Seeds and seedlings of two neotropical montane understory shrubs respond differently to anthropogenic edges and treefall gaps

Edges resulting from forest clear-cutting and treefall gaps can affect plant populations and consequently the distribution of species across landscapes. These two types of disturbance might interact to exacerbate or ameliorate “edge effects”, a rarely tested possibility. We focused on the effects of distance from forest edge (0–10, 30–40, 60–70, and 190–200 m) and habitat within forest fragments (treefall gaps and intact forest) on the early stages of development of Palicourea gibbosa and Faramea affinis, two common shrubs of montane forests in southwest Colombia. Seed germination and seedling growth did not change with distance from forest edge. Within forest fragments, however, seed germination and seedling growth were higher in treefall gaps than in intact forest understory for both species. In contrast, seed predation was influenced by distance from forest edge and in P gibbosa it depended on habitat. Seed predation was highest in the forest interior (190–200 m from forest edge) and in P. gibbosa this was true only in treefall gap habitats. These results suggest that animal mediated processes such as post-dispersal seed predation are more likely than physiological processes to be affected by anthropogenic edges. Our results provide some evidence that treefall gaps may interact with “edge effects”, however, they are inconclusive as to whether they exacerbate or ameliorate them. Received: 31 August 1998 / Accepted: 18 February 1999     

Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues

The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a given protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the Escherichia coli proteome using several proteomic methodologies and globally measured oxidation rates of methionine residues in the presence and absence of tertiary structure, as well as the folding stabilities of methionine-containing domains. These data indicated that buried methionines have a wide range of protection factors against oxidation that correlate strongly with folding stabilities. Consistent with this, we show that in comparison to E. coli, the proteome of the thermophile Thermus thermophilus is significantly more stable and thus more resistant to methionine oxidation. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and propose a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures. Overall, these results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability.     

Selection on embryonic haemoglobin in an elevational generalist songbird

Animals developing at high elevation experience a suite of environmental challenges, most notably the low partial pressure of oxygen (PO₂) in ambient air. In low PO₂, bird species with high-elevation ancestry consistently demonstrate higher hatching success than lowland counterparts, suggesting highland birds are adapted to restricted O₂ (hypoxia) in early development. Haemoglobin (Hb), the critical oxygen-transport protein, is a likely target of PO₂-related selection across ontogeny since Hb isoforms expressed at distinct developmental stages demonstrate different O₂ affinities. To test if Hb function is under PO₂-related selection at different ontogenetic stages, we sampled a songbird, the hooded siskin (Spinus magellanicus), across two approximately 4000 m elevational transects. We sequenced all of the loci that encode avian Hb isoforms, and tested for signatures of spatially varying selection by comparing divergence patterns in Hb loci to other loci sampled across the genome. We found strong signatures of diversifying selection at non-synonymous sites in loci that contribute to embryonic (α^π, β^H) and definitive (β^A) Hb isoforms. This is the first evidence for selection on embryonic haemoglobin in high-elevation Neoaves. We conclude that selection on Hb function at brief, but critical stages of ontogeny may be a vital component to high elevation adaptation in birds.     

Tabular strategies for metadata in ecology,evolution, and the environmental sciences

Data support knowledge development and theory advances in ecology and evolution. We are increasingly reusing data within our teams and projects and through the global, openly archived datasets of others. Metadata can be challenging to write and interpret, but it is always crucial for reuse. The value metadata cannot be overstated—even as a relatively independent research object because it describes the work that has been done in a structured format. We advance a new perspective and classify methods for metadata curation and development with tables. Tables with templates can be effectively used to capture all components of an experiment or project in a single, easy‐to‐read file familiar to most scientists. If coupled with the R programming language, metadata from tables can then be rapidly and reproducibly converted to publication formats including extensible markup language files suitable for data repositories. Tables can also be used to summarize existing metadata and store metadata across many datasets. A case study is provided and the added benefits of tables for metadata, a priori, are developed to ensure a more streamlined publishing process for many data repositories used in ecology, evolution, and the environmental sciences. In ecology and evolution, researchers are often highly tabular thinkers from experimental data collection in the lab and/or field, and representations of metadata as a table will provide novel research and reuse insights.     

水牛、大额牛和牦牛抑制素α亚基编码基因外显子1多态性分析

为了揭示牛科物种INHA基因的遗传特征,该文采用PCR产物直接测序法对水牛、大额牛和牦牛INHA基因外显子1及其侧翼序列进行多态性检测,并结合已发表的包括牛科物种在内的一些哺乳动物数据进行了比较分析。结果表明,在水牛INHA基因外显子1中存在c.73C>A替换,为同义替换,河流型和沼泽型水牛编码产物一致;在大额牛的INHA基因外显子1中发现c.62C>T、c.187G>A替换,分别引起INHA中氨基酸发生p.P21L、p.V63M改变,两者均为相同性质氨基酸的替换;在牦牛中发现c.62C>T、c.129A>G替换,前者也引起编码氨基酸发生p.P21L替换,后者为同义替换。在INHA基因5’侧翼区所测出的序列中,水牛、大额牛和牦牛等物种内均未发现SNP位点,但在种间发现存在c.-6T>G的替换,大额牛、牦牛和普通牛均为c.-6G,而水牛为c.-6T。在INHA基因内含子中,水牛的第31～36位核苷酸处发现有6个碱基的缺失,即c.262+31₂62+36delTCTGAC;该位点在河流型水牛中野生型（+/+）占主体,而在沼泽型水牛中则缺失型（-/-）占主体。在大额牛、牦牛和普通牛等其它牛科物种的内含子中均未发现该缺失,但与水牛相比,大额牛、牦牛和普通牛内含子中发现缺失c.262+78₂62+79delTG。序列比对显示,INHA基因外显子1序列中c.43A和c.67G为水牛中所特有,而c.173A和c.255G为大额牛、牦牛和普通牛所共有,c.24C、c.47G、c.174T和c.206T为山羊所特有。大额牛、牦牛和普通牛间INHA基因外显子1序列差异较小,而山羊和水牛与它们间的差异相对较大。     

狭果茶藨子果实多糖提取及其抗氧化和流变特性

以狭果茶藨子果实为原料,多糖提取量为考察指标,通过单因素试验及响应面试验对多糖提取工艺进行优化,结果表明最佳多糖制备工艺条件为:提取温度40℃,时间30 min,料液比1∶30 g/mL,此时狭果茶藨子中多糖提取量达115.32 mg/g;流变学特性研究表明狭果茶藨子果实多糖溶液属于非牛顿流体,多糖溶液表现出剪切稀化的现象,当多糖质量浓度为1.0%时,其流变学特性与0.1%的羧甲基纤维素钠溶液相似,且过酸、过碱的环境均不会改变狭果茶藨子果实多糖溶液的流变学特性;抗氧化试验结果表明狭果茶藨子果实多糖具有潜在的抗氧化能力,对DPPH自由基的清除能力低于抗坏血酸,而对羟自由基的清除能力显著高于抗坏血酸。本研究结果可为狭果茶藨子果实多糖在食品领域的开发利用提供理论依据。     

隐喻加工复合模式的ERP研究

本研究使用S1→S2范式研究中国人大脑隐喻加工模式是否与"等级显性理论"一致。被试对隐喻匹配任务和不相关匹配模式进行"是"和"否"隐喻的判断,同时脑电设备记录他们进行任务加工时的事件相关电位(ERP)。通过对相关电极N400的分析发现,右脑加工两个任务时,激活程度呈递增的趋势,与"等级显性理论"一致。另外,两个任务中顶叶空间加工区参与程度的差异说明,隐喻意义的整合需要对相似性、熟悉度等确定后再进行空间联系。     

Effect of temperature and storage time on cellular analysis of fresh pleural fluid samples

L. Antonangelo, F. S. Vargas, M. M. P. Acencio, A. P. Corá, L. R. Teixeira, E. H. Genofre and R. K. B. Sales
Effect of temperature and storage time on cellular analysis of fresh pleural fluid samples Objective: Despite the methodological variability in preparation techniques for pleural fluid cytology, it is fundamental that the cells should be preserved, permitting adequate morphological classification. We evaluated numerical and morphological changes in pleural fluid specimens processed after storage at room temperature or under refrigeration. Methods: Aliquots of pleural fluid from 30 patients, collected in ethylenediaminetetraacetic acid‐coated tubes and maintained at room temperature (21 °C) or refrigeration (4 °C) were evaluated after 2 and 6 hours and 1, 2, 3, 4, 7 and 14 days. Evaluation of cytomorphology and global and percentage counts of leucocytes, macrophages and mesothelial cells were included . Results: The samples had quantitative cellular variations from day 3 or 4 onwards, depending on the storage conditions. Morphological alterations occurred earlier in samples maintained at room temperature (day 2) than in those under refrigeration (day 4). Conclusions: This study confirms that storage time and temperature are potential pre‐analytical causes of error in pleural fluid cytology.     

Influence of aging and caloric restriction on activation of Ras/MAPK, calcineurin, and CaMK-IV activities in rat T cells

The signaling cascade mediated by Ras (p21ras) and MAPK (mitogen-activated protein kinase) and calcium/calmodulin regulating enzymes, calcineurin (CaN) and CaMK-IV, are considered to be essential for T-cell growth and function. In the present study, the effect of aging and caloric restriction (CR) on the induction of Ras and MAPK activation by concanavalin A (ConA) was studied. Splenic T cells were isolated from young (4-6 months) and old (22-24 months) rats that had free access to food (control group), and from caloric restricted old (22-24 months) rats that beginning at 6 weeks of age were fed 60%(40% caloric restriction) of the diet consumed by the control rats. We found that the induction of Ras activity in T cells isolated from control old rats was lower (P<0.001) than that in control young rats. However, the levels of Ras activity in T cells isolated from CR old rats were similar to the levels in the age-matched control rats. The induction of MAPK activity in T cells isolated from control old rats and CR old rats was significantly less than in T cells isolated from control young rats, and caloric restriction significantly (P<0.05) reduced the age-related decline in MAPK activation. We also measured the induction of CaN and CaMK-IV activities by ConA in T cells from control young and old and CR old rats. The induction of both CaN and CaMK-IV activity decreased with age. Caloric restriction significantly (P<0.05) reduced the age-related decline in CaN activity, but had no significant effect on CaMK-IV activity. The changes in Ras/MAPK activation and in CaN and CaMK-IV activity with age or with CR were not associated with alterations in their corresponding protein levels. Thus, caloric restriction has a differential effect on the activation of the upstream signaling molecules that are altered with age.