Inhibitory effects on phospholipase A2 and antivenin activity of melanin extracted from Thea sinensis Linn

Antivenin activity of melanin extracted from black tea (MEBT) was reported for the first time. The antagonistic effect of MEBT was evaluated for Agkistrodon contortrix laticinctus (broadbanded copperhead), Agkistrodon halys blomhoffii (Japanese mamushi), and Crotalus atrox (western diamondback rattlesnake) snake venoms administered i.p. to ICR mice. MEBT was injected i.p. immediately after the venom administration in dose of 3 mg per mouse in the same place of venom injection. MEBT demonstrated neutralization effect against all venoms tested. The greatest antivenin effect of MEBT was found against Japanese mamushi snake venom. In this case, half the mice died within 2.5 +/- 0.7 h after injection of 0.9 mg/kg of venom. An immediate injection of MEBT substantially reduced the toxic effect of venom and extended time at the 50% level of survival up to 52.3 +/- 2.3 h. The antivenin activity of MEBT is due to chelating of Ca++ and non-specific binding of phospholipase A2. The inhibitory effect of MEBT on phospholipase A2 assessed for different venoms was similar to that obtained with pure enzyme. Low toxicity of MEBT in combination with its antagonistic activity against different venoms may allow effective life-saving treatment against snakebites. Such application of MEBT is important when identification of the snake is impossible or if specific treatment is unavailable.     

Inhibition of voltage-gated Na(+) current by nanosecond pulsed electric field (nsPEF) is not mediated by Na(+) influx or Ca(2+) signaling

In earlier studies, we found that permeabilization of mammalian cells with nsPEF was accompanied by prolonged inhibition of voltage-gated (VG) currents through the plasma membrane. This study explored if the inhibition of VG Na(+) current (I(Na)) resulted from (i) reduction of the transmembrane Na(+) gradient due to its influx via nsPEF-opened pores, and/or (ii) downregulation of the VG channels by a Ca(2+)-dependent mechanism. We found that a single 300 ns electric pulse at 1.6-5.3 kV/cm triggered sustained Na(+) influx in exposed NG108 cells and in primary chromaffin cells, as detected by increased fluorescence of a Sodium Green Dye. In the whole-cell patch clamp configuration, this influx was efficiently buffered by the pipette solution so that the increase in the intracellular concentration of Na(+) ([Na](i)) did not exceed 2-3 mM. [Na](i) increased uniformly over the cell volume and showed no additional peaks immediately below the plasma membrane. Concurrently, nsPEF reduced VG I(Na) by 30-60% (at 4 and 5.3 kV/cm). In control experiments, even a greater increase of the pipette [Na(+)] (by 5 mM) did not attenuate VG I(Na), thereby indicating that the nsPEF-induced Na(+) influx was not the cause of VG I(Na) inhibition. Similarly, adding 20 mM of a fast Ca(2+) chelator 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA) into the pipette solution did not prevent or attenuate the inhibition of the VG I(Na) by nsPEF. These findings point to possible Ca(2+)-independent downregulation of the VG Na(+) channels (e.g., caused by alteration of the lipid bilayer) or the direct effect of nsPEF on the channel.     

Aptorchis glandularis n. sp. (Digenea: Plagiorchioidea) from the northwestern red-faced turtle, Emydura australis, (Pleurodira: Chelidae) in the Kimberley, Western Australia

Aptorchis glandularis n. sp. is described from the intestine of the northwestern red-faced turtle, Emydura australis (Pleurodira: Chelidae), in the Kimberley, Western Australia. This digenean is morphologically most similar to Aptorchis aequalis but can be differentiated readily from the latter species by the presence of ventral glands arranged in 3 rows. This feature is unique among plagiorhioidean digeneans and resembles the glands observed in some monostome digeneans in Notocotylidae and Microscaphidiidae. Comparison of approximately 2,600 bases of ribosomal DNA (partial 18S, complete ITS1+5.8S+ITS2, partial 28S), obtained from all 5 known Aptorchis species, strongly supports the status of Aptorchis glandularis n. sp. as a new species. Phylogenetic analysis of these sequence data demonstrates 2 strongly supported clades (A. pearsoni + A. megacetabulus) and (A. aequalis + A. glandularis n. sp.), with A. megapharynx representing a separate lineage. This is the first report of an endoparasite from Emydura australis.     

Four-alpha-helix bundle with designed anesthetic binding pockets. Part I: structural and dynamical analyses

The four-α-helix bundle mimics the transmembrane domain of the Cys-loop receptor family believed to be the protein target for general anesthetics. Using high resolution NMR, we solved the structure (Protein Data Bank ID: 2I7U) of a prototypical dimeric four-α-helix bundle, (Aα₂-L1M/L38M)₂, with designed specific binding pockets for volatile anesthetics. Two monomers of the helix-turn-helix motif form an antiparallel dimer as originally designed, but the high-resolution structure exhibits an asymmetric quaternary arrangement of the four helices. The two helices from the N-terminus to the linker (helices 1 and 1′) are associated with each other in the dimer by the side-chain ring stacking of F12 and W15 along the long hydrophobic core and by a nearly perfect stretch of hydrophobic interactions between the complementary pairs of L4, L11, L18, and L25, all of which are located at the heptad e position along the helix-helix dimer interface. In comparison, the axes of the two helices from the linker to the C-terminus (helices 2 and 2′) are wider apart from each other, creating a lateral access pathway around K47 from the aqueous phase to the center of the designed hydrophobic core. The site of the L38M mutation, which was previously shown to increase the halothane binding affinity by ∼3.5-fold, is not part of the hydrophobic core presumably involved in the anesthetic binding but shows an elevated transverse relaxation (R₂) rate. Qualitative analysis of the protein dynamics by reduced spectral density mapping revealed exchange contributions to the relaxation at many residues in the helices. This observation was confirmed by the quantitative analysis using the Modelfree approach and by the NMR relaxation dispersion measurements. The NMR structures and Autodock analysis suggest that the pocket with the most favorable amphipathic property for anesthetic binding is located between the W15 side chains at the center of the dimeric hydrophobic core, with the possibility of two additional minor binding sites between the F12 and F52 ring stacks of each monomer. The high-resolution structure of the designed anesthetic-binding protein offers unprecedented atomistic details about possible sites for anesthetic-protein interactions that are essential to the understanding of molecular mechanisms of general anesthesia.     

New structural–optical effect in LiF–Li2B4O7 thin-film structures in the crystallization

The effect of optical radiation during the phase transition from the amorphous to the crystalline state of matter was investigated for the first time. The results were obtained on nanoscale films of (LiF)_x(Li₂B₄O₇)_1-x compositions by sputtering on cold Ni substrates. The starting materials for films were chosen due to their wide use for tissue-equivalent ionizing radiation dosimetry. It is shown that the detected thermoluminescence effect is sensitive to the thickness of the films. The paper compares the results of these studies with the study of the thermoluminescence characteristics of films irradiated by an M-30 microtron with bremsstrahlung radiation with a maximum energy of 6 MeV. The absorbed radiation dose was 1 kGy. Differences in the luminescence characteristics of irradiated and nonirradiated films were revealed. The nature of the demonstrated structural–optical effect is discussed.     

The Psilostomidae Looss, 1900 (<Emphasis Type="Italic">sensu stricto</Emphasis>) (Digenea: Echinostomatoidea): description of three new genera and a key to the genera of the family

Three new psilostomid genera, Byrdtrema n. g., Longisaccus n. g. and Macracetabulum n. g., each with a single species, are described from ducks, Aix sponsa (L.) and Bucephala albeola (L.) in North America. Byrdtrema n. g. and Macracetabulum n. g. possess a bipartite seminal vesicle and share this character with four psilostomid genera, Grysoma Byrd, Bogitsh & Maples, 1961, Neopsilotrema Kudlai, Pulis, Kostadinova & Tkach, 2016, Psilostomum Looss, 1899 and Psilotornus Byrd & Prestwood, 1969. Byrdtrema n. g. differs from Macracetabulum n. g. in the shape of the body (elongate vs elongate-oval); the position of the ventral sucker (in first third of body vs just pre-equatorial); the shorter forebody; as well as in the smaller size of the eggs in relation to body length. Both new genera differ from (i) Grysoma by the nature of the vitellarium (large, compact follicles with small vitelline cells vs weakly defined follicles with large vitelline cells, respectively) and the smaller size of the eggs in relation to body length; (ii) Psilostomum in the posterior extend of the cirrus-sac in relation to ventral sucker (slightly posterior vs more posterior), the location of the genital pore (at the level of oesophagus vs just postbifurcal), the shorter length of uterine and longer post-testicular fields in relation to body length, and the anterior limits of vitellarium (at the level of ventral sucker vs posterior to ventral sucker); (iii) Psilotornus by the presence of a muscular pharynx (vs absent or rudimentary) and the location of the cirrus-sac (antero-dorsal to ventral sucker or more posterior vs entirely anterior to ventral sucker) and ovary (in hindbody vs in forebody). Byrdtrema n. g. differs from Neopsilotrema in the shape of the body (elongate vs subspherical to elongate-oval) and ventral sucker (elongate-oval vs subspherical to transversely oval), the shorter forebody and smaller eggs in relation to body length. Macracetabulum n. g. differs from Neopsilotrema by the shape of the ventral sucker (elongate-oval vs subspherical to transversely oval), the anterior limits of vitellarium (level of middle of ventral sucker vs level of intestinal bifurcation or anterior testis); and the slightly smaller size of eggs in relation to body length. Among the psilostomid genera, Longisaccus n. g. shows close affinities to Psilochasmus Lühe, 1909 in the presence of the long cirrus-sac and tubular internal seminal vesicle but can be clearly distinguished from the latter by the absence of the retractile tail-like process. In combination with molecular data, the above differences justify the recognition of three new genera. A key to the genera of the Psilostomidae is provided.     

Erysiphe kenjiana (Erysiphales), a new invasive fungus in Europe

An Asian powdery mildew fungus Erysiphe (Uncinula) kenjiana (Erysiphales, Ascomycota) has been found in Ukraine. This is the first record of this fungus in Europe. In 2007, E. kenjiana was collected on four Ulmus species in Kiev. All locations adjoined railways or an airport. Development of E. kenjiana was epiphytotic. This species was not found on elms surveyed at towns situated north-east, east or south of Kiev. The fungus may have been brought directly to Ukraine by rail or air transport. In 2008, the fungus was also collected in Chernihiv situated north-east of Kiev. It is likely that E. kenjiana will spread over all Ukraine and into countries of central and western Europe in 2009 or later. Molecular phylogenetic analyses using D1/D2 domains of the 28S rDNA and ITS sequences revealed that the Ulmaceae-Cannabaceae-parasitic powdery mildews, including E. kenjiana, form a clade with strong supports, suggesting that these species diverged from a single ancestor and expanded their host ranges within the Ulmaceae and allied Cannabaceae. This hypothesis is supported by these species sharing the unique morphology of enlarged apices on their chasmothecial appendages. These fungi formed part of a larger grouping with species on Fagaceae, Nothofagaceae, Rosaceae, and Sapindaceae with strong statistical supports. These results suggest that Uncinula-like powdery mildew fungi on these plant families exhibit close evolutionary relationships with their hosts.     

RankAggreg, an R package for weighted rank aggregation

Background  

Researchers in the field of bioinformatics often face a challenge of combining several ordered lists in a proper and efficient manner. Rank aggregation techniques offer a general and flexible framework that allows one to objectively perform the necessary aggregation. With the rapid growth of high-throughput genomic and proteomic studies, the potential utility of rank aggregation in the context of meta-analysis becomes even more apparent. One of the major strengths of rank-based aggregation is the ability to combine lists coming from different sources and platforms, for example different microarray chips, which may or may not be directly comparable otherwise.     

New Macroderoides (Digenea: Macroderoididae) from Florida gar, with molecular phylogeny of the genus

Macroderoides minutus n. sp. is described based on specimens collected from the Florida gar (Lepisosteus platyrhincus) from Orange Lake, Alachua County, Florida. The new species is the ninth recognized species of Macroderoides and is morphologically closest to Macroderoides flavus and Macroderoides typicus. It differs from both species in having a smaller body, ventral sucker larger than the oral sucker, substantially lower body length to width ratio, fewer and larger eggs, and other characters. A comparison of sequences of nuclear rDNA (partial 18S, complete ITS region, and partial 28S) of the new species, with sequences of 5 other Macroderoides, convincingly supports the status of M. minutus as a new species. Molecular phylogenetic analysis, including all North American Macroderoides species except for Macroderoides parvus, has demonstrated the presence of 2 distinct clades, 1 including Macroderoides spinifer + (Macroderoides minutus n. sp. + Macroderoides texanus) and the other including Macroderoides trilobatus + (M. typicus + M. flavus). The tree topology suggests that the similarity in body proportions among M. minutus n. sp., M. typicus + M. flavus is not a result of close phylogenetic relationship. It has also revealed for the first time the phylogenetic affinities of M. flavus, which is the only North American member of Macroderoides that switched from holostean fishes to teleosts.     

Paraoistosomum novaeguineae n. gen., n. sp. (Digenea) from a New Guinea crocodile: a surprising relative of the enigmatic Oistosomum caduceus Odhner, 1902

Paraoistosomum novaeguineae n. gen., n. sp. is described based on specimens from the kidneys of a New Guinea crocodile Crocodylus novaeguineae collected in Papua New Guinea. The body shape and the topology of most internal organs of the new species are strongly reminiscent of Oistosomum caduceus Odhner 1902, the sole member of Oistosomum, a genus of unclear phylogenetic relationships and systematic position described from the Nile crocodile in Sudan in 1902 and never reported since then. At the same time, the new species has a number of significant differences from Oistosomum caduceus. Among them are much shorter intestinal ceca, a relatively larger ventral sucker, ovary anterolateral to ventral sucker (posterolateral in O. caduceus ), vitellaria arranged in 2 clusters of loosely organized follicles at the level of ventral sucker (2 narrow long lateral fields in O. caduceus ), much longer esophagus, and other characters. Most importantly, the new species has the genital pore situated at the anterior body end adjacent to the oral sucker, whereas O. caduceus has the genital pore in front of the ventral sucker. These dramatic differences suggest establishment of a new genus for the species from Papua New Guinea. The anatomy of P. novaeguineae n. gen., n. sp. suggests that these genera may not belong to the Plagiorchiidae, the current familial allocation of Oistosomum. Scarcity of material and lack of molecular data do not permit clarification of this problem at the present time.