银沙槐内生放线菌抗菌活性及其与内生细菌的拮抗关系

从荒漠濒危植物银沙槐根部分离到内生放线菌12株和内生细菌31株.以大肠杆菌、金黄色葡萄球菌和枯草芽孢杆菌为指示菌对内生放线菌进行了抗菌活性筛选.结果表明：3株放线菌对3种指示菌均有抑制作用,2株完全无抑菌作用.采用菌块抑制法分析内生放线菌对来自同一植物内生细菌的抑制效果,44.9%的组合出现抑制现象,最大抑菌圈直径为28.5mm,最小者仅8.25 mm,主要抑制对象是革兰氏阴性菌和芽孢菌;55.1%的组合无抑制现象.说明内生菌的相互作用具有多样性.     

苯并[α]芘对不同修复潜力羊茅属植物的根系分泌物中几种低分子量有机物的影响

根系分泌物是植物与土壤间进行物质交换和信息传递的重要载体, 是植物响应外界胁迫的重要途径, 也是构成根际微生态特征的关键因素。根系分泌物与有机污染物的植物修复密切相关, 研究胁迫条件下不同修复潜力植物间根系分泌物的释放特征有助于揭示植物修复的内在机制。该文借助根际袋土培试验研究了苯并[α]芘(BaP)胁迫下5种羊茅属(Festuca)植物根系不同生长期(30-70天)几种低分子量有机物的分泌特征。结果表明: 1) BaP浓度在10.25-161.74 mg·kg^-1范围内时, 待试植物能有效地促进土壤中BaP的去除, 其修复潜力依次为苇状羊茅(F. arundinacea) > 草原羊茅(F. chelungkiangnica) ≥ 毛稃羊茅(F. rubra subsp. arctica) ≥ 贫芒羊茅(F. sinomutica) > 细芒羊茅(F. stapfii)。2) BaP胁迫增强了植物根系对可溶性糖的分泌: 随着胁迫强度的增大、胁迫期的延长, 其分泌量变化呈“先升后降”趋势。3) BaP胁迫促进了植物根系低分子量有机酸的释放, 植物的修复潜力越大, 有机酸高峰值出现时的胁迫浓度越高; 组成成分较稳定, 草酸、乙酸、乳酸和苹果酸为主要组分(>97.34%), 在修复潜力较强植物的根系分泌物中检测出微量的反丁烯二酸。4) BaP胁迫对氨基酸种类影响不大, 但对分泌量影响较大。其中, 苏氨酸、丝氨酸、甘氨酸、丙氨酸的分泌量随BaP胁迫强度的增强而剧增; 脯氨酸、羟脯氨酸和天冬氨酸近乎以加和效应甚至协同效应的形式参与植物对BaP胁迫的应激反应: 参与应激组分的分泌量随胁迫强度的增强而剧增, 植物的修复潜力越强, 参与的组分越多。可见BaP胁迫下, 5种羊茅属植物根系分泌物中几种低分子量有机物的释放特征与植物自身的修复潜力有关: 修复潜力越强, 释放量越多且成分也越复杂, 并呈现出较强的环境适应性及生理可塑性。     

A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae

A multispecies-based taxonomic microarray targeting coding sequences of diverged orthologous genes in Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces mikatae, Saccharomyces bayanus, Saccharomyces kudriavzevii, Naumovia castellii, Lachancea kluyveri and Candida glabrata was designed to allow identification of isolates of these species and their interspecies hybrids. Analysis of isolates of several Saccharomyces species and interspecies hybrids demonstrated the ability of the microarray to differentiate these yeasts on the basis of their specific hybridization patterns. Subsequent analysis of 183 supposed S. cerevisiae isolates of various ecological and geographical backgrounds revealed one misclassified S. bayanus or Saccharomyces uvarum isolate and four aneuploid interspecies hybrids, one between S. cerevisiae and S. bayanus and three between S. cerevisiae and S. kudriavzevii . Furthermore, this microarray design allowed the detection of multiple introgressed S. paradoxus DNA fragments in the genomes of three different S. cerevisiae isolates. These results show the power of multispecies-based microarrays as taxonomic tools for the identification of species and interspecies hybrids, and their ability to provide a more detailed characterization of interspecies hybrids and recombinants.     

Conserved amino acid networks involved in antibody variable domain interactions

Engineered antibodies are a large and growing class of protein therapeutics comprising both marketed products and many molecules in clinical trials in various disease indications. We investigated naturally conserved networks of amino acids that support antibody V_H and V_L function, with the goal of generating information to assist in the engineering of robust antibody or antibody‐like therapeutics. We generated a large and diverse sequence alignment of V‐class Ig‐folds, of which V_H and V_L domains are family members. To identify conserved amino acid networks, covariations between residues at all possible position pairs were quantified as correlation coefficients (?‐values). We provide rosters of the key conserved amino acid pairs in antibody V_H and V_L domains, for reference and use by the antibody research community. The majority of the most strongly conserved amino acid pairs in V_H and V_L are at or adjacent to the V_H–V_L interface suggesting that the ability to heterodimerize is a constraining feature of antibody evolution. For the V_H domain, but not the V_L domain, residue pairs at the variable‐constant domain interface (V_H–C_H1 interface) are also strongly conserved. The same network of conserved V_H positions involved in interactions with both the V_L and C_H1 domains is found in camelid V_HH domains, which have evolved to lack interactions with V_L and C_H1 domains in their mature structures; however, the amino acids at these positions are different, reflecting their different function. Overall, the data describe naturally occurring amino acid networks in antibody Fv regions that can be referenced when designing antibodies or antibody‐like fragments with the goal of improving their biophysical properties. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Streptococcus pneumoniae detects and responds to foreign bacterial peptide fragments in its environment

Streptococcus pneumoniae is an important cause of bacterial meningitis and pneumonia but usually colonizes the human nasopharynx harmlessly. As this niche is simultaneously populated by other bacterial species, we looked for a role and pathway of communication between pneumococci and other species. This paper shows that two proteins of non-encapsulated S. pneumoniae, AliB-like ORF 1 and ORF 2, bind specifically to peptides matching other species resulting in changes in the pneumococci. AliB-like ORF 1 binds specifically peptide SETTFGRDFN, matching 50S ribosomal subunit protein L4 of Enterobacteriaceae, and facilitates upregulation of competence for genetic transformation. AliB-like ORF 2 binds specifically peptides containing sequence FPPQS, matching proteins of Prevotella species common in healthy human nasopharyngeal microbiota. We found that AliB-like ORF 2 mediates the early phase of nasopharyngeal colonization in vivo. The ability of S. pneumoniae to bind and respond to peptides of other bacterial species occupying the same host niche may play a key role in adaptation to its environment and in interspecies communication. These findings reveal a completely new concept of pneumococcal interspecies communication which may have implications for communication between other bacterial species and for future interventional therapeutics.     

At home with the birds: Kalahari tree skinks associate with sociable weaver nests despite African pygmy falcon presence

The way in which animals use habitat can affect their access to key resources or how they are buffered from environmental variables such as the extreme temperatures of deserts. One strategy of animals is to modify the environment or take advantage of structures constructed by other species. The sociable weaver bird (Philetairus socius) constructs enormous colonial nests in trees. These nests are frequented by Kalahari tree skinks (Trachylepis spilogaster) and the two species coexist over a large portion of the Kalahari Desert in South Africa. We tested whether skinks were more abundant in trees containing sociable weaver nests and asked whether the physical features of trees were important predictors of skink abundance. We then focused on potential costs of this association by examining the relationship between skink abundance and the presence of a potential predator, the pygmy falcon (Polihierax semitorquatus), which exclusively uses weaver nest colonies for roosting and nesting. Finally, we simulated a predatory threat to determine if skinks assess risk differently if a weaver nest is present. We found a significant positive association between the presence of weaver nests and skink abundance. In the absence of nests, the type of tree did not influence skink abundance. Skinks used weaver nests and were more likely to perch on the nest than the tree. When threatened with predation, skinks preferred to take refuge in nests. Surprisingly, the presence of nesting pygmy falcons in nests did not influence skink abundance, perhaps because of the abundance of nearby refuges within nests, tree crevices, or in debris at the tree base. We suggest that sociable weaver nests provide multiple benefits to skinks including lowered predation risk, thermal refuges and greater prey availability, although this requires experimental testing. In the current era of global climate change, sociable weaver nests may become a crucial resource for skinks seeking refuge as the Kalahari climate warms.     

Crematogaster chiarinii ants as a potential biological control agent for protecting honeybee colonies from attack by Dorylus quadratus driver ants in Ethiopia (Hymenoptera: Formicidae)

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Spatial synchrony in the response of a long range migratory species (Salmo salar) to climate change in the North Atlantic Ocean

A major challenge in understanding the response of populations to climate change is to separate the effects of local drivers acting independently on specific populations, from the effects of global drivers that impact multiple populations simultaneously and thereby synchronize their dynamics. We investigated the environmental drivers and the demographic mechanisms of the widespread decline in marine survival rates of Atlantic salmon (Salmo salar) over the last four decades. We developed a hierarchical Bayesian life cycle model to quantify the spatial synchrony in the marine survival of 13 large groups of populations (called stock units, SU) from two continental stock groups (CSG) in North America (NA) and Southern Europe (SE) over the period 1971–2014. We found strong coherence in the temporal variation in postsmolt marine survival among the 13 SU of NA and SE. A common North Atlantic trend explains 37% of the temporal variability of the survivals for the 13 SU and declines by a factor of 1.8 over the 1971–2014 time series. Synchrony in survival trends is stronger between SU within each CSG. The common trends at the scale of NA and SE capture 60% and 42% of the total variance of temporal variations, respectively. Temporal variations of the postsmolt survival are best explained by the temporal variations of sea surface temperature (SST, negative correlation) and net primary production indices (PP, positive correlation) encountered by salmon in common domains during their marine migration. Specifically, in the Labrador Sea/Grand Banks for populations from NA, 26% and 24% of variance is captured by SST and PP, respectively and in the Norwegian Sea for populations from SE, 21% and 12% of variance is captured by SST and PP, respectively. The findings support the hypothesis of a response of salmon populations to large climate‐induced changes in the North Atlantic simultaneously impacting populations from distant continental habitats.