Bicalcasura maculata n. gen., n. sp. (Curculionoidea: Dryophthoridae) with a list of weevils described from Dominican amber

A new genus and species, Bicalcasura maculata n. gen., n. sp. (Coleoptera: Curculionoidea: Rhynchophorinae: Dryophthoridae) is described from Dominican amber as the first fossil member of the Tribe Diocalandrini. The new genus is characterised by procoxae located in the middle of the prothorax; a thick, short and strongly curved rostrum with the scape not reaching the pronotum; a weak extension of the rostrum in respect to the antennal attachment; slightly elongated fifth ventrite; narrow (not bilobed) third tarsomere and a pair of apical spurs on the protibiae. This set of characters separates the fossil from the extant genus Diocalandra Faust, 1894, the only other member of this tribe. A list of weevils (Curculionoidea) described from Dominican amber is included.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:D25F7915-3C49-4E22-A37C-F574F573C67D     

Dependencies of Substitution Steps Number on Hamming Distance Are Identical For One-parameter Discrete Models of Both Direct and Parallel Genetic Diversity

Abstract

With the help of previously introduced enumeration procedure (M.Yu. Shchelkanov, A.N. Yudin, A.V Antonov, N.S. Starikov, A.A. Vedenov, E.V. Karamov, J. Biomol. Struct. Dyn. 15, 217–229 (1997)) and probability distribution function for the enumeration after some substitution steps (M.Yu. Shchelkanov, L.A. Soinov, V.V. Zalunin, D.A. Gumennyi, A.N. Yudin, A.A. Natan, V.B. Kireev, E.V. Karamov, J. Biomol. Struct. Dyn. 15, N 4, (1998)) we have demonstrated that dependencies of replication acts number on Hamming distance are identical for one-parameter discrete models of both direct and parallel genetic diversity.     

A Kinetic Approach to the Prediction of RNA Secondary Structures

Abstract

A new approach to the prediction of secondary RNA structures based on the analysis of the kinetics of molecular self-organisation is proposed herein. The Markov process is used to describe structural reconstructions during secondary structure formation. This process is modelled by a Monte-Carlo method. Examples of the calculation by this method of the secondary structures kinetic ensemble are given. Distribution of time-dependent probabilities within the ensembles is obtained.

An effective method for search for the equilibrium ensemble is also suggested. This method is based on the construction of a tree of all possible secondary structures of RNA. By ascribing a probability for each structure (according to its free energy) the Boltzmann equilibrium ensemble can be obtained.     

The chromosome cycle of prokaryotes

In both eukaryotes and prokaryotes, chromosomal DNA undergoes replication, condensation–decondensation and segregation, sequentially, in some fixed order. Other conditions, like sister‐chromatid cohesion (SCC), may span several chromosomal events. One set of these chromosomal transactions within a single cell cycle constitutes the ‘chromosome cycle’. For many years it was generally assumed that the prokaryotic chromosome cycle follows major phases of the eukaryotic one: –replication–condensation–segregation–(cell division)–decondensation–, with SCC of unspecified length. Eventually it became evident that, in contrast to the strictly consecutive chromosome cycle of eukaryotes, all stages of the prokaryotic chromosome cycle run concurrently. Thus, prokaryotes practice ‘progressive’ chromosome segregation separated from replication by a brief SCC, and all three transactions move along the chromosome at the same fast rate. In other words, in addition to replication forks, there are ‘segregation forks’ in prokaryotic chromosomes. Moreover, the bulk of prokaryotic DNA outside the replication–segregation transition stays compacted. I consider possible origins of this concurrent replication–segregation and outline the ‘nucleoid administration’ system that organizes the dynamic part of the prokaryotic chromosome cycle.     

Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors: Prime side chromane-containing inhibitors

The structure activity relationship of the prime region of conformationally restricted hydroxyethylamine (HEA) BACE inhibitors is described. Variation of the P1′ region provided selectivity over Cat-D with a series of 2,2-dioxo-isothiochromanes and optimization of the P2′ substituent of chromane–HEA(s) with polar substituents provided improvements in the compound’s in vitro permeability. Significant potency gains were observed with small aliphatic substituents such as methyl, n-propyl, and cyclopropyl when placed at the C-2 position of the chromane.     

Taxonomic review of genus Diaparsis Förster (Hymenoptera: Ichneumonidae: Tersilochinae) from South Korea

Eleven species of the genus Diaparsis, including two unidentified species, are recorded from South Korea. One new species, D. koreana Khalaim, et al., sp. nov., is described, and six species, D. carinifer (Thomson), D. convexa Khalaim, D. egregia Khalaim, D. hyperae Kusigemati, D. jucunda (Holmgren) and D. neoplicator Khalaim, are recorded from this country for the first time. Diaparsis hyperae and D. pulchra are the most abundant species of the genus in the Korean fauna. A key to eleven species of Diaparsis occurring in South Korea is provided.     

Role of the ectodomain serine 275 in shaping the binding pocket of the ATP-gated P2X3 receptor

ATP-activated P2X3 receptors expressed in nociceptive sensory neurons play an important role in pain signaling. Basic properties of this receptor subtype, including very strong desensitization, depend on the rate of dissociation of the agonist from the binding site. Even though the rough structure of the ATP binding site has been proposed on the basis of the X-ray structure of the zebrafish P2X4 receptor and mutagenesis studies, the fine subunit-specific structural properties predisposing the receptor to tight capture of the agonist inside the binding pocket have not been elucidated. In this work, by exploring in silico the functional role for the left flipper located in the ectodomain region, we identified within this loop a candidate residue S275, which could contribute to the closure of the agonist-binding pocket. Testing of the S275 mutants using the patch-clamp technique revealed a crucial role for S275 in agonist binding and receptor desensitization. The S275A mutant showed a reduced rate of onset of desensitization and accelerated resensitization and was weakly inhibited by nanomolar agonist. Extracellular calcium application produced inhibition instead of facilitation of membrane currents. Moreover, some full agonists became only partial agonists when applied to the S275A receptor. These effects were stronger with the more hydrophobic mutants S275C and S275V. Taken together, our data suggest that S275 contributes to the closure of the agonist-binding pocket and that effective capture of the agonist provided by the left flipper in calcium-dependent manner determines the high rate of desensitization, slow recovery, and sensitivity to nanomolar agonist of the P2X3 receptor.     

Linker and/or transmembrane regions of influenza A/Group-1, A/Group-2, and type B virus hemagglutinins are packed differently within trimers

Influenza virus hemagglutinin is a homotrimeric spike glycoprotein crucial for virions' attachment, membrane fusion, and assembly reactions. X-ray crystallography data are available for hemagglutinin ectodomains of various types/subtypes but not for anchoring segments. To get structural information for the linker and transmembrane regions of hemagglutinin, influenza A (H1-H16 subtypes except H8 and H15) and B viruses were digested with bromelain or subtilisin Carlsberg, either within virions or in non-ionic detergent micelles. Proteolytical fragments were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Within virions, hemagglutinins of most influenza A/Group-1 and type B virus strains were more susceptible to digestion with bromelain and/or subtilisin compared to A/Group-2 hemagglutinins. The cleavage sites were always located in the hemagglutinin linker sequence. In detergent, 1) bromelain cleaved hemagglutinin of every influenza A subtype in the linker region; 2) subtilisin cleaved Group-2 hemagglutinins in the linker region; 3) subtilisin cleaved Group-1 hemagglutinins in the transmembrane region; 4) both enzymes cleaved influenza B virus hemagglutinin in the transmembrane region. We propose that the A/Group-2 hemagglutinin linker and/or transmembrane regions are more tightly associated within trimers than type A/Group-1 and particularly type B ones. This hypothesis is underpinned by spatial trimeric structure modeling performed for transmembrane regions of both Group-1 and Group-2 hemagglutinin representatives. Differential S-acylation of the hemagglutinin C-terminal anchoring segment with palmitate/stearate residues possibly contributes to fine tuning of transmembrane trimer packing and stabilization since decreased stearate amount correlated with deeper digestion of influenza B and some A/Group-1 hemagglutinins.     

Manipulation of cell volume and membrane pore comparison following single cell permeabilization with 60- and 600-ns electric pulses

Intense nanosecond-duration electric pulses (nsEP) open stable nanopores in the cell membrane, followed by cell volume changes due to water uptake or expulsion, as regulated by the osmolality balance of pore-impermeable solutes inside and outside the cell. The size of pores opened by either fifty 60-ns EP (~13 kV/cm) or five, 600-ns EP (~6 kV/cm) in GH3 cells was estimated by isoosmotic replacement of bath NaCl with polyethylene glycols and sugars. Such replacement reduced cell swelling or resulted in transient or sustained cell shrinking in response to EP. depending on the availability of pores permeable to the test solute. Unexpectedly, solute substitutions showed that for the same integral area of pores opened by 60- and 600-ns treatments (as estimated by cell volume changes), the pore sizes were similar. However, the 600-ns exposure triggered significantly higher cell uptake of propidium. We concluded that 600-ns EP opened a greater number of larger (propidium-permeable pores), but the fraction of the larger pores in the entire pore population was insufficient to contribute to cell volume changes. For both the 60- and 600-ns exposures, cell volume changes were determined by pores smaller than 0.9 nm in diameter; however, the diameter increased with increasing the nsEP intensity.