Vc生产菌“神舟七号”搭载育种

选取3株性状不同的Vc二步发酵生产菌搭载于"神舟七号"飞船进行空间诱变,返回地面后,经富集培养和分离,获得近12000株诱变菌株。采用试管微量培养并监测pH值法作3次初筛,获300余株优良株,再经摇瓶发酵定酸、糖法作3次复筛,选出12株优良菌株。新菌株摇瓶发酵转化率提高了5%～7%。研究了新菌株生产的最适发酵条件,调整了部分工艺过程,应用于大生产,转化率提高4%～5%。     

Did the introduction of maize into Europe provide enemy‐free space to Ostrinia nubilalis? Parasitism differences between two sibling species of the genus Ostrinia

We examined whether maize offers enemy‐free space (EFS) to its pest Ostrinia nubilalis, and may thereby have contributed to its divergence from the sibling species, Ostrinia scapulalis, feeding mainly on mugwort, when introduced into Europe five centuries ago. We collected Ostrinia larvae on maize (70 populations, 8425 individuals) and mugwort (10 populations, 1184 individuals) and recorded parasitism using both traditional (counting emerging parasitoids) and molecular methods (detection by specific polymerase chain reaction). The main parasitoid was Macrocentrus cingulum (Braconidae). On mugwort, parasitism was twice that on maize, and parasitoid‐related mortality was 8 times higher. This suggests that maize affords substantial EFS to Ostrinia feeding on it. The lower Mortality:Infestation ratio in maize suggests that O. nubilalis’ immune response might be stronger than that of O. scapulalis. If so, adapting to maize and diverging from O. scapulalis would decrease the impact of parasitism on O. nubilalis at both ecological and evolutionary levels.     

Competing species in a changing climate: effects of recruitment disturbances on two interacting barnacle species

1. The climate is changing and data-based simulation models can be a valuable tool for predicting population response to such changes and investigate the mechanisms of population change. In this study, a data-based two-species matrix model was constructed to explore the possible effects of elevated sea surface temperature (i.e. climate change) on the interaction between open populations of the south Atlantic barnacle species Chthamalus montagui and the boreal species Semibalanus balanoides in the north-east Atlantic. 2. First, the model was used to perform an elasticity analysis to determine the relative importance of recruitment and survival in the interaction. Further, three scenarios of changes in recruitment, related to climate change, were investigated with model simulations: (i) increased frequencies of low recruitment for S. balanoides; (ii) increased frequencies of high recruitment for C. montagui; (iii) a combination of (i) and (ii). 3. Model simulations showed that in present environmental conditions, S. balanoides occupied most of the space and dominated the interaction through high recruitment and survival. These results matched independent field observations, which validated the model for further analyses. 4. The elasticity analyses showed that although free space was available there was competition for space during recruitment intervals. It was also shown that both populations were sensitive to changes in recruitment. 5. Introducing the three scenarios of recruitment disturbances led to large changes in species abundance and free space. The most significant changes were found when scenario (i) and (ii) were combined, producing a shift in species dynamics towards C. montagui dominance. This demonstrates that recruitment can be an important mechanism in the interaction between populations and that the population response to changes in recruitment depends on the added response of interacting species. 6. In a more general context, this model shows that increased sea surface temperature could rapidly lead to increased competition from southern species at higher latitudes. This might accelerate the effects of climate change on the species distribution at these latitudes and eventually lead to changes in community dynamics on temperate and subarctic shores.     

Prediction of protease types in a hybridization space

Regulating most physiological processes by controlling the activation, synthesis, and turnover of proteins, proteases play pivotal regulatory roles in conception, birth, digestion, growth, maturation, ageing, and death of all organisms. Different types of proteases have different functions and biological processes. Therefore, it is important for both basic research and drug discovery to consider the following two problems. (1) Given the sequence of a protein, can we identify whether it is a protease or non-protease? (2) If it is, what protease type does it belong to? Although the two problems can be solved by various experimental means, it is both time-consuming and costly to do so. The avalanche of protein sequences generated in the post-genetic era has challenged us to develop an automated method for making a fast and reliable identification. By hybridizing the functional domain composition and pseudo-amino acid composition, we have introduced a new method called "FunD-PseAA predictor" that is operated in a hybridization space. To avoid redundancy and bias, demonstrations were performed on a dataset where none of the proteins has >or=25% sequence identity to any other. The overall success rate thus obtained by the jackknife cross-validation test in identifying protease and non-protease was 92.95%, and that in identifying the protease type was 94.75% among the following six types: (1) aspartic, (2) cysteine, (3) glutamic, (4) metallo, (5) serine, and (6) threonine. Demonstration was also made on an independent dataset, and the corresponding overall success rates were 98.36% and 97.11%, respectively, suggesting the FunD-PseAA predictor is very powerful and may become a useful tool in bioinformatics and proteomics.     

Fine‐scale movements and behaviors of coyotes (Canis latrans) during their reproductive period

In canids, resident breeders hold territories but require different resources than transient individuals (i.e., dispersers), which may result in differential use of space, land cover, and food by residents and transients. In the southeastern United States, coyote (Canis latrans) reproduction occurs during spring and is energetically demanding for residents, but transients do not reproduce and therefore can exhibit feeding behaviors with lower energetic rewards. Hence, how coyotes behave in their environment likely differs between resident and transient coyotes. We captured and monitored 36 coyotes in Georgia during 2018–2019 and used data from 11 resident breeders, 12 predispersing residents (i.e., offspring of resident breeders), and 11 transients to determine space use, movements, and relationships between these behaviors and landcover characteristics. Average home range size for resident breeders and predispersing offspring was 20.7 ± 2.5 km² and 50.7 ± 10.0 km², respectively. Average size of transient ranges was 241.4 ± 114.5 km². Daily distance moved was 6.3 ± 3.0 km for resident males, 5.5 ± 2.7 km for resident females, and 6.9 ± 4.2 km for transients. We estimated first‐passage time values to assess the scale at which coyotes respond to their environment, and used behavioral change‐point analysis to determine that coyotes exhibited three behavioral states. We found notable differences between resident and transient coyotes in regard to how landcover characteristics influenced their behavioral states. Resident coyotes tended to select for areas with denser vegetation while resting and foraging, but for areas with less dense vegetation and canopy cover when walking. Transient coyotes selected areas closer to roads and with lower canopy cover while resting, but for areas farther from roads when foraging and walking. Our findings suggest that behaviors of both resident and transient coyotes are influenced by varying landcover characteristics, which could have implications for prey.     

A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES

The molecular chaperone, GroEL, essential for correct protein folding in E. coli, is composed of 14 identical subunits organized in two interacting rings, each providing a folding chamber for non‐native substrate proteins. The oligomeric assembly shows positive cooperativity within each ring and negative cooperativity between the rings. Although it is well known that ATP and long‐range allosteric interactions drive the functional cycle of GroEL, an atomic resolution view of how ligand binding modulates conformational adaptations over long distances remains a major challenge. Moreover, little is known on the relation between equilibrium dynamics at physiological temperatures and the allosteric transitions in GroEL. Here we present multiple all‐atom molecular dynamics simulations of the GroEL‐GroES assemblies at different stages of the functional cycle. Combined with an extensive analysis of the complete set of experimentally available structures, principal component analysis and conformer plots, we provide an explicit evaluation of the accessible conformational space of unliganded GroEL. Our results suggest the presence of pre‐existing conformers at the equatorial domain level, and a shift of the conformational ensemble upon ATP‐binding. At the inter‐ring interface the simulations capture a remarkable offset motion of helix D triggered by ATP‐binding to the folding active ring. The reorientation of helix D, previously only observed upon GroES association, correlates with a change of the internal dynamics in the opposite ring. This work contributes to the understanding of the molecular mechanisms in GroEL and highlights the ability of all‐atom MD simulations to model long‐range structural changes and allosteric events in large systems. Proteins 2012;. © 2012 Wiley Periodicals, Inc.     

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.     

Natural foliar variegation without costs? The case of Begonia

Background and Aims

Foliar variegation is recognized as arising from two major mechanisms: leaf structure and pigment-related variegation. Begonia has species with a variety of natural foliar variegation patterns, providing diverse examples of this phenomenon. The aims of this work are to elucidate the mechanisms underlying different foliar variegation patterns in Begonia and to determine their physiological consequences.

Methods

Six species and one cultivar of Begonia were investigated. Light and electron microscopy revealed the leaf structure and ultrastructure of chloroplasts in green and light areas of variegated leaves. Maximum quantum yields of photosystem II were measured by chlorophyll fluorescence. Comparison with a cultivar of Ficus revealed key features distinguishing variegation mechanisms.

Key Results

Intercellular space above the chlorenchyma is the mechanism of variegation in these Begonia. This intercellular space can be located (a) below the adaxial epidermis or (b) below the adaxial water storage tissue (the first report for any taxa), creating light areas on a leaf. In addition, chlorenchyma cell shape and chloroplast distribution within chlorenchyma cells differ between light and green areas. Chloroplasts from both areas showed dense stacking of grana and stroma thylakoid membranes. The maximum quantum yield did not differ significantly between these areas, suggesting minimal loss of function with variegation. However, the absence of chloroplasts in light areas of leaves in the Ficus cultivar led to an extremely low quantum yield.

Conclusions

Variegation in these Begonia is structural, where light areas are created by internal reflection between air spaces and cells in a leaf. Two forms of air space structural variegation occur, distinguished by the location of the air spaces. Both forms may have a common origin in development where dermal tissue becomes loosely connected to mesophyll. Photosynthetic functioning is retained in light areas, and these areas do not include primary veins, potentially limiting the costs of variegation.     

Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117–200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.