Polarity in higher plant dictyosomes

Summary Dictyosomes in three higher plant cell secretory systems,Zea root cap cells,Tradescantia pollen tubes and digestive glands ofDionaea fly traps, are shown to possess a structural polarity in terms of either the production of secretory vesicles, or the reaction of individual cisternae to the osmium-zinc-iodide impregnation procedure. These observations contradict previous claims that higher plant dictyosomes lack structural polarity. Doubts about the applicability of the endomembrane flow concept to higher plant cell dictyosomes are discussed in relation to the relative balance between carbohydrate and protein in secreted products. The lack of dictyosome-associated endoplasmic reticulum in some of these plant cell systems is confirmed.     

Combinations of non-invasive indicators to detect dairy cows submitted to high-starch-diet challenge

High-starch diets (HSDs) fed to high-producing ruminants are often responsible for rumen dysfunction and could impair animal health and production. Feeding HSDs are often characterized by transient rumen pH depression, accurate monitoring of which requires costly or invasive methods. Numerous clinical signs can be followed to monitor such diet changes but no specific indicator is able to make a statement at animal level on-farm. The aim of this pilot study was to assess a combination of non-invasive indicators in dairy cows able to monitor a HSD in experimental conditions. A longitudinal study was conducted in 11 primiparous dairy cows fed with two different diets during three successive periods: a 4-week control period (P1) with a low-starch diet (LSD; 13% starch), a 4-week period with an HSD (P2, 35% starch) and a 3-week recovery period (P3) again with the LSD. Animal behaviour was monitored throughout the experiment, and faeces, urine, saliva, milk and blood were sampled simultaneously in each animal at least once a week for analysis. A total of 136 variables were screened by successive statistical approaches including: partial least squares-discriminant analysis, multivariate analysis and mixed-effect models. Finally, 16 indicators were selected as the most representative of a HSD challenge. A generalized linear mixed model analysis was applied to highlight parsimonious combinations of indicators able to identify animals under our experimental conditions. Eighteen models were established and the combination of milk urea nitrogen, blood bicarbonate and feed intake was the best to detect the different periods of the challenge with both 100% of specificity and sensitivity. Other indicators such as the number of drinking acts, fat:protein ratio in milk, urine, and faecal pH, were the most frequently used in the proposed models. Finally, the established models highlight the necessity for animals to have more than 1 week of recovery diet to return to their initial control state after a HSD challenge. This pilot study demonstrates the interest of using combinations of non-invasive indicators to monitor feed changes from a LSD to a HSD to dairy cows in order to improve prevention of rumen dysfunction on-farm. However, the adjustment and robustness of the proposed combinations of indicators need to be challenged using a greater number of animals as well as different acidogenic conditions before being applied on-farm.     

放线菌分类地位的变迁及其系统学研究最新进展

放线菌是目前细菌域最大的谱系之一,门下物种繁多。放线菌作为人类生产和生活极为密切的微生物类群,其强大的代谢产物编码能力为人们所共识。放线菌系统学是以实现对放线菌进行分类、鉴定、命名为目标的基础学科,因此它是放线菌资源研究和开发利用的重要理论基础。近期,我们放线菌资源与利用团队对2009年版放线菌分类系统再次进行了更新和修订,并被国际权威分类学期刊IJSEM杂志接受发表,进一步巩固了我国在本领域的国际领先地位。重点对放线菌的概念演变、分类地位变迁,以及放线菌系统学研究的最新进展做全面概述,并对其未来发展方向进行了展望,以供国内从事本领域研究的同行参考。     

Is population subdivision different from speciation? From phylogeography to species delimitation

Species‐level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model‐based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species.     

人为干扰对溪流鱼类功能多样性及其纵向梯度格局的影响

溪流鱼类多样性沿着河流纵向梯度的空间分布规律已得到大量报道, 但这些研究大多聚焦基于物种组成的分类α多样性, 而有关分类β多样性和功能多样性的纵向梯度分布规律及其对人类干扰的响应研究较少。本文以青弋江上游3条人为干扰程度不同的河源溪流为研究区域, 比较研究了人为干扰对溪流鱼类功能α和β多样性及其纵向梯度分布格局的影响。结果显示, 人类干扰改变了河源溪流鱼类功能多样性的纵向梯度格局——由线性变化变为二项式分布。此外, 我们发现, 人为干扰导致土著种被本地入侵种取代, 且较强的土地利用和水污染排放可能增大环境的不连续性, 而群落周转和嵌套变化往往取决于环境的变化。尽管功能β多样性由嵌套成分主导, 但周转成分占比相对于人为干扰较小的溪流而言明显增加。人为干扰显著改变了受干扰溪流鱼类的物种组成和功能多样性, 且功能多样性的纵向梯度格局在不同的多样性指标上存在差异。本研究强调, 在评估人为干扰下多样性的变化时, 需要从多方面考虑, 包括空间尺度和多样性指标等。     

A mixed finite element formulation for a non-linear,transversely isotropic material model for the cardiac tissue

In this paper we present a mixed finite element method for modeling the passive properties of the myocardium. The passive properties are described by a non-linear, transversely isotropic, hyperelastic material model, and the myocardium is assumed to be almost incompressible. Single-field, pure displacement-based formulations are known to cause numerical difficulties when applied to incompressible or slightly compressible material cases. This paper presents an alternative approach in the form of a mixed formulation, where a separately interpolated pressure field is introduced as a primary unknown in addition to the displacement field. Moreover, a constraint term is included in the formulation to enforce (almost) incompressibility. Numerical results presented in the paper demonstrate the difficulties related to employing a pure displacement-based method, applying a set of physically relevant material parameter values for the cardiac tissue. The same problems are not experienced for the proposed mixed method. We show that the mixed formulation provides reasonable numerical results for compressible as well as nearly incompressible cases, also in situations of large fiber stretches. There is good agreement between the numerical results and the underlying analytical models.     

eScience and the need for data standards in the life sciences: in pursuit of objectivity rather than truth

Referring to European history of natural sciences as an example, I discuss the relation between development of standards and the emergence of new epistemic virtues. I distinguish standards relating to scientific argumentation from standards relating to data production. The former are based on truth-seeking epistemic virtues and use criteria of logical coherence and empirical grounding. They are important for the justification of an explanatory hypothesis. Data and metadata standards, on the other hand, concern the data record itself and all steps and actions taken during data production and are based on virtues of objectivity. In the second part I focus on data and metadata standards and argue that, in order to meet the requirements of eScience, the specification of the currently popular minimum information checklists should be complemented to cover four aspects: (i) content standards, which increase reproducibility and operational transparency of data production, (ii) concept standards, which increase the semantic transparency of the terms used in data records, (iii) nomenclatural standards, which provide stable and unambiguous links between the terms used and their underlying definitions or their real referents, and (iv) format standards, which increase compatibility and computer-parsability of data records. I discuss the role of scientific terminology for standardizing data and the need for using semantically standardized and formalized data-reporting languages in the form of controlled vocabularies and ontologies for establishing content standards for data in the life sciences. Finally I comment on the necessity of community participation in the development and application of standards and in making data openly available.     

Switching from usual brand cigarettes to a tobacco-heating cigarette or snus: Part 2. Biomarkers of exposure

Abstract

A randomized, multi-center study of adult cigarette smokers switched to tobacco-heating cigarettes, snus or ultra-low machine yield tobacco-burning cigarettes (50/group) was conducted, and subjects’ experience with the products was followed for 24 weeks. Differences in biomarkers of tobacco exposure between smokers and never smokers at baseline and among groups relative to each other and over time were assessed. Results indicated reduced exposure to many potentially harmful constituents found in cigarette smoke following product switching. Findings support differences in exposure from the use of various tobacco products and are relevant to the understanding of a risk continuum among tobacco products.

Trial registration: ClinicalTrials.gov identifier: NCT02061917.     

Fusion Peptide Interaction with Lipid Bilayer: Modeling with Monte Carlo Simulation and Continuum Electrostatics Calculation

Abstract

Conformation of 20-residue peptide E5, an analog of the fusion peptide of influenza virus hemagglutinin, was explored by Monte-Carlo technique starting with the fully buried in the membrane ideal α-helix. The lipid bilayer (of 30 Å width) together with surrounding water were modeled by the atomic solvation parameters. During the simulation, residues 2–18 of the peptide retained α-helical conformation, and the peptide was found to be partially immersed into the bilayer. In the resulting low-energy conformers, the N-terminus was buried inside the membrane, its position with respect to the bilayer surface (Z_NT) being varied from 2.5 to 7.5 Å, and the orientation of the helical axis relative to the membrane plane (Θ) – from 10 to 35°. The low-energy conformers (below -200kcal/mol) were clustered in the space (Z_NT, Θ) into 4 groups. To select low-energy states of the peptide compatible with NMR data, we calculated pKa values of E5 ionizable groups and compared them with the experimental values. It was shown that the best correlation coefficient (0.87) and rmsd (0.68 in pH units) were obtained for the group of states which is characterized by Θ = 15–19° and Z_NT = 3.5–4.5Å.