1,338 research outputs found
New genes from old: asymmetric divergence of gene duplicates and the evolution of development
Gene duplications and gene losses have been frequent events in the evolution of animal genomes, with the balance between these two dynamic processes contributing to major differences in gene number between species. After gene duplication, it is common for both daughter genes to accumulate sequence change at approximately equal rates. In some cases, however, the accumulation of sequence change is highly uneven with one copy radically diverging from its paralogue. Such âasymmetric evolutionâ seems commoner after tandem gene duplication than after whole-genome duplication, and can generate substantially novel genes. We describe examples of asymmetric evolution in duplicated homeobox genes of moths, molluscs and mammals, in each case generating new homeobox genes that were recruited to novel developmental roles. The prevalence of asymmetric divergence of gene duplicates has been underappreciated, in part, because the origin of highly divergent genes can be difficult to resolve using standard phylogenetic methods.
This article is part of the themed issue âEvo-devo in the genomics era, and the origins of morphological diversityâ.</jats:p
Adaptive mutation using statistics mechanism for genetic algorithms
Copyright @ 2004 Springer-Verla
Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan
Background: Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide.
Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular C. trachomatis
previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia
(A/SA1). No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan.
Methods: This study sequenced twenty ocular C. trachomatis isolates to improve understanding of pathogen diversity
in North-East Africa and examine for genomic variation specific to Sudan, possibly related to the persistence of
trachoma in surveyed communities. High quality, whole genome sequences were obtained from 12/20 isolates.
Results: All isolates were serovar A and had tarP and trpA sequences typical of classical, ocular C. trachomatis isolates.
The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of C. trachomatis phylogeny
distinct from geographically disparate ocular isolates, with little intra-population diversity. We found 333 SNPs that
were conserved in Sudanese ocular isolates but rare compared to other ocular C. trachomatis populations, which were
focused in two genomic loci (CTA0172-CTA0173 and CTA0482).
Conclusions: Limited intra-population diversity and geographical clustering of ocular C. trachomatis suggests minimal
transmission between and slow diversification within trachoma-endemic communities. However, diversity may
have been higher pre-treatment in these communities. Over-representation of Sudan-specific SNPs in three genes
suggests they may have an impact on C. trachomatis growth and transmission in this population
A Regularized Graph Layout Framework for Dynamic Network Visualization
Many real-world networks, including social and information networks, are
dynamic structures that evolve over time. Such dynamic networks are typically
visualized using a sequence of static graph layouts. In addition to providing a
visual representation of the network structure at each time step, the sequence
should preserve the mental map between layouts of consecutive time steps to
allow a human to interpret the temporal evolution of the network. In this
paper, we propose a framework for dynamic network visualization in the on-line
setting where only present and past graph snapshots are available to create the
present layout. The proposed framework creates regularized graph layouts by
augmenting the cost function of a static graph layout algorithm with a grouping
penalty, which discourages nodes from deviating too far from other nodes
belonging to the same group, and a temporal penalty, which discourages large
node movements between consecutive time steps. The penalties increase the
stability of the layout sequence, thus preserving the mental map. We introduce
two dynamic layout algorithms within the proposed framework, namely dynamic
multidimensional scaling (DMDS) and dynamic graph Laplacian layout (DGLL). We
apply these algorithms on several data sets to illustrate the importance of
both grouping and temporal regularization for producing interpretable
visualizations of dynamic networks.Comment: To appear in Data Mining and Knowledge Discovery, supporting material
(animations and MATLAB toolbox) available at
http://tbayes.eecs.umich.edu/xukevin/visualization_dmkd_201
Earth science: Redox state of early magmas
International audienceA study of cerium in zircon minerals has allowed an assessment of the redox conditions that prevailed when Earth's earliest magmas formed. The results suggest that the mantle became oxidized sooner than had been though
Anthropometric indices of Gambian children after one or three annual rounds of mass drug administration with azithromycin for trachoma control.
BACKGROUND: Mass drug administration (MDA) with azithromycin, carried out for the control of blinding trachoma, has been linked to reduced mortality in children. While the mechanism behind this reduction is unclear, it may be due, in part, to improved nutritional status via a potential reduction in the community burden of infectious disease. To determine whether MDA with azithromycin improves anthropometric indices at the community level, we measured the heights and weights of children aged 1 to 4 years in communities where one (single MDA arm) or three annual rounds (annual MDA arm) of azithromycin had been distributed. METHODS: Data collection took place three years after treatment in the single MDA arm and one year after the final round of treatment in the annual MDA arm. Mean height-for-age, weight-for-age and weight-for-height z scores were compared between treatment arms. RESULTS: No significant differences in mean height-for-age, weight-for-age or weight-for-height z scores were found between the annual MDA and single MDA arms, nor was there a significant reduction in prevalence of stunting, wasting or underweight between arms. CONCLUSIONS: Our data do not provide evidence that community MDA with azithromycin improved anthropometric outcomes of children in The Gambia. This may suggest reductions in mortality associated with azithromycin MDA are due to a mechanism other than improved nutritional status
Modelling Hurricane Exposure and Wind Speed on a Mesoclimate Scale: A Case Study from Cusuco NP, Honduras
High energy weather events are often expected to play a substantial role in biotic community dynamics and large scale diversity patterns but their contribution is hard to prove. Currently, observations are limited to the documentation of accidental records after the passing of such events. A more comprehensive approach is synthesising weather events in a location over a long time period, ideally at a high spatial resolution and on a large geographic scale. We provide a detailed overview on how to generate hurricane exposure data at a meso-climate level for a specific region. As a case study we modelled landscape hurricane exposure in Cusuco National Park (CNP), Honduras with a resolution of 50 mĂ50 m patches. We calculated actual hurricane exposure vulnerability site scores (EVVS) through the combination of a wind pressure model, an exposure model that can incorporate simple wind dynamics within a 3-dimensional landscape and the integration of historical hurricanes data. The EVSS was calculated as a weighted function of sites exposure, hurricane frequency and maximum wind velocity. Eleven hurricanes were found to have affected CNP between 1995 and 2010. The highest EVSS's were predicted to be on South and South-East facing sites of the park. Ground validation demonstrated that the South-solution (i.e. the South wind inflow direction) explained most of the observed tree damage (90% of the observed tree damage in the field). Incorporating historical data to the model to calculate actual hurricane exposure values, instead of potential exposure values, increased the model fit by 50%
A Prospective Study of the Association of Metacognitive Beliefs and Processes with Persistent Emotional Distress After Diagnosis of Cancer
Two hundred and six patients, diagnosed with primary breast or prostate cancer completed self-report questionnaires on two occasions: before treatment (T1) and 12 months later (T2). The questionnaires included: the Hospital Anxiety and Depression Scale; Impact of Events Scale; the Metacognitions Questionnaire-30 (MCQ-30) and the Illness Perceptions Questionnaire-revised. A series of regression analyses indicated that metacognitive beliefs at T1 predicted between 14 and 19 % of the variance in symptoms of anxiety, depression and trauma at T2 after controlling for age and gender. For all three outcomes, the MCQ-30 subscale ânegative beliefs about worryâ made the largest individual contribution with âcognitive confidenceâ also contributing in each case. For anxiety, a third metacognitive variable, âpositive beliefs about worryâ also predicted variance in T2 symptoms. In addition, hierarchical analyses indicated that metacognitive beliefs explained a small but significant amount of variance in T2 anxiety (2 %) and T2 depression (4 %) over and above that explained by demographic variables, T1 symptoms and T1 illness perceptions. The findings suggest that modifying metacognitive beliefs and processes has the potential to alleviate distress associated with cancer
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