GONOME: measuring correlations between GO terms and genomic positions

Background: Current methods to find significantly under- and over-represented gene ontology (GO) terms in a set of genes consider the genes as equally probable balls in a bag, as may be appropriate for transcripts in micro-array data. However, due to the varying length of genes and intergenic regions, that approach is inappropriate for deciding if any GO terms are correlated with a set of genomic positions. Results: We present an algorithm - GONOME - that can determine which GO terms are significantly associated with a set of genomic positions given a genome annotated with (at least) the starts and ends of genes. We show that certain GO terms may appear to be significantly associated with a set of randomly chosen positions in the human genome if gene lengths are not considered, and that these same terms have been reported as significantly over-represented in a number of recent papers. This apparent over-representation disappears when gene lengths are considered, as GONOME does. For example, we show that, when gene length is taken into account, the term development is not significantly enriched in genes associated with human CpG islands, in contradiction to a previous report. We further demonstrate the efficacy of GONOME by showing that occurrences of the proteosome-associated control element (PACE) upstream activating sequence in the S. cerevisiae genome associate significantly to appropriate GO terms. An extension of this approach yields a whole-genome motif discovery algorithm that allows identification of many other promoter sequences linked to different types of genes, including a large group of previously unknown motifs significantly associated with the terms 'translation' and 'translational elongation'. Conclusion: GONOME is an algorithm that correctly extracts over-represented GO terms from a set of genomic positions. By explicitly considering gene size, GONOME avoids a systematic bias toward GO terms linked to large genes. Inappropriate use of existing algorithms that do not take gene size into account has led to erroneous or suspect conclusions. Reciprocally GONOME may be used to identify new features in genomes that are significantly associated with particular categories of genes.

Kidney volume, blood pressure, and albuminuria: Findings in an Australian Aboriginal community

Background. Australian Aborigines are experiencing epidemic proportions of renal disease, marked by albuminuria and, variably, hematuria. They also have high rates of low birth weight, which have been associated with lower kidney volumes and higher blood pressures. The authors evaluated relationships between kidney volume, blood pressure, albuminuria, and hematuria in 1 homogeneous group. Methods Forty-three percent (672 of 1,560) of the population in a remote coastal Australian Aboriginal community aged 4.4 to 72.1 years participated in the study. Results: Kidney size correlated closely with body size. Systolic blood pressure (SBP) was correlated inversely with kidney length and kidney volume, after adjusting for age, sex, and body surface area (BSA); a 1-cm increase in mean kidney length was associated with a 2.2-mm Hg decrease in SBP, and a 10-mL increase in mean kidney volume was associated with a 0.6-mm Hg decrease in SBP (P = 0.001). Mean kidney volume explained 10% of the variance in SBP in a multivariate model containing age, sex, and BSA. In addition to higher SBP, adults who had the lowest quartiles of kidney volume also had the highest levels of overt albuminuria (P = 0.044). Conclusion: Smaller kidneys predispose to higher blood pressures and albuminuria in this population. The lower volumes possibly represent kidneys with reduced nephron numbers, which might be related to an adverse intrauterine environment. Susceptibility to renal disease could be a direct consequence of reduced nephron numbers; the higher blood pressures with which they are associated could also contribute to, as well as derive from, this association.

Belief in dealing with depression alone: Results from community surveys of adolescents and adults

Background: Community surveys have found that some people believe that it is better to deal with depression alone rather than seek help. However, there has been little research into the characteristics of this group. Methods: Data were drawn from three Australian surveys: (1) a national survey of 1001 adults aged 18+ years; (2) a school survey of 552 students aged 14-16 years from two regions; (3) a survey of 577 young people aged 12-17 years from the Melbourne region. In all three surveys, participants who believed it would be helpful to deal with depression alone were contrasted with those who believed it would be harmful in terms of sociodemographic characteristics, recognition of depression in a vignette, contact with people who experienced depression, beliefs about treatments, beliefs about using substances, beliefs about long-term outcomes, and beliefs about causes. Results: In both adolescents and adults, belief in dealing with depression alone was associated with male gender, less favourable views about mental health professionals, more favourable views about using substances to deal with depression, and a more positive expectation about the outcome if treatment is not sought. Adolescents believing in dealing with depression alone had more favourable views about some potential helpers, such as church workers and pharmacists. In adults, but not adolescents, there was an association with the belief that depression is caused by personal weakness. Limitations: The surveys did not directly ask about reasons for believing that dealing with depression alone would be helpful and did not assess actual help-seeking. Conclusions: Factors encouraging dealing with depression alone are a belief that it is a self-limiting disorder, that substances are an effective way to deal with it and, in adults, that depression is due to personal weakness. Consistent with previous research, males are an important target group for encouraging seeking help to deal with depression. (c) 2006 Elsevier B.V. All rights reserved.

Inhibition studies of purple acid phosphatases: Implications for the catalytic mechanism

Purple acid phosphatases (PAPs) belong to the family of binuclear metallohydrolases and catalyse the hydrolysis of a large group of phosphoester substrates at acidic pH. Despite structural conservation in their active sites PAPs appear to display mechanistic versatility. Here, aspects of the catalytic mechanism of two PAPs are investigated using the inhibitors vanadate and fluoride as probes. While the magnitude of their vanadate inhibition constants are similar the two enzymes differ with respect to the mode of inhibition; vanadate interacts in a non-competitive fashion with pig PAP (K-i = 40 mu mol L-1) while it inhibits red kidney bean PAP competitively (K-i = 30 mu mol L-1). Similarly, fluoride also acts as a competitive inhibitor for red kidney bean PAP, independent of pH, while the inhibition of pig PAP by fluoride is uncompetitive at low pH and non-competitive at higher pH, independent of metal ion composition. Furthermore, while fluoride acts as a slow-binding inhibitor in pig PAP it binds rapidly to the catalytic site of the red kidney bean enzyme. Since vanadate and fluoride are proposed to act as transition state and nucleophile mimics, respectively, the observed differences in inhibition kinetics indicate subtle but distinct variations in the reaction mechanism of these enzymes.

Large scale experiments on gravel and mixed beaches: Experimental procedure, data documentation and initial results

This paper provides information on the experimental set-up, data collection methods and results to date for the project Large scale modelling of coarse grained beaches, undertaken at the Large Wave Channel (GWK) of FZK in Hannover by an international group of researchers in Spring 2002. The main objective of the experiments was to provide full scale measurements of cross-shore processes on gravel and mixed beaches for the verification and further development of cross-shore numerical models of gravel and mixed sediment beaches. Identical random and regular wave tests were undertaken for a gravel beach and a mixed sand/gravel beach set up in the flume. Measurements included profile development, water surface elevation along the flume, internal pressures in the swash zone, piezometric head levels within the beach, run-up, flow velocities in the surf-zone and sediment size distributions. The purpose of the paper is to present to the scientific community the experimental procedure, a summary of the data collected, some initial results, as well as a brief outline of the on-going research being carried out with the data by different research groups. The experimental data is available to all the scientific community following submission of a statement of objectives, specification of data requirements and an agreement to abide with the GWK and EU protocols. (C) 2005 Elsevier B.V. All rights reserved.