Biopython: freely available Python tools for computational molecular biology and bioinformatics

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected]

Early evolution of the extraordinary Nova Del 2013 (V339 Del)

We determine the temporal evolution of the luminosity L(WD), radius R(WD) and effective temperature Teff of the white dwarf (WD) pseudophotosphere of V339 Del from its discovery to around day 40. Another main objective was studying the ionization structure of the ejecta. These aims were achieved by modelling the optical/near-IR spectral energy distribution (SED) using low-resolution spectroscopy (3500 - 9200 A), UBVRcIc and JHKLM photometry. During the fireball stage (Aug. 14.8 - 19.9, 2013), Teff was in the range of 6000 - 12000 K, R(WD) was expanding non-uniformly in time from around 66 to around 300 (d/3 kpc) R(Sun), and L(WD) was super-Eddington, but not constant. After the fireball stage, a large emission measure of 1.0-2.0E+62 (d/3 kpc)**2 cm**(-3) constrained the lower limit of L(WD) to be well above the super-Eddington value. The evolution of the H-alpha line and mainly the transient emergence of the Raman-scattered O VI 1032 A line suggested a biconical ionization structure of the ejecta with a disk-like H I region persisting around the WD until its total ionization, around day 40. It is evident that the nova was not evolving according to the current theoretical prediction. The unusual non-spherically symmetric ejecta of nova V339 Del and its extreme physical conditions and evolution during and after the fireball stage represent interesting new challenges for the theoretical modelling of the nova phenomenon.Comment: 14 pages, 9 figures, 3 tables, accepted for Astronomy and Astrophysic

All-organic and organic-silicon photonic ring micro-resonators

Organic electro-optic materials offer exceptional processability (both from solution and the gas phase) that permit fabrication of flexible and conformal device structures and the integration of organic materials with a wide range of disparate materials. In addition, organic electro-optical materials have fundamental response times that are in the terahertz region, and useable electro-optic coefficients that are approaching 300 pm/V (at telecommunication wavelengths). In addition to fabrication by traditional lithographic methods, multiple devices on a single wafer have been fabricated by soft and nano-imprint lithography. In this presentation, we review the fabrication and performance evaluation of a number of all-organic and organic-silicon photonic ring microresonator devices. Both electrical and thermal tuning of devices, including both single and multiple ring micro-resonators, are demonstrated

Evidence for directional selection at a novel major histocompatibility class I marker in wild common frogs (Rana temporaria) exposed to a viral pathogen (Ranavirus).

(c) 2009 Teacher et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Whilst the Major Histocompatibility Complex (MHC) is well characterized in the anuran Xenopus, this region has not previously been studied in another popular model species, the common frog (Rana temporaria). Nor, to date, have there been any studies of MHC in wild amphibian host-pathogen systems. We characterise an MHC class I locus in the common frog, and present primers to amplify both the whole region, and specifically the antigen binding region. As no more than two expressed haplotypes were found in over 400 clones from 66 individuals, it is likely that there is a single class I locus in this species. This finding is consistent with the single class I locus in Xenopus, but contrasts with the multiple loci identified in axolotls, providing evidence that the diversification of MHC class I into multiple loci likely occurred after the Caudata/Anura divergence (approximately 350 million years ago) but before the Ranidae/Pipidae divergence (approximately 230 mya). We use this locus to compare wild populations of common frogs that have been infected with a viral pathogen (Ranavirus) with those that have no history of infection. We demonstrate that certain MHC supertypes are associated with infection status (even after accounting for shared ancestry), and that the diseased populations have more similar supertype frequencies (lower F(ST)) than the uninfected. These patterns were not seen in a suite of putatively neutral microsatellite loci. We interpret this pattern at the MHC locus to indicate that the disease has imposed selection for particular haplotypes, and hence that common frogs may be adapting to the presence of Ranavirus, which currently kills tens of thousands of amphibians in the UK each year

The surged faradic stimulation to the pelvic floor muscles as an adjunct to the medical management in children with rectal prolapse

<p>Abstract</p> <p>Background</p> <p>To assess the role of the surged faradic stimulation to the pelvic floor muscles as an adjunct to the conservative management in the children of idiopathic rectal prolapse</p> <p>Methods</p> <p><it>Study design</it>: Prospective</p> <p><it>Setting</it>: Pediatric Surgery Department, Pt BD Sharma, Post Graduate Institute of Medical Sciences, Rohtak</p> <p><it>Subjects</it>: 47 consecutive children with idiopathic rectal prolapse attending the Pediatric Surgery out patient department from July 2005 to June 2006</p> <p><it>Methodology</it>: The information pertaining to duration and the extent of rectal prolapse, predisposing or associated medical conditions, results of local clinical examination were noted. Surged faradic stimulation using modified intraluminal rectal probe, was given on the alternate days. The conventional conservative medical management was also continued. The extent of relief and the number of the sittings of faradic stimulation required were noted at various stages of follow-ups</p> <p><it>Statistical Methods</it>: Mean values between those completely cured and others; poor responders and others were compared with t-test and proportions were compared with Chi square test. The p-value < 0.05 was considered statistically significant.</p> <p>Results</p> <p>The mean number of sittings in the completely cured group (n = <b>28</b>(64%)) was (12.4 ± 7.8) and was comparable with very poor responder (n = 6(13%). There was higher percentage of relief (76%) at the first follow up (at 15 days) in completely cured Vs other (37%) and also the poor responders showed (20%) Vs other (68%) and was statistically significant.</p> <p>Conclusion</p> <p>With use of faradic stimulation, even the long-standing rectal prolapse can be fully cured. The follow up visit at 2 weeks is very important to gauge the likely success of this modality in treatment of the patients with rectal prolapse. Those showing poor response at this stage may require alternative treatment or take a long time to get cured</p

Plasmodium vivax Diversity and Population Structure across Four Continents

Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations

EB Ford revisited: assessing the long-term stability of wing-spot patterns and population genetic structure of the meadow brown butterfly on the Isles of Scilly

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Data files of wing spot sizes and AFLP genotypes available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.j7v42.Understanding selection in the wild remains a major aim of evolutionary ecology and work by Ford and colleagues on the meadow brown butterfly Maniola jurtina did much to ignite this agenda. A great deal of their work was conducted during the 1950s on the Isles of Scilly. They documented island-specific wing-spot patterns that remained consistent over about a decade, but patterns on some islands changed after environmental perturbation. It was suggested that these wing-spot patterns reflected island-specific selection and that there was little migration between islands. However, genetic studies to test the underlying assumption of restricted migration are lacking and it is also unknown whether the originally described wing-spot patterns have persisted over time. We therefore collected female butterflies from five of Ford's original study locations, including three large islands (St Mary's, St Martin's and Tresco) and two small islands (Tean and St Helen's). Wing-spot patterns had not changed appreciably over time on three of the islands (two large and one small), but were significantly different on the other two. Furthermore, analysis of 176 amplified fragment length polymorphisms revealed significant genome-wide differentiation among the five islands. Our findings are consistent with Ford's conclusions that despite the close proximity of these islands, there is restricted gene flow among them.Heredity advance online publication, 2 November 2016; doi:10.1038/hdy.2016.94.We thank the Genetics Society for a fieldwork grant (to DJH) that funded the collection trip and DJH thanks Mike Johnson for sparking interest in this area. SWB is supported by the Australian Research Council and a Ramsay Fellowship, NW by a Royal Society Wolfson Fellowship and NERC and DJH by the Leverhulme Trust

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species

All-organic and organic-silicon photonic ring micro-resonators

Organic electro-optic materials offer exceptional processability (both from solution and the gas phase) that permit fabrication of flexible and conformal device structures and the integration of organic materials with a wide range of disparate materials. In addition, organic electro-optical materials have fundamental response times that are in the terahertz region, and useable electro-optic coefficients that are approaching 300 pm/V (at telecommunication wavelengths). In addition to fabrication by traditional lithographic methods, multiple devices on a single wafer have been fabricated by soft and nano-imprint lithography. In this presentation, we review the fabrication and performance evaluation of a number of all-organic and organic-silicon photonic ring microresonator devices. Both electrical and thermal tuning of devices, including both single and multiple ring micro-resonators, are demonstrated