conventional techniques such as isoelectric focusing.