气候变化对冬季东海外海中下层游泳动物群落结构及重要经济种类的影响

以全球气候变暖为主要特征的全球气候变化对海洋生物和海洋生态系统造成的影响已引起国际学者的高度关注。根据中国14家国营渔业公司底拖网渔业生产和渔业资源大面定点调查获得的17种中下层渔业数据,结合1960—2011年东海北部水域海表温度的变化情况,利用Fox模型移除捕捞效应产生的趋势变化后,分析了气候变化对中、下层游泳动物群落结构及几种重要经济种类的影响。通过气候跃变检验分析发现,海表温度在整体变暖的趋势上叠加有年代际波动,研究水域分别在1982/1983年发生了从寒冷期(1960—1982年)向升温期(1983—1998)、经由1998/1999年再到温暖期(1999—2011年)的跃变。群落结构变化特征显示:相比于寒冷期,温暖期间底层类和大型捕食类资源指数降低,中层类和无脊椎类升高;暖水种资源指数升高,暖温种降低;生物多样性指数略有增加。移除捕捞效应后,对不同生态属性种类CPUE与海表温度距平进行相关分析显示:底层类、中层类和无脊椎类残差与海表温度距平均呈正相关关系,其中中层类与海表温度距平显著正相关,而大型捕食类则呈负相关关系;暖水种残差与海表温度距平呈正相关,而暖温种则呈负相关关系。中层类中的黄鲫(Setipinna taty)、银鲳(Pampus argenteus)的CPUE残差均与海表温度距平呈显著正相关关系,近底层类中的带鱼(Trichiurus japonicus)和头足类(Squid)的CPUE残差均与海表温度距平呈正相关关系,而底层类小黄鱼(Larimichthys polyactis)和对虾(Shrimp)则呈负相关关系。在气候变化的大背景下,需加强其对海洋生态系统结构和功能影响的研究,查明渔业资源对气候变化的响应机制和机理,制定科学有效的渔业管理制度,实现渔业资源的可持续发展。     

基于过程参数相关分析的鸟苷发酵过程优化

本文分析鸟苷产生菌枯草芽孢杆菌(Bacilus subtilis)在50L多参数自控发酵罐上的发酵过程特点,基于多种在线及离线参数的检测,通过相关分析将生理调控的工艺参数和生物合成过程中的代谢流分布相联系,发现了发酵过程中的代谢流向糖酵解和TCA循环的迁移,并初步分析了产生代谢流迁移的原因,在此基础上优化发酵过程使产苷水平稳定在30g/L。     

Use of a generalised linear model to test habitat preferences: the example of Zingel asper, an endemic endangered percid of the River Rhône

SUMMARY 1. A study of microhabitat preferences was conducted on Zingel asper , an endangered endemic species from the Rhône catchment. A generalised linear model allowed us to test statistically the non-random habitat selection and the effect of season and site on this habitat selection.
2. The analysis detected significant preferences for the three physical variables considered: water depth, water velocity and substratum size.
3. A seasonal shift in the substratum size preference was found: preference for stones increasing during the spawning season. Depth preference varied between sites, suggesting a possible plasticity in habitat selection.
4. These results suggest that the availability of suitable physical habitat plays a significant role in determining fish distribution in the River Beaume.     

Population Dynamics of Pseudomonas syringae pv. tomato Strains on Tomato Cultivars Rio Grande and Rio Grande-Pto under Field Conditions

We examined the effects of the Pto resistance locus on the population dynamics of Pseudomonas syringae pv. tomato (Pst) strains in field experiments with the nearly isogenic tomato lines Rio Grande (RG, susceptible to Pst races 0 and 1) and Rio Grande-Pto (RG-Pto, resistant to Pst race 0, susceptible to Pst race 1). Pst strain SM78-1Sm^r (race 0) grew well under field conditions and caused ample bacterial speck disease on susceptible RG plants. In contrast, strain DC3000 failed to establish large populations when inoculated onto field grown RG plants. Mean population sizes of SM78-1Sm^r were 4–5 orders of magnitude larger on RG than RG-Pto plants indicating that RG-Pto plants were highly effective in attenuating pathogen population development. Most of the sampled leaflets from RG-Pto field plots harboured small numbers of SM78-1Sm^r. However, population sizes SM78-1Sm^r as large as 10⁵–10⁶ CFU were found on a few leaflets. Bacteria isolated from these leaflets had phenotypes characteristic of Pst race 1 strains. In growth chamber plant assays, the bacterial strains grew well and caused typical speck lesions on RG-Pto plants. The strains appeared to be race-shift mutants of SM SM78-1Sm^r. Interestingly, results from DNA hybridization experiments demonstrated that the race-shift mutants were deleted for the avirulence gene, avrPto but not for avrPtoB.     

Kinematic motion of the anterior cruciate ligament deficient knee during functionally high and low demanding tasks

The purpose of this study was to determine whether mechanical adaptations were present in patients with anterior cruciate ligament (ACL)-deficient knees during high-demand activities. Twenty-two subjects with unilateral ACL deficiency (11 males and 11 females, 19.6 months after injury) performed five different activities at a comfortable speed (level walking, ascending and descending steps, jogging, jogging to a 90-degree side cutting toward the opposite direction of the tested side). Three-dimensional knee kinematics for the ACL-deficient knees and uninjured contralateral knees were evaluated using the Point Cluster Technique. There was no significant difference in knee flexion angle, but an offset toward the knee in less valgus and more external tibial rotation was observed in the ACL-deficient knee. The tendency was more obvious in high demand motions, and a significant difference was clearly observed in the side cutting motions. These motion patterns, with the knee in less valgus and more external tibial rotation, are proposed to be an adaptive movement to avoid pivot shift dynamically, and reveal evidence in support of a dynamic adaptive motion occurring in ACL-deficient knees.     

Identification of Zinc-ligated Cysteine Residues Based on 13Cα and 13Cβ Chemical Shift Data

Although a significant number of proteins include bound metals as part of their structure, the identification of amino acid residues coordinated to non-paramagnetic metals by NMR remains a challenge. Metal ligands can stabilize the native structure and/or play critical catalytic roles in the underlying biochemistry. An atom’s chemical shift is exquisitely sensitive to its electronic environment. Chemical shift data can provide valuable insights into structural features, including metal ligation. In this study, we demonstrate that overlapped ¹³Cβ chemical shift distributions of Zn-ligated and non-metal-ligated cysteine residues are largely resolved by the inclusion of the corresponding ¹³Cα chemical shift information, together with secondary structural information. We demonstrate this with a bivariate distribution plot, and statistically with a multivariate analysis of variance (MANOVA) and hierarchical logistic regression analysis. Using 287 ¹³Cα/¹³Cβ shift pairs from 79 proteins with known three-dimensional structures, including 86 ¹³Cα and¹³Cβ shifts for 43 Zn-ligated cysteine residues, along with corresponding oxidation state and secondary structure information, we have built a logistic regression model that distinguishes between oxidized cystines, reduced (non-metal ligated) cysteines, and Zn-ligated cysteines. Classifying cysteines/cystines with a statisical model incorporating all three phenomena resulted in a predictor of Zn ligation with a recall, precision and F-measure of 83.7%, and an accuracy of 95.1%. This model was applied in the analysis of Bacillus subtilis IscU, a protein involved in iron–sulfur cluster assembly. The model predicts that all three cysteines of IscU are metal ligands. We confirmed these results by (i) examining the effect of metal chelation on the NMR spectrum of IscU, and (ii) inductively coupled plasma mass spectrometry analysis. To gain further insight into the frequency of occurrence of non-cysteine Zn ligands, we analyzed the Protein Data Bank and found that 78% of the Zn ligands are histidine and cysteine (with nearly identical frequencies), and 18% are acidic residues aspartate and glutamate. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Population shift of binding pocket size and dynamic correlation analysis shed new light on the anticooperative mechanism of PII protein

P_II protein is one of the largest families of signal transduction proteins in archaea, bacteria, and plants, controlling key processes of nitrogen assimilation. An intriguing characteristic for many P_II proteins is that the three ligand binding sites exhibit anticooperative allosteric regulation. In this work, P_II protein from Synechococcus elongatus, a model for cyanobacteria and plant P_II proteins, is utilized to reveal the anticooperative mechanism upon binding of 2‐oxoglutarate (2‐OG). To this end, a method is proposed to define the binding pocket size by identifying residues that contribute greatly to the binding of 2‐OG. It is found that the anticooperativity is realized through population shift of the binding pocket size in an asymmetric manner. Furthermore, a new algorithm based on the dynamic correlation analysis is developed and utilized to discover residues that mediate the anticooperative process with high probability. It is surprising to find that the T‐loop, which is believed to be responsible for mediating the binding of P_II with its target proteins, also takes part in the intersubunit signal transduction process. Experimental results of P_II variants further confirmed the influence of T‐loop on the anticooperative regulation, especially on binding of the third 2‐OG. These discoveries extend our understanding of the P_II T‐loop from being essential in versatile binding of target protein to signal‐mediating in the anticooperative allosteric regulation. Proteins 2014; 82:1048–1059. © 2013 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

Shift work parameters and disruption of diurnal cortisol production in female hospital employees

Shift work is associated with an increased risk of cardiovascular diseases (CVD). Disruption of cortisol production is a potential underlying mechanism. This study explored the associations of diurnal quantity and pattern of cortisol production in relation to (1) current shift work status (exclusive day versus rotating days and nights), (2) years of past shift work and (3) parameters of rotating shift work (timing, length and intensity). Female hospital employees (160 day workers and 168 rotating shift workers) from southeastern Ontario, Canada, participated in a cross-sectional study. Participants completed a baseline questionnaire and measures of body height, weight, and waist circumference were taken. Midstream urine samples were collected over two separate 24-hour periods to measure creatinine-adjusted cortisol. Total diurnal cortisol production and pattern were described with two measures of the area under the curve. The effect of shift work on cortisol was modeled using multivariable linear regression analyses. Cortisol production in day workers and shift workers on their day shift were similar; however, shift workers on the night shift had flatter diurnal cortisol curves and produced less cortisol. This suggests that night work is associated with an acute attenuation of cortisol production.     

Tracing specific synonymous codon-secondary structure correlations through evolution

Abstract We previously showed that GAU codons are preferred (relative to synonymous GAC codons) for encoding aspartates specifically at the N-termini of α-helices in human, but not in E. coli, proteins. To test if this difference reflected a general difference between eucaryotes and procaryotes, we now extended the analysis to include the proteins and coding sequences of mammals, vertebrates, S. cerevisiae, and plants. We found that the GAU-α-helix correlation is also strong in non-human mammalian and vertebrate proteins but is much weaker or insignificant in S. cerevisiae and plants. The vertebrate correlations are of sufficient strength to enhance α-helix N-terminus prediction. Additional results, including the observation that the correlation is significantly enhanced when proteins that are known to be correctly expressed in recombinant procaryotic systems are excluded, suggest that the correlation is induced at the level of protein translation and folding and not at the nucleic acid level. To the best of our knowledge, it is not explicable by the canonical picture of protein expression and folding, suggesting the existence of a novel evolutionary selection mechanism. One possible explanation is that some α-helix N-terminal GAU codons may facilitate correct co-translational folding in vertebrates.     

大蹄蝠多普勒正负补偿效应的声波特征与比较

利用单摆装置模拟大蹄蝠的飞行状态并实时记录其回声定位信号,以研究其多普勒频移补偿行为。与其静息状态下的超声波特征比较,发现大蹄蝠在接近目标的过程中有多普勒正补偿效应:叫声频率随相对速度改变而成正相关变化;当相对速度最大时,其叫声频率相对静息状态频率降低最多,而相对速度为零时,叫声频率回复到静息时频率。而当大蹄蝠远离目标时,有多普勒负补偿效应:叫声频率随相对速度改变成正相关变化,叫声频率在相对速度最大时,升高最多,但相同速度下升高之值较正补偿值低得多。另外,负补偿效应出现的频率较正补偿值低,这可能是由蝙蝠生理结构的限制以及自然状态下罕见的多普勒负补偿条件所决定。     

Stability parameters and performance of interregional crosses in durum wheat (Triticum durum Desf.)

Summary Twelve durum wheat varieties originating from 3 ecologically diverse regions and their 48 intergroup crosses were evaluated for stability of performance with respect to grain yield and certain component traits. The linear component of the genotype-environment interaction was revealed for grain yield, 100-grain weight and plant height, non-linear for tiller number whereas for grains per spike both components were equally important. However, except for tiller number, the linear component appeared to be contributing to a large extent towards the prevalent interactions. NP 404, Bijaga Yellow and Giorgio VZ 331 depicted stable performance for grain yield. However, considering all the attributes, the parents NP 404, Bijaga Yellow, Anhinga s and Mexicali 75 and hybrids NP 401 x Mexicali 75, NP 404 x Anhinga s, NP 412 x Mexicali 75, NP 404 x Gerardo VZ 466 and Anhinga s x Capeiti appeared promising. The Mexican group as a whole exhibited a more stable performance than the other two evaluated groups. Compensating shift among the component characters was evident in the case of parents as well as hybrids and stability of performance appeared to be under genetic control. Effective utilization of these two aspects through introduction in otherwise desirable varieties has been advocated.Part of Ph.D. thesis of senior author submitted to the Punjab Agricultural University     

Effects of coexistence on habitat use and trophic ecology of interacting native and invasive amphipods

1. Invasive species in aquatic systems are major drivers of changes in biodiversity. Amphipods are key species in freshwaters, with invasive amphipods either replacing or coexisting with native species and often damaging local biodiversity. However, the consequences of interactions among native and invasive amphipods for their habitat use and feeding ecology and ecosystem function are not yet well understood. 2. We examined a number of streams in Brittany and Northern Ireland, with native and invasive amphipods, to evaluate the consequences of species interactions for both habitat use and diet. Our field studies centred on testing two proposed models: a cohabitation model without competition between two native species (Gammarus pulex vs Echinogammarus berilloni), and a competition model between an invasive and a native species (Gammarus pulex vs Gammarus duebeni celticus). For these three species, alone and in combination, we assessed their habitat use and feeding patterns, the latter through gut contents and stable C and N isotope analyses of their tissues. 3. When existing as single‐species populations, all three species used stream habitats broadly similarly, although G. pulex was more strongly associated with leaf litter and vegetation compared to pebble substrata than the other species. When G. pulex coexisted with either E. berilloni or G. d. celticus, the latter two changed to using all habitats equally, whereas the former retained its habitat preferences. 4. Similarly, all three species when alone had similar gut contents, with inorganic material predominating, followed by leaf and woody material and more rarely algae and invertebrates. When G. pulex coexisted with E. berilloni, the diet of the latter did not change; however, the frequency of inorganic matter, leaves and wood declined in the gut contents of G. pulex. When G. pulex coexisted with G. d. celticus, the pattern of gut contents did not change in either species. 5. When existing as single‐species populations, G. pulex had a broader range of isotopic signatures, both for δ¹³C and for δ¹⁵N, than the two other species, indicating a more variable diet among individuals. When G. pulex coexisted with either E. berilloni or G. d. celticus, the latter two had similar ranges of δ¹³C and δ¹⁵N, whereas for G. pulex the range was much less for δ¹³C and δ¹⁵N, suggesting a less diverse diet. 6. Our results infer two different modes of coexistence between native and non‐native amphipods. We have shown that the native species, which coexist stably, appear to show interference competition, leading to spatial habitat segregation, whereas competition for food and possible intraguild predation by G. pulex on G. d. celticus would explain why the distribution and density of the latter is affected by G. pulex. However, since all the species have a similar diet and feeding habit, we expect no great overall effect on ecosystem processes as a consequence of species interactions and displacements.     

荣成天鹅湖湿地越冬大天鹅食性分析

2005年12月～2006年3月以大天鹅(Cygnus cygnus)为对象,研究其越冬期间的食性,利用粪便显微组织分析法定量调查其食物组成。结果表明,大天鹅的越冬食物主要为小麦(Triticum aestivum)、海带(Laminaria japonica)和大叶藻(Zostera marina),其中,小麦的比例最大,分别占冬季食物组成的99.67%和早春的90.17%。对冬季与早春的食物组成的差异进行分析,发现大天鹅在天鹅湖保护区发生了食物替代现象。结合以往资料,认为生态污染和湿地结构性破坏导致大天鹅传统食物减少,致使食物替代现象的发生。     

鸟苷发酵过程代谢流迁移的分析

以典型的代谢控制发酵产品鸟苷为例说明了一种基于过程参数的相关分析来研究发酵过程中代谢流迁移的方法。通过对发酵过程多参数的相关性分析,结合生物合成代谢途径、氨基酸和有机酸积累的分析,确认了发酵过程代谢流向EMP途径的迁移,认为造成这种代谢流迁移的原因可能是过程铵离子积累。在此基础上,通过对过程参数实时检测分析和及时调整EMP和HMP代谢通量使产率提高了35％。      

Quantifying light-dependent circadian disruption in humans and animal models

Although circadian disruption is an accepted term, little has been done to develop methods to quantify the degree of disruption or entrainment individual organisms actually exhibit in the field. A variety of behavioral, physiological and hormonal responses vary in amplitude over a 24-h period and the degree to which these circadian rhythms are synchronized to the daily light–dark cycle can be quantified with a technique known as phasor analysis. Several studies have been carried out using phasor analysis in an attempt to measure circadian disruption exhibited by animals and by humans. To perform these studies, species-specific light measurement and light delivery technologies had to be developed based upon a fundamental understanding of circadian phototransduction mechanisms in the different species. When both nocturnal rodents and diurnal humans, experienced different species-specific light–dark shift schedules, they showed, based upon phasor analysis of the light–dark and activity–rest patterns, similar levels of light-dependent circadian disruption. Indeed, both rodents and humans show monotonically increasing and quantitatively similar levels of light-dependent circadian disruption with increasing shift-nights per week. Thus, phasor analysis provides a method for quantifying circadian disruption in the field and in the laboratory as well as a bridge between ecological measurements of circadian entrainment in humans and parametric studies of circadian disruption in animal models, including nocturnal rodents.     

Climate change and the outbreak ranges of two North American bark beetles

Abstract

• 1 One expected effect of global climate change on insect populations is a shift in geographical distributions toward higher latitudes and higher elevations. Southern pine beetle Dendroctonus frontalis and mountain pine beetle Dendroctonus ponderosae undergo regional outbreaks that result in large‐scale disturbances to pine forests in the south‐eastern and western United States, respectively.
• 2 Our objective was to investigate potential range shifts under climate change of outbreak areas for both bark beetle species and the areas of occurrence of the forest types susceptible to them.
• 3 To project range changes, we used discriminant function models that incorporated climatic variables. Models to project bark beetle ranges employed changed forest distributions as well as changes in climatic variables.
• 4 Projected outbreak areas for southern pine beetle increased with higher temperatures and generally shifted northward, as did the distributions of the southern pine forests.
• 5 Projected outbreak areas for mountain pine beetle decreased with increasing temperature and shifted toward higher elevation. That trend was mirrored in the projected distributions of pine forests in the region of the western U.S. encompassed by the study.
• 6 Projected outbreak areas for the two bark beetle species and the area of occurrence of western pine forests increased with more precipitation and decreased with less precipitation, whereas the area of occurrence of southern pine forests decreased slightly with increasing precipitation.
• 7 Predicted shifts of outbreak ranges for both bark beetle species followed general expectations for the effects of global climate change and reflected the underlying long‐term distributional shifts of their host forests.