Cofactor‐binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle,cavity, and fold space

Small molecules are recognized in protein‐binding pockets through surface‐exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein–ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise tounexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein–cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein‐binding pockets, and the local folding patterns next to the cofactor‐binding site. State‐of‐the‐art clustering techniques have been applied to group the different protein–cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process. Proteins 2012. © 2011 Wiley Periodicals, Inc.     

重引入狗獾秋冬季行为的初步研究

2010年11月至2011年2月在上海奉贤申亚生态园内,对从山东重引入的狗獾(Meles meles)在围栏内进行了秋冬季行为的初步研究。结果表明,重引入狗獾在冬季活动时间低,取食食物以肉类饲料为主,平均2～4 d出洞活动一次,受温度影响大。研究表明,重引入狗獾能适应人工饲养并顺利越冬。     

Mating system and early viability resistance to habitat fragmentation in a bird-pollinated eucalypt

Habitat fragmentation has been shown to disrupt ecosystem processes such as plant-pollinator mutualisms. Consequently, mating patterns in remnant tree populations are expected to shift towards increased inbreeding and reduced pollen diversity, with fitness consequences for future generations. However, mating patterns and phenotypic assessments of open-pollinated progeny have rarely been combined in a single study. Here, we collected seeds from 37 Eucalyptus incrassata trees from contrasting stand densities following recent clearance in a single South Australian population (intact woodland=12.6 trees ha⁻¹; isolated pasture=1.7 trees ha⁻¹; population area=10 km²). 649 progeny from these trees were genotyped at eight microsatellite loci. We estimated genetic diversity, spatial genetic structure, indirect contemporary pollen flow and mating patterns for adults older than the clearance events and open-pollinated progeny sired post-clearance. A proxy of early stage progeny viability was assessed in a common garden experiment. Density had no impact on mating patterns, adult and progeny genetic diversity or progeny growth, but was associated with increased mean pollen dispersal. Weak spatial genetic structure among adults suggests high historical gene flow. We observed preliminary evidence for inbreeding depression related to stress caused by fungal infection, but which was not associated with density. Higher observed heterozygosities in adults compared with progeny may relate to weak selection on progeny and lifetime-accumulated mortality of inbred adults. E. incrassata appears to be resistant to the negative mating pattern and fitness changes expected within fragmented landscapes. This pattern is likely explained by strong outcrossing and regular long-distance pollen flow.     

The role of tumor necrosis factor-α for interleukin-10 production by murine dendritic cells

In the present study, we examined the role of tumor necrosis factor (TNF) in interleukin (IL)-10 production by dendritic cells (DCs) using bone-marrow derived DCs from wild type (WT) and TNF-α knockout (TNF-α^−/−) mice. Toll-like receptor (TLR) stimulation induced substantial level of IL-10 production by WT DCs, but significantly low level of IL-10 production by TNF-α^−/− DCs. In contrast, no significant difference was detected in IL-12 p40 production between WT and TNF-α^−/− DCs. Addition of TNF-α during TLR stimulation recovered the impaired ability of TNF-α^−/− DCs for IL-10 production. This recovery appeared to be associated with an activation of extracellular signal-regulated kinase, p38 mitogen-activated protein kinase, and phosphatidylinositol 3-kinase/Akt following the TNF-α addition. Blocking these kinases significantly inhibited IL-10 production by TNF-α^−/− DCs stimulated with TLR ligands plus TNF-α. Thus, TNF-α may be a key molecule to regulate the balance between anti-inflammatory versus inflammatory cytokine production in DCs.     

Mutations Altering a Structurally Conserved Loop-Helix-Loop Region of a Viral Packaging Motor Change DNA Translocation Velocity and Processivity

Many double-stranded DNA viruses employ ATP-driven motors to translocate their genomes into small, preformed viral capsids against large forces resisting confinement. Here, we show via direct single-molecule measurements that a mutation T194M downstream of the Walker B motif in the phage λ gpA packaging motor causes an 8-fold reduction in translocation velocity without substantially changing processivity or force dependence, whereas the mutation G212S in the putative C (coupling) motif causes a 3-fold reduction in velocity and a 6-fold reduction in processivity. Meanwhile a T194M pseudorevertant (T194V) showed a near restoration of the wild-type dynamics. Structural comparisons and modeling show that these mutations are in a loop-helix-loop region that positions the key residues of the catalytic motifs, Walker B and C, in the ATPase center and is structurally homologous with analogous regions in chromosome transporters and SF2 RNA helicases. Together with recently published studies of SpoIIIE chromosome transporter and Ded1 RNA helicase mutants, these findings suggest the presence of a structurally conserved region that may be a part of the mechanism that determines motor velocity and processivity in several different types of nucleic acid translocases.     

Influence of Dry Season and Food Quality and Quantity on Behavior and Feeding Strategy of Propithecus verreauxi in Kirindy, Madagascar

According to optimal foraging theory, herbivores can base food choice mainly on the quality or the quantity of food, or both. Among herbivorous primates, folivorous lemurs living in the highly seasonal environment of Madagascar have to cope with the shortage of high-quality food during the dry season, at least in deciduous forests. We studied (Verreaux's sifaka) in Kirindy, western Madagascar, to understand the influence of dry season and food quality and quantity on behavioral patterns and feeding strategy (qualitative vs. quantitative dietary choice) of a folivorous lemur in a deciduous forest. We followed 7 groups (4 groups/period; 3 individuals/group/month) during 4 periods of the year (wet season: February–March; early/middle/late dry season: May–June; July–September; October–November). We collected samples of plants eaten and examined behavioral and feeding patterns, considering food quality (macronutrients, proteins/fibers ratio, and tannins) and abundance. We found 1) a significant reduction of home range, core area, and daily path length from the wet to the dry season, possibly related to dietary change and 2) a daily period of inactivity in the dry season for energy conservation. Regarding the feeding strategy, Kirindy sifakas showed 1) high variation and selection in choosing food items and 2) a dietary choice based mainly on quality: Kirindy sifakas fed on plant species/families independently from their abundance and tannins represented a feeding deterrent during the dry season. Overall, behavioral and dietary adaptations allow Kirindy sifakas to overcome the shortage of high-quality food in the lean period.     

昆虫记忆的形成机制及生态适应性

介绍近十几年来利用蜜蜂Apis mellifera L.、果蝇Drosophila melanogaster Meigen和寄生蜂等昆虫对学习和记忆行为研究的成果。这些研究表明昆虫的记忆形成是多阶段的。从短时记忆向长时记忆的形成过程中,cAMP反应元件结合蛋白(cAMP response element-bindingprotein,CREB)起重要的作用;而蘑菇体是学习、记忆形成的主要位点。已有的研究还表明昆虫记忆的动态是适应于不同物种的生态学需要。这些研究为探索昆虫和其它动物记忆的形成和生态适应性提供了理论基础。     

Automated engineering of synthetic metabolic pathways for efficient biomanufacturing

Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals for health, food, energy, materials and others. A systems approach to metabolic engineering has gained traction in recent years thanks to advances in strain engineering, leading to an accelerated scaling from rapid prototyping to industrial production. Metabolic engineering is nowadays on track towards a truly manufacturing technology, with reduced times from conception to production enabled by automated protocols for DNA assembly of metabolic pathways in engineered producer strains. In this review, we discuss how the success of the metabolic engineering pipeline often relies on retrobiosynthetic protocols able to identify promising production routes and dynamic regulation strategies through automated biodesign algorithms, which are subsequently assembled as embedded integrated genetic circuits in the host strain. Those approaches are orchestrated by an experimental design strategy that provides optimal scheduling planning of the DNA assembly, rapid prototyping and, ultimately, brings forward an accelerated Design-Build-Test-Learn cycle and the overall optimization of the biomanufacturing process. Achieving such a vision will address the increasingly compelling demand in our society for delivering valuable biomolecules in an affordable, inclusive and sustainable bioeconomy.