断尾对胎生蜥蜴运动能力和选择体温的影响

尾自切是蜥蜴为了降低被捕食危险而采取的一种反捕食适应策略,但断尾可导致体重减轻、热量收支平衡改变,并影响蜥蜴的运动能力和体温调节.为检验断尾对蜥蜴运动能力和选择体温的影响,于2006年5月选取黑龙江省小兴安岭地区的一个胎生蜥蜴种群进行实验.结果表明:在30 ℃和24℃两个实验温度下,断尾后胎生蜥蜴的运动能力均明显下降,表现在停顿次数增多、最大可持续距离和最大疾跑速度减少等方面;断尾、温度和性别对胎生蜥蝎运动能力的影响在一定程度上是相互独立的,断尾是影响胎生蜥蜴运动能力的主要因素;断尾对胎生蜥蝎的选择体温没有显著影响.     

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.     

One-step targeted maximum likelihood estimation for time-to-event outcomes

Researchers in observational survival analysis are interested in not only estimating survival curve nonparametrically but also having statistical inference for the parameter. We consider right-censored failure time data where we observe n independent and identically distributed observations of a vector random variable consisting of baseline covariates, a binary treatment at baseline, a survival time subject to right censoring, and the censoring indicator. We assume the baseline covariates are allowed to affect the treatment and censoring so that an estimator that ignores covariate information would be inconsistent. The goal is to use these data to estimate the counterfactual average survival curve of the population if all subjects are assigned the same treatment at baseline. Existing observational survival analysis methods do not result in monotone survival curve estimators, which is undesirable and may lose efficiency by not constraining the shape of the estimator using the prior knowledge of the estimand. In this paper, we present a one-step Targeted Maximum Likelihood Estimator (TMLE) for estimating the counterfactual average survival curve. We show that this new TMLE can be executed via recursion in small local updates. We demonstrate the finite sample performance of this one-step TMLE in simulations and an application to a monoclonal gammopathy data.     

Contrasting sensitivity of nestling and fledgling Barn Swallow Hirundo rustica body mass to local weather conditions

Local weather can influence the growth and development of young birds either indirectly, by modifying prey availability, or directly, by affecting energetic trade-offs. Such effects can have lasting implications for life history traits, but the nature of these effets may vary with the developmental stage of the birds, and over timescales from days to weeks. We examined the interactive effects of temperature, rainfall and wind speed on the mass of nestling and fledgling Barn Swallows Hirundo rustica both on the day of capture and averaging weather across the time since hatching. At the daily timescale, nestling mass was negatively correlated with temperature, but the strength of this association depended on the level of rainfall and wind speed; nestlings were typically heavier on dry or windy days, and the negative effect of temperature was strongest under calm or wet conditions. At the early lifetime timescale (i.e. from hatching to pre-fledging), nestling mass was negatively correlated with temperature at low wind speed. Fledgling body mass was less sensitive to weather; the only weather effect evident was a negative correlation with temperature at the daily scale under high rainfall that became slightly positive under low rainfall. These changes are consistent with weather effects on the availability and distribution of insects within the landscape (e.g. causing high concentrations of flying insects) and with the effects of weather variation on nest microclimate. These results together demonstrate the impacts of weather on chick growth, over immediate (daily) and longer term (nestling/fledgling lifetime) timescales. This shows that sensitivity to local weather conditions varies across the early lifetime of young birds (nestling–fledgling stages) and illustrates the mechanisms by which larger scale (climate) variations influence the body condition of individuals.     

染色质重塑调控生物温度适应性的研究进展

温度是限制物种适应性分布的重要环境因子,对极端环境温度的耐受性决定生物分布和扩散范围,而表观遗传可以提供快速的响应机制,促使生物快速适应极端环境温度。染色质重塑作为表观遗传的重要组成部分之一,其可以通过调控胁迫相关基因的表达从而促进生物适应不良环境条件。本文主要阐述了染色质重塑复合物的分类、组成和染色质重塑的方式,梳理了染色质重塑在生物温度适应性中的研究进展,提出染色质重塑在生物适应不良环境温度过程中发挥重要作用,并对未来染色质重塑与温度适应性研究提出建议。     

Interaction between eggshell temperature and carbon dioxide concentration after day 8 of incubation on broiler chicken embryo development

Carbon dioxide (CO₂) is considered to be an important factor during incubation of eggs. Effects attributed to higher CO₂ concentrations during experiment might be due to confounding effects of other environmental conditions, such as incubation temperature. To disentangle effects of eggshell temperature (EST) and CO₂ concentration, an experiment was conducted. A total of 630 Cobb 500 hatching eggs from 37 to 45 wk commercial breeder flocks were collected and incubated according to treatments. The experiment was setup as a complete randomized 2 × 3 factorial design, resulting in 6 treatments. From day 8 of incubation onward, broiler eggs were exposed to one of two EST (37.8 or 38.9 °C) and one of three CO₂ concentrations (0.1, 0.4 or 0.8%). Eggs were incubated in climate-respiration chambers and metabolic heat production was determined continuously. At day 18 of incubation and at 6 h after hatching, embryo and chicken quality were determined by evaluation of organ weights, navel condition, blood metabolites and hepatic glycogen. Hatching time and chicken length at 6 h after hatching showed an interaction between EST and CO₂ concentration (both P = 0.001). Furthermore, no effect of CO₂ concentration was found on embryo development or chicken quality. Metabolic heat production between day 8 and 18 of incubation was not affected by either EST or CO₂. At day 18 of incubation, an EST of 38.9 °C resulted in a higher egg weight loss, longer embryos, higher yolk free body mass (YFBM) and lower heart weight than an EST of 37.8 °C (all P < 0.008). At 6 h after hatching, an EST of 38.9 °C resulted in a higher residual yolk weight and lower YFBM, liver weight and heart weight than an EST of 37.8 °C (all P < 0.003). Lactate, uric acid and hepatic glycogen were not affected by EST at either day 18 of incubation or at hatch. Glucose was not affected by EST at day 18 of incubation, but at hatch, it was higher at an EST of 37.8 °C than at an EST of 38.9 °C (P = 0.02). It can be concluded that effects of CO₂ concentration (at concentrations ≤0.8%) on embryonic development and chicken quality appear to be limited when EST is maintained at a constant level. Moreover, a higher EST from day 8 of incubation onward appears to negatively affect chicken quality at hatch.     

Effects of Different Ambient Temperatures on Caecal Microbial Composition in Broilers

Short-term or acute temperature stress affect the immune responses and alters the gut microbiota of broilers, but the influences of long-term temperature stress on stress biomarkers and the intestinal microbiota remains largely unknown. Therefore, we examined the effect of three long-term ambient temperatures (high (HC), medium (MC), and low (LC) temperature groups) on the gene expression of broilers’ heat shock proteins (Hsps) and inflammation – related genes, as well as the caecal microbial composition. The results revealed that Hsp70 and Hsp90 levels in HC group significantly increased, and levels of Hsp70, Hsp90, IL-6, TNF-α, and NFKB1 in LC group were significantly higher than in MC group (p < 0.05). In comparison with the MC group, the proportion of Firmicutes increased in HC and LC groups, while that of Bacteroidetes decreased in LC group at phylum level (p < 0.05). At genus level, the proportion of Escherichia/Shigella, Phascolarctobacterium, Parabacteroides,and Enterococcus increased in HC group; the fraction of Faecalibacterium was higher in LC group; and the percentage of Barnesiella and Alistipes decreased in both HC and LC groups (p < 0.05). Functional analysis based on communities’ phylogenetic investigation revealed that the pathways involved in environmental information processing and metabolism were enriched in the HC group. Those involved in cellular processes and signaling, metabolism, and gene regulation were enriched in LC group. Hence, we conclude that the long-term temperature stress can greatly alter the intestinal microbial communities in broilers and may further affect the host’s immunity and health.     

草菇低温胁迫初期应答关键通路的探究

本研究利用表达谱芯片技术解析了低温胁迫初期（0-120min）不同低温处理时间草菇转录组水平的变化。芯片结果分析发现在低温诱导过程中,低温处理20min内变化基因的功能为单加氧酶、氧化还原酶和细胞内的氧化还原。低温处理40min时表达差异基因具有结合RNA的功能。80min的时间段内,基因的功能比较集中于核酸物质和能量的代谢。CYP450的代谢途径在20-40min、60-80min和100-120min低温处理的菌丝体中均有显著性变化,表明这一通路在草菇低温处理过程中表现活跃。基因表达趋势分析发现34个表达差异基因富集到显著表达趋势模型,基因共表达网络分析发现VVO_04066位于网络的核心地位,推测VVO_04066通过提高磷酸肌醇特异性磷脂酶C（PI-PLC）的胞内水平,促进糖蛋白和几丁质的合成,从而完成草菇细胞的低温胁迫应答。