The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1

Genome wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of common disorders. However, since the large majority of these risk SNPs reside outside gene-coding regions, GWAS generally provide no information about causal mechanisms regarding the specific gene(s) that are affected or the tissue(s) in which these candidate gene(s) exert their effect. The ‘gold standard’ method for understanding causal genes and their mechanisms of action are laborious basic science studies often involving sophisticated knockin or knockout mouse lines, however, these types of studies are impractical as a high-throughput means to understand the many risk variants that cause complex diseases like coronary artery disease (CAD). As a solution, we developed a streamlined, data-driven informatics pipeline to gain mechanistic insights on complex genetic loci. The pipeline begins by understanding the SNPs in a given locus in terms of their relative location and linkage disequilibrium relationships, and then identifies nearby expression quantitative trait loci (eQTLs) to determine their relative independence and the likely tissues that mediate their disease-causal effects. The pipeline then seeks to understand associations with other disease-relevant genes, disease sub-phenotypes, potential causality (Mendelian randomization), and the regulatory and functional involvement of these genes in gene regulatory co-expression networks (GRNs). Here, we applied this pipeline to understand a cluster of SNPs associated with CAD within and immediately adjacent to the gene encoding HDAC9. Our pipeline demonstrated, and validated, that this locus is causal for CAD by modulation of TWIST1 expression levels in the arterial wall, and by also governing a GRN related to metabolic function in skeletal muscle. Our results reconciled numerous prior studies, and also provided clear evidence that this locus does not govern HDAC9 expression, structure or function. This pipeline should be considered as a powerful and efficient way to understand GWAS risk loci in a manner that better reflects the highly complex nature of genetic risk associated with common disorders.     

Lack of both Fas ligand and perforin protects from flavivirus-mediated encephalitis in mice

The mechanism by which encephalitic flaviviruses enter the brain to inflict a life-threatening encephalomyelitis in a small percentage of infected individuals is obscure. We investigated this issue in a mouse model for flavivirus encephalitis in which the virus was administered to 6-week-old animals by the intravenous route, analogous to the portal of entry in natural infections, using a virus dose in the range experienced following the bite of an infectious mosquito. In this model, infection with 0.1 to 10(5) PFU of virus gave mortality in approximately 50% of animals despite low or undetectable virus growth in extraneural tissues. We show that the cytolytic effector functions play a crucial role in invasion of the encephalitic flavivirus into the brain. Mice deficient in either the granule exocytosis- or Fas-mediated pathway of cytotoxicity showed delayed and reduced mortality. Mice deficient in both cytotoxic effector functions were resistant to a low-dose peripheral infection with the neurotropic virus.     

Honeybee foraging in differentially structured landscapes

Honeybees communicate the distance and location of resource patches by bee dances, but this spatial information has rarely been used to study their foraging ecology. We analysed, for the first time to the best of the authors' knowledge, foraging distances and dance activities of honeybees in relation to landscape structure, season and colony using a replicated experimental approach on a landscape scale. We compared three structurally simple landscapes characterized by a high proportion of arable land and large patches, with three complex landscapes with a high proportion of semi-natural perennial habitats and low mean patch size. Four observation hives were placed in the centre of the landscapes and switched at regular intervals between the six landscapes from the beginning of May to the end of July. A total of 1137 bee dances were observed and decoded. Overall mean foraging distance was 1526.1 +/- 37.2 m, the median 1181.5 m and range 62.1-10037.1 m. Mean foraging distances of all bees and foraging distances of nectar-collecting bees did not significantly differ between simple and complex landscapes, but varied between month and colonies. Foraging distances of pollen-collecting bees were significantly larger in simple (1743 +/- 95.6 m) than in complex landscapes (1543.4 +/- 71 m) and highest in June when resources were scarce. Dancing activity, i.e. the number of observed bee dances per unit time, was significantly higher in complex than in simple landscapes, presumably because of larger spatial and temporal variability of resource patches in complex landscapes. The results facilitate an understanding of how human landscape modification may change the evolutionary significance of bee dances and ecological interactions, such as pollination and competition between honeybees and other bee species.     

Genetic and cytological characterization of the recombination protein RAD-51 in<Emphasis Type="Italic"> Caenorhabditis elegans</Emphasis>

We investigated the role of Caenorhabditis elegans rad-51 during meiotic prophase. We showed that rad-51 mutant worms are viable, have no defects in meiotic homology recognition and synapsis but exhibit abnormal chromosomal morphology and univalent formation at diakinesis. During meiosis RAD-51 becomes localized to distinct foci in nuclei of the transition zone of the gonad and is most abundant in nuclei at late zygotene/early pachytene. Foci then gradually disappear from chromosomes and no foci are observed in late pachytene. RAD-51 localization requires the recombination genes spo-11 and mre-11 as well as chk-2, which is necessary for homology recognition and presynaptic alignment. Mutational analysis with synapsis- and recombination-defective strains, as well as the analysis of strains bearing heterozygous translocation chromosomes, suggests that presynaptic alignment may be required for RAD-51 focus formation, whereas homologous synaptonemal complex formation is required to remove RAD-51 foci.     

Understanding base-assisted desulfurization using a variety of disulfide-bridged peptides

A recently rediscovered reaction of base-assisted lanthionine formation has been applied to several systems of disulfide-bridged peptides. In addition to previously described nonapeptides consisting of i, i+3 cystine linkages, the reaction has now been extended to systems consisting of shorter (i, i+2) and longer (i, i+4) disulfide bridges. The desulfurization reaction is also compatible with disulfide bridges formed through homocysteines and penicillamines, yielding unusual amino acids such as cystathionine and beta,beta-dimethyl lanthionine (referred to as "penthionine") in a peptide chain, respectively. Systematic study of this transformation has provided several new insights into its mechanism. We have observed formation of dehydroalanine and dehydrovaline residues resulting from i, i+2-bridged cysteines and i, i+3-bridged cysteine/penicillamine peptides, respectively, thereby supporting a beta-elimination/Michael-addition mechanism for this transformation. Amino acid analysis and NMR data from total correlation spectroscopy (TOCSY) and (1)H-(13)C heteronuclear single quantum correlation (HSQC) experiments show three diastereomeric lanthionine-bridged peptides in the product mixture. But in the case of desulfurization of a cysteine/homocysteine containing disulfide-bridged peptide, Michael addition appears to be stereoselective, yielding a single stereoisomer of cystathionine within the peptide. According to molecular modeling and CD spectroscopy, constrained peptides such as those containing penicillamine are less likely to undergo facile desulfurization. Flexibility of the torsional angles (C(alpha)H-C(alpha)-C(beta)-S) corresponding to the cysteine residues and temperature appear to be contributing factors determining the extent of desulfurization.     

Uncertainty analysis of penicillin V production using Monte Carlo simulation

Uncertainty and variability affect economic and environmental performance in the production of biotechnology and pharmaceutical products. However, commercial process simulation software typically provides analysis that assumes deterministic rather than stochastic process parameters and thus is not capable of dealing with the complexities created by variance that arise in the decision-making process. Using the production of penicillin V as a case study, this article shows how uncertainty can be quantified and evaluated. The first step is construction of a process model, as well as analysis of its cost structure and environmental impact. The second step is identification of uncertain variables and determination of their probability distributions based on available process and literature data. Finally, Monte Carlo simulations are run to see how these uncertainties propagate through the model and affect key economic and environmental outcomes. Thus, the overall variation of these objective functions are quantified, the technical, supply chain, and market parameters that contribute most to the existing variance are identified and the differences between economic and ecological evaluation are analyzed. In our case study analysis, we show that final penicillin and biomass concentrations in the fermenter have the highest contribution to variance for both unit production cost and environmental impact. The penicillin selling price dominates return on investment variance as well as the variance for other revenue-dependent parameters.     

Long-chain fatty acid uptake into adipocytes depends on lipid raft function

This study investigates the role of lipid rafts and caveolae, a subclass of lipid raft microdomains, in the binding and uptake of long-chain fatty acids (LCFA) by 3T3-L1 cells during differentiation. Disruption of lipid rafts by beta-cyclodextrin (betaCD) or selective inhibition of caveolae by overexpression of a dominant-negative mutant of caveolin-3 (Cav(DGV)) resulted in disassembly of caveolae structures at the cell surface, as assessed by electron microscopy. While in 3T3-L1 fibroblasts, which express few caveolae, Cav(DGV) or betaCD had no effect on LCFA uptake, in 3T3-L1 adipocytes the same treatments decreased the level of [(3)H]oleic acid uptake by up to 55 +/- 8 and 49 +/- 7%, respectively. In contrast, cholesterol loading of 3T3-L1 adipocytes resulted in a 4-fold increase in the extent of caveolin-1 expression and a 1.7-fold increase in the level of LCFA uptake. Both the inhibitory and enhancing effects of these treatments were constantly increasing with the [(3)H]oleic acid incubation time up to 5 min. Incubation of 3T3-L1 adipocytes with [(3)H]stearate followed by isolation of a caveolin-1 positive detergent-resistant membrane (DRM) fraction revealed that [(3)H]stearate binds to caveolae. Fatty acid translocase (FAT/CD36) was found to be present in this DRM fraction as well. Our data thus strongly indicate a critical involvement of lipid rafts in the binding and uptake of LCFA into 3T3-L1 adipocytes. Furthermore, our findings suggest that caveolae play a pivotal role in lipid raft-dependent LCFA uptake. This transport mechanism is induced in conjunction with cell differentiation and might be mediated by FAT/CD36.     

The multidrug resistance gene mdr1a influences resistance to ectromelia virus infection by mechanisms other than conventional immunity

P-glycoprotein (P-gp), an ATP-dependent membrane pump encoded by mdr, plays, in addition to its ability to efflux toxins, a role in the resistance to pathogens. We employed mdr1a gene knock out (mdr1a-/-) mice and ectromelia virus (EV) to elucidate the role of P-gp in resistance to EV. Mdr1a-/- mice are more susceptible to EV infection than wild type (wt) mice, showing increased mortality and morbidity. Unexpectedly, virus titres in liver, and in vitro in macrophages and splenocytes were significantly lower in the more susceptible mdr1a-/- mice than wt littermates. Analysis of immunological mechanisms known to influence resistance to EV infection, such as NK and cytotoxic T cell responses, EV specific antibody and cytokine levels did not reveal significant differences between the two strains of mice. Only dendritic cells from mdr1a-/- mice showed impaired migration to the draining lymph nodes compared to wt mice. Our data show that P-gp plays an important role in EV infection by as yet undefined mechanisms.     

Characterization of a human angiotensinogen cleaved in its reactive center loop by a proteolytic activity from Chinese hamster ovary cells

Angiotensinogen, the renin (E.C. 3.4.23.15) substrate, belongs to the serpins superfamily and has been classified as a noninhibitory serpin. Using mass spectroscopy, angiotensinogen purified from Chinese hamster ovary cell supernatant shows a broad spectrum. The absence of protease inhibitors throughout the purification leads to an angiotensinogen cleaved within the reactive center loop. This cleavage does not affect the Ang I generation because kinetic parameters are similar to the values of the full-length angiotensinogen. Although cleavage is complete, the cleaved angiotensinogen migrates after deglycosylation on SDS-polyacrylamide gel electrophoresis as a doublet differing by 4 kDa. To test whether the circulating angiotensinogen is cleaved in the reactive center loop, it was purified from a pool of human plasma and was shown to be uncleaved. Its migration was obviously slower than of cleaved angiotensinogen but also consisted of two bands pointing to a so far unexplained residual heterogeneity. We then compared the heat-induced polymerization of full-length- and reactive center loop-cleaved angiotensinogens. Both monomers were able to aggregate, revealing a particular behavior of angiotensinogen distinct from that of reactive center loop-cleaved serpins. Lacking the three-dimensional structure of angiotensinogen, we propose and discuss a structural model of the serpin fold within the renin substrate.     

Application of the Ancient Forest Concept to Potential Natural Vegetation Mapping in Flanders, A Strongly Altered Landscape in Northern Belgium

Construction of potential natural vegetation (PNV) poses particular challenges in landscapes heavily altered by human activity and must be based on transparent, repeatable methods. We integrated the concept of ancient forest (AF) and ancient forest species (AFS) into a four-step procedure of PNV mapping: 1) classification of forest vegetation relevés; 2) selection of those vegetation types that can serve as PNV units, based on AF and AFS; 3) merging of selected vegetation types into five PNV units that can be predicted from a digital morphogenetic soil map; 4) mapping of three additional PNV units based on additional environmental data. The second step, concerning the selection of reference forest vegetation, is of particular interest for PNV construction in Flanders (northern Belgium), where forest cover has been subject to temporal disruption and spatial fragmentation. Among the variety of extant forest recovery states, we chose as PNV units those vegetation types for which a high proportion of relevés had been located in AF and that contained many AFS. As the frequency of AFS depends on site conditions, we only compared and selected vegetation types that are found on similar sites according to average Ellenberg indicator values. While succession is irrelevant for the definition of PNV, colonization rates of AFS can be used to estimate the time required for PNV to be restored in a site.