Functional characterization of the atypical Hsp70 subunit of yeast ribosome-associated complex

Eukaryotic ribosomes carry a stable chaperone complex termed ribosome-associated complex consisting of the J-domain protein Zuo1 and the Hsp70 Ssz1. Zuo1 and Ssz1 together with the Hsp70 homolog Ssb1/2 form a functional triad involved in translation and early polypeptide folding processes. Strains lacking one of these components display slow growth, cold sensitivity, and defects in translational fidelity. Ssz1 diverges from canonical Hsp70s insofar that neither the ability to hydrolyze ATP nor binding to peptide substrates is essential in vivo. The exact role within the chaperone triad and whether or not Ssz1 can hydrolyze ATP has remained unclear. We now find that Ssz1 is not an ATPase in vitro, and even its ability to bind ATP is dispensable in vivo. Furthermore, Ssz1 function was independent of ribosome-associated complex formation, indicating that Ssz1 is not merely a structural scaffold for Zuo1. Finally, Ssz1 function in vivo was inactivated when both nucleotide binding and Zuo1 interaction via the C-terminal domain were disrupted in the same mutant. The two domains of this protein thus cooperate in a way that allows for severe interference in either but not in both of them.     

Geographical Distribution and Diversity of Bacteria Associated with Natural Populations of Drosophila melanogaster

Drosophila melanogaster is one of the most widely used model systems in biology. However, little is known about its associated bacterial community. As a first step towards understanding these communities, we compared bacterial 16S rRNA gene sequence libraries recovered from 11 natural populations of adult D. melanogaster. Bacteria from these sequence libraries were grouped into 74 distinct taxa, spanning the phyla Proteobacteria, Bacteroidetes, and Firmicutes, which were unevenly spread across host populations. Summed across populations, the distribution of abundance of genera was closely fit by a power law. We observed differences among host population locations both in bacterial community richness and in composition. Despite this significant spatial variation, no relationship was observed between species richness and a variety of abiotic factors, such as temperature and latitude. Overall, bacterial communities associated with adult D. melanogaster hosts are diverse and differ across host populations.     

The relationship between locomotor behavior and limb morphology in brown (Cebus apella) and weeper (Cebus olivaceus) capuchins

This study is a comparison of locomotor behavior and postcranial form in two species of capuchin monkey, the brown capuchin (Cebus apella), and the weeper capuchin (Cebus olivaceus). Behavioral data from groups of wild C. apella and C. olivaceus in Guyana were collected during the period of December 1999 through November 2000. Postcranial variables including 40 measurements and three indices were taken from 43 adult and subadult specimens of C. apella and 14 adult and subadult specimens of C. olivaceus housed in American museums, as well as two wild-caught adult specimens of C. olivaceus from the Georgetown Zoo in Guyana. The results of this study indicate that these two capuchins exhibit similar patterns of locomotor behavior, but that there are important differences in how they move through their homerange, particularly with respect to quadrupedalism. These differences in behavior are reflected in their postcranial morphology and can be related to differences in foraging strategies. This study provides an example of the importance of using more exclusive categories of quadrupedal behaviors when comparing closely related arboreal quadrupeds, as well as an alternative explanation for some of the postcranial features of C. apella that may relate to foraging postures and foraging strategy rather than traditionally categorized patterns of locomotor behavior.     

An amphibious bryozoan from living mangrove leaves - Amphibiobeania new genus (Beaniidae)

Amphibiobeania epiphylla is a new, monotypic taxon of Beaniidae (Cheilostomata) from Darwin, Northern Territory. It is unique among the 6,000 living species of Bryozoa in that it encrusts mainly living tree leaves (chiefly the mangrove Rhizophora stylosa). The consequence of living in such a specialized habitat is that colonies are emergent (subaerial) for a significant part of the tidal cycle-around 12 of every 24 hours during spring tides and for several days during neap tides. Desiccation is prevented or minimized by the high humidity of the habitat and a cohesive coating of silt covering the colony. Zooids are weakly calcified and lie alternately on their left and right sides in a lineal series, with opercula displaced to the outer corner of the distal zooidal rim. Organisms associated with A. epiphylla include a colony-damaging ceratopogonid (Diptera) larva and a tarsonemid mite that may use dead zooidal interiors, beneath the silt crust, for shelter.     

Middle phalanx skeletal morphology in the hand: Can it predict flexor tendon size and attachments?

Specific sites on the palmar diaphysis of the manual middle phalanges provide attachment for the flexor digitorum superficialis (FDS) tendon. It has been assumed in the literature that lateral palmar fossae on these bones reflect locations for these attachments and offer evidence for relative size of the flexor tendon. This assumption has led to predictions about relative FDS muscle force potential from sizes of fossae on fossil hominin middle phalanges. Inferences about locomotor capabilities of fossil hominins in turn have been drawn from the predicted force potential of the flexor muscle. The study reported here provides a critical first step in evaluating hypotheses about behavioral implications of middle phalangeal morphology in fossil hominins, by testing the hypothesis that the lateral fossae reflect the size of the FDS tendon and the location of the terminal FDS tendon attachments on the middle phalanx. The middle phalangeal region was dissected in 43 individuals from 16 primate genera, including humans. Qualitative observations were made of tendon attachment locations relative to the lateral fossae. Length measurements of the fossae were tested as predictors of FDS tendon cross-sectional area and of FDS attachment tendon lengths. Our results lead to the conclusion that the hypothesis must be rejected, and that future attention should focus on functional implications of the palmar median bar associated with the lateral fossae.     

Stable Isotope Ratios and Forensic Analysis of Microorganisms

In the aftermath of the anthrax letters of 2001, researchers have been exploring various analytical signatures for the purpose of characterizing the production environment of microorganisms. One such signature is stable isotope ratios, which in heterotrophs, are a function of nutrient and water sources. Here we discuss the use of stable isotope ratios in microbial forensics, using as a database the carbon, nitrogen, oxygen, and hydrogen stable isotope ratios of 247 separate cultures of Bacillus subtilis 6051 spores produced on a total of 32 different culture media. In the context of using stable isotope ratios as a signature for sample matching, we present an analysis of variations between individual samples, between cultures produced in tandem, and between cultures produced in the same medium but at different times. Additionally, we correlate the stable isotope ratios of carbon, nitrogen, oxygen, and hydrogen for growth medium nutrients or water with those of spores and show examples of how these relationships can be used to exclude nutrient or water samples as possible growth substrates for specific cultures.     

Evidence for statistical epistasis between catechol-<Emphasis Type="Italic">O</Emphasis>-methyltransferase (COMT) and polymorphisms in RGS4, G72 (DAOA), GRM3, and DISC1: influence on risk of schizophrenia

Catechol-O-methyltransferase (COMT) regulates dopamine degradation and is located in a genomic region that is deleted in a syndrome associated with psychosis, making it a promising candidate gene for schizophrenia. COMT also has been shown to influence prefrontal cortex processing efficiency. Prefrontal processing dysfunction is a common finding in schizophrenia, and a background of inefficient processing may modulate the effect of other candidate genes. Using the NIMH sibling study (SS), a non-independent case-control set, and an independent German (G) case-control set, we performed conditional/unconditional logistic regression to test for epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes. Evidence for interaction was evaluated using a likelihood ratio test (LRT) between nested models. SNPs in RGS4, G72, GRM3, and DISC1 showed evidence for significant statistical epistasis with COMT. A striking result was found in RGS4: three of five SNPs showed a significant increase in risk [LRT P-values: 90387 = 0.05 (SS); SNP4 = 0.02 (SS), 0.02 (G); SNP18 = 0.04 (SS), 0.008 (G)] in interaction with COMT; main effects for RGS4 SNPs were null. Significant results for SNP4 and SNP18 were also found in the German study. We were able to detect statistical interaction between COMT and polymorphisms in candidate genes for schizophrenia, many of which had no significant main effect. In addition, we were able to replicate other studies, including allelic directionality. The use of epistatic models may improve replication of psychiatric candidate gene studies.     

Common genetic variation in eight genes of the <Emphasis Type="Italic">GH</Emphasis>/<Emphasis Type="Italic">IGF1</Emphasis> axis does not contribute to adult height variation

Stature (adult height) is one of the most heritable human traits, yet few genes, if any, have been convincingly associated with adult height variation in the general population. Here, we selected 150 tag SNPs from eight candidate genes in the growth hormone (GH)/insulin-like growth factor-1 (IGF1) axis (GHR, GHRH, GHRHR, IGF1, IGFALS, IGFBP3, JAK2, STAT5B), and genotyped them in ∼2,200 individuals ascertained for short or tall stature. Nominally significant tag SNPs were then tested in three additional replication cohorts, including a family-based panel to rule out spurious associations owing to population stratification. Across the four height cohorts (N = 6,075 individuals), we did not observe any consistent associations between stature and common variants (≥5% minor allele frequency) in these eight genes, including a common deletion of the growth hormone receptor gene exon 3. Tests of epistatic interactions between these genes did not yield any results beyond those expected by chance. Although we have not tested all genes in the GH/IGF1 axis, our results indicate that common variation in these GH/IGF1 axis genes is not a major determinant of stature, and suggest that if common variation contributes to adult height variation in the general population, the variants are in other, possibly unanticipated genes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

5-Heteroatom substituted pyrazoles as canine COX-2 inhibitors. Part III: molecular modeling studies on binding contribution of 1-(5-methylsulfonyl)pyrid-2-yl and 4-nitrile

The structure-activity relationship toward canine COX-1 and COX-2 in vitro whole blood activity of 4-hydrogen versus 4-cyano substituted 5-aryl or 5-heteroatom substituted N-phenyl versus N-2-pyridyl sulfone pyrazoles is discussed. The differences between the pairs of compounds with the 4-nitrile pyrazole derivatives having substantially improved in vitro activity are highlighted for both COX-2 and COX-1. This difference in activity may be due to the contribution of the hydrogen bond of the 4-cyano group with Ser 530 as shown by our molecular modeling studies. In addition, our model suggests a potential contribution from hydrogen bonding of the pyridyl nitrogen to Tyr 355 for the increased activity over the phenyl sulfone analogs.