87 research outputs found
Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices
Position-specific scoring matrices (PSSMs) are useful for detecting weak
homology in protein sequence analysis, and they are thought to contain some
essential signatures of the protein families. In order to elucidate what kind
of ingredients constitute such family-specific signatures, we apply singular
value decomposition to a set of PSSMs and examine the properties of dominant
right and left singular vectors. The first right singular vectors were
correlated with various amino acid indices including relative mutability, amino
acid composition in protein interior, hydropathy, or turn propensity, depending
on proteins. A significant correlation between the first left singular vector
and a measure of site conservation was observed. It is shown that the
contribution of the first singular component to the PSSMs act to disfavor
potentially but falsely functionally important residues at conserved sites. The
second right singular vectors were highly correlated with hydrophobicity
scales, and the corresponding left singular vectors with contact numbers of
protein structures. It is suggested that sequence alignment with a PSSM is
essentially equivalent to threading supplemented with functional information.
The presented method may be used to separate functionally important sites from
structurally important ones, and thus it may be a useful tool for predicting
protein functions.Comment: 22 pages, 7 figures, 4 table
Determinants of cognitive function in childhood: A cohort study in a middle income context
BACKGROUND: There is evidence that poverty, health and nutrition affect children's cognitive development. This study aimed to examine the relative contributions of both proximal and distal risk factors on child cognitive development, by breaking down the possible causal pathways through which poverty affects cognition. METHODS: This cohort study collected data on family socioeconomic status, household and neighbourhood environmental conditions, child health and nutritional status, psychosocial stimulation and nursery school attendance. The effect of these on Wechsler Pre-School and Primary Scale of Intelligence scores at five years of age was investigated using a multivariable hierarchical analysis, guided by the proposed conceptual framework. RESULTS: Unfavourable socioeconomic conditions, poorly educated mother, absent father, poor sanitary conditions at home and in the neighbourhood and low birth weight were negatively associated with cognitive performance at five years of age, while strong positive associations were found with high levels of domestic stimulation and nursery school attendance. CONCLUSION: Children's cognitive development in urban contexts in developing countries could be substantially increased by interventions promoting early psychosocial stimulation and preschool experience, together with efforts to prevent low birth weight and promote adequate nutritional status
Coastal Upwelling Supplies Oxygen-Depleted Water to the Columbia River Estuary
Low dissolved oxygen (DO) is a common feature of many estuarine and shallow-water
environments, and is often attributed to anthropogenic nutrient enrichment from
terrestrial-fluvial pathways. However, recent events in the U.S. Pacific
Northwest have highlighted that wind-forced upwelling can cause naturally
occurring low DO water to move onto the continental shelf, leading to
mortalities of benthic fish and invertebrates. Coastal estuaries in the Pacific
Northwest are strongly linked to ocean forcings, and here we report observations
on the spatial and temporal patterns of oxygen concentration in the Columbia
River estuary. Hydrographic measurements were made from transect (spatial
survey) or anchor station (temporal survey) deployments over a variety of wind
stresses and tidal states during the upwelling seasons of 2006 through 2008.
During this period, biologically stressful levels of dissolved oxygen were
observed to enter the Columbia River estuary from oceanic sources, with minimum
values close to the hypoxic threshold of 2.0 mg L−1. Riverine
water was consistently normoxic. Upwelling wind stress controlled the timing and
magnitude of low DO events, while tidal-modulated estuarine circulation patterns
influenced the spatial extent and duration of exposure to low DO water. Strong
upwelling during neap tides produced the largest impact on the estuary. The
observed oxygen concentrations likely had deleterious behavioral and
physiological consequences for migrating juvenile salmon and benthic crabs.
Based on a wind-forced supply mechanism, low DO events are probably common to
the Columbia River and other regional estuaries and if conditions on the shelf
deteriorate further, as observations and models predict, Pacific Northwest
estuarine habitats could experience a decrease in environmental quality
Relative Impacts of Adult Movement, Larval Dispersal and Harvester Movement on the Effectiveness of Reserve Networks
Movement of individuals is a critical factor determining the effectiveness of
reserve networks. Marine reserves have historically been used for the management
of species that are sedentary as adults, and, therefore, larval dispersal has
been a major focus of marine-reserve research. The push to use marine reserves
for managing pelagic and demersal species poses significant questions regarding
their utility for highly-mobile species. Here, a simple conceptual
metapopulation model is developed to provide a rigorous comparison of the
functioning of reserve networks for populations with different admixtures of
larval dispersal and adult movement in a home range. We find that adult movement
produces significantly lower persistence than larval dispersal, all other
factors being equal. Furthermore, redistribution of harvest effort previously in
reserves to remaining fished areas (‘fishery squeeze’) and fishing
along reserve borders (‘fishing-the-line’) considerably reduce
persistence and harvests for populations mobile as adults, while they only
marginally changes results for populations with dispersing larvae. Our results
also indicate that adult home-range movement and larval dispersal are not simply
additive processes, but rather that populations possessing both modes of
movement have lower persistence than equivalent populations having the same
amount of ‘total movement’ (sum of larval and adult movement spatial
scales) in either larval dispersal or adult movement alone
Detecting Clusters of Mutations
Positive selection for protein function can lead to multiple mutations within a small stretch of DNA, i.e., to a cluster of mutations. Recently, Wagner proposed a method to detect such mutation clusters. His method, however, did not take into account that residues with high solvent accessibility are inherently more variable than residues with low solvent accessibility. Here, we propose a new algorithm to detect clustered evolution. Our algorithm controls for different substitution probabilities at buried and exposed sites in the tertiary protein structure, and uses random permutations to calculate accurate P values for inferred clusters. We apply the algorithm to genomes of bacteria, fly, and mammals, and find several clusters of mutations in functionally important regions of proteins. Surprisingly, clustered evolution is a relatively rare phenomenon. Only between 2% and 10% of the genes we analyze contain a statistically significant mutation cluster. We also find that not controlling for solvent accessibility leads to an excess of clusters in terminal and solvent-exposed regions of proteins. Our algorithm provides a novel method to identify functionally relevant divergence between groups of species. Moreover, it could also be useful to detect artifacts in automatically assembled genomes
Recreational fisheries in the UK: natural capital, ecosystem services, threats, and management
Innate immune properties of selected human neuropeptides against Moraxella catarrhalis and nontypeable Haemophilus influenzae
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