Assessing Allowable Take of Migratory Birds

Legal removal of migratory birds from the wild occurs for several reasons, including subsistence, sport harvest, damage control, and the pet trade. We argue that harvest theory provides the basis for assessing the impact of authorized take, advance a simplified rendering of harvest theory known as potential biological removal as a useful starting point for assessing take, and demonstrate this approach with a case study of depredation control of black vultures (Coragyps atratus) in Virginia, USA. Based on data from the North American Breeding Bird Survey and other sources, we estimated that the black vulture population in Virginia was 91,190 (95% credible interval = 44,520–212,100) in 2006. Using a simple population model and available estimates of life-history parameters, we estimated the intrinsic rate of growth (rmax) to be in the range 7–14%, with 10.6% a plausible point estimate. For a take program to seek an equilibrium population size on the conservative side of the yield curve, the rate of take needs to be less than that which achieves a maximum sustained yield (0.5 x rmax). Based on the point estimate for rmax and using the lower 60% credible interval for population size to account for uncertainty, these conditions would be met if the take of black vultures in Virginia in 2006 was rmax. Further, the ratio of desired harvest rate to 0.5 x rmax may be a useful metric for ascertaining the applicability of specific requirements of the National Environmental Protection Act

Human Movement Is Both Diffusive and Directed

Understanding the influence of the built environment on human movement requires quantifying spatial structure in a general sense. Because of the difficulty of this task, studies of movement dynamics often ignore spatial heterogeneity and treat movement through journey lengths or distances alone. This study analyses public bicycle data from central London to reveal that, although journey distances, directions, and frequencies of occurrence are spatially variable, their relative spatial patterns remain largely constant, suggesting the influence of a fixed spatial template. A method is presented to describe this underlying space in terms of the relative orientation of movements toward, away from, and around locations of geographical or cultural significance. This produces two fields: one of convergence and one of divergence, which are able to accurately reconstruct the observed spatial variations in movement. These two fields also reveal categorical distinctions between shorter journeys merely serving diffusion away from significant locations, and longer journeys intentionally serving transport between spatially distinct centres of collective importance. Collective patterns of human movement are thus revealed to arise from a combination of both diffusive and directed movement, with aggregate statistics such as mean travel distances primarily determined by relative numbers of these two kinds of journeys

Nonparametric identification of regulatory interactions from spatial and temporal gene expression data

<p>Abstract</p> <p>Background</p> <p>The correlation between the expression levels of transcription factors and their target genes can be used to infer interactions within animal regulatory networks, but current methods are limited in their ability to make correct predictions.</p> <p>Results</p> <p>Here we describe a novel approach which uses nonparametric statistics to generate ordinary differential equation (ODE) models from expression data. Compared to other dynamical methods, our approach requires minimal information about the mathematical structure of the ODE; it does not use qualitative descriptions of interactions within the network; and it employs new statistics to protect against over-fitting. It generates spatio-temporal maps of factor activity, highlighting the times and spatial locations at which different regulators might affect target gene expression levels. We identify an ODE model for <it>eve </it>mRNA pattern formation in the <it>Drosophila melanogaster </it>blastoderm and show that this reproduces the experimental patterns well. Compared to a non-dynamic, spatial-correlation model, our ODE gives 59% better agreement to the experimentally measured pattern. Our model suggests that protein factors frequently have the potential to behave as both an activator and inhibitor for the same <it>cis</it>-regulatory module depending on the factors' concentration, and implies different modes of activation and repression.</p> <p>Conclusions</p> <p>Our method provides an objective quantification of the regulatory potential of transcription factors in a network, is suitable for both low- and moderate-dimensional gene expression datasets, and includes improvements over existing dynamic and static models.</p

Level of Arterial Ligation in Rectal Cancer Surgery: Low Tie Preferred over High Tie. A Review

Consensus does not exist on the level of arterial ligation in rectal cancer surgery. From oncologic considerations, many surgeons apply high tie arterial ligation (level of inferior mesenteric artery). Other strategies include ligation at the level of the superior rectal artery, just caudally to the origin of the left colic artery (low tie), and ligation at a level without any intraoperative definition of the inferior mesenteric or superior rectal arteries

β1 Integrin Maintains Integrity of the Embryonic Neocortical Stem Cell Niche

IInteractions between laminins and integrin receptors hold neural stem cells in place at the ventricular surface of embryonic brain. Transient disruption leads to abnormal stem cell divisions and permanent cortical malformation

Dissecting Oct3/4-Regulated Gene Networks in Embryonic Stem Cells by Expression Profiling

POU transcription factor Pou5f1 (Oct3/4) is required to maintain ES cells in an undifferentiated state. Here we show that global expression profiling of Oct3/4-manipulated ES cells delineates the downstream target genes of Oct3/4. Combined with data from genome-wide chromatin-immunoprecipitation (ChIP) assays, this analysis identifies not only primary downstream targets of Oct3/4, but also secondary or tertiary targets. Furthermore, the analysis also reveals that downstream target genes are regulated either positively or negatively by Oct3/4. Identification of a group of genes that show both activation and repression depending on Oct3/4 expression levels provides a possible mechanism for the requirement of appropriate Oct3/4 expression to maintain undifferentiated ES cells. As a proof-of-principle study, one of the downstream genes, Tcl1, has been analyzed in detail. We show that Oct3/4 binds to the promoter region of Tcl1 and activates its transcription. We also show that Tcl1 is involved in the regulation of proliferation, but not differentiation, in ES cells. These findings suggest that the global expression profiling of gene-manipulated ES cells can help to delineate the structure and dynamics of gene regulatory networks

Inhibition of Effector Function but Not T Cell Activation and Increase in FoxP3 Expression in T Cells Differentiated in the Presence of PP14

Background: T-helper polarization of naïve T cells is determined by a complex mechanism that involves many factors, eventually leading to activation of Th1, Th2, or Th17 responses or alternatively the generation of regulatory T cells. Placental Protein 14 (PP14) is a 28 kDa glycoprotein highly secreted in early pregnancy that is able to desensitize T cell receptor (TCR) signaling and modulate T cell activation. Methodology/Principal Findings: Prolonged antigen-specific stimulation of T cells in the presence of PP14 resulted in an impaired secretion of IFN-c, IL-5 and IL-17 upon restimulation, although the cells proliferated and expressed activation markers. Furthermore, the generation of regulatory CD4 + CD25 high Foxp3 + T cells was induced in the presence of PP14, in both antigen-specific as well as polyclonal stimulation. In accordance with previous reports, we found that the induction of FoxP3 expression by PP14 is accompanied by down regulation of the PI3K-mTOR signaling pathway. Conclusions/Significance: These data suggest that PP14 arrests T cells in a unique activated state that is not accompanied with the acquisition of effector function, together with promoting the generation of regulatory T cells. Taken together, our results may elucidate the role of PP14 in supporting immune tolerance in pregnancy by reducing T cell effector function

Understory Bird Communities in Amazonian Rainforest Fragments: Species Turnover through 25 Years Post-Isolation in Recovering Landscapes

Inferences about species loss following habitat conversion are typically drawn from short-term surveys, which cannot reconstruct long-term temporal dynamics of extinction and colonization. A long-term view can be critical, however, to determine the stability of communities within fragments. Likewise, landscape dynamics must be considered, as second growth structure and overall forest cover contribute to processes in fragments. Here we examine bird communities in 11 Amazonian rainforest fragments of 1–100 ha, beginning before the fragments were isolated in the 1980s, and continuing through 2007. Using a method that accounts for imperfect detection, we estimated extinction and colonization based on standardized mist-net surveys within discreet time intervals (1–2 preisolation samples and 4–5 post-isolation samples). Between preisolation and 2007, all fragments lost species in an area-dependent fashion, with loss of as few as <10% of preisolation species from 100-ha fragments, but up to 70% in 1-ha fragments. Analysis of individual time intervals revealed that the 2007 result was not due to gradual species loss beginning at isolation; both extinction and colonization occurred in every time interval. In the last two samples, 2000 and 2007, extinction and colonization were approximately balanced. Further, 97 of 101 species netted before isolation were detected in at least one fragment in 2007. Although a small subset of species is extremely vulnerable to fragmentation, and predictably goes extinct in fragments, developing second growth in the matrix around fragments encourages recolonization in our landscapes. Species richness in these fragments now reflects local turnover, not long-term attrition of species. We expect that similar processes could be operating in other fragmented systems that show unexpectedly low extinction

The Core and Accessory Genomes of Burkholderia pseudomallei: Implications for Human Melioidosis

Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, can exhibit significant ecological flexibility that is likely reflective of a dynamic genome. Using whole-genome Bp microarrays, we examined patterns of gene presence and absence across 94 South East Asian strains isolated from a variety of clinical, environmental, or animal sources. 86% of the Bp K96243 reference genome was common to all the strains representing the Bp “core genome”, comprising genes largely involved in essential functions (eg amino acid metabolism, protein translation). In contrast, 14% of the K96243 genome was variably present across the isolates. This Bp accessory genome encompassed multiple genomic islands (GIs), paralogous genes, and insertions/deletions, including three distinct lipopolysaccharide (LPS)-related gene clusters. Strikingly, strains recovered from cases of human melioidosis clustered on a tree based on accessory gene content, and were significantly more likely to harbor certain GIs compared to animal and environmental isolates. Consistent with the inference that the GIs may contribute to pathogenesis, experimental mutation of BPSS2053, a GI gene, reduced microbial adherence to human epithelial cells. Our results suggest that the Bp accessory genome is likely to play an important role in microbial adaptation and virulence

Ecological Energetics of an Abundant Aerial Insectivore, the Purple Martin

We thank T. Fagin for help with estimating the seasonal range area occupied by Purple Martins. We thank an anonymous reviewer, Mark Brigham, and J Boyles for their comments on this manuscript.Conceived and designed the experiments: JFK ESB WFF PBC. Performed the experiments: JFK PBC. Analyzed the data: JFK PBC. Wrote the manuscript: JFK ESB WFF PBC. Developed the model in Matlab: JFK PBC.The atmospheric boundary layer and lower free atmosphere, or aerosphere, is increasingly important for human transportation, communication, environmental monitoring, and energy production. The impacts of anthropogenic encroachment into aerial habitats are not well understood. Insectivorous birds and bats are inherently valuable components of biodiversity and play an integral role in aerial trophic dynamics. Many of these insectivores are experiencing range-wide population declines. As a first step toward gaging the potential impacts of these declines on the aerosphere’s trophic system, estimates of the biomass and energy consumed by aerial insectivores are needed. We developed a suite of energetics models for one of the largest and most common avian aerial insectivores in North America, the Purple Martin (Progne subis). The base model estimated that Purple Martins consumed 412 (± 104) billion insects*y-1 with a biomass of 115,860 (± 29,192) metric tonnes*y-1. During the breeding season Purple Martins consume 10.3 (+ 3.0) kg of prey biomass per km3 of aerial habitat, equal to about 36,000 individual insects*km-3. Based on these calculations, the cumulative seasonal consumption of insects*km-3 is greater in North America during the breeding season than during other phases of the annual cycle, however the maximum daily insect consumption*km-3 occurs during fall migration. This analysis provides the first range-wide quantitative estimate of the magnitude of the trophic impact of this large and common aerial insectivore. Future studies could use a similar modeling approach to estimate impacts of the entire guild of aerial insectivores at a variety of temporal and spatial scales. These analyses would inform our understanding of the impact of population declines among aerial insectivores on the aerosphere’s trophic dynamics.Yeshttp://www.plosone.org/static/editorial#pee