Secondary structure determines protein topology

Using a test set of 13 small, compact proteins, we demonstrate that a remarkably simple protocol can capture native topology from secondary structure information alone, in the absence of long-range interactions. It has been a long-standing open question whether such information is sufficient to determine a protein's fold. Indeed, even the far simpler problem of reconstructing the three-dimensional structure of a protein from its exact backbone torsion angles has remained a difficult challenge owing to the small, but cumulative, deviations from ideality in backbone planarity, which, if ignored, cause large errors in structure. As a familiar example, a small change in an elbow angle causes a large displacement at the end of your arm; the longer the arm, the larger the displacement. Here, correct secondary structure assignments (alpha-helix, beta-strand, beta-turn, polyproline II, coil) were used to constrain polypeptide backbone chains devoid of side chains, and the most stable folded conformations were determined, using Monte Carlo simulation. Just three terms were used to assess stability: molecular compaction, steric exclusion, and hydrogen bonding. For nine of the 13 proteins, this protocol restricts the main chain to a surprisingly small number of energetically favorable topologies, with the native one prominent among them.     

The ‘home advantage’ is necessary for a full winner effect and changes in post-encounter testosterone

Winning aggressive contests can both enhance future winning ability and change post-encounter hormones; however, it remains unclear if the context of a fight also influences such winner effects and hormone changes. We investigated this issue by using California mice (Peromyscus californicus) to test if the effect of residency status is necessary to improve future winning ability and alter post-encounter hormones. Male mice were subjected to an aggressive contest and their blood was collected 45 min after the fight. Upon contest initiation, focal mice had a ‘home advantage’ and three prior winning experiences, only one of these factors, or neither factor. Only individuals with a ‘home advantage’ and prior winning experience showed a full winner effect. Post-encounter changes in testosterone and progesterone resulted from an interaction between residency status and winning experience. These data indicate that in male California mice a ‘home advantage’ is necessary to produce the full winner effect and that residency status helps regulate inter-individual variation in the expression of post-encounter testosterone pulses and progesterone changes. Furthermore, these respective behavioral and physiological phenomena might be modulated in a context-specific manner, in part by the surrounding physical environment.     

The Biology and Ecology of Feral Alfalfa (Medicago sativa L.) and Its Implications for Novel Trait Confinement in North America

Alfalfa (Medicago sativa) is an important forage crop worldwide. Apart from cultivated fields, alfalfa is also found along roadsides and in natural and semi-natural habitats. However, little information is available on the establishment capabilities of alfalfa in noncultivated areas and the potential of these founding populations to become feral. Some crop species have not lost all their wild characteristics during the domestication process and with several inherent traits favoring weediness, alfalfa could be one among those that can become feral. There is great interest in the feral potential of alfalfa, particularly due to the concerns that feral plants could act as genetic bridges and facilitate novel trait movement at the landscape level. Alfalfa is the first perennial, insect-pollinated crop to be genetically engineered and approved for unconfined release into the environment. This review investigates and compiles information in the literature that reveals the life history components that can influence ferality in alfalfa. Characteristics that can contribute to ferality in alfalfa include high genetic diversity, perenniality, quick regrowth potential, persistence, symbiotic nitrogen fixation, deep tap root system, drought and cold tolerance, and seed dormancy. With these traits, alfalfa is equipped to invade and dominate unmanaged habitats. Feral alfalfa populations can and will act as bridges for long-distance gene flow and facilitate the adventitious presence of novel traits in the environment. As such, feral populations will become a potential barrier for achieving coexistence of transgenic and nontransgenic alfalfa fields. Implications of ferality, including gene flow and hybridization with compatible wild relatives are also discussed in detail. This review serves as a resource for environmental risk assessment for the release of alfalfa containing novel traits.     

Choice of analytical method can have dramatic effects on primate home range estimates

Primate home range sizes can vary tremendously as a consequence of the analytical technique chosen to estimate home range. This is exemplified by a recent dataset on free ranging snub-nosed monkeys (Rhinopithecus bieti) in Northwest Yunnan, China. Our findings show that the grid cell method cannot substitute for the minimum convex polygon (MCP) method and vice versa. MCP-based estimates are far too large, especially when the form of the home range is irregular due to forays into peripheral areas. Here, we propose an adjusted polygon method, whereby unsuitable and never visited areas are clipped out from the polygon, thus producing more accurate results. Compared to the grid cell method, the adjusted MCP is much more robust when the number of group relocations is limited; MCP turned out to be the method of choice for calculation of monthly and seasonal home ranges. The grid cell method on the other hand yielded the most precise estimates for total or annual home ranges. The style of ranging exhibited by a given primate taxon or population determines which analytical procedures should be applied to estimate home range size, and we would stress the need for thorough evaluation of the pros and cons of home range estimators before conducting field work and analysing data.     

蜂桶寨自然保护区小熊猫巢域初步研究

2002年5~11月,在蜂桶寨自然保护区利用无线电遥测技术对6只小熊猫的巢域利用进行了初步研究。结果表明,6只戴颈圈个体M1、M2、M3、F1、F2、F3的巢域面积分别为330·26hm~2、135·18hm~2、190·67hm~2、98·23hm~2、141·60hm~2、204·80hm~2;雄性个体平均巢域面积为218·70hm~2,雌性个体为148·21hm~2。小熊猫个体间巢域重叠普遍,平均重叠率达25·33%,其中雄性个体之间为26·00%,雌性个体之间为23·67%,两性个体之间为25·67%。可能受人为干扰的影响,M1在6只监测个体中巢域面积、日均移动距离均为最大。     

宠物的福利和管理

＂家庭动物＂或＂伴侣动物＂的提法较＂宠物＂而言,更为确切并规范。伴侣动物往往因为种种原因成为城镇的流浪动物,在一定程度上,已经成为社会问题。遗弃宠物的原因尽管多种多样,深层次原因主要还是伦理道德的缺失。流浪动物日益泛滥,正在拷问人类的精神文明,有必要引起全社会的关注。动物福利在当今社会已不仅仅是概念化的一般性号召,一些发达国家出版的动物法典对犬、猫的福利有专题阐述。法典不仅对伴侣动物的各种福利条件作了具体规定,同时还提出了最低标准和最佳方案。本文以犬的食物饲喂、饮水及犬舍的要求为例,逐一介绍。     

Effects of fragmented breeding habitat and resource distribution on behavior and survival of the bank vole (Myodes glareolus)

Habitat fragmentation causes negative population trends or even local extinction in many species. Understanding the role of fragmentation on behavior and space use of animals is an essential part of revealing the mechanism behind observed population declines. We studied experimentally the effects of small-scale habitat fragmentation on the distribution and movement of bank voles (Myodes glareolus) in seminatural enclosures. We predicted that besides habitat structure, availability of two resources, food for both sexes, and receptive females for males, determine individual distribution. We manipulated female density (either 0, 4, or 12 per enclosure) and followed movements of radio-collared males. We also studied the effect of unequal food distribution between the fragments on vole distribution. The habitat of 0.25-ha enclosures was manipulated by forming either one large, two medium-sized, or four small habitat patches surrounded by an inhospitable matrix. Female density and distribution clearly affected male spacing behavior. Males had larger home ranges in the medium female density enclosures. Furthermore, the use of the inhospitable and risky matrix area increased with habitat fragmentation. Food supplementation improved individual condition measured as body mass but did not affect breeding success. Our experiments demonstrated that both small-scale habitat fragmentation and resource distribution affect the behavior and condition of individuals. Increased fragmentation led to increased risk taking in both mating and foraging behavior. This should have direct survival and fitness consequences, and therefore our results may be extrapolated to population-level consequences of habitat fragmentation.     

Assessing Risk of Unintended Antigen Occurrence in Food: A Case Instance for Maize-Expressed LT-B

Plant-based antigen production represents an innovative strategy for low cost vaccine production and delivery. Successfully advancing plant-made antigen production in open field systems requires understanding of confinement integrity and consequences of inadvertent occurrence in the food supply. The food safety implications of confinement loss and inadvertent antigen occurrence in the food supply can be effectively addressed using quantitative exposure assessment along with knowledge of properties of specific antigens. We report here a food safety risk assessment for the maize-expressed heat-labile enterotoxin subunit B of Escherichia coli (LT-B). In addition to dietary exposure assessment, food safety considerations for maize-expressed LT-B included assessment of allergenic potential, levels and sites of transgenic protein expression, history of use, post-translational glycosylation, protein processing and digestive stability, mammalian functionality and toxicity, and compositional characteristics of the transformed plant. As shown for LT-B, inadvertent occurrence in the food supply of a plant-produced antigen constitutes a minimal human health concern principally because of limited exposure potential.     

Territorial behavior of the plethodontid salamander Plethodon kentucki: influence of habitat structure and population density

To investigate the possible influence of variation in ecological and demographic factors on the spatial organization of the terrestrial plethodontid salamander Plethodon kentucki, I conducted a 3-year capture-recapture study and determined home-range characteristics and spatial relationships of individuals at two field sites that differed in predominant cover type and population density. Home ranges of adults were fixed and the home ranges of same-sex adult neighbors were mostly exclusive. The spatial arrangement of adult home ranges exhibited overall regularity or regularity within aggregations, whereas the distribution of juvenile home ranges was usually random. Analysis of nearest-neighbor sex indicated a positive intersexual association of adult home ranges. Removal studies provided evidence for defense of adult home ranges only at the high-density site. The distribution of home ranges was influenced by the presence of cover objects, but there was no significant relationship between adult body size and percent of home-range area with cover. Males overlapped the home ranges of gravid females significantly more often than those of non-gravid females, indicating that the distribution of gravid females had a strong influence on the distribution of male home ranges. In laboratory tests, increased male-male aggression during the breeding season suggests that males may compete for access to mates. At the high-density site, larger males may have benefited by having greater reproductive success than smaller males because they were more dominant and their home ranges overlapped a greater number of gravid-female home ranges. My results indicate that habitat structure and population density may influence the spatial organization and mating system of P. kentucki. Received: 26 May 1997 / Accepted: 9 October 1997     

黑顶麻雀的活动区及其影响因素

2017和2018年每年6至10月,在甘肃安西极旱荒漠国家级自然保护区利用无线电遥测技术对繁殖期16只黑顶麻雀(Passer ammodendri)(9♀,7♂)和繁殖期后1个月内雌雄各1只的活动区进行了监测。使用95%固定核空间法(FK)计算活动区面积,60%固定核空间法求得的活动区面积作为核心区面积。结果显示,在繁殖期雌雄黑顶麻雀个体间的平均活动区面积分别为(23.88±4.50)hm²(n=9)和(32.36±7.24)hm²(n=7),核心区面积分别为(3.92±0.70)hm²和(5.55±1.55)hm²,繁殖期雌雄个体间的活动区和核心区面积均无显著差异。繁殖结束后一个月内雌雄活动区面积分别为123.86hm²和272.40 hm²,核心区面积分别为23.68 hm²和64.88 hm²。雌、雄性个体繁殖期的活动区面积和核心区面积均显著小于繁殖期后。个性表现为羞怯的个体活动区面积显著小于个性表现为勇敢...