Structural plasticity of an invariant hydrophobic triad in the switch regions of Rab GTPases is a determinant of effector recognition

Rab GTPases function as regulatory components of an evolutionarily conserved machinery that mediates docking, priming, and fusion of vesicles with intracellular membranes. We have previously shown that the active conformation of Rab3A is stabilized by a substantial hydrophobic interface between the putative conformational switch regions (Dumas, J. J., Zhu, Z., Connolly, J. L., and Lambright, D. G. (1999) Structure 7, 413-423). A triad of invariant hydrophobic residues at this switch interface (Phe-59, Trp-76, and Tyr-91) represents a major interaction determinant between the switch regions of Rab3A and the Rab3A-specific effector Rabphilin3A (Ostermeier, C., and Brunger, A. T. (1999) Cell 96, 363-374). Here, we report the crystal structure of the active form of Rab5C, a prototypical endocytic Rab GTPase. As is true for Rab3A, the active conformation of Rab5C is stabilized by a hydrophobic interface between the switch regions. However, the conformation of the invariant hydrophobic triad (residues Phe-58, Trp-75, and Tyr-90 in Rab5C) is dramatically altered such that the resulting surface is noncomplementary to the switch interaction epitope of Rabphilin3A. This structural rearrangement reflects a set of nonconservative substitutions in the hydrophobic core between the central beta sheet and the alpha2 helix. These observations demonstrate that structural plasticity involving an invariant hydrophobic triad at the switch interface contributes to the mechanism by which effectors recognize distinct Rab subfamilies. Thus, the active conformation of the switch regions conveys information about the identity of a particular Rab GTPase as well as the state of the bound nucleotide.     

Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Background  

The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words.     

U.K. winter egg survival in the field and laboratory diapause of Typhlodromips montdorensis

Abstract. Typhlodromips montdorensis has potential for release as a glasshouse biological control agent in the U.K. against thrips and spider mites. This study investigates the field survival in the U.K. of T. montdorensis when released as eggs, and the diapause response when reared in a regime related to its location of origin. All acclimated and nonacclimated eggs of T. montdorensis die in the field within 7 days of exposure. It is not possible to induce diapause in T. montdorensis reared at 21 °C under a LD 11 : 13 h photoperiod. The results presented here support the view that T. montdorensis is unlikely to survive a U.K. winter outside of the glasshouse environment, and contribute to the understanding of the biology of this little known species.     

Establishment potential of the predatory mirid <Emphasis Type="Italic">Dicyphus hesperus</Emphasis> in northern Europe

The predatory mirid Dicyphus hesperus Knight (Hemiptera: Miridae) is native to North America. The species has been used for the control of glasshouse whitefly on aubergine in the Netherlands, and is currently being evaluated for continued and wider release in Europe. Field and laboratory studies were conducted on a population collected from southern California, USA, to assess the cold tolerance and potential for outdoor establishment under prevailing northern European climates. The supercooling points (whole animal freezing temperatures) of nymphal and adult insects were around −20°C. The lethal temperatures (LTemp₅₀) of non-diapausing nymphs and adults and diapausing adults were close to their respective freezing temperatures at −17.6, −17.6 and −19.2°C. At 5°C, the LTime₅₀ was 54, 101.7 and 117.5 days for fed nymphs, non-diapausing and diapausing adults respectively. When first instar nymphs were placed in the field in winter, starved samples died out after 70 days, but 5% of the fed nymphs survived until the end of winter (140 days) and developed to adult on return to the laboratory. After a similar 5-month field exposure, 50% of fed diapausing adults and 15% of fed non-diapausing adults were still alive at the end of winter, whereas starved diapausing adults died after 140 days. On return to the laboratory after 5 months in the field, both diapausing and non-diapausing adults mated and laid eggs, forming viable populations. Overall, the field and laboratory experiments indicate that this population of D. hesperus is able to enter diapause and that winter temperatures are not a barrier to establishment in northern Europe.     

Estimating the rate of evolution of the rate of molecular evolution

A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.      

Intraguild Predation and Feeding Preferences in Three Species of Phytoseiid Mite Used for Biological Control

The ecological impact of introduced biological control agents on native species of arthropods is a matter of considerable debate. This study investigated the ability of the non-native predatory mite Neoseiulus californicus to feed on the native Typhlodromus pyri and vice versa, as both species now co-occur in UK orchards. Typhlodromips montdorensis is a candidate for introduction into the UK as a glasshouse biological control agent. The ability of T. montdorensis to feed on the widely used N. californicus was investigated to identify possible intraguild predation, which might influence the effectiveness of either or both species as predators of Tetranychus urticae. Both N. californicus and T. pyri consumed larval stages of each other, but in choice experiments both showed a preference for T. urticae. Both N. californicus and T. montdorensis also fed on each other, but whereas N. californicus again showed a preference for T. urticae, T. montdorensis fed equally on T. urticae and N. californicus. Interactions between N. californicus and T. pyri and N. californicus and T. montdorensis are discussed in relation to their effectiveness as biological control agents in the glasshouse and the natural control of spider mite in the field.     

Evaluation of a candidate International Standard for Meningococcal Group C polysaccharide

Meningococcal group C (MenC) plain polysaccharide (PS) and conjugate vaccines are primarily evaluated by physicochemical methods to ensure that batches are consistently manufactured. As different assays are employed to quantify the MenC PS content of final formulations and bulk intermediaries, there is a need for an International MenC PS Standard to calibrate internal references used in the different laboratories. Twelve laboratories from nine different countries participated in a collaborative study to determine the MenC PS content of a candidate International Standard MenC PS preparation (08/214) and to assess its suitability. On the basis of the results from this study the candidate standard 08/214 was established as an International Standard for the quantification of MenC PS content in vaccines and components. It has a content of 1.192 ± 0.192 mg MenC PS/ampoule (expanded uncertainty with coverage factor of k = 2.365 corresponding to a 95% level of confidence), as determined by the resorcinol assays carried out by eight of the participating laboratories. The standard is available from The National Institute of Biological Standards and Control who act as guardians and distributors of the material under the auspices of WHO.     

Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features

Background  

Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and utilizes ideas from statistical information retrieval to discover and characterize properties shared by subsets of the list. The practical utility of this method is demonstrated by employing it in a retrospective study of two non-overlapping sets of genes defined by a published investigation as markers for normal human breast luminal epithelial cells and myoepithelial cells.     

Thermal biology of Typhlodromips montdorensis: implications for its introduction as a glasshouse biological control agent in the UK

The recent unexpected local establishment of a non‐native predatory mite, Neoseiulus californicus (McGregor) (Acari: Phytoseiidae), in the UK prompted us to undertake this study, which investigated the thermal biology of an alien species Typhlodromips montdorensis (Schicha) (Acari: Phytoseiidae). Laboratory and field experiments on its cold tolerance were used to assess its establishment potential outside of glasshouse environments in the UK. Currently, T. montdorensis is being tested as a glasshouse biological control agent against thrips and spider mites, but is not yet licensed for release in the UK. Typhlodromips montdorensis has a developmental threshold of between 10.3 and 10.7 °C, and a thermal budget of between 108.7 and 105.3 degree‐days when estimated by weighted and simple linear regression, respectively. Under outdoor conditions, T. montdorensis could theoretically complete up to six generations a year. The supercooling points of female and larval T. montdorensis were ?22 to ?24 °C with 100% pre‐freeze mortality apparent in both acute and chronic low temperature exposures. Typhlodromips montdorensis were unable to enter diapause under a selected laboratory regime. No reproduction occurred in the field from November to March, with 100% mortality within 7–14 days of release during this period. It is concluded that T. montdorensis would be a ‘safe candidate’ for introduction as a glasshouse biological control agent in the UK.     

Influence of Boar and Semen Parameters on Motility and Acrosome Integrity in Liquid Boar Semen Stored for Five Days

Ninety ejaculates from a total of 76 AI boars were extended in Beltsville Thawing Solution (BTS). Boar identity, breed, weight of the ejaculate and sperm concentration were registered. Motility and acrosome integrity were assessed after storage at 16–18°C for 6, 30, 54, 78, and 102 h. Storage time had a significant influence on both motility (p < 0.01) and acrosome integrity (p < 0.001). The Least Square Means for percentage of motility showed a small decline from 79.8% after 6 h of storage to 78.4% at 102 h. Motility at 78 and 102 h was significantly different from motility at 6 h (p < 0.05). The percentage of sperm cells with normal acrosomes declined throughout the experiment. The Least Square Means for 6, 30, 54, 78, and 102 h of storage were 93.9%, 90.6%, 88.0%, 84.8%, and 78.2%, respectively. The decrease in acrosome integrity from one storage time to the next was highly significant throughout the trial (p < 0.001). There was a significant influence of boar (p < 0.001) and sperm concentration (p < 0.01) on motility, while acrosome integrity was affected only by boar (p < 0.001). Breed of the boars and weight of the ejaculate did not influence the dependent variables.