Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector anopheles arabiensis

Association mapping is a widely applied method for elucidating the genetic basis of phenotypic traits. However, factors such as linkage disequilibrium and levels of genetic diversity influence the power and resolution of this approach. Moreover, the presence of population subdivision among samples can result in spurious associations if not accounted for. As such, it is useful to have a detailed understanding of these factors before conducting association mapping experiments. Here we conducted whole-genome sequencing on 24 specimens of the malaria mosquito vector, Anopheles arabiensis, to further understanding of patterns of genetic diversity, population subdivision and linkage disequilibrium in this species. We found high levels of genetic diversity within the An. arabiensis genome, with ~800,000 high-confidence, single- nucleotide polymorphisms detected. However, levels of nucleotide diversity varied significantly both within and between chromosomes. We observed lower diversity on the X chromosome, within some inversions, and near centromeres. Population structure was absent at the local scale (Kilombero Valley, Tanzania) but detected between distant populations (Cameroon vs. Tanzania) where differentiation was largely restricted to certain autosomal chromosomal inversions such as 2Rb. Overall, linkage disequilibrium within An. arabiensis decayed very rapidly (within 200 bp) across all chromosomes. However, elevated linkage disequilibrium was observed within some inversions, suggesting that recombination is reduced in those regions. The overall low levels of linkage disequilibrium suggests that association studies in this taxon will be very challenging for all but variants of large effect, and will require large sample sizes

A 17O Paramagnetic NMR Study of Sm2O3, Eu2O3, and Sm-/Eu- Substituted CeO2

Paramagnetic solid-state NMR of lanthanide (Ln) containing materials can be challenging due to the high electron spin states possible for the Ln f electrons, which result in large paramagnetic shifts, and these difficulties are compounded for 17O due to the low natural abundance and quadrupolar character. In this work, we present examples of 17O NMR experiments for lanthanide oxides and strategies to overcome these difficulties. In particular, we record and assign the 17O NMR spectra of monoclinic Sm2O3 and Eu2O3 for the first time, as well as performing density functional theory (DFT) calculations to gain further insight into the spectra. The temperature dependence of the Sm3+ and Eu3+ magnetic susceptibilities are investigated by measuring the 17O shift of the cubic sesquioxides over a wide temperature range, which reveal non-Curie temperature dependence due to the presence of low-lying electronic states. This behaviour is reproduced by calculating the electron spin as a function of temperature, yielding shifts which agree well with the experimental values. Using the understanding of the magnetic behaviour gained from the sesquioxides, we then explore the local oxygen environments in 15 at% Sm- and Eu-substituted CeO2, with the 17O NMR spectrum exhibiting signals due to environments with zero, one and two nearest neighbour Ln ions, as well as further splitting due to oxygen vacancies. Finally, we extract an activation energy for oxygen vacancy motion in these systems of 0.35 ± 0.02 eV from the Arrhenius temperature dependence of the 17O T1 relaxation constants, which is found to be independent of the Ln ion within error. The relation of this activation energy to literature values for oxygen diffusion in Ln-substituted CeO2 is discussed to infer mechanistic information which can be applied to further develop these materials as solid-state oxide-ion conductors.Oppenheimer Foundation. NECCES, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award No. DE-SC0012583. Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility Scientific Data and Computing Center, a component of the Computational Science Initiative, at Brookhaven National Laboratory, under Contract No. DE-SC001270

BCL-W has a fundamental role in B cell survival and lymphomagenesis.

Compromised apoptotic signaling is a prerequisite for tumorigenesis. The design of effective therapies for cancer treatment depends on a comprehensive understanding of the mechanisms that govern cell survival. The antiapoptotic proteins of the BCL-2 family are key regulators of cell survival and are frequently overexpressed in malignancies, leading to increased cancer cell survival. Unlike BCL-2 and BCL-XL, the closest antiapoptotic relative BCL-W is required for spermatogenesis, but was considered dispensable for all other cell types. Here, however, we have exposed a critical role for BCL-W in B cell survival and lymphomagenesis. Loss of Bcl-w conferred sensitivity to growth factor deprivation-induced B cell apoptosis. Moreover, Bcl-w loss profoundly delayed MYC-mediated B cell lymphoma development due to increased MYC-induced B cell apoptosis. We also determined that MYC regulates BCL-W expression through its transcriptional regulation of specific miR. BCL-W expression was highly selected for in patient samples of Burkitt lymphoma (BL), with 88.5% expressing BCL-W. BCL-W knockdown in BL cell lines induced apoptosis, and its overexpression conferred resistance to BCL-2 family-targeting BH3 mimetics. Additionally, BCL-W was overexpressed in diffuse large B cell lymphoma and correlated with decreased patient survival. Collectively, our results reveal that BCL-W profoundly contributes to B cell lymphoma, and its expression could serve as a biomarker for diagnosis and aid in the development of better targeted therapies

Police, public, and offender perceptions of body-worn video: a single jurisdictional multiple-perspective analysis

Objectives. Police, public, and offender survey responses from a single jurisdiction give a multiple-perspective insight into the use of body-worn video (BWV) cameras by police. Methods. Police attitudinal data was collected from before (n = 190), during (n = 139), and at the conclusion (n = 221) of a BWV implementation trial. Public attitudes were collected at the conclusion of the BWV implementation trial via online survey (n = 995 respondents) and intercept survey (n = 428 respondents). Offender attitudes (n = 302) were collected in police custody over a 6-month period immediately preceding the BWV trial. Results. The extent to which police felt BWV influenced their behavior tempered during the trial. All three perspectives were supportive of the use of BWV. The public who had encountered BWV-wearing officers and the offender sample indicated limited belief that BWV would reduce bad behavior. There was also clear contention about the policy and practice decisions around recording. Conclusions. These findings have significance for BWV trials, commenting on the importance of (a) collecting police attitudes at multiple points, (b) separating the attitudes of public who did encounter police wearing BWV, and (c) data collection and policy for evaluation outcomes

Salmonella flagellin activates NAIP/NLRC4 and canonical NLRP3 inflammasomes in human macrophages

Infection of human macrophages with Salmonella enterica serovar Typhimurium (S. Typhimurium) leads to inflammasome activation. Inflammasomes are multi-protein complexes facilitating caspase–1 activation and subsequent gasdermin D-mediated cell death and interleukin–1β and interleukin–18 cytokine release. The NAIP/NLRC4 inflammasome is activated by multiple bacterial protein ligands including flagellin from the flagellum and the needle protein PrgI from the S. Typhimurium type III secretion system. Here we show that transfected ultrapure flagellin from S. Typhimurium induced cell death and cytokine secretion in THP–1 cells and primary human monocyte-derived macrophages (hMDM). In THP–1 cells, NAIP/NLRC4 and NLRP3 played redundant roles in inflammasome activation during infection with S. Typhimurium. Knock-out of NAIP or NLRC4 in THP–1 cells revealed that flagellin, but not PrgI, now activated the NLRP3 inflammasome through a ROS- and/or cathepsin-dependent mechanism that was independent of caspase–4/5 activity. In conclusion, our data suggest that NLRP3 can be activated by flagellin to act as a “safety net” to maintain inflammasome activation under conditions of suboptimal NAIP/NLRC4 activation, as observed in THP–1 cells, possibly explaining the redundant role of NLRP3 and NAIP/NLRC4 during S. Typhimurium infection.Wellcome Trus

The effects of climatic fluctuations and extreme events on running water ecosystems

Most research on the effects of environmental change in freshwaters has focused on incremental changes in average conditions, rather than fluctuations or extreme events such as heatwaves, cold snaps, droughts, floods or wildfires, which may have even more profound consequences. Such events are commonly predicted to increase in frequency, intensity and duration with global climate change, with many systems being exposed to conditions with no recent historical precedent. We propose a mechanistic framework for predicting potential impacts of environmental fluctuations on running water ecosystems by scaling up effects of fluctuations from individuals to entire ecosystems. This framework requires integration of four key components: effects of the environment on individual metabolism, metabolic and biomechanical constraints on fluctuating species interactions, assembly dynamics of local food webs and mapping the dynamics of the meta-community onto ecosystem function. We illustrate the framework by developing a mathematical model of environmental fluctuations on dynamically assembling food webs. We highlight (currently limited) empirical evidence for emerging insights and theoretical predictions. For example, widely supported predictions about the effects of environmental fluctuations are: high vulnerability of species with high per capita metabolic demands such as large-bodied ones at the top of food webs; simplification of food web network structure and impaired energetic transfer efficiency; reduced resilience and top-down relative to bottom-up regulation of food web and ecosystem processes. We conclude by identifying key questions and challenges that need to be addressed to develop more accurate and predictive bio-assessments of the effects of fluctuations, and implications of fluctuations for management practices in an increasingly uncertain world

Studying changes in the practice of two teachers developing assessment for learning

This paper describes changes in the practice of two teachers, observed over an eighteen month period, who were participating in a study intended to support teachers in developing their use of assessment in support of learning. The design of the intervention allowed each teacher to choose for themselves which aspects of their practice to develop. Analysis of lesson observations, journal entries and interviews indicate that both teachers were keen to change their practice, but were concerned about the disruption to their established routines, and in particular about the potential for loss of control of their classes. Both teachers did effect significant changes in their classrooms, but these tended to be developments of existing preferred ways of working, rather than radical innovations. In conclusion, it is suggested that to be most effective, teacher professional development needs to be structured strongly enough to afford teacher growth, but flexible enough to allow different teachers to take their practice in different ways

Simultaneous non-negative matrix factorization for multiple large scale gene expression datasets in toxicology

Non-negative matrix factorization is a useful tool for reducing the dimension of large datasets. This work considers simultaneous non-negative matrix factorization of multiple sources of data. In particular, we perform the first study that involves more than two datasets. We discuss the algorithmic issues required to convert the approach into a practical computational tool and apply the technique to new gene expression data quantifying the molecular changes in four tissue types due to different dosages of an experimental panPPAR agonist in mouse. This study is of interest in toxicology because, whilst PPARs form potential therapeutic targets for diabetes, it is known that they can induce serious side-effects. Our results show that the practical simultaneous non-negative matrix factorization developed here can add value to the data analysis. In particular, we find that factorizing the data as a single object allows us to distinguish between the four tissue types, but does not correctly reproduce the known dosage level groups. Applying our new approach, which treats the four tissue types as providing distinct, but related, datasets, we find that the dosage level groups are respected. The new algorithm then provides separate gene list orderings that can be studied for each tissue type, and compared with the ordering arising from the single factorization. We find that many of our conclusions can be corroborated with known biological behaviour, and others offer new insights into the toxicological effects. Overall, the algorithm shows promise for early detection of toxicity in the drug discovery process

Inflammasome activation causes dual recruitment of NLRC4 and NLRP3 to the same macromolecular complex.

Pathogen recognition by nucleotide-binding oligomerization domain-like receptor (NLR) results in the formation of a macromolecular protein complex (inflammasome) that drives protective inflammatory responses in the host. It is thought that the number of inflammasome complexes forming in a cell is determined by the number of NLRs being activated, with each NLR initiating its own inflammasome assembly independent of one another; however, we show here that the important foodborne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) simultaneously activates at least two NLRs, whereas only a single inflammasome complex is formed in a macrophage. Both nucleotide-binding domain and leucine-rich repeat caspase recruitment domain 4 and nucleotide-binding domain and leucine-rich repeat pyrin domain 3 are simultaneously present in the same inflammasome, where both NLRs are required to drive IL-1β processing within the Salmonella-infected cell and to regulate the bacterial burden in mice. Superresolution imaging of Salmonella-infected macrophages revealed a macromolecular complex with an outer ring of apoptosis-associated speck-like protein containing a caspase activation and recruitment domain and an inner ring of NLRs, with active caspase effectors containing the pro-IL-1β substrate localized internal to the ring structure. Our data reveal the spatial localization of different components of the inflammasome and how different members of the NLR family cooperate to drive robust IL-1β processing during Salmonella infection.S.M.M was supported by a Cambridge International Scholarship. T.P.M was supported by a Wellcome Trust Research Career Development Fellowship (WT085090MA). This study was supported by Biotechnology and Biological Sciences Research Council (BBSRC) grants (BB/H003916/1 and BB/K006436/1) and a BBSRC Research Development Fellowship (BB/H021930/1) awarded to C.E.B.http://www.pnas.org/content/early/2014/05/05/1402911111.abstrac