Curvularia tsudae comb. nov. et nom. nov., formerly Pseudocochliobolus australiensis, and a revised synonymy for Curvularia australiensis

Cultures originally identified as Drechslera australiensis, from seeds of Chloris gayana in Japan, were the basis for Tsuda and Ueyama's new combination, Bipolaris australiensis, and its associated sexual morph Pseudocochliobolus australiensis. By studying ex-type materials of both Drechslera australiensis, which was originally isolated from seeds of Oryza sativa in Australia, and Pseudocochliobolus australiensis, we show by morphological and molecular phylogenetic analysis that these two specimens represent different species. Taxonomic confusion is resolved by the transfer of Pseudocochliobolus australiensis to Curvularia tsudae comb. nov. et nom. nov., together with a revised synonymy for Curvularia australiensis.

Proton NMR and infrared investigations of secondary dithiocarbamate ester: molecular conformation and vibrational assignment of S-methyl N-methyl dithiocarbamate

Rotational isomerism of S-methyl N-methyl dithiocarbamate (MMDTC) has been investigated by means of variable temperature proton NMR and i.r. spectroscopy. The i.r. spectra of MMDTC as neat, solution and at sub-ambient temperatures have been examined. Normal vibrational analysis of all the fundamentals of MMDTC has been carried out, the vibrational assignment has been compared with those of related secondary thioamides to note the consistency in the assignments and to obtain the pattern characteristic of the secondary thioamide vibrations.

Fungal Planet description sheets: 281–319

Novel species of fungi described in the present study include the following from South Africa: Alanphillipsia aloeicola from Aloe sp., Arxiella dolichandrae from Dolichandra unguiscati, Ganoderma austroafricanum from Jacaranda mimosifolia, Phacidiella podocarpi and Phaeosphaeria podocarpi from Podocarpus latifolius, Phyllosticta mimusopisicola from Mimusops zeyheri and Sphaerulina pelargonii from Pelargonium sp. Furthermore, Barssia maroccana is described from Cedrus atlantica (Morocco), Codinaea pini from Pinus patula (Uganda), Crucellisporiopsis marquesiae from Marquesia acuminata (Zambia), Dinemasporium ipomoeae from Ipomoea pes-caprae (Vietnam), Diaporthe phragmitis from Phragmites australis (China), Marasmius vladimirii from leaf litter (India), Melanconium hedericola from Hedera helix (Spain), Pluteus albotomentosus and Pluteus extremiorientalis from a mixed forest (Russia), Rachicladosporium eucalypti from Eucalyptus globulus (Ethiopia), Sistotrema epiphyllum from dead leaves of Fagus sylvatica in a forest (The Netherlands), Stagonospora chrysopyla from Scirpus microcarpus (USA) and Trichomerium dioscoreae from Dioscorea sp. (Japan). Novel species from Australia include: Corynespora endiandrae from Endiandra introrsa, Gonatophragmium triuniae from Triunia youngiana, Penicillium coccotrypicola from Archontophoenix cunninghamiana and Phytophthora moyootj from soil. Novelties from Iran include Neocamarosporium chichastianum from soil and Seimatosporium pistaciae from Pistacia vera, Xenosonderhenia eucalypti and Zasmidium eucalyptigenum are newly described from Eucalyptus urophylla in Indonesia. Diaporthe acaciarum and Roussoella acacia are newly described from Acacia tortilis in Tanzania. New species from Italy include Comoclathris spartii from Spartium junceum and Phoma tamaricicola from Tamarix gallica. Novel genera include (Ascomycetes): Acremoniopsis from forest soil and Collarina from water sediments (Spain), Phellinocrescentia from a Phellinus sp. (French Guiana), Neobambusicola from Strelitzia nicolai (South Africa), Neocladophialophora from Quercus robur (Germany), Neophysalospora from Cotymbia henryi (Mozambique) and Xenophaeosphaeria from Grewia sp. (Tanzania). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Discovering hidden structures in molecular data using a Bayesian partition model approach

Advancements in the analysis techniques have led to a rapid accumulation of biological data in databases. Such data often are in the form of sequences of observations, examples including DNA sequences and amino acid sequences of proteins. The scale and quality of the data give promises of answering various biologically relevant questions in more detail than what has been possible before. For example, one may wish to identify areas in an amino acid sequence, which are important for the function of the corresponding protein, or investigate how characteristics on the level of DNA sequence affect the adaptation of a bacterial species to its environment. Many of the interesting questions are intimately associated with the understanding of the evolutionary relationships among the items under consideration. The aim of this work is to develop novel statistical models and computational techniques to meet with the challenge of deriving meaning from the increasing amounts of data. Our main concern is on modeling the evolutionary relationships based on the observed molecular data. We operate within a Bayesian statistical framework, which allows a probabilistic quantification of the uncertainties related to a particular solution. As the basis of our modeling approach we utilize a partition model, which is used to describe the structure of data by appropriately dividing the data items into clusters of related items. Generalizations and modifications of the partition model are developed and applied to various problems. Large-scale data sets provide also a computational challenge. The models used to describe the data must be realistic enough to capture the essential features of the current modeling task but, at the same time, simple enough to make it possible to carry out the inference in practice. The partition model fulfills these two requirements. The problem-specific features can be taken into account by modifying the prior probability distributions of the model parameters. The computational efficiency stems from the ability to integrate out the parameters of the partition model analytically, which enables the use of efficient stochastic search algorithms.

Diagnostic Molecular Markers for Phosphine Resistance in U.S. Populations of Tribolium castaneum and Rhyzopertha dominica

Stored product beetles that are resistant to the fumigant pesticide phosphine (hydrogen phosphide) gas have been reported for more than 40 years in many places worldwide. Traditionally, determination of phosphine resistance in stored product beetles is based on a discriminating dose bioassay that can take up to two weeks to evaluate. We developed a diagnostic cleaved amplified polymorphic sequence method, CAPS, to detect individuals with alleles for strong resistance to phosphine in populations of the red flour beetle, Tribolium castaneum, and the lesser grain borer, Rhyzopertha dominica, according to a single nucleotide mutation in the dihydrolipoamide dehydrogenase (DLD) gene. We initially isolated and sequenced the DLD genes from susceptible and strongly resistant populations of both species. The corresponding amino acid sequences were then deduced. A single amino acid mutation in DLD in populations of T.castaneum and R.dominica with strong resistance was identified as P45S in T.castaneum and P49S in R.dominica, both collected from northern Oklahoma, USA. PCR products containing these mutations were digested by the restriction enzymes MboI and BstNI, which revealed presence or absence, respectively of the resistant (R) allele and allowed inference of genotypes with that allele. Seven populations of T.castaneum from Kansas were subjected to discriminating dose bioassays for the weak and strong resistance phenotypes. Application of CAPS to these seven populations confirmed the R allele was in high frequency in the strongly resistant populations, and was absent or at a lower frequency in populations with weak resistance, which suggests that these populations with a low frequency of the R allele have the potential for selection of the strong resistance phenotype. CAPS markers for strong phosphine resistance will help to detect and confirm resistant beetles and can facilitate resistance management actions against a given pest population.

Novel Pathotypes of Elsinoe australis Associated with Citrus australasica and Simmondsia chinensis in Australia

Molecular phylogenetic analysis, morphology and pathogenicity to citrus fruit were used to study two isolates of Elsinoe australis associated with scab-like symptoms on a fruit of Citrus australasica (finger lime) and Simmondsia chinensis (jojoba) in Australia. In addition to being associated with finger lime, the isolate from finger lime could cause scab symptoms on C. x aurantium cv. Murcott tangor in pathogenicity tests, but could not cause scab symptoms on the other orange, mandarin, lemon or grapefruit tested. Pathogenicity tests also support previous studies showing the isolate from jojoba could not produce symptoms on fruit of C. natsudaidai. Based on the findings of this study, two novel pathotypes of E. australis are designated from Australia; namely the Finger Lime (FL) pathotype associated with finger lime, and the Jojoba Black Scab (JBS) pathotype associated with black scab of jojoba. The significance of these novel E. australis pathotypes on market access and biosecurity issues for citrus are briefly discussed.

Polyphasic characterization of four new plant pathogenic Phyllosticta species from China, Japan, and the United States

The black rot disease of Vitis species and other host genera of Vitacease is caused by Phyllosticta ampelicida and allied taxa which is considered to be a species complex. In this paper, we introduce four new species of Phyllosticta, including two from the P. ampelicida complex, based on a polyphasic characterization including disease symptoms and host association, morphology, and molecular phylogeny. The phylogenetic analysis was conducted based on the ribosomal internal transcribed spacer (ITS) region and a combined multi-locus alignment of the ITS, actin (ACT), partial translation elongation factor 1-alpha (TEF-1), and glyceraldehydes 3-phosphate dehydrogenase (GPDH) gene regions. Our study confirms the phylogenetic distinctions of the four new species, as well as their phenotypic differences with known species in the genus.

Mathematical models on the impact of noise and dyadic molecular structures on the properties of a cardiac myocyte

In cardiac myocytes (heart muscle cells), coupling of electric signal known as the action potential to contraction of the heart depends crucially on calcium-induced calcium release (CICR) in a microdomain known as the dyad. During CICR, the peak number of free calcium ions (Ca) present in the dyad is small, typically estimated to be within range 1-100. Since the free Ca ions mediate CICR, noise in Ca signaling due to the small number of free calcium ions influences Excitation-Contraction (EC) coupling gain. Noise in Ca signaling is only one noise type influencing cardiac myocytes, e.g., ion channels playing a central role in action potential propagation are stochastic machines, each of which gates more or less randomly, which produces gating noise present in membrane currents. How various noise sources influence macroscopic properties of a myocyte, how noise is attenuated and taken advantage of are largely open questions. In this thesis, the impact of noise on CICR, EC coupling and, more generally, macroscopic properties of a cardiac myocyte is investigated at multiple levels of detail using mathematical models. Complementarily to the investigation of the impact of noise on CICR, computationally-efficient yet spatially-detailed models of CICR are developed. The results of this thesis show that (1) gating noise due to the high-activity mode of L-type calcium channels playing a major role in CICR may induce early after-depolarizations associated with polymorphic tachycardia, which is a frequent precursor to sudden cardiac death in heart failure patients; (2) an increased level of voltage noise typically increases action potential duration and it skews distribution of action potential durations toward long durations in cardiac myocytes; and that (3) while a small number of Ca ions mediate CICR, Excitation-Contraction coupling is robust against this noise source, partly due to the shape of ryanodine receptor protein structures present in the cardiac dyad.

Molecular evidence of Ebola Reston virus infection in Philippine bats

Background: In 2008-09, evidence of Reston ebolavirus (RESTV) infection was found in domestic pigs and pig workers in the Philippines. With species of bats having been shown to be the cryptic reservoir of filoviruses elsewhere, the Philippine government, in conjunction with the Food and Agriculture Organization of the United Nations, assembled a multi-disciplinary and multi-institutional team to investigate Philippine bats as the possible reservoir of RESTV. Methods: The team undertook surveillance of bat populations at multiple locations during 2010 using both serology and molecular assays. Results: A total of 464 bats from 21 species were sampled. We found both molecular and serologic evidence of RESTV infection in multiple bat species. RNA was detected with quantitative PCR (qPCR) in oropharyngeal swabs taken from Miniopterus schreibersii, with three samples yielding a product on conventional hemi-nested PCR whose sequences differed from a Philippine pig isolate by a single nucleotide. Uncorroborated qPCR detections may indicate RESTV nucleic acid in several additional bat species (M. australis, C. brachyotis and Ch. plicata). We also detected anti-RESTV antibodies in three bats (Acerodon jubatus) using both Western blot and ELISA. Conclusions: The findings suggest that ebolavirus infection is taxonomically widespread in Philippine bats, but the evident low prevalence and low viral load warrants expanded surveillance to elaborate the findings, and more broadly, to determine the taxonomic and geographic occurrence of ebolaviruses in bats in the region. © 2015 Jayme et al.

Neutron Scattering and Molecular Dynamics Evidence for Levitation Effect in Nanopores

Neutron Scattering and Molecular Dynamics Evidence for Levitation Effect in Nanopores ... Neutron scattering measurements and molecular dynamics simulations have been carried out on the three isomers of pentane (neopentane (neo), isopentane (iso), and n-pentane (n-)) adsorbed in zeolite NaY. ... In order to understand this surprising dependence, the dimensionless levitation parameter, γ, for atomic systems may be modified to suit molecular systems.

Baobabopsis, a new genus of graminicolous downy mildews from tropical Australia, with an updated key to the genera of downy mildews

So far 19 genera of downy mildews have been described, of which seven are parasitic to grasses. Here, we introduce a new genus, Baobabopsis, to accommodate two distinctive downy mildews, B. donbarrettii sp. nov., collected on Perotis rara in northern Australia, and B. enneapogonis sp. nov., collected on Enneapogon spp. in western and central Australia. Baobabopsis donbarrettii produced both oospores and sporangiospores that are morphologically distinct from other downy mildews on grasses. Molecular phylogenetic analyses showed that the two species of Baobabopsis occupied an isolated position among the known genera of graminicolous downy mildews. The importance of the Poaceae for the evolution of downy mildews is highlighted by the observation that more than a third of the known genera of downy mildews occur on grasses, while more than 90 % of the known species of downy mildews infect eudicots.

Molecular vibrations and conformation of primary dithiocarbamate ester. Infrared and NMR studies on S-methyl dithiocarbamate

The i.r. spectra of a primary dithiocarbamate ester namely, S-methyl dithiocarbamate (SMDTC) and its N-dideuterated compound have been measured between 4000 and 30 cm−1. Spectra in solution and at liquid nitrogen temperature have also been obtained. Assignment of all the fundamentals has been proposed and supported from a full normal coordinate analysis. The band assignments for SMDTC have been compared with those of related molecules and the characteristic bands of primary thioamides are derived. Conformational flexibility of SMDTC has been examined by i.r. and proton NMR spectroscopy. The hindered rotation around the C---N bond has been studied by a complete line shape analysis. The magnitude of ---NH2 and ---CH3 torsional barriers is also estimated from vibrational frequencies and force constants.

Molecular structures of cytidine-5-diphosphate and cytidine-5-diphospho-choline, and their role in intermediary metabolism

The nucleotide coenzyme cytidine-5-diphospho-choline is highly folded. The CMP-5 parts of the molecules in the crystal structure are strongly linked by metal ligation and hydrogen bonds leaving the phosphoryl-choline residues relatively free. Cytidine-5-diphosphoric acid exists as a zwitterion with N31 protonated. The P−O bond lengths from the anhydride bridging oxygen in the pyrophosphate are significantly different.

Molecular structure of nicotinamide adenine dinucleotide

NICOTINAMIDE adenine dinucleotide (NAD) has a fundamental role in metabolic processes as an electron transport molecule. Although its chemical structure was elucidated1 in 1934, its detailed conformation remains still to be established in spite of numerous physicochemical applications2. NAD analogues with a variety of substitutions on the bases are known to retain considerable activity of the natural coenzyme as long as the pyrophosphate diester group has been retained3,4. The geometry of this backbone moiety is therefore indispensable to our understanding of the conformation and function of the coenzyme. We have so far no experimental evidence on this in NAD or any other nucleotide coenzyme molecule. X-ray studies have been possible only on those analogues5,6 where the nicotinamide and adenine rings are linked by a trimethylene bridge. The results are conflicting and it is difficult to use them to provide a structural basis for the NAD molecule itself, particularly as the phosphate backbone is absent from these analogues.

An uncommon nucleotide conformation shown by molecular structure of deoxyuridine-5-phosphate and nucleic acid stereochemistry

CRYSTAL structure determinations of nucleic acid fragments have shown that several of the conformational features found in the monomeric building blocks are also manifested at the nucleic acid level. Stereochemical variations between thymine and uracil nucleotides are therefore of interest as they can provide a structural basis for some of the differences between the conformations of DNA and RNA. X-ray studies have so far not shown any major dissimilarities between these two nucleotide species although the sugar ring of deoxyribonucleotides is found to possess greater flexibility than that in ribonucleotides. We report here the molecular structure of deoxyuridine-5'-phosphate (dUMP-5') which is not a common monomer unit of DNAs as it is replaced by its 5-methyl analogue deoxythymidine-5'-phosphate (dTMP-5'). The investigation was undertaken to help determine whether or not this implied a fundamental difference between the geometries of these two molecules.