Estimating density of a forest-dwelling bat: a predictive model for Rafinesque’s big-eared bat

Data on species distribution and abundance are the foundation of population ecology. However, due to difficulties in surveying bats, abundance estimates for tree-roosting microchiropterans are non-existent. Therefore, our objective was to develop methods for estimating colony abundance and density, taking as our model Rafinesque’s big-eared bat Corynorhinus rafinesquii, a species of conservation concern found in cypress-gum swamps of the southeastern United States. We searched 123 transects at eight study sites in the Coastal Plain of Georgia, USA to locate and characterize diurnal summer roosts of C. rafinesquii. We modeled the relationship between the number of bat colonies and landscape-scale habitat variables with zero-inflated negative binomial regression and used Akaike’s information criterion to select the most parsimonious models. We generated a predictive density map to identify areas of high colony density and to estimate overall abundance. Colony density was predicted by the duration of wetland flooding, wetland width, and study site. Application of the regression model to a GIS indicated there were 3,734 colonies containing 6,910 adult bats on the eight study sites. Predicted density ranged from 0.07 colonies/ha and 0.07 adult bats/ha in saturated wetlands to 0.47 colonies/ha and 1.18 adult bats/ha in semi-permanently flooded wetlands. This study is the first to estimate density and abundance of forest-dwelling microchiropterans over a large area. Such data can serve as a baseline for future work on population trends in C. rafinesquii. In addition, our approach could be replicated for other bat species with moderately cryptic roosts.     

Core concepts of spatial prioritisation in systematic conservation planning

Systematic conservation planning (SCP) is a field of conservation biology concerned with delivering on‐the‐ground actions that achieve conservation goals. It describes a set of operational models that cover both design and implementation of conservation, with a strong focus on mobilising the collective action typically required to implement conservation. SCP, as it was originally described, was composed of six different stages: collection of data, identification of conservation goals, evaluation of the existing protected area network, design of expansions, implementation of conservation action, and long‐term maintenance of biodiversity in the network. Since then, the operational model has been expanded into several different variants. Conservation actions applied inside SCP include establishment and expansion of reserve networks and allocation of habitat restoration and management. Within the broader context of SCP, there is a fundamental biogeographic‐economic analysis frequently called spatial conservation prioritisation or conservation assessment, which is used for identifying where important areas for biodiversity are and how conservation goals might be achieved efficiently. Here, we review the usage and meaning of the 12 biogeographic‐economic core concepts of SCP: adequacy, complementarity, comprehensiveness, effectiveness, efficiency, flexibility, irreplaceability, replacement cost, representation, representativeness, threat, and vulnerability. Some of the concepts have clear definitions whereas others may have alternative and possibly conflicting definitions. With a comprehensive literature review literature, we elucidate the historical backgrounds of these concepts, the first definitions and usages, alternative later definitions, key applications, and prior reviews. This review reduces linguistic uncertainty in the application of SCP. Since SCP is a global activity with a multitude of different stakeholders involved, it is vital that those involved can speak the same language. Through these concepts, this review serves as a source of information about the historical development of SCP. It provides a comprehensive review for anyone wishing to understand the key concepts of spatial prioritisation within SCP.     

Evidence for interplay between genes and maternal stress in utero: monoamine oxidase A polymorphism moderates effects of life events during pregnancy on infant negative emotionality at 5 weeks

The low activity variant of the monoamine oxidase A (MAOA) functional promoter polymorphism, MAOA‐LPR, in interaction with adverse environments (G × E) is associated with child and adult antisocial behaviour disorders. MAOA is expressed during foetal development so in utero G × E may influence early neurodevelopment. We tested the hypothesis that MAOA G × E during pregnancy predicts infant negative emotionality soon after birth. In an epidemiological longitudinal study starting in pregnancy, using a two stage stratified design, we ascertained MAOA‐LPR status (low vs. high activity variants) from the saliva of 209 infants (104 boys and 105 girls), and examined predictions to observed infant negative emotionality at 5 weeks post‐partum from life events during pregnancy. In analyses weighted to provide estimates for the general population, and including possible confounders for life events, there was an MAOA status by life events interaction (P = 0.017). There was also an interaction between MAOA status and neighbourhood deprivation (P = 0.028). Both interactions arose from a greater effect of increasing life events on negative emotionality in the MAOA‐LPR low activity, compared with MAOA‐LPR high activity infants. The study provides the first evidence of moderation by MAOA‐LPR of the effect of the social environment in pregnancy on negative emotionality in infancy, an early risk for the development of child and adult antisocial behaviour disorders .     

Cu3P Binary Phosphide: Synthesis via a Wet Mechanochemical Method and Electrochemical Behavior as Negative Electrode Material for Lithium‐Ion Batteries

Mechanochemical synthesis of Cu₃P in the presence of n‐dodecane results in a material with a secondary particle size distribution of 10 μm, secondary particles which consist of homogeneously agglomerated 20 nm primary particles. The electrochemical performance of Cu₃P with lithium is influenced by the reaction depth, in other words by the lower potential cut‐off. During the electrochemical reaction, the displacement of copper by lithium from the Cu₃P structure until the formation of Li₃P and Cu deteriorates the capacity retention. Improved performance was obtained when the charge potential was limited to 0.50 V (vs. Li/Li⁺) and the formation of the Li_xCu_3‐xP phase (0 ≤ × ≤ 2). In this case, when the potential is limited to 0.5 V, the capacity is stable for more than 50 cycles. Acceptable electrochemical performances in Li‐ion cells within the voltage range 0.50–2.0 V (vs. Li/Li⁺) were shown when Cu₃P was used as an anode and Li_1.2(Ni_0.13Mn_0.54Co_0.13)O₂ and LiNi_0.5Mn_1.5O₄ as positive electrode materials.     

藜磷酸肌醇5-磷酸酶基因(CaP5P)的表达分析和胁迫响应检测

植物通过多种信号途径感知外界环境变化,从而引发一系列的信号级联反应,其中磷脂信号途径起着重要的作用。本研究从藜盐胁迫差减文库中获得了一个EST05序列,利用RT-PCR检测了其在非生物胁迫下表达趋势,显示EST05序列在非生物胁迫下的表达有升高。随后利用RACE技术获得其全长编码序列,测序结果显示其与蓖麻(Ricinus communis) 的磷酸肌醇5-磷酸酶基因(P5P)的同源性达56%,遂将其命名为CaP5P。最后过量表达CaP5P在拟南芥中初步验证了功能,转基因植株表现对盐胁迫耐受性降低的趋势,呈现负调控的特征。本研究对磷酸肌醇5-磷酸酶基因功能的初步研究为磷脂信号途径中负调控组分的分析提供了参考依据。     

Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis

Experiments that longitudinally collect RNA sequencing (RNA-seq) data can provide transformative insights in biology research by revealing the dynamic patterns of genes. Such experiments create a great demand for new analytic approaches to identify differentially expressed (DE) genes based on large-scale time-course count data. Existing methods, however, are suboptimal with respect to power and may lack theoretical justification. Furthermore, most existing tests are designed to distinguish among conditions based on overall differential patterns across time, though in practice, a variety of composite hypotheses are of more scientific interest. Finally, some current methods may fail to control the false discovery rate. In this paper, we propose a new model and testing procedure to address the above issues simultaneously. Specifically, conditional on a latent Gaussian mixture with evolving means, we model the data by negative binomial distributions. Motivated by Storey (2007) and Hwang and Liu (2010), we introduce a general testing framework based on the proposed model and show that the proposed test enjoys the optimality property of maximum average power. The test allows not only identification of traditional DE genes but also testing of a variety of composite hypotheses of biological interest. We establish the identifiability of the proposed model, implement the proposed method via efficient algorithms, and demonstrate its good performance via simulation studies. The procedure reveals interesting biological insights, when applied to data from an experiment that examines the effect of varying light environments on the fundamental physiology of the marine diatom Phaeodactylum tricornutum.     

Reduction of nuclear Y654-p-β-catenin expression through SH3GL2-meditated downregulation of EGFR in chemotolerance TNBC: Clinical and prognostic importance

Triple negative breast cancer (TNBC) originates from a less differentiated ductal cell of breast, which is less sensitive to chemotherapy. The chemotolerance mechanism of TNBC has not yet been studied in detail. For this reason, molecular profiles (expression/genetic/epigenetic) of Y654-p-β-catenin (active) and its kinase epidermal growth factor receptor (EGFR) along with SH3GL2 (regulator of EGFR homeostasis) were compared between neoadjuvant chemotherapy treated (NACT) and pretherapeutic TNBC samples. Reduced nuclear expression of Y654-p-β-catenin protein with low proliferation index and CD44 prevalence showed concordance with reduced expression of EGFR/Y1045-p-EGFR proteins in the NACT samples than the pretherapeutic TNBC samples. Infrequent messenger RNA expression, gene amplification (10–32.5%), and mutation (1%) of EGFR were seen in the TNBC samples irrespective of therapy, suggesting the importance of EGFR protein stabilization in this tumor. The upregulation of SH3GL2 seen in the NACT samples in contrast to the pretherapeutic samples might be due to its promoter hypomethylation, as seen in the quantitative methylation assay. A similar trend of upregulation of SH3GL2 and downregulation of EGFR, Y1045-p-EGFR, Y654-p-β-catenin were seen in the MDA-MB-231 cell line using antharacycline antitumor drugs (doxorubicin/nogalamycin). The NACT patients with reduced expression of Y654-p-β-catenin and/or EGFR and high expression of SH3GL2 showed comparatively better prognosis than the pretherapeutic patients. Thus, our study showed that reduced nuclear expression of Y654-p-β-catenin in NACT samples due to downregulation of EGFR protein through promoter hypomethylation-mediated upregulation of SH3GL2, resulting in low proliferation index/CD44 prevalence with better prognosis of the NACT patients, might have an important role in the chemotolerance of TNBC.     

Training of laboratory-housed non-human primates in the UK

Abstract

Laboratory-housed non-human primates may experience a range of potential stressors, including physical and chemical restraint, venepuncture, injection, catching and cage-change. Training them to co-operate, using positive reinforcement techniques, is one means of significantly reducing the adverse impact of such procedures upon them and, therefore, is a refinement. Furthermore, the additional time that staff spend with the primates, and the need for individual recognition and close observation of animal behavior, mean that the trainer develops a relationship with each individual animal which can be beneficial for animal welfare (e.g., by reducing the occurrence of abnormal behavior and fear of humans). We surveyed use of training in thirteen UK establishments using and breeding primates, utilizing a mixed-mode questionnaire. The survey demonstrated that there is widespread awareness of training as a refinement and appreciation of its diverse benefits, but training is not used as widely or as fully as it might be. This is largely due to real constraints (principally staff and time and a lack of confidence in ability to train), and perceived constraints (such as a supposed lack of information on how to train and assessment of the benefits, and an overestimation of the time investment needed). There is also considerable variation between establishments in the purposes of training and techniques used, with a reliance on negative reinforcement in three. We conclude that there is considerable scope for refinement of common scientific, veterinary and husbandry procedures, and refer to some resources designed to help establishments take action (e.g., Prescott and Buchanan-Smith 2003).