Neutral space analysis for a Boolean network model of the fission yeast cell cycle network

Background

Interactions between genes and their products give rise to complex circuits known as gene regulatory networks (GRN) that enable cells to process information and respond to external stimuli. Several important processes for life, depend of an accurate and context-specific regulation of gene expression, such as the cell cycle, which can be analyzed through its GRN, where deregulation can lead to cancer in animals or a directed regulation could be applied for biotechnological processes using yeast. An approach to study the robustness of GRN is through the neutral space. In this paper, we explore the neutral space of a Schizosaccharomyces pombe (fission yeast) cell cycle network through an evolution strategy to generate a neutral graph, composed of Boolean regulatory networks that share the same state sequences of the fission yeast cell cycle.

Results

Through simulations it was found that in the generated neutral graph, the functional networks that are not in the wildtype connected component have in general a Hamming distance more than 3 with the wildtype, and more than 10 between the other disconnected functional networks. Significant differences were found between the functional networks in the connected component of the wildtype network and the rest of the network, not only at a topological level, but also at the state space level, where significant differences in the distribution of the basin of attraction for the G₁ fixed point was found for deterministic updating schemes.

Conclusions

In general, functional networks in the wildtype network connected component, can mutate up to no more than 3 times, then they reach a point of no return where the networks leave the connected component of the wildtype. The proposed method to construct a neutral graph is general and can be used to explore the neutral space of other biologically interesting networks, and also formulate new biological hypotheses studying the functional networks in the wildtype network connected component.     

Time-budgeting and foraging strategy of the stoplight parrotfish Sparisoma viride Bonnaterre,in Jamaica

Quantitative data on the ways in which the different phases of the stoplight parrotfish (Sparisomaviride Bonnaterre) distribute their time among various activities in different habitats are presented. Individuals spent from 84–97% of their diurnal time swimming, feeding, and hovering. Additionally, large adults spent a significant amount of time sheltering among crevices. Phase-related differences in these activities are statistically significant, as are differences in duration and rates of change of the activities. Large individuals spent more time swimming, while small individuals spent more time hovering. In addition, large individuals performed longer bouts of activity and switched activities less frequently than small individuals. Adult males and females spent approximately equal proportions of time in each of the activity states. Stochastic analyses of behavioural sequences show second order Markov chain dependencies, suggesting that preceding activity states affect subsequent behaviour. Possible relationships between behavioural sequencing and the species foraging strategy are discussed, and it is suggested that the sequence of behavioural activities can provide an estimation of the distribution of food resources in the environment.     

四川白水河国家级大熊猫自然保护区生态旅游发展战略研究

通过对白水河国家级自然保护区生态旅游资源的参与式调查与评估,确定了白水河生态旅游的可行的优先区域,比选出本区生态旅游资源特色,提出了白水河生态旅游“以大熊猫栖息地探秘、观鸟、生态教育与体验为核心的生态旅游目的地”的主题定位,以及“飞来的大熊猫原生栖息地”等形象定位,以及生态旅游活动布局,价格策略、营销策略、管理策略等战略。     

Potential causes and life-history consequences of sexual size dimorphism in mammals

1. Male-biased sexual size dimorphism (SSD) in mammals has been explained by sexual selection favouring large, competitive males. However, new research has identified other potential factors leading to SSD. The aim of this review is to evaluate current research on the causes of SSD in mammals and to investigate some consequences of SSD, including costs to the larger sex and sexual segregation. 2. While larger males appear to gain reproductive benefits from their size, studies have also identified alternative mating strategies, unexpected variance in mating success and found no clear relationship between degree of polygyny and dimorphism. This implies that sexual selection is unlikely to be the single selective force directing SSD. 3. Latitude seems to influence SSD primarily through variation in overall body size and seasonal food availability, which affect potential for polygyny. Likewise, population density influences resource availability and evidence suggests that food scarcity differentially constrains the growth of the sexes. Diverging growth patterns between the sexes appear to be the primary physiological mechanism leading to SSD. 4. Female-biased dimorphism is most adequately explained by reduced male–male competition resulting in a decrease in male size. Female–female competition for dominance and resources, including mates, may also select for increased female size. 5. Most studies found that sexual segregation arises through asynchrony of activity budgets between the sexes. The larger sex can suffer sex-biased mortality through increased parasite load, selective predation and the difficulty associated with sustaining a larger body size under conditions of resource scarcity. 6. None of the variables considered here appears to contribute a disproportionate amount to SSD in mammals. Several promising avenues of research are currently overlooked and long-term studies, which have previously been biased toward ungulates, should be carried out on a variety of taxa.     

生物多样性相关传统知识的国际保护及中国应对策略

数个国际多边协定、政府间组织和机构都涉及生物多样性相关的传统知识, 包括《生物多样性公约》(CBD)、关于遗传资源获取与惠益分享的《名古屋议定书》(NP)、《粮食和农业植物遗传资源国际条约》(ITPGRFA)、世界知识产权组织(WIPO)、世贸组织下的《与贸易相关的知识产权协定》(WTO/TRIPS)以及生物多样性与生态系统服务政府间科学-政策平台(IPBES)等。然而, 各个国际文书所界定的传统知识内涵和外延却有所区别和侧重。中国是生物多样性极为丰富的多民族大国, 各族人民在数千年的生产和生活实践中创造了丰富的与保护和持续利用生物遗传资源相关的传统知识、创新和实践做法。作为多个相关国际公约或协定的缔约方, 中国应厘清各相关国际公约或协定中生物多样性相关传统知识的内涵、保护目标及国际义务, 加强国家在履行相关国际公约或协定过程中的协同增效, 从而在相关传统知识的国际谈判中统一立场, 维护国家及地方社区利益。本文系统梳理了各相关国际多边协定、组织和机构对于传统知识的界定, 以及国际多边体系在保护遗传资源相关传统知识方面的工作, 根据中国遗传资源相关传统知识的现状和已有的措施, 结合当前履行国际多边协定的大背景, 提出了促进中国生物多样性相关传统知识保护的5项具体建议, 包括: (1)采取立法、行政和政策措施; (2)加强相关研究, 强化技术支撑; (3)加强传统知识保护的能力建设; (4)在国内履约过程中, 强化传统知识相关工作的协调; (5)在国际层面上加强中国传统知识的宣传力度。     

Effects of starvation on death‐feigning in adult Eucryptorrhynchus brandti (Coleoptera: Curculionidae)

In insects, death‐feigning is an effective defence strategy. Eucryptorrhynchus brandti, a major borer pest in China, has a weak flight ability and exhibits obvious death‐feigning behaviour when disturbed. Despite a large number of studies of its biological and ecological properties as well as control methods, the death‐feigning behaviour has not been specifically described. In laboratory conditions, we recorded the survival rate under starvation and feeding conditions and evaluated the effect of starvation on the duration and occurrence of death‐feigning. In a continuous experiment, we examined variation in the death‐feigning duration every day over 7 day. Then, we evaluated the effects of starvation for 3, 6 and 9 day in a non‐continuous experiment and further observed variation in the death‐feigning intensity. We found that starvation significantly affected the survival rate. Survival time was significantly longer in the starvation group than in the feeding group, and females had longer survival times than males (female: 14 day, male: 8 day). In the continuous experiment, starved E. brandti had the longest duration of death‐feigning at 2 day, followed by a significant decrease. In the non‐continuous experiment, the duration and proportion of death‐feigning decreased significantly as the duration of starvation increased and were significantly lower than feeding. These observations suggest that starvation is a non‐negligible factor in the death‐feigning behaviour of E. brandti adults, facilitating the interpretation of future ecological and behavioural data of thanatosis.     

基于区域剖分算法的土壤碳通量空间采样策略

由于土壤碳通量在空间分布上具有很强的异质性,传统的采样方法难以对区域土壤碳通量进行精确估算,因此确定适当的采样策略对区域土壤碳通量的估算具有重要意义.本文提出一种逐点递增式采样的区域剖分部署策略(RDPG):设定初始采样点,使用改进的凸包插值算法构造Delaunay三角网,根据邻近已知采样点插值计算三角形各边垂直平分线的交点的离散度,选择离散度最大的点作为新增采样点.采用该方法对变异系数为0.42～0.59的仿真试验区域进行多次试验,结果表明:在相同试验条件下,RDPG布局策略能够获得比随机采样和均匀采样策略更高的区域土壤碳通量估算准确度.RDPG方法考虑了区域土壤碳通量的空间异质性,提高了区域土壤碳通量拟合精度.     

Critical threshold meal size and molt initiation in Rhodnius prolixus

The molting process and body growth in Rhodnius prolixus (Hemiptera: Reduviidae) (Ståhl, 1859) are significantly influenced by the availability and quality of food. Based on the body weight of each stage, the present study provides estimates of a potential critical weight threshold required for molt initiation in R. prolixus. In addition, a new measure given by the area under the weight curve is proposed, which encapsulates both body weight and time. It is shown that this measure is consistent with the data, and allows the estimation of a pre‐refractory period (i.e. the time interval between the moment at which the critical weight threshold is reached and the moment when no further meals are accepted). The present analysis estimates the critical weight threshold as 1.6, 5.3, 12.9, 42.0 and 97.0 mg for stages 1–5, respectively, whereas the values of the area under the curve threshold as 5, 16, 31.2, 159.7 and 329.9 mg days for stages 1–5, respectively. The results of the present study confirm the existence of a weight‐dependent mechanism for the initiation of molting in R. prolixus.     

应用球孢白僵菌防治马尾松毛虫的策略及其生物多样性基础的研究

对３种不同方式应用球孢白僵菌防治马尾松毛虫的结果表明,３个林场的虫口在连续４年内均被抑制在低水平,但松毛虫种群动态不同：以淹没式施放白僵菌为主,但有时也淹没式施放化学杀虫剂的麻姑山林场平均虫口密度为３．１６±４．９４条·株－１,波动最大;长期接种式应用白僵菌的戴公山林场平均虫口密度只有０．０９±０．１４条·株－１,一直处于低密度状态;以化学农药处理小面积虫源地结合不频繁地淹没式施放白僵菌的金寺山林场平均虫口密度为１．４５±２．２９条·株－１,偶可达防治指标．对群落组成的调查结果表明,从麻姑山、金寺山到戴公山,动物和虫生真菌群落各物种的总个体数递减,而总物种数、总物种数与总个体数的比值,天敌与害虫种数和个体数的比值以及群落多样性指数皆递增,表明群落多样性渐趋丰富,食物链网渐趋复杂,群落稳定性和对害虫的自然控制能力逐渐增强．对群落动态的主成分分析进一步表明,从麻姑山、金寺山到戴公山,动物和虫生真菌群落的演化时序分明,趋于稳定,自我调节力强．     

Assessing age,breeding stage,and mating activity as drivers of variation in the reproductive microbiome of female tree swallows

Sexually transmitted microbes are hypothesized to influence the evolution of reproductive strategies. Though frequently discussed in this context, our understanding of the reproductive microbiome is quite nascent. Indeed, testing this hypothesis first requires establishing a baseline understanding of the temporal dynamics of the reproductive microbiome and of how individual variation in reproductive behavior and age influence the assembly and maintenance of the reproductive microbiome as a whole. Here, we ask how mating activity, breeding stage, and age influence the reproductive microbiome. We use observational and experimental approaches to explain variation in the cloacal microbiome of free‐living, female tree swallows (Tachycineta bicolor). Using microsatellite‐based parentage analyses, we determined the number of sires per brood (a proxy for female mating activity). We experimentally increased female sexual activity by administering exogenous 17ß‐estradiol. Lastly, we used bacterial 16S rRNA amplicon sequencing to characterize the cloacal microbiome. Neither the number of sires per brood nor the increased sexual activity of females significantly influenced female cloacal microbiome richness or community structure. Female age, however, was positively correlated with cloacal microbiome richness and influenced overall community structure. A hypothesis to explain these patterns is that the effect of sexual activity and the number of mates on variation in the cloacal microbiome manifests over an individual''s lifetime. Additionally, we found that cloacal microbiome alpha diversity (Shannon Index, Faith''s phylogenetic distance) decreased and community structure shifted between breeding stages. This is one of few studies to document within‐individual changes and age‐related differences in the cloacal microbiome across successive breeding stages. More broadly, our results contribute to our understanding of the role that host life history and behavior play in shaping the cloacal microbiomes of wild birds.