Promise and pitfalls of the Immunochip

Genomewide association studies (GWAS) have proven a powerful hypothesis-free method to identify common disease-associated variants. Even quite large GWAS, however, have only at best identified moderate proportions of the genetic variants contributing to disease heritability. To provide cost-effective genotyping of common and rare variants to map the remaining heritability and to fine-map established loci, the Immunochip Consortium has developed a 200,000 SNP chip that has been produced in very large numbers for a fraction of the cost of GWAS chips. This chip provides a powerful tool for immunogenetics gene mapping.     

Proteomic analysis of phytopathogenic fungus <Emphasis Type="Italic">Botrytis cinerea</Emphasis> as a potential tool for identifying pathogenicity factors,therapeutic targets and for basic research

Botrytis cinerea is a phytopathogenic fungus causing disease in a substantial number of economically important crops. In an attempt to identify putative fungal virulence factors, the two-dimensional gel electrophoresis (2-DE) protein profile from two B. cinerea strains differing in virulence and toxin production were compared. Protein extracts from fungal mycelium obtained by tissue homogenization were analyzed. The mycelial 2-DE protein profile revealed the existence of qualitative and quantitative differences between the analyzed strains. The lack of genomic data from B. cinerea required the use of peptide fragmentation data from MALDI-TOF/TOF and ESI ion trap for protein identification, resulting in the identification of 27 protein spots. A significant number of spots were identified as malate dehydrogenase (MDH) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The different expression patterns revealed by some of the identified proteins could be ascribed to differences in virulence between strains. Our results indicate that proteomic analysis are becoming an important tool to be used as a starting point for identifying new pathogenicity factors, therapeutic targets and for basic research on this plant pathogen in the postgenomic era.     

The ALDH gene superfamily of Arabidopsis

Aldehyde dehydrogenases (ALDHs) represent a protein superfamily of NAD(P)(+)-dependent enzymes that oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes. The Arabidopsis genome contains 14 unique ALDH sequences encoding members of nine ALDH families, including eight known families and one novel family (ALDH22) that is currently known only in plants. Here, we identify members of the ALDH gene superfamily in Arabidopsis; provide a revised, unified nomenclature for these ALDH genes; analyze the molecular relationship among Arabidopsis ALDH genes and compare them to ALDH genes from other species, including prokaryotes and mammals; and describe the role of ALDHs in cytoplasmic male sterility, plant defense and abiotic stress tolerance.     

Oligomeric State and Thermal Stability of Apo- and Holo- Human Ornithine δ-Aminotransferase

Human ornithine δ-aminotransferase (hOAT) (EC 2.6.1.13) is a mitochondrial pyridoxal 5′-phosphate (PLP)-dependent aminotransferase whose deficit is associated with gyrate atrophy, a rare autosomal recessive disorder causing progressive blindness and chorioretinal degeneration. Here, both the apo- and holo-form of recombinant hOAT were characterized by means of spectroscopic, kinetic, chromatographic and computational techniques. The results indicate that apo and holo-hOAT (a) show a similar tertiary structure, even if apo displays a more pronounced exposure of hydrophobic patches, (b) exhibit a tetrameric structure with a tetramer-dimer equilibrium dissociation constant about fivefold higher for the apoform with respect to the holoform, and (c) have apparent T_m values of 46 and 67?°C, respectively. Moreover, unlike holo-hOAT, apo-hOAT is prone to unfolding and aggregation under physiological conditions. We also identified Arg217 as an important hot-spot at the dimer–dimer interface of hOAT and demonstrated that the artificial dimeric variant R217A exhibits spectroscopic properties, T_m values and catalytic features similar to those of the tetrameric species. This finding indicates that the catalytic unit of hOAT is the dimer. However, under physiological conditions the apo-tetramer is slightly less prone to unfolding and aggregation than the apo-dimer. The possible implications of the data for the intracellular stability and regulation of hOAT are discussed.     

Modifying ligand-induced and constitutive signaling of the human 5-HT4 receptor

G protein-coupled receptors (GPCRs) signal through a limited number of G-protein pathways and play crucial roles in many biological processes. Studies of their in vivo functions have been hampered by the molecular and functional diversity of GPCRs and the paucity of ligands with specific signaling effects. To better compare the effects of activating different G-protein signaling pathways through ligand-induced or constitutive signaling, we developed a new series of RASSLs (receptors activated solely by synthetic ligands) that activate different G-protein signaling pathways. These RASSLs are based on the human 5-HT(4b) receptor, a GPCR with high constitutive G(s) signaling and strong ligand-induced G-protein activation of the G(s) and G(s/q) pathways. The first receptor in this series, 5-HT(4)-D(100)A or Rs1 (RASSL serotonin 1), is not activated by its endogenous agonist, serotonin, but is selectively activated by the small synthetic molecules GR113808, GR125487, and RO110-0235. All agonists potently induced G(s) signaling, but only a few (e.g., zacopride) also induced signaling via the G(q) pathway. Zacopride-induced G(q) signaling was enhanced by replacing the C-terminus of Rs1 with the C-terminus of the human 5-HT(2C) receptor. Additional point mutations (D(66)A and D(66)N) blocked constitutive G(s) signaling and lowered ligand-induced G(q) signaling. Replacing the third intracellular loop of Rs1 with that of human 5-HT(1A) conferred ligand-mediated G(i) signaling. This G(i)-coupled RASSL, Rs1.3, exhibited no measurable signaling to the G(s) or G(q) pathway. These findings show that the signaling repertoire of Rs1 can be expanded and controlled by receptor engineering and drug selection.     

羊血铜锌超氧化物歧化酶(Cu-ZnSOD)的分离纯化

目的:对羊血进行提取SOD。方法:采用有机溶剂去除血红蛋白、热变性、丙酮沉淀、DEAE-32离子交换柱层析的方法,对羊红细胞Cu,Zn-SOD进行分离纯化。利用非变性凝胶电泳NBT活性染色鉴定SOD,SDS-PAGE测定分子量。结果:表明1 000ml羊血中得到SOD干粉1 257mg,总活力为79 453U,比活力为3 871.4U/mg。活性染色结果证明羊血SOD有2条带,表明已达到电泳纯。SDS-PAGE测得SOD亚基分子量分别为16.71kDa、15.97kDa。H2O2对羊血CuZn-SOD活性有抑制作用,通过紫外光谱扫描,羊血SOD在231nm处有最大吸收峰。     

Moose summer and winter diets along a large scale gradient of forage availability in southern Norway

Studies on dietary functional responses in large herbivores are traditionally conducted by following individual animals. The method is very time-consuming, and hence, typically provides only a narrow array of forage species compositions. Here we use a range level approach to look at moose (Alces alces) selectivity for and utilization of forage species in relation to availability in both summer and winter. We compare 12 Norwegian ranges representing a large scale gradient in plant communities. The most important forage species in the diet were birches (Betula spp., comprising 43% of all trees browsed in summer and 27% in winter), rowan (Sorbus aucuparia, 25% of trees browsed in summer, 37% in winter), and bilberry (Vaccinum myrtillus, 42% of herbaceous epidermal fragments in summer feces). Selectivity for birches was positively related to its availability and negatively related to availability of rowan, Salix spp., and aspen (Populus tremula) together (all more selected for than birches). Multiple regression models including availability of several forage species were thus superior to single-species models in explaining the diet content of main forage plants. Selectivity for birches was also stronger in summer than in winter, while the opposite pattern was found for rowan. The finding is relevant for our evaluation of the quality of summer and winter ranges, and hence, their relative influence on population productivity. Our study underlines the need to incorporate species composition of available forage when quantifying dietary functional responses in selective herbivores such as moose. Furthermore, care should be taken when extrapolating data on moose diet across ranges or seasons.     

Habitat Use and Ranging Behavior of <Emphasis Type="Italic">Callimico goeldii</Emphasis>

We studied the diet, habitat use, and ranging behavior of 1 group of Callimico goeldii (callimicos) over 12 mo in northwestern Bolivia. The group’s diet was comprised of fungi (39%), fruits (31%), arthropods (14%), exudates (14%), and other matter (2%). Callimicos concentrated their ranging activities in secondary forest (50%), primary forest with dense understory (30%), and bamboo (17%) habitats. The group’s total home range was 114 ha; on average they used 38.4 ha/ mo and had a day range of 925 m. Monthly average day ranges—but not monthly home ranges—increased as frugivory declined, suggesting that subjects foraged on fungi and exudates by rechecking resources within a core area, making their day ranges longer than during months when they concentrated on fruit resources. The callimicos formed polyspecific associations with tamarins (Saguinus labiatus and S. fuscicollis) during 81% of observations. Day ranges increased in months with higher association rates which appears to result from the callimicos using a broader set of habitats when with tamarins than when alone. The ranging pattern of callimicos appears to be influenced primarily by 3 factors: their seasonal shift in diet requires that they forage in a variety of habitats across the year; their depletion of resources causes them to shift their core area over time; and their lack of territorial behavior eliminates the need to patrol boundaries as part of their daily movement. As a result, callimicos differ from many other callitrichids in their low ratio of day range length to home range size.     

Translational machinery of the chaetognath <Emphasis Type="Italic">Spadella cephaloptera</Emphasis>: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

Background  

Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies.     

Science and Sentiment: Grinnell’s Fact-Based Philosophy of Biodiversity Conservation

At the beginning of the twentieth century, the biologist Joseph Grinnell made a distinction between science and sentiment for producing fact-based generalizations on how to conserve biodiversity. We are inspired by Grinnellian science, which successfully produced a century-long impact on studying and conserving biodiversity that runs orthogonal to some familiar philosophical distinctions such as fact versus value, emotion versus reason and basic versus applied science. According to Grinnell, unlike sentiment-based generalizations, a fact-based generalization traces its diverse commitments and thus becomes tractable for its audience. We argue that foregrounding tractability better explains Grinnell’s practice in the context of his time as well as in the context of current discourse among scientists over the political “biases” of biodiversity research and its problem of “reproducibility.”