New features of the cell wall of the radio-resistant bacterium Deinococcus radiodurans

We have analyzed the cell wall of the radio-resistant bacterium Deinococcus radiodurans. Unexpectedly, the bacterial envelope appears to be organized in different complexes of high molecular weight. Each complex is composed of several proteins, most of which are coded by genes of unknown function and the majority are constituents of the inner/outer membrane system. One of the most abundant complexes is constituted by the gene DR_0774. This protein is a type of secretin which is a known subunit of the homo-oligomeric channel that represents the main bulk of the type IV piliation family. Finally, a minor component of the pink envelope consists of several inner-membrane proteins. The implications of these findings are discussed.     

FDR control by the BH procedure for two-sided correlated tests with implications to gene expression data analysis

The multiple testing problem attributed to gene expression analysis is challenging not only by its size, but also by possible dependence between the expression levels of different genes resulting from coregulations of the genes. Furthermore, the measurement errors of these expression levels may be dependent as well since they are subjected to several technical factors. Multiple testing of such data faces the challenge of correlated test statistics. In such a case, the control of the False Discovery Rate (FDR) is not straightforward, and thus demands new approaches and solutions that will address multiplicity while accounting for this dependency. This paper investigates the effects of dependency between bormal test statistics on FDR control in two-sided testing, using the linear step-up procedure (BH) of Benjamini and Hochberg (1995). The case of two multiple hypotheses is examined first. A simulation study offers primary insight into the behavior of the FDR subjected to different levels of correlation and distance between null and alternative means. A theoretical analysis follows in order to obtain explicit upper bounds to the FDR. These results are then extended to more than two multiple tests, thereby offering a better perspective on the effect of the proportion of false null hypotheses, as well as the structure of the test statistics correlation matrix. An example from gene expression data analysis is presented.     

低压舱模拟飞行对于脑力负荷影响的初步探讨

目的：通过低压舱模拟飞行环境下被试人员生理指标的变化,探讨飞行员脑力负荷的变化规律。方法：21名男性志愿者参加低压舱模拟飞行的实验过程,座舱内的压力高度模拟2400米高空压力,持续时间1．5h,重复两次,中间出舱休息0．5h,检测指标为心率变异性（HRV）,心理运动测验以及NASA—TLX主观评定量表。结果：研究表明,NASA－TLX量表从主观感受上很好的反映了低压舱模拟飞行后脑力负荷的变化,HRV、心理运动测验也发生了相应的变化。结论：本研究结果提示低压舱模拟飞行所导致的脑力负荷变化是具有一定规律的,生理心理测验可能是测定变化规律的一种间接方法。     

Organisms and responses to environmental change

There is great concern currently over environmental change and the biotic responses, actual or potential, to that change. There is also great concern over biodiversity and the observed losses to date. However, there has been little focus on the diversity of potential responses that organisms can make, and how this would influence both the focus of investigation and conservation efforts. Here emphasis is given to broad scale approaches, from gene to ecosystem and where a better understanding of diversity of potential response is needed. There is a need for the identification of rare, key or unique genomes and physiologies that should be made priorities for conservation because of their importance to global biodiversity. The new discipline of conservation physiology is one aspect of the many ways in which organismal responses to environmental variability and change can be investigated, but wider approaches are needed. Environmental change, whether natural or human induced occurs over a very wide range of scales, from nanometres to global and seconds to millennia. The processes involved in responses also function over a wide range of scales, from the molecular to the ecosystem. Organismal responses to change should be viewed in these wider frameworks. Within this overall framework the rate of change of an environmental variable dictates which biological process will be most important in the success or failure of the response. Taking this approach allows an equation to be formulated that allows the likely survival of future change to be estimated:Ps=(f(PF)xf(GM)xf(NP)xf(F)xf(D)xf(RA))/(ΔExf(C)xf(PR)xF(HS)),where Ps = Probability of survival; PF = Physiological flexibility; GM = Gene pool modification rate; NP = number in population; F = Fitness; D = Dispersal capability; RA = Resource availability; ΔE = rate of change of the environment; C = Competition; PR = Predation and parasitism; HS = Habitat separation. Functions (f) are used here to denote that factors may interact and respond in a non-linear fashion.     

Fecundity determines the extinction threshold in a Canadian assemblage of longhorned beetles (Coleoptera: Cerambycidae)

Reproductive rate has been suggested to have a positive effect on the amount of habitat loss a species can tolerate while emigration from habitat patches has been suggested to have both positive and negative effects. Forest fragmentation has been suggested to have negative effects on forest species. We determined the extinction threshold for 12 species of saproxylic (dead wood dependent) longhorned beetles (Coleoptera: Cerambycidae) using trap catch data from Ontario, Canada. We also determined the maximum egg production of each species and whether they were likely to move outside of forest patches. We found a strong negative relationship between reproductive rate and the minimum habitat amount required for species presence. This relationship is obscured if the scale of investigation is not appropriate for the study organism. As well, species caught moving outside forest habitat had lower extinction thresholds than species not caught moving outside forest but this was not significant after accounting for reproductive rate. Fragmentation did not have an effect on the minimum habitat requirements. These relationships can inform predictions of which species will be most affected by habitat loss.     

开花对两种杓兰光合作用和同化产物分配的影响

对同一生境下黄花杓兰（Cypripedium flavum）和西藏杓兰（Cypripedium tibeticum）开花株与非开花株的气体交换、光系统Ⅱ实际光化学效率（φPSⅡ）和^14C分配进行了测定,目的在于了解开花对杓兰光合作用以及同化产物分配的影响。结果表明这两种杓兰开花均能通过提高电子传递速率来提升植株的光合作用。相对于黄花杓兰,西藏杓兰开花显著提高植株的呼吸速率,以致其最大净光合速率（Amax）的提升不显著。两种杓兰的花和地下部分（包括根状茎和芽）在同化产物分配上存在竞争关系,因而开花减少了同化产物向植株地下部分的分配。     

Relations between biochemical thermodynamics and biochemical kinetics

The parameters in steady-state or rapid-equilibrium rate equations for enzyme-catalyzed reactions depend on the temperature, pH, and ionic strength, and may depend on the concentrations of specific species in the buffer. When the complete rate equation (i.e. the equation with parameters for the reverse reaction as well as the forward reaction) is determined, there are one or more Haldane relations between some of the kinetic parameters and the apparent equilibrium constant for the reaction that is catalyzed. When the apparent equilibrium constant can be calculated from the kinetic parameters, the equilibrium composition can be calculated. This is remarkable because the kinetic parameters all depend on the properties of the enzymatic site, but the apparent equilibrium constant and the equilibrium composition do not. The effects of ionic strength and pH on the unoccupied enzymatic site and the occupied enzymatic site have to cancel in the Haldane relation or in the calculation of the apparent equilibrium constant using the rate constants for the steps in the mechanism. Several simple enzymatic mechanisms and their complete rate equations are discussed.     

Accounting for variation of substitution rates through time in Bayesian phylogeny reconstruction of Sapotoideae (Sapotaceae)

We used Bayesian phylogenetic analysis of 5 kb of chloroplast DNA data from 68 Sapotaceae species to clarify phylogenetic relationships within Sapotoideae, one of the two major clades within Sapotaceae. Variation in substitution rates through time was shown to be a very important aspect of molecular evolution for this data set. Relative rates tests indicated that changes in overall rate have taken place in several lineages during the history of the group and Bayes factors strongly supported a covarion model, which allows the rate of a site to vary over time, over commonly used models that only allow rates to vary across sites. Rate variation over time was actually found to be a more important model component than rate variation across sites. The covarion model was originally developed for coding gene sequences and has so far only been tested for this type of data. The fact that it performed so well with the present data set, consisting mainly of data from noncoding spacer regions, suggests that it deserves a wider consideration in model based phylogenetic inference. Repeatability of phylogenetic results was very difficult to obtain with the more parameter rich models, and analyses with identical settings often supported different topologies. Overparameterization may be the reason why the MCMC did not sample from the posterior distribution in these cases. The problem could, however, be overcome by using less parameter rich evolutionary models, and adjusting the MCMC settings. The phylogenetic results showed that two taxa, previously thought to belong in Sapotoideae, are not part of this group. Eberhardtia aurata is the sister of the two major Sapotaceae clades, Chrysophylloideae and Sapotoideae, and Neohemsleya usambarensis belongs in Chrysophylloideae. Within Sapotoideae two clades, Sideroxyleae and Sapoteae, were strongly supported. Bayesian analysis of the character history of some floral morphological traits showed that the ancestral type of flower in Sapotoideae may have been characterized by floral parts (sepals, petals, stamens, and staminodes) in single whorls of five, entire corolla lobes, and seeds with an adaxial hilum.