Matching methods to produce maps for pest risk analysis to resources

Decision support systems (DSSs) for pest risk mapping are invaluable for guiding pest risk analysts seeking to add maps to pest risk analyses (PRAs). Maps can help identify the area of potential establishment, the area at highest risk and the endangered area for alien plant pests. However, the production of detailed pest risk maps may require considerable time and resources and it is important to match the methods employed to the priority, time and detail required. In this paper, we apply PRATIQUE DSSs to Phytophthora austrocedrae, a pathogen of the Cupressaceae, Thaumetopoea pityocampa, the pine processionary moth, Drosophila suzukii, spotted wing Drosophila, and Thaumatotibia leucotreta, the false codling moth. We demonstrate that complex pest risk maps are not always a high priority and suggest that simple methods may be used to determine the geographic variation in relative risks posed by invasive alien species within an area of concern

Transition in housing design and thermal comfort in rural Tanzania

This study evaluates the performance of three low-income passive housing designs at providing thermal comfort for their inhabitants in temperate tropical rural Tanzania. Severe climatic conditions in these upland regions include large daily oscillations in air temperature (14°C-36°C) and high levels of solar radiation, causing overheating which affects inhabitant health and wellbeing. Inadequate shelter in these difficult climatic conditions is a widespread problem with 71% of Tanzanians living in rural areas, of which 28% of are below the national poverty line. Over the last 10 years an increasing number of houses are using modern building materials (brick or concrete walls and iron roof) rather than traditional vernacular design (mud-pole walls and thatch roof). Three designs were chosen to describe this transition. The performances of the three houses were simulated across a study year using IES and then compared against five chosen criteria to assess thermal comfort. Detailed analyses of critical times of day and specific areas of the building envelope were used to identify critical areas of design. The traditional house overheated significantly less often with smaller diurnal indoor temperature swings than the modern houses (due to its higher roof insulation and wall thermal mass). It also experienced uncomfortably low temperatures least often but maintained higher temperatures for longer during hot evenings. The modern houses outperformed the traditional house in ventilation gains with constant heat rejection throughout the day and night. The traditional house’s open structure resulted in high daytime ventilation gains and night-time heat rejection. Consideration of the position and internal gains of each room was found to be an important design factor. Across the study year the traditional design provided greater thermal comfort. However, as durability and social pressures are important factors in the choice of building materials, the design of modern materials that can mimic and improve on traditional material performance is critical to improving the health of inhabitants

Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease

Copyright: © 2013 Eyre 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 creditedClostridium difficile whole genome sequencing has the potential to identify related isolates, even among otherwise indistinguishable strains, but interpretation depends on understanding genomic variation within isolates and individuals.Serial isolates from two scenarios were whole genome sequenced. Firstly, 62 isolates from 29 timepoints from three in vitro gut models, inoculated with a NAP1/027 strain. Secondly, 122 isolates from 44 patients (2–8 samples/patient) with mostly recurrent/on-going symptomatic NAP-1/027 C. difficile infection. Reference-based mapping was used to identify single nucleotide variants (SNVs).Across three gut model inductions, two with antibiotic treatment, total 137 days, only two new SNVs became established. Pre-existing minority SNVs became dominant in two models. Several SNVs were detected, only present in the minority of colonies at one/two timepoints. The median (inter-quartile range) [range] time between patients’ first and last samples was 60 (29.5–118.5) [0–561] days. Within-patient C. difficile evolution was 0.45 SNVs/called genome/year (95%CI 0.00–1.28) and within-host diversity was 0.28 SNVs/called genome (0.05–0.53). 26/28 gut model and patient SNVs were non-synonymous, affecting a range of gene targets.The consistency of whole genome sequencing data from gut model C. difficile isolates, and the high stability of genomic sequences in isolates from patients, supports the use of whole genome sequencing in detailed transmission investigations.Peer reviewe

Linear-Time Algorithms for Computing Maximum-Density Sequence Segments with Bioinformatics Applications

We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a_i,w_i) for i = 1,..,n and w_i>0, a segment A(i,j) is a consecutive subsequence of A starting with index i and ending with index j. The width of A(i,j) is w(i,j) = sum_{i <= k <= j} w_k, and the density is (sum_{i<= k <= j} a_k)/ w(i,j). The maximum-density segment problem takes A and two values L and U as input and asks for a segment of A with the largest possible density among those of width at least L and at most U. When U is unbounded, we provide a relatively simple, O(n)-time algorithm, improving upon the O(n \log L)-time algorithm by Lin, Jiang and Chao. When both L and U are specified, there are no previous nontrivial results. We solve the problem in O(n) time if w_i=1 for all i, and more generally in O(n+n\log(U-L+1)) time when w_i>=1 for all i.Comment: 23 pages, 13 figures. A significant portion of these results appeared under the title, "Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics," in Proceedings of the Second Workshop on Algorithms in Bioinformatics (WABI), volume 2452 of Lecture Notes in Computer Science (Springer-Verlag, Berlin), R. Guigo and D. Gusfield editors, 2002, pp. 157--17

The role of mutation rate variation and genetic diversity in the architecture of human disease

Background We have investigated the role that the mutation rate and the structure of genetic variation at a locus play in determining whether a gene is involved in disease. We predict that the mutation rate and its genetic diversity should be higher in genes associated with disease, unless all genes that could cause disease have already been identified. Results Consistent with our predictions we find that genes associated with Mendelian and complex disease are substantially longer than non-disease genes. However, we find that both Mendelian and complex disease genes are found in regions of the genome with relatively low mutation rates, as inferred from intron divergence between humans and chimpanzees, and they are predicted to have similar rates of non-synonymous mutation as other genes. Finally, we find that disease genes are in regions of significantly elevated genetic diversity, even when variation in the rate of mutation is controlled for. The effect is small nevertheless. Conclusions Our results suggest that gene length contributes to whether a gene is associated with disease. However, the mutation rate and the genetic architecture of the locus appear to play only a minor role in determining whether a gene is associated with disease

Transformational agronomy by growing summer crops in winter: Crop establishment in cold soils

Winter sown sorghum reduces the impact of heat and water stresses around flowering and increases cropping intensity, though, achieving uniform plant establishment remains challenging. Sowing sorghum in winter will require crops to uniformly germinate and emerge in soils which are cooler than the recommended >16ºC minimum daily temperature, during the driest time of the year. Prolonged emergence periods and reduced total emergence can decrease canopy uniformity with negative impacts on yield, crop management and cropping system intensity. Acceptable establishment percentages (>80%) were achieved for some site by seedlot combinations, though large differences in establishment rate between seedlots were observed. The differences in seedlot emerge rate were related to final establishment. This calls for seed vigour testing, novel seed production technologies, management of seedbed hydrothermal conditions and breeding programs for cold tolerance

Treating depression and depression-like behavior with physical activity: An immune perspective

The increasing burden of major depressive disorder makes the search for an extended understanding of etiology, and for the development of additional treatments highly significant. Biological factors may be useful biomarkers for treatment with physical activity (PA), and neurobiological effects of PA may herald new therapeutic development in the future. This paper provides a thorough and up-to-date review of studies examining the neuroimmunomodulatory effects of PA on the brain in depression and depression-like behaviors. From a neuroimmune perspective, evidence suggests PA does enhance the beneficial and reduce the detrimental effects of the neuroimmune system. PA appears to increase the following factors: interleukin (IL)-10, IL-6 (acutely), macrophage migration inhibitory factor, central nervous system-specific autoreactive CD4+ T cells, M2 microglia, quiescent astrocytes, CX3CL1, and insulin-like growth factor-1. On the other hand, PA appears to reduce detrimental neuroimmune factors such as: Th1/Th2 balance, pro-inflammatory cytokines, C-reactive protein, M1 microglia, and reactive astrocytes. The effect of other mechanisms is unknown, such as: CD4+CD25+ T regulatory cells (T regs), CD200, chemokines, miRNA, M2-type blood-derived macrophages, and tumor necrosis factor (TNF)-α [via receptor 2 (R2)]. The beneficial effects of PA are likely to occur centrally and peripherally (e.g., in visceral fat reduction). The investigation of the neuroimmune effects of PA on depression and depression-like behavior is a rapidly developing and important field.Harris A. Eyre, Evan Papps and Bernhard T. Baun