ProDy: protein dynamics inferred from theory and experiments

SUMMARY: We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods. AVAILABILITY: ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/.     

Kebab: kinetochore and EB1 associated basic protein that dynamically changes its localisation during Drosophila mitosis

Microtubule plus ends are dynamic ends that interact with other cellular structures. Microtubule plus end tracking proteins are considered to play important roles in the regulation of microtubule plus ends. Recent studies revealed that EB1 is the central regulator for microtubule plus end tracking proteins by recruiting them to microtubule plus ends through direct interaction. Here we report the identification of a novel Drosophila protein, which we call Kebab (kinetochore and EB1 associated basic protein), through in vitro expression screening for EB1-interacting proteins. Kebab fused to GFP shows a novel pattern of dynamic localisation in mitosis. It localises to kinetochores weakly in metaphase and accumulates progressively during anaphase. In telophase, it associates with microtubules in central-spindle and centrosomal regions. The localisation to kinetochores depends on microtubules. The protein has a domain most similar to the atypical CH domain of Ndc80, and a coiled-coil domain. The interaction with EB1 is mediated by two SxIP motifs but is not required for the localisation. Depletion of Kebab in cultured cells by RNA interference did not show obvious defects in mitotic progression or microtubule organisation. Generation of mutants lacking the kebab gene indicated that Kebab is dispensable for viability and fertility.     

DNA methylation changes associated with risk factors in tumors of the upper aerodigestive tract

Cancers of the upper aerodigestive tract (UADT) are common forms of malignancy associated with tobacco and alcohol exposures, although human papillomavirus and nutritional deficiency are also important risk factors. While somatically acquired DNA methylation changes have been associated with UADT cancers, what triggers these events and precise epigenetic targets are poorly understood. In this study, we applied quantitative profiling of DNA methylation states in a panel of cancer-associated genes to a case-control study of UADT cancers. Our analyses revealed a high frequency of aberrant hypermethylation of several genes, including MYOD1, CHRNA3 and MTHFR in UADT tumors, whereas CDKN2A was moderately hypermethylated. Among differentially methylated genes, we identified a new gene (the nicotinic acetycholine receptor gene) as target of aberrant hypermethylation in UADT cancers, suggesting that epigenetic deregulation of nicotinic acetycholine receptors in non-neuronal tissues may promote the development of UADT cancers. Importantly, we found that sex and age is strongly associated with the methylation states, whereas tobacco smoking and alcohol intake may also influence the methylation levels in specific genes. This study identifies aberrant DNA methylation patterns in UADT cancers and suggests a potential mechanism by which environmental factors may deregulate key cellular genes involved in tumor suppression and contribute to UADT cancers.Key words: DNA methylation, upper aerodigestive tract, cancer, risk factors, biomarkers     

The role of the housefly, Musca domestica, in the spread of Aujeszky''s disease (pseudorabies)

Starved houseflies were held over a suspension of Aujeszky's virus (PRV-1) for 24-48 h. One group was rinsed in 70% ethanol to kill virus attached to the body surface. No virus was isolated from this group. For the other group the titre of virus decreased more rapidly on the body surface of flies than in the environment. Model experiments demonstrated that the Aujeszky's virus cannot survive in the body of the housefly but the body surface may be contaminated for a period of time depending on the initial viral titre. Experiments showed that susceptible pigs fed on flies contaminated with Aujeszky's virus may become infected. The quantity of virus (5 x 10(5) pfu ml-1) shed by a single housefly during biting and vomiting on the cornea or abraded skin proved to be sufficient to cause infection in susceptible pigs, rabbits and a lamb. It is possible that houseflies could play a role in transmission of infection within herds. Transmission between herds is much less likely.     

Circadian rest-activity rhythm in chronic obstructive pulmonary disease

To characterize circadian rest-activity rhythm in COPD, 26 cases (66.9 ± 8.5y) and 15 controls (63.0 ± 10.7y) were assessed by actimetry. Rhythm fragmentation was measured by intradaily variability (IV), while synchronization to the 24-h light-dark cycle was measured by interdaily stability (IS). The average activity during the least active 5-h period (L5) and the average activity during the most active 10-h period (M10) were used to calculate the relative amplitude mean [RAm = (M10-L5)/(M10+L5)]. COPD patients presented higher IVm (0.242 ± 0.097 vs 0.182 ± 0.063) and L5 (36.849 ± 18.239 vs 19.888 ± 12.268) and lower RAm (0.696 ± 0.134 vs 0.833 ± 0.093) than controls. Future studies on the effects of chronotherapy measures in COPD are warranted.     

Influence of prior experience on shell selection by the white spotwrist hermit crab Pagurus criniticornis (Crustacea: Paguridae)

Individuals of Pagurus criniticornis in a free-choice situation were experimentally tested under different laboratory conditions. In order to assess the effect of recently occupied shells on the size- and type-preference by hermit crabs, individuals were held for 30 days under one of the following two conditions: (1) excess of shells and (2) absence of shells. The crabs were then allowed to select shells from a wide array of empty gastropod shells of the two most-occupied species, as observed previously in the field: Cerithium atratum and Morula nodulosa. Preferred shell type (species) and size (shell aperture width and length) were correlated with hermit-crab size. The crabs showed a strong (100%) preference for C. atratum shells, demonstrating that recent and past experience did not influence either shell-type or shell-size preferences in this pagurid. Handling editor: K. Martens     

Synthesis and properties of new trinuclear Mo(II) complexes containing imidazole and benzimidazole ferrocene units

The reaction of FcCOCl (Fc = (C₅H₅)Fe(C₅H₄)) with benzimidazole or imidazole in 1:1 ratio gives the ferrocenyl derivatives FcCO(benzim) (L1) or FcCO(im) (L2), respectively. Two molecules of L1 or L2 can replace two nitrile ligands in [Mo(η³-C₃H₅)(CO)₂(CH₃CN)₂Br] or [Mo(η³- C₅H₅O)(CO)₂(CH₃CN)₂Br] leading to the new trinuclear complexes [Mo(η³-C₃H₅)(CO)₂(L)₂Br] (C1 for L = L1; C3 for L = L2) and [Mo(η³-C₅H₅O)(CO)₂(L)₂Br] (C2 for L = L1; C4 for L = L2) with L1 and L2 acting as N-monodentade ligands. L1, L2 and C2 were characterized by X-ray diffraction studies. [Mo(η³-C₅H₅O)(CO)₂(L1)₂Br] was shown to be a trinuclear species, with the two L1 molecules occupying one equatorial and one axial position in the coordination sphere of Mo(II). Cyclic voltammetric studies were performed for the two ligands L1 and L2, as well as for their molybdenum complexes, and kinetic and thermodynamic data for the corresponding redox processes obtained. In agreement with the nature of the frontier orbitals obtained from DFT calculations, L1 and L2 exhibit one oxidation process at the Fe(II) center, while C1, C3, and C4 display another oxidation wave at lower potentials, associated with the oxidation of Mo(II).