1,843 research outputs found
Lightning Talk: Biopython (bio) Geography Module
For Google Summer of Code 2009/NESCENT Phyloinformatics Summer of Code 2009, I built a Geography module for Biopython. The purpose of the module is to search, download, and process biogeographical data from GBIF, much as Biopython currently accesses Genbank. Application of the tool to a historical biogeography study on bivalves will be illustrated.

As required by Google Summer of Code and Biopython, the code is open access and is released under the Biopython License:
"http://www.biopython.org/DIST/LICENSE":http://www.biopython.org/DIST/LICENSE

The module is described, and a tutorial is presented, on the Biopython wiki:
http://biopython.org/wiki/BioGeography

The page contains links to the source hosted on Github; here is the direct link:
"http://github.com/nmatzke/biopython/tree/Geography":http://github.com/nmatzke/biopython/tree/Geograph
Effects of Aneuploidy on Genome Structure, Expression, and Interphase Organization in Arabidopsis thaliana
Aneuploidy refers to losses and/or gains of individual chromosomes from the
normal chromosome set. The resulting gene dosage imbalance has a noticeable
affect on the phenotype, as illustrated by aneuploid syndromes, including Down
syndrome in humans, and by human solid tumor cells, which are highly aneuploid.
Although the phenotypic manifestations of aneuploidy are usually apparent,
information about the underlying alterations in structure, expression, and
interphase organization of unbalanced chromosome sets is still sparse. Plants
generally tolerate aneuploidy better than animals, and, through colchicine
treatment and breeding strategies, it is possible to obtain inbred sibling
plants with different numbers of chromosomes. This possibility, combined with
the genetic and genomics tools available for Arabidopsis
thaliana, provides a powerful means to assess systematically the
molecular and cytological consequences of aberrant numbers of specific
chromosomes. Here, we report on the generation of Arabidopsis
plants in which chromosome 5 is present in triplicate. We compare the global
transcript profiles of normal diploids and chromosome 5 trisomics, and assess
genome integrity using array comparative genome hybridization. We use live cell
imaging to determine the interphase 3D arrangement of transgene-encoded
fluorescent tags on chromosome 5 in trisomic and triploid plants. The results
indicate that trisomy 5 disrupts gene expression throughout the genome and
supports the production and/or retention of truncated copies of chromosome 5.
Although trisomy 5 does not grossly distort the interphase arrangement of
fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations
between transgene alleles. Our analysis reveals the complex genomic changes that
can occur in aneuploids and underscores the importance of using multiple
experimental approaches to investigate how chromosome numerical changes
condition abnormal phenotypes and progressive genome instability
A Bayesian approach for estimating the probability of trigger failures in the stop-signal paradigm
Response inhibition is frequently investigated using the stop-signal paradigm, where participants perform a two-choice response time task that is occasionally interrupted by a stop signal instructing them to withhold their response. Stop-signal performance is formalized as a race between a go and a stop process. If the go process wins, the response is executed; if the stop process wins, the response is inhibited. Successful inhibition requires fast stop responses and a high probability of triggering the stop process. Existing methods allow for the estimation of the latency of the stop response, but are unable to identify deficiencies in triggering the stop process. We introduce a Bayesian model that addresses this limitation and enables researchers to simultaneously estimate the probability of trigger failures and the entire distribution of stopping latencies. We demonstrate that trigger failures are clearly present in two previous studies, and that ignoring them distorts estimates of stopping latencies. The parameter estimation routine is implemented in the BEESTS software (Matzke et al., Front. Quantitative Psych. Measurement, 4, 918; 2013a) and is available at http://dora.erbe-matzke.com/software.html
Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication
<p>Abstract</p> <p>Background</p> <p>DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (<it>Equus caballus</it>) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets.</p> <p>Results</p> <p>In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (<it>Equus przewalski</it>) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago.</p> <p>Conclusions</p> <p>Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the domestic horse mtDNA gene pool.</p
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