Mitochondrial phylogeography and demographic history of the Vicuña: implications for conservation

The vicuña (Vicugna vicugna; Miller, 1924) is a conservation success story, having recovered from near extinction in the 1960s to current population levels estimated at 275 000. However, lack of information about its demographic history and genetic diversity has limited both our understanding of its recovery and the development of science-based conservation measures. To examine the evolution and recent demographic history of the vicuña across its current range and to assess its genetic variation and population structure, we sequenced mitochondrial DNA from the control region (CR) for 261 individuals from 29 populations across Peru, Chile and Argentina. Our results suggest that populations currently designated as Vicugna vicugna vicugna and Vicugna vicugna mensalis comprise separate mitochondrial lineages. The current population distribution appears to be the result of a recent demographic expansion associated with the last major glacial event of the Pleistocene in the northern (18 to 22°S) dry Andes 14–12 000 years ago and the establishment of an extremely arid belt known as the 'Dry Diagonal' to 29°S. Within the Dry Diagonal, small populations of V. v. vicugna appear to have survived showing the genetic signature of demographic isolation, whereas to the north V. v. mensalis populations underwent a rapid demographic expansion before recent anthropogenic impacts

Effect of incarceration and opioid agonist treatment transitions on risk of hospitalisation with injection drug use-associated bacterial infections: A self-controlled case series in New South Wales, Australia

Background: Transitional times in opioid use, such as release from prison and discontinuation of opioid agonist treatment (OAT), are associated with health harms due to changing drug consumption practices and limited access to health and social supports. Using a self-controlled (within-person) study design, we aimed to understand if these transitions increase risks of injection drug use-associated bacterial infections. Methods: We performed a self-controlled case series among a cohort of people with opioid use disorder (who had all previously accessed OAT) in New South Wales, Australia, 2001-2018. The outcome was hospitalisation with injecting-related bacterial infections. We divided participants’ observed days into time windows related to incarceration and OAT receipt. We compared hospitalization rates during focal (exposure) windows and referent (control) windows (i.e., 5-52 weeks continuously not incarcerated or continuously receiving OAT). We estimated adjusted incidence rate ratios (aIRR) using conditional logistic regression, adjusted for time-varying confounders. Results: There were 7590 participants who experienced hospitalisation with injecting-related bacterial infections (35% female; median age 38 years; 78% hospitalised with skin and soft-tissue infections). Risk for injecting-related bacterial infections was elevated for two weeks following release from prison (aIRR 1.45; 95%CI 1.22–1.72). Risk was increased during two weeks before (aIRR 1.89; 95%CI 1.59–2.25) and after (aIRR 1.91; 95%CI 1.54–2.36) discontinuation of OAT, and during two weeks before (aIRR 3.63; 95%CI 3.13–4.22) and after (aIRR 2.52; 95%CI 2.09–3.04) OAT initiation. Conclusion: Risk of injecting-related bacterial infections varies greatly within-individuals over time. Risk is raised immediately after prison release, and around initiation and discontinuation of OAT. Social contextual factors likely contribute to excess risks at transitions in incarceration and OAT exposure

Passive phloem loading and long-distance transport in a synthetic tree-on-a-chip

Vascular plants rely on differences of osmotic pressure to export sugars from regions of synthesis (mature leaves) to sugar sinks (roots, fruits). In this process, known as M\"unch pressure flow, the loading of sugars from photosynthetic cells to the export conduit (the phloem) is crucial, as it sets the pressure head necessary to power long-distance transport. Whereas most herbaceous plants use active mechanisms to increase phloem concentration above that of the photosynthetic cells, in most tree species, for which transport distances are largest, loading seems to occur via passive symplastic diffusion from the mesophyll to the phloem. Here, we use a synthetic microfluidic model of a passive loader to explore the nonlinear dynamics that arise during export and determine the ability of passive loading to drive long-distance transport. We first demonstrate that in our device, phloem concentration is set by the balance between the resistances to diffusive loading from the source and convective export through the phloem. Convection-limited export corresponds to classical models of M\"unch transport, where phloem concentration is close to that of the source; in contrast, diffusion-limited export leads to small phloem concentrations and weak scaling of flow rates with the hydraulic resistance. We then show that the effective regime of convection-limited export is predominant in plants with large transport resistances and low xylem pressures. Moreover, hydrostatic pressures developed in our synthetic passive loader can reach botanically relevant values as high as 10 bars. We conclude that passive loading is sufficient to drive long-distance transport in large plants, and that trees are well suited to take full advantage of passive phloem loading strategies

Lovelock theories, holography and the fate of the viscosity bound

We consider Lovelock theories of gravity in the context of AdS/CFT. We show that, for these theories, causality violation on a black hole background can occur well in the interior of the geometry, thus posing more stringent constraints than were previously found in the literature. Also, we find that instabilities of the geometry can appear for certain parameter values at any point in the geometry, as well in the bulk as close to the horizon. These new sources of causality violation and instability should be related to CFT features that do not depend on the UV behavior. They solve a puzzle found previously concerning unphysical negative values for the shear viscosity that are not ruled out solely by causality restrictions. We find that, contrary to previous expectations, causality violation is not always related to positivity of energy. Furthermore, we compute the bound for the shear viscosity to entropy density ratio of supersymmetric conformal field theories from d=4 till d=10 - i.e., up to quartic Lovelock theory -, and find that it behaves smoothly as a function of d. We propose an approximate formula that nicely fits these values and has a nice asymptotic behavior when d goes to infinity for any Lovelock gravity. We discuss in some detail the latter limit. We finally argue that it is possible to obtain increasingly lower values for the shear viscosity to entropy density ratio by the inclusion of more Lovelock terms.Comment: 42 pages, 17 figures, JHEP3.cls. v2: reference adde

Rotation and Spin in Physics

We delineate the role of rotation and spin in physics, discussing in order Newtonian classical physics, special relativity, quantum mechanics, quantum electrodynamics and general relativity. In the latter case, we discuss the generalization of the Kepler formula to post-Newtonian order $(c^{-2}$) including spin effects and two-body effects. Experiments which verify the theoretical results for general relativistic spin-orbit effects are discussed as well as efforts being made to verify the spin-spin effects

TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets

<p>Abstract</p> <p>Background</p> <p>The nucleotide sequence flanking the translation initiation codon (start codon context) affects the translational efficiency of eukaryotic mRNAs, and may indicate the presence of an alternative translation initiation site (TIS) to produce proteins with different properties. Multi-targeting may reflect the translational variability of these other protein forms. In this paper we present a web server that performs computations to investigate the usage of alternative translation initiation sites for the synthesis of new protein variants that might have different functions.</p> <p>Results</p> <p>An efficient web-based tool entitled TISs-ST (Translation Initiation Sites and Secretory Targets) evaluates putative translation initiation sites and indicates the prediction of a signal peptide of the protein encoded from this site. The TISs-ST web server is freely available to both academic and commercial users and can be accessed at <url>http://ipe.cbmeg.unicamp.br/pub/TISs-ST</url>.</p> <p>Conclusion</p> <p>The program can be used to evaluate alternative translation initiation site consensus with user-specified sequences, based on their composition or on many position weight matrix models. TISs-ST provides analytical and visualization tools for evaluating the periodic frequency, the consensus pattern and the total information content of a sequence data set. A search option allows for the identification of signal peptides from predicted proteins using the PrediSi software.</p

Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies

Gene and SNP annotation are among the first and most important steps in analyzing a genome. As the number of sequenced genomes continues to grow, a key question is: how does the quality of the assembled sequence affect the annotations? We compared the gene and SNP annotations for two different Bos taurus genome assemblies built from the same data but with significant improvements in the later assembly. The same annotation software was used for annotating both sequences. While some annotation differences are expected even between high-quality assemblies such as these, we found that a staggering 40% of the genes (>9,500) varied significantly between assemblies, due in part to the availability of new gene evidence but primarily to genome mis-assembly events and local sequence variations. For instance, although the later assembly is generally superior, 660 protein coding genes in the earlier assembly are entirely missing from the later genome's annotation, and approximately 3,600 (15%) of the genes have complex structural differences between the two assemblies. In addition, 12–20% of the predicted proteins in both assemblies have relatively large sequence differences when compared to their RefSeq models, and 6–15% of bovine dbSNP records are unrecoverable in the two assemblies. Our findings highlight the consequences of genome assembly quality on gene and SNP annotation and argue for continued improvements in any draft genome sequence. We also found that tracking a gene between different assemblies of the same genome is surprisingly difficult, due to the numerous changes, both small and large, that occur in some genes. As a side benefit, our analyses helped us identify many specific loci for improvement in the Bos taurus genome assembly

Impact of progressive global warming on the global-scale yield of maize and soybean

Global surface temperature is projected to warm over the coming decades, with regional differences expected in temperature change, rainfall and the frequency of extreme events. Temperature is a major determinant of crop growth and development, affecting planting date, growing season length and yield. We investigated the effects of increments of mean global temperature warming from 0.5 °C to 4 °C on soybean and maize development and yield, both globally and for the main producing countries, and simulated adaptation through changing planting date and variety. Increasing temperature resulted in reduced growing season lengths and ultimately reduced yields for both crops. The global yield for maize decreased as temperature increased, although the severity of the decrease was dependent on geographic region. Small temperature increases of 0.5 °C had no effect on soybean yield, although yield decreased as temperature increased. These negative effects, however, were partly compensated for by the implementation of adaptation strategies including planting earlier in the season and changing variety. The degree of compensation was dependent on geographical area and crop, with maize adaptation delaying the negative effects of temperature on yield, compared to soybean adaptation which increased yield in China, India and Korea DPR as well as delaying the effects in the remaining countries. The results of this paper indicate the degree to which farmer-controlled adaptation strategies can alleviate the negative impacts of increasing temperature on two major crop species

Bright spots, physical activity investments that work : sweatcoin : a steps generated virtual currency for sustained physical activity behaviour change

Sweatcoin converts the step count recorded on smartphones into a virtual currency. Using this app, users generate financial rewards through physical activity, with higher levels of activity creating a higher ‘income’. Sweatcoins can subsequently be used to purchase commercially available products from an in-app marketplace