1,075 research outputs found
Apparent absence of Batrachochytrium salamandrivorans in wild urodeles in the United Kingdom
This is the final version. Available from the publisher via the DOI in this record.Whether an infectious disease threat to wildlife arises from pathogen introduction or the increased
incidence of an already-present agent informs mitigation policy and actions. The prior absence of a
pathogen can be difcult to establish, particularly in free-living wildlife. Subsequent to the epidemic
emergence of the fungus, Batrachochytrium salamandrivorans (Bsal), in mainland Europe in 2010 and
prior to its detection in captive amphibians in the United Kingdom (UK), we tested archived skin swabs
using a Bsal-specifc qPCR. These samples had been collected in 2011 from 2409 wild newts from ponds
across the UK. All swabs were negative for Bsal. Bayesian hierarchical modelling suggests that Bsal
was absent from, or present at very low levels in, these ponds at the time of sampling. Additionally,
surveillance of newt mortality incidents, 2013–2017, failed to detect Bsal. As this pathogen has been
shown to be widespread in British captive amphibian collections, there is an urgent need to raise
awareness of the importance of efective biosecurity measures, especially amongst people with captive
amphibians, to help minimise the risk of Bsal spreading to the wild. Continued and heightened wild
amphibian disease surveillance is a priority to provide an early warning system for potential incursion
eventsDepartment for Environment, Food and Rural Affairs (DEFRA)Animal & Plant Health Agency (APHA
Comparison of Cross-Sectional and Daily Reports in Studying the Relationship Between Depression and Use of Alcohol in Response to Stress in College Students
Alcohol use in response to stress in college students may be affected by the presence of symptoms of depression. However, this is a challenging issue to study due to the various methodologies used as well as the possible effect of depressed mood on the accuracy of self-report. This study focused on methodological issues as possible sources of equivocal findings regarding the relationship between depressed mood and alcohol use in response to stress in a college student population. Findings may differ when these variables are examined cross-sectionally versus longitudinally. Methods : Depressed mood and alcohol coping were assessed both cross-sectionally and repeatedly over time in 125 college students. Participants were assessed at baseline using a diagnostic self-report measure of depression as well as a measure of typical coping style. In addition, daily measures of stress, symptoms of depression, and coping were completed for 45 consecutive days. Results : Different relationships between depressed mood and alcohol coping were found when depressed individuals were analyzed separately from those who were not depressed. Although a significant correlation between daily use of alcohol coping and daily depressed mood was found, there were no differences between depressed and nondepressed participants (as assessed at baseline) on daily alcohol coping. Conclusions : These findings have implications for research design as well as clinical assessment regarding the relationships between mood and use of alcohol for coping; the findings suggest that cross-sectional measures of mood and alcohol use may obscure differences as assessed repeatedly over time. In addition, these findings support the utility of frequent assessment of depressive symptoms when implementing or evaluating programs that target coping skills in college students.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65757/1/j.1530-0277.2000.tb04552.x.pd
Score regularization for peptide identification
<p>Abstract</p> <p>Background</p> <p>Peptide identification from tandem mass spectrometry (MS/MS) data is one of the most important problems in computational proteomics. This technique relies heavily on the accurate assessment of the quality of peptide-spectrum matches (PSMs). However, current MS technology and PSM scoring algorithm are far from perfect, leading to the generation of incorrect peptide-spectrum pairs. Thus, it is critical to develop new post-processing techniques that can distinguish true identifications from false identifications effectively.</p> <p>Results</p> <p>In this paper, we present a consistency-based PSM re-ranking method to improve the initial identification results. This method uses one additional assumption that two peptides belonging to the same protein should be correlated to each other. We formulate an optimization problem that embraces two objectives through regularization: the smoothing consistency among scores of correlated peptides and the fitting consistency between new scores and initial scores. This optimization problem can be solved analytically. The experimental study on several real MS/MS data sets shows that this re-ranking method improves the identification performance.</p> <p>Conclusions</p> <p>The score regularization method can be used as a general post-processing step for improving peptide identifications. Source codes and data sets are available at: <url>http://bioinformatics.ust.hk/SRPI.rar</url>.</p
Efimov effect in quantum magnets
Physics is said to be universal when it emerges regardless of the underlying
microscopic details. A prominent example is the Efimov effect, which predicts
the emergence of an infinite tower of three-body bound states obeying discrete
scale invariance when the particles interact resonantly. Because of its
universality and peculiarity, the Efimov effect has been the subject of
extensive research in chemical, atomic, nuclear and particle physics for
decades. Here we employ an anisotropic Heisenberg model to show that collective
excitations in quantum magnets (magnons) also exhibit the Efimov effect. We
locate anisotropy-induced two-magnon resonances, compute binding energies of
three magnons and find that they fit into the universal scaling law. We propose
several approaches to experimentally realize the Efimov effect in quantum
magnets, where the emergent Efimov states of magnons can be observed with
commonly used spectroscopic measurements. Our study thus opens up new avenues
for universal few-body physics in condensed matter systems.Comment: 7 pages, 5 figures; published versio
A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal
Embryonic stem (ES) cell self-renewal efficiency is determined by the Nanog protein level. However, the protein partners of Nanog that function to direct self-renewal are unclear. Here, we identify a Nanog interactome of over 130 proteins including transcription factors, chromatin modifying complexes, phosphorylation and ubiquitination enzymes, basal transcriptional machinery members, and RNA processing factors. Sox2 was identified as a robust interacting partner of Nanog. The purified Nanog–Sox2 complex identified a DNA recognition sequence present in multiple overlapping Nanog/Sox2 ChIP-Seq data sets. The Nanog tryptophan repeat region is necessary and sufficient for interaction with Sox2, with tryptophan residues required. In Sox2, tyrosine to alanine mutations within a triple-repeat motif (S X T/S Y) abrogates the Nanog–Sox2 interaction, alters expression of genes associated with the Nanog-Sox2 cognate sequence, and reduces the ability of Sox2 to rescue ES cell differentiation induced by endogenous Sox2 deletion. Substitution of the tyrosines with phenylalanine rescues both the Sox2–Nanog interaction and efficient self-renewal. These results suggest that aromatic stacking of Nanog tryptophans and Sox2 tyrosines mediates an interaction central to ES cell self-renewal
The Origin of Malarial Parasites in Orangutans
Background
Recent findings of Plasmodium in African apes have changed our perspectives on the evolution of malarial parasites in hominids. However, phylogenetic analyses of primate malarias are still missing information from Southeast Asian apes. In this study, we report molecular data for a malaria parasite lineage found in orangutans.
Methodology/Principal Findings
We screened twenty-four blood samples from Pongo pygmaeus (Kalimantan, Indonesia) for Plasmodium parasites by PCR. For all the malaria positive orangutan samples, parasite mitochondrial genomes (mtDNA) and two antigens: merozoite surface protein 1 42 kDa (MSP-142) and circumsporozoite protein gene (CSP) were amplified, cloned, and sequenced. Fifteen orangutans tested positive and yielded 5 distinct mitochondrial haplotypes not previously found. The haplotypes detected exhibited low genetic divergence among them, indicating that they belong to one species. We report phylogenetic analyses using mitochondrial genomes, MSP-142 and CSP. We found that the orangutan malaria parasite lineage was part of a monophyletic group that includes all the known non-human primate malaria parasites found in Southeast Asia; specifically, it shares a recent common ancestor with P. inui (a macaque parasite) and P. hylobati (a gibbon parasite) suggesting that this lineage originated as a result of a host switch. The genetic diversity of MSP-142 in orangutans seems to be under negative selection. This result is similar to previous findings in non-human primate malarias closely related to P. vivax. As has been previously observed in the other Plasmodium species found in non-human primates, the CSP shows high polymorphism in the number of repeats. However, it has clearly distinctive motifs from those previously found in other malarial parasites.
Conclusion
The evidence available from Asian apes indicates that these parasites originated independently from those found in Africa, likely as the result of host switches from other non-human primates
Emerging Infectious Disease leads to Rapid Population Decline of Common British Birds
Emerging infectious diseases are increasingly cited as threats to wildlife, livestock and humans alike. They can threaten geographically isolated or critically endangered wildlife populations; however, relatively few studies have clearly demonstrated the extent to which emerging diseases can impact populations of common wildlife species. Here, we report the impact of an emerging protozoal disease on British populations of greenfinch Carduelis chloris and chaffinch Fringilla coelebs, two of the most common birds in Britain. Morphological and molecular analyses showed this to be due to Trichomonas gallinae. Trichomonosis emerged as a novel fatal disease of finches in Britain in 2005 and rapidly became epidemic within greenfinch, and to a lesser extent chaffinch, populations in 2006. By 2007, breeding populations of greenfinches and chaffinches in the geographic region of highest disease incidence had decreased by 35% and 21% respectively, representing mortality in excess of half a million birds. In contrast, declines were less pronounced or absent in these species in regions where the disease was found in intermediate or low incidence. Also, populations of dunnock Prunella modularis, which similarly feeds in gardens, but in which T. gallinae was rarely recorded, did not decline. This is the first trichomonosis epidemic reported in the scientific literature to negatively impact populations of free-ranging non-columbiform species, and such levels of mortality and decline due to an emerging infectious disease are unprecedented in British wild bird populations. This disease emergence event demonstrates the potential for a protozoan parasite to jump avian host taxonomic groups with dramatic effect over a short time period
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