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]

Rapid evolution of novel biotic interactions in the UK Brown Argus butterfly uses genomic variation from across its geographical range

Understanding the rate and extent to which populations can adapt to novel environments at their ecological margins is fundamental to predicting the persistence of biological communities during ongoing and rapid global change. Recent range expansion in response to climate change in the UK butterfly Aricia agestis is associated with the evolution of novel interactions with a larval food plant, and the loss of its ability to use an ancestral host species. Using ddRAD analysis of 61,210 variable SNPs from 261 females from throughout the UK range of this species, we identify genomic regions at multiple chromosomes that are associated with evolutionary responses, and their association with demographic history and ecological variation. Gene flow appears widespread throughout the range, despite the apparently fragmented nature of the habitats used by this species. Patterns of haplotype variation between selected and neutral genomic regions suggest that evolution associated with climate adaptation is polygenic, resulting from the independent spread of alleles throughout the established range of this species, rather than the colonization of pre-adapted genotypes from coastal populations. These data suggest that rapid responses to climate change do not depend on the availability of pre-adapted genotypes. Instead, the evolution of novel forms of biotic interaction in A. agestis has occurred during range expansion, through the assembly of novel genotypes from alleles from multiple localities

Dusty Wind-Blown Bubbles

Spurred by recent observations of 24 micron emission within wind-blown bubbles, we study the role that dust can play in such environments, and build an approximate model of a particular wind-blown bubble, `N49.' First, we model the observations with a dusty wind-blown bubble, and then ask whether dust could survive within N49 to its present age (estimated to be 5x10^5 to 10^6 years). We find that dust sputtering and especially dust-gas friction would imply relatively short timescales (t ~ 10^4 years) for dust survival in the wind-shocked region of the bubble. To explain the 24 micron emission, we postulate that the grains are replenished within the wind-blown bubble by destruction of embedded, dense cloudlets of ISM gas that have been over-run by the expanding wind-blown bubble. We calculate the ablation timescales for cloudlets within N49 and find approximate parameters for the embedded cloudlets that can replenish the dust; the parameters for the cloudlets are roughly similar to those observed in other nebula. Such dust will have an important effect on the bubble: including simple dust cooling in a wind-blown bubble model for N49, we find that the luminosity is higher by approximately a factor of six at a bubble age of about 10^4 years. At ages of 10^7 years, the energy contained in the bubble is lower by about a factor of eight if dust is included; if dust must be replenished within the bubble, the associated accompanying gas mass will also be very important to wind-blown bubble cooling and evolution. While more detailed models are certainly called for, this work illustrates the possible strong importance of dust in wind-blown bubbles, and is a first step toward models of dusty, wind-blown bubbles.Comment: 13 pages, 14 figures, Accepted to Ap

Parathyroid hormone-related protein exhibits antioxidant features in osteoblastic cells through its N-terminal and osteostatin domains

Objectives: Oxidative stress plays a major role in the onset and progression of involutional osteoporosis. However, classical antioxidants fail to restore osteoblast function. Interestingly, the bone anabolism of parathyroid hormone (PTH) has been shown to be associated with its ability to counteract oxidative stress in osteoblasts. The PTH counterpart in bone, which is the PTHrelated protein (PTHrP), displays osteogenic actions through both its N-terminal PTH-like region and the C-terminal domain. Methods: We examined and compared the antioxidant capacity of PTHrP (1-37) with the C-terminal PTHrP domain comprising the 107-111 epitope (osteostatin) in both murine osteoblastic MC3T3-E1 cells and primary human osteoblastic cells. Results: We showed that both N- and C-terminal PTHrP peptides at 100 nM decreased reactive oxygen species production and forkhead box protein O activation following hydrogen peroxide (H 2 O 2 )-induced oxidation, which was related to decreased lipid oxidative damage and caspase-3 activation in these cells. This was associated with their ability to restore the deleterious effects of H 2 O 2 on cell growth and alkaline phosphatase activity, as well as on the expression of various osteoblast differentiation genes. The addition of Rp-cyclic 3',5'-hydrogen phosphorothioate adenosine triethylammonium salt (a cyclic 3',5'-adenosine monophosphate antagonist) and calphostin C (a protein kinase C inhibitor), or a PTH type 1 receptor antagonist, abrogated the effects of N-terminal PTHrP, whereas protein phosphatase 1 (an Src kinase activity inhibitor), SU1498 (a vascular endothelial growth factor receptor 2 inhibitor), or an anti osteostatin antiserum, inhibited the effects of C-terminal PTHrP. Conclusion: These findings indicate that the antioxidant properties of PTHrP act through its N- and C-terminal domains and provide novel insights into the osteogenic action of PTHrP.This work has been funded by grants from the Fundacion para la Investigacion Osea y Metabolismo Mineral-FEIOMM and the Instituto de Salud Carlos III (PI11/00449, PI15/00340, PI1600065, RD12/0043/0029, RD12/0043/0008 and RD12/0043/0018,). J. A. Ardua, D. Lozano, and S. Portal-Nunez are recipients of postdoctoral contracts from the Ministerio de Economia y Competitividad, Juan de la Cierva program JCI-2011-09548, FPDI-2013-17268, and RETICEF [FEDER “una manera de hacer Europa” (RD12/0043/0008)

Insights from international environmental legislation and protocols for the global plastic treaty

Correction to: Insights from international environmental legislation and protocols for the global plastic treaty (Scientific Reports, (2024), 14, 1, (2750), 10.1038/s41598-024-53099-9) Margrethe Aanesen, Julide C. Ahi, Tenaw G. Abate, Farhan R. Khan, Frans P. de Vries, Hauke Kite-Powell, Nicola J. Beaumont, 2024, vol. 14, issue 1. Scientific Reports http://www.scopus.com/inward/record.url?scp=85188545299&partnerID=8YFLogxK, https://doi.org/10.1038/s41598-024-57568-zPeer reviewe

‘Christians, out here?’ Encountering Street-Pastors in the post-secular spaces of the UK’s night-time economy

This paper explores the concept of the post-secular city by examining the growing presence of Street-Pastors in the night-time economy of British cities. Street-Pastors are Christian volunteers who work to ensure the safety of people on a ‘night out’. We contribute to work that has called for greater attention to be placed on the ways in which religious faith and ethics are performed to create liminal spaces of understanding in urban areas. Drawing upon in-depth ethnographic research conducted in a range of UK towns and cities, we consider this distinct form of faith-based patrolling in relation to the spatial processes and practices of urban-nightscapes. By exploring the geographies of Street-Pastors, we not only contribute to more nuanced accounts of ‘drinking spaces’ but provide an empirical engagement with the growing body of work on urban rhythms and encounters

Impact of Scottish vocational qualifications on residential child care : have they fulfilled the promise?

This article will present findings from a doctoral study exploring the impact of 'SVQ Care: Promoting Independence (level III)' within children's homes. The study focuses on the extent to which SVQs enhance practice and their function within a 'learning society'. A total of 30 staff were selected from seven children's homes in two different local authority social work departments in Scotland. Each member of staff was interviewed on four separate occasions over a period of 9 months. Interviews were structured using a combination of repertory grids and questions. Particular focus was given to the assessment process, the extent to which SVQs enhance practice and the learning experiences of staff. The findings suggest that there are considerable deficiencies both in terms of the SVQ format and the way in which children's homes are structured for the assessment of competence. Rather than address the history of failure within residential care, it appears that SVQs have enabled the status quo to be maintained whilst creating an 'illusion' of change within a learning society