Effects of dietary n-3 fatty acids on the phospholipid molecular species of monkey brain.

PubMed

Lin, D S; Connor, W E; Anderson, G J; Neuringer, M

1990-10-01

We examined the changes in the molecular species of brain ethanolamine glycerophospholipids of monkeys fed diets containing widely ranging amounts of n-3 fatty acids. Two groups of rhesus monkeys were fed pre- and postnatally either a control diet (soy oil; containing 8% of fatty acids as 18:3n-3) or a deficient diet (safflower oil; containing less than 0.3% 18:3n-3). The brains of these animals were analyzed at 22 months of age. A third group of monkeys was fed the safflower oil diet to 22 months of age and then switched to a fish oil diet (28% long-chain n-3 fatty acids) for 1-2 years before autopsy. The molecular species of the diacyl, alkylacyl, and alkenylacyl ethanolamine glycerophospholipids from frontal cortex were separated by HPLC. A total of 24 molecular species were identified. Fatty acids in the sn-2 position differed markedly among the diet groups, but the sn-1 position always contained only 16:0, 18:0, or 18:1. In the diacyl subclass of the control brain, the n-3 molecular species represented 41% of total and the n-6 species 45%, whereas in the deficient brain the n-3 molecular species decreased to 9% and n-6 molecular species increased to 77%. The fatty acid 22:5n-6 did not replace 22:6n-3 in a symmetrical fashion in the molecular species of the deficient brain. In the brains of the fish oil-fed monkeys, the n-3 molecular species amounted to 61% and n-6 molecular species were reduced to 25%. The species 18:1-22:6, 16:0-22:6, and 18:0-22:6 generally changed proportionally in response to diet.(ABSTRACT TRUNCATED AT 250 WORDS)

The activation strain model and molecular orbital theory

PubMed Central

Wolters, Lando P; Bickelhaupt, F Matthias

2015-01-01

The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324–343. doi: 10.1002/wcms.1221 PMID:26753009

Molecular characterization and RAPD analysis of Juniperus species from Iran.

PubMed

Kasaian, J; Behravan, J; Hassany, M; Emami, S A; Shahriari, F; Khayyat, M H

2011-06-07

The genus Juniperus L. (Cupressaceae), an aromatic evergreen plant, consists of up to 68 species around the world. We classified five species of Juniperus found in Iran using molecular markers to provide a means for molecular identification of Iranian species. Plants were collected (three samples of each species) from two different provinces of Iran (Golestan and East Azarbayejan). The DNA was extracted from the leaves using a Qiagen Dneasy Plant Mini Kit. Amplification was performed using 18 ten-mer RAPD primers. Genetic distances were estimated based on 187 RAPD bands to construct a dendrogram by means of unweighted pair group method of arithmetic means. It was found that J. communis and J. oblonga were differentiated from the other species. Genetic distance values ranged from 0.19 (J. communis and J. oblonga) to 0.68 (J. communis and J. excelsa). Juniperus foetidissima was found to be most similar to J. sabina. Juniperus excelsa subspecies excelsa and J. excelsa subspecies polycarpos formed a distinct group.

Molecular tools for cryptic Candida species identification with applications in a clinical laboratory.

PubMed

Gamarra, Soledad; Dudiuk, Catiana; Mancilla, Estefanía; Vera Garate, María Verónica; Guerrero, Sergio; Garcia-Effron, Guillermo

2013-01-01

Candida spp. includes more than 160 species but only 20 species pose clinical problems. C. albicans and C. parapsilosis account for more than 75% of all the fungemias worldwide. In 1995 and 2005, one C. albicans and two C. parapsilosis-related species were described, respectively. Using phenotypic traits, the identification of these newly described species is inconclusive or impossible. Thus, molecular-based procedures are mandatory. In the proposed educational experiment we have adapted different basic molecular biology techniques designed to identify these species including PCR, multiplex PCR, PCR-based restriction endonuclease analysis and nuclear ribosomal RNA amplification. During the classes, students acquired the ability to search and align gene sequences, design primers, and use bioinformatics software. Also, in the performed experiments, fungal molecular taxonomy concepts were introduced and the obtained results demonstrated that classic identification (phenotypic) in some cases needs to be complemented with molecular-based techniques. As a conclusion we can state that we present an inexpensive and well accepted group of classes involving important concepts that can be recreated in any laboratory. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Method of molecular specie alteration by nonresonant laser induced dielectric breakdown

DOEpatents

Ronn, Avigdor M.

1980-01-01

Irradiation of a molecular specie by itself or in the presence of a secondary material at a pressure above a threshold value for the particular system by a laser of predetermined minimum power and having a frequency displaced from an absorption line of the specie causes severance of the weakest bond and a yield of products containing at least one dissociative fragment from said specie. A Rogowski type TEA CO.sub.2 --N.sub.2 --He laser has been used successfully on a wide variety of molecular species. Solid, liquid and gaseous end products have been obtained depending upon the starting materials. When solids have been produced they are in the form of microfine particles or microfine aggregates. A neodymium glass laser has also been used successfully.

Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China.

PubMed

Feng, Shang-Guo; Lu, Jiang-Jie; Gao, Ling; Liu, Jun-Jun; Wang, Hui-Zhong

2014-04-01

Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.

Anti-inflammatory and antioxidant properties of Piper species: a perspective from screening to molecular mechanisms.

PubMed

Kumar, Sarvesh; Malhotra, Shashwat; Prasad, Ashok K; Van der Eycken, Erik V; Bracke, Marc E; Stetler-Stevenson, William G; Parmar, Virinder S; Ghosh, Balaram

2015-01-01

Identifying novel therapeutic agents from natural sources and their possible intervention studies has been one of the major areas in biomedical research in recent years. Piper species are highly important - commercially, economically and medicinally. Our groups have been working for more than two decades on the identification and characterization of novel therapeutic lead molecules from Piper species. We have extensively studied the biological activities of various extracts of Piper longum and Piper galeatum, and identified and characterized novel molecules from these species. Using synthetic chemistry, various functional groups of the lead molecules were modified and structure activity relationship (SAR) studies identified synthetic molecules with better efficacy and lower IC50 values. Moreover, the mechanisms of actions of some of these molecules were studied at the molecular level. The objective of this review is to summarize experimental data published from our laboratories and others on antioxidant and anti-inflammatory potentials of Piper species and their chemical constituents.

A new Sparassis species from Spain described using morphological and molecular data.

PubMed

Blanco-Dios, Jaime B; Wang, Zheng; Binder, Manfred; Hibbett, David S

2006-10-01

Sparassis miniensis, collected in Pinus pinaster forests in Galicia (northwest Iberian Peninsula) is described as a new species, based on morphological and molecular data. Sparassis miniensis is morphologically distinct from all other species in the genus Sparassis based on scattered flabellae, which are strongly laciniated, azonate, and arise from an orange to rose-purplish base. The sporadic presence of clamp connections is restricted to subhymenial hyphae. Molecular data from LSU-rDNA, ITS and partial gene coding RNA polymerase subunit II (rpb2) suggest a close relationship between the new species S. miniensis and S. brevipes, another European species producing large fruiting bodies but with entire flabellae and no clamp connections.

Molecular convergence of the parasitic plant species Cuscuta reflexa and Phelipanche aegyptiaca.

PubMed

Rehker, Jan; Lachnit, Magdalena; Kaldenhoff, Ralf

2012-08-01

The parasitic plant species Cuscuta reflexa and Phelipanche aegyptiaca have independently developed parasitism, the former parasitizing on shoots and the latter attaching to roots. Regardless of these differences, the two species use similar organs, termed haustoria, to attach to the host plant. In this study, we show that this morphological similarity can be extended to the molecular level. An attAGP-promoter from Solanum lycopersicum, which is activated by Cuscuta infections, was also induced after infection by P. aegyptiaca. Furthermore, we show by validation of transcriptome sequencing data that the Phelipanche orthologue of a haustorium-specific Cuscuta gene, which codes for a cysteine proteinase, was activated in the early stages of Phelipanche invasion. Inhibition of the Phelipanche cysteine proteinase was achieved by 35S- or attAGP-promoter-driven expression of its intrinsic inhibitory polypeptide. A reduction in P. aegyptiaca infection rates during experiments in flower pots and in an in vitro polybag system in comparison to controls was recorded.

Phylogenetic Molecular Species Delimitations Unravel Potential New Species in the Pest Genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae)

PubMed Central

Dumas, Pascaline; Barbut, Jérôme; Le Ru, Bruno; Silvain, Jean-François; Clamens, Anne-Laure; d’Alençon, Emmanuelle; Kergoat, Gael J.

2015-01-01

Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence). As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae), a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster) species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens) ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808), S. frugiperda (J.E. Smith, 1797) and S. mauritia (Boisduval, 1833)) and support the synonymy of S. marima (Schaus, 1904) with S. ornithogalli (Guenée, 1852). They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858) and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities. PMID:25853412

Low molecular weight species in humic and fulvic fractions

USGS Publications Warehouse

Wilson, M.A.; Collin, P.J.; Malcolm, R.L.; Perdue, E. Michael; Cresswell, P.

1988-01-01

Fourier transform solution 1H nuclear magnetic resonance (NMR) spectrometry with homogated water peak irradiation is a useful method for detecting low molecular weight substances in humic extracts. Succinate, acetate, methanol, formate, lactate and some aryl methoxyl compounds have been detected in extracts from a wide range of sources. In view of the controversy over whether low molecular weight substances are contaminants in humic extracts introduced by the concentration procedure, we report that some of these materials are not contaminants since 1H-NMR can be used to follow their formation from higher molecular weight species. ?? 1988.

Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae, Pucciniales) on Willows in China

PubMed Central

Zhao, Peng; Wang, Qing-Hong; Tian, Cheng-Ming; Kakishima, Makoto

2015-01-01

The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was

Molecular Identification of Cryptosporidium Species from Pet Snakes in Thailand.

PubMed

Yimming, Benjarat; Pattanatanang, Khampee; Sanyathitiseree, Pornchai; Inpankaew, Tawin; Kamyingkird, Ketsarin; Pinyopanuwat, Nongnuch; Chimnoi, Wissanuwat; Phasuk, Jumnongjit

2016-08-01

Cryptosporidium is an important pathogen causing gastrointestinal disease in snakes and is distributed worldwide. The main objectives of this study were to detect and identify Cryptosporidium species in captive snakes from exotic pet shops and snake farms in Thailand. In total, 165 fecal samples were examined from 8 snake species, boa constrictor (Boa constrictor constrictor), corn snake (Elaphe guttata), ball python (Python regius), milk snake (Lampropeltis triangulum), king snake (Lampropeltis getula), rock python (Python sebae), rainbow boa (Epicrates cenchria), and carpet python (Morelia spilota). Cryptosporidium oocysts were examined using the dimethyl sulfoxide (DMSO)-modified acid-fast staining and a molecular method based on nested-PCR, PCR-RFLP analysis, and sequencing amplification of the SSU rRNA gene. DMSO-modified acid-fast staining revealed the presence of Cryptosporidium oocysts in 12 out of 165 (7.3%) samples, whereas PCR produced positive results in 40 (24.2%) samples. Molecular characterization indicated the presence of Cryptosporidium parvum (mouse genotype) as the most common species in 24 samples (60%) from 5 species of snake followed by Cryptosporidium serpentis in 9 samples (22.5%) from 2 species of snake and Cryptosporidium muris in 3 samples (7.5%) from P. regius.

Molecular Identification of Cryptosporidium Species from Pet Snakes in Thailand

PubMed Central

Yimming, Benjarat; Pattanatanang, Khampee; Sanyathitiseree, Pornchai; Inpankaew, Tawin; Kamyingkird, Ketsarin; Pinyopanuwat, Nongnuch; Chimnoi, Wissanuwat; Phasuk, Jumnongjit

2016-01-01

Cryptosporidium is an important pathogen causing gastrointestinal disease in snakes and is distributed worldwide. The main objectives of this study were to detect and identify Cryptosporidium species in captive snakes from exotic pet shops and snake farms in Thailand. In total, 165 fecal samples were examined from 8 snake species, boa constrictor (Boa constrictor constrictor), corn snake (Elaphe guttata), ball python (Python regius), milk snake (Lampropeltis triangulum), king snake (Lampropeltis getula), rock python (Python sebae), rainbow boa (Epicrates cenchria), and carpet python (Morelia spilota). Cryptosporidium oocysts were examined using the dimethyl sulfoxide (DMSO)-modified acid-fast staining and a molecular method based on nested-PCR, PCR-RFLP analysis, and sequencing amplification of the SSU rRNA gene. DMSO-modified acid-fast staining revealed the presence of Cryptosporidium oocysts in 12 out of 165 (7.3%) samples, whereas PCR produced positive results in 40 (24.2%) samples. Molecular characterization indicated the presence of Cryptosporidium parvum (mouse genotype) as the most common species in 24 samples (60%) from 5 species of snake followed by Cryptosporidium serpentis in 9 samples (22.5%) from 2 species of snake and Cryptosporidium muris in 3 samples (7.5%) from P. regius. PMID:27658593

Phosphatidylglycerol molecular species of photosynthetic membranes analyzed by high-performance liquid chromatography: theoretical considerations.

PubMed

Xu, Y; Siegenthaler, P A

1996-02-01

A reversed-phase high-performance liquid chromatography technique was developed to separate, identify, and quantify individual phosphatidylglycerol (PG) molecular species in thylakoid membranes isolated from higher plant leaves. PG was first separated by thin-layer chromatography; then the dinitrobenzoyl derivatives of diacylglycerols produced after phospholipase C hydrolysis of PG were separated by a C18 reversed-phase column and detected at 254 nm. A linear response of the detector was observed in the range of 0.025 to 12 nmol of PG molecular species. It was established that there was an excellent correlation (r = 0.996) between the carbon and double-bond number in the aliphatic residues and the relative retention time of dinitrobenzoyl derivatives. A new equivalent carbon number value (ECN*) which takes into consideration the number of cis-(nc) and trans-(nt) double bonds per molecular species was defined as ECN* = CN - 2nc - nt, where CN is the number of carbon atoms in the aliphatic residues. The logarithm of the retention time increased linearily as a function of ECN* value. However, in this type of correlation, it may happen that two molecular species of PG having distinct relative retention times had the same ECN* value. In this case, the two molecular species can be identified by the linear correlation (r = 1) existing between the reciprocal of the relative retention time and the number of double bonds (0 < or = n < or = 3) in the separate 18:n/delta 3-trans-hexadecenoic acid -16:1(3t)- and 18:n/16:0 molecular species series. The advantages of this method are good separation, cohort elution time, quantitative precision, and predictable retention times of PG molecular species from chloroplast membranes. The method has been used routinely to identify the ten PG molecular species of thylakoid membranes in squash, potato, lettuce, and spinach leaf: 18:3/16:1(3t), 18:3/16:0, 18:2/16:1(3t), 18:2/16:0, 18:1/16:1(3t), 18:1/16:0, 18:0/16:1(3t), 18:0/16:0, 16

Molecular ecology studies of species radiations: current research gaps, opportunities and challenges.

PubMed

de la Harpe, Marylaure; Paris, Margot; Karger, Dirk N; Rolland, Jonathan; Kessler, Michael; Salamin, Nicolas; Lexer, Christian

2017-05-01

Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations. © 2017 John Wiley & Sons Ltd.

Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles.

PubMed

Fujisawa, Tomochika; Vogler, Alfried P; Barraclough, Timothy G

2015-01-22

Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.

Comparative molecular cytogenetic characterization of seven Deschampsia (Poaceae) species.

PubMed

Amosova, Alexandra V; Bolsheva, Nadezhda L; Zoshchuk, Svyatoslav A; Twardovska, Maryana O; Yurkevich, Olga Yu; Andreev, Igor O; Samatadze, Tatiana E; Badaeva, Ekaterina D; Kunakh, Viktor A; Muravenko, Olga V

2017-01-01

The genus Deschampsia P. Beauv (Poaceae) involves a group of widespread polymorphic species. Some of them are highly tolerant to stressful and variable environmental conditions, and D. antarctica is one of the only two vascular plants growing in Antarctic. This species is a source of useful for selection traits and a valuable model for studying an environmental stress tolerance in plants. Genome diversity and comparative chromosomal phylogeny within the genus have not been studied yet as karyotypes of most Deschampsia species are poorly investigated. We firstly conducted a comparative molecular cytogenetic analysis of D. antarctica (Antarctic Peninsula) and related species from various localities (D. cespitosa, D. danthonioides, D. elongata, D. flexuosa (= Avenella flexuosa), D. parvula and D. sukatschewii by fluorescence in situ hybridization with 45S and 5S rDNA, DAPI-banding and sequential rapid in situ hybridization with genomic DNA of D. antarctica, D. cespitosa, and D. flexuosa. Based on patterns of distribution of the examined markers, chromosomes of the studied species were identified. Within these species, common features as well as species peculiarities in their karyotypic structure and chromosomal distribution of molecular cytogenetic markers were characterized. Different chromosomal rearrangements were detected in D. antarctica, D. flexuosa, D. elongata and D. sukatschewii. In karyotypes of D. antarctica, D. cespitosa, D. elongata and D. sukatschewii, 0-3 B chromosomes possessed distinct DAPI-bands were observed. Our findings suggest that the genome evolution of the genus Deschampsia involved polyploidy and also different chromosomal rearrangements. The obtained results will help clarify the relationships within the genus Deschampsia, and can be a basis for the further genetic and biotechnological studies as well as for selection of plants tolerant to extreme habitats.

Complexity in Dioryctria zimmermani Species Group: Incongruence Between Species Limits and Molecular Diversity

Treesearch

Amanda D. Roe; Daniel R. Miller; Susan J. Weller

2011-01-01

Dioryctria (Zeller 1846) (Lepidoptera: Pyralidae: Phycitinae) moths, commonlyknown as coneworms, are a group of important coniferous pests. InterspeciÞc overlap of molecular, morphological, and behavioral traits has made identiÞcation and delimitation of these species problematic, impeding their management and control. In particular, delimitation of members of the...

Comparative molecular cytogenetic characterization of seven Deschampsia (Poaceae) species

PubMed Central

Bolsheva, Nadezhda L.; Zoshchuk, Svyatoslav A.; Twardovska, Maryana O.; Yurkevich, Olga Yu; Andreev, Igor O.; Samatadze, Tatiana E.; Badaeva, Ekaterina D.; Kunakh, Viktor A.; Muravenko, Olga V.

2017-01-01

The genus Deschampsia P. Beauv (Poaceae) involves a group of widespread polymorphic species. Some of them are highly tolerant to stressful and variable environmental conditions, and D. antarctica is one of the only two vascular plants growing in Antarctic. This species is a source of useful for selection traits and a valuable model for studying an environmental stress tolerance in plants. Genome diversity and comparative chromosomal phylogeny within the genus have not been studied yet as karyotypes of most Deschampsia species are poorly investigated. We firstly conducted a comparative molecular cytogenetic analysis of D. antarctica (Antarctic Peninsula) and related species from various localities (D. cespitosa, D. danthonioides, D. elongata, D. flexuosa (= Avenella flexuosa), D. parvula and D. sukatschewii by fluorescence in situ hybridization with 45S and 5S rDNA, DAPI-banding and sequential rapid in situ hybridization with genomic DNA of D. antarctica, D. cespitosa, and D. flexuosa. Based on patterns of distribution of the examined markers, chromosomes of the studied species were identified. Within these species, common features as well as species peculiarities in their karyotypic structure and chromosomal distribution of molecular cytogenetic markers were characterized. Different chromosomal rearrangements were detected in D. antarctica, D. flexuosa, D. elongata and D. sukatschewii. In karyotypes of D. antarctica, D. cespitosa, D. elongata and D. sukatschewii, 0–3 B chromosomes possessed distinct DAPI-bands were observed. Our findings suggest that the genome evolution of the genus Deschampsia involved polyploidy and also different chromosomal rearrangements. The obtained results will help clarify the relationships within the genus Deschampsia, and can be a basis for the further genetic and biotechnological studies as well as for selection of plants tolerant to extreme habitats. PMID:28407010

[Differentiation of species within the Mycobacterium tuberculosis complex by molecular techniques].

PubMed

Herrera-León, Laura; Pozuelo-Díaz, Rodolfo; Molina Moreno, Tamara; Valverde Cobacho, Azucena; Saiz Vega, Pilar; Jiménez Pajares, María Soledad

2009-11-01

The Mycobacterium tuberculosis complex includes the following species: Mycobacterium tuberculosis, Mycobacterium africanum, Mycobacterium bovis, Mycobacterium bovis-BCG, Mycobacterium microti, Mycobacterium caprae, Mycobacterium pinnipedii, and Mycobacterium canettii. These species cause tuberculosis in humans and animals. Identification of mycobacterial strains has classically been performed by phenotype study. Over the last years, laboratories have developed several molecular techniques to differentiate between these species. The aim of this study is to evaluate these methods and develop a simple, fast, identification scheme. We analyzed 251 strains randomly obtained from the strains studied in 2004, and 797 strains received by the Reference Laboratory between 2005 and 2007. Phenotype characterization of 4183 strains isolated during that period was done by studying the colony morphology, characteristics in culture, nitrate reduction, niacin accumulation, and growth in the presence of thiophen-2-carboxylic acid hydrazide 10 microg/mL and pyrazinamide 50 microg/mL. The molecular identification scheme designed was as follows: 1) gyrB PCR-RFLP with RsaI, TaqI or SacII and hsp65 RFLP/PCR with HhaI., and 2) multiplex-PCR to determine the presence/absence of the RD9 and RD1 regions. The results showed 100% agreement between phenotype study and the molecular scheme. This molecular identification scheme is a simple and fast method, with 100% sensitivity and specificity, that can be implemented in most clinical laboratories at a low cost.

Abiotic stresses activate a MAPkinase in the model grass species Lolium temulentum L.

USDA-ARS?s Scientific Manuscript database

Forage and turf grasses are utilized in diverse environments which exposes them to a variety of abiotic stresses, however very little is known concerning the perception or molecular responses to these various stresses. In the model grass species Lolium temulentum (Lt), a 46 kDa mitogen-activated pro...

Advances in conservation endocrinology: the application of molecular approaches to the conservation of endangered species.

PubMed

Tubbs, Christopher; McDonough, Caitlin E; Felton, Rachel; Milnes, Matthew R

2014-07-01

Among the numerous societal benefits of comparative endocrinology is the application of our collective knowledge of hormone signaling towards the conservation of threatened and endangered species - conservation endocrinology. For several decades endocrinologists have used longitudinal hormone profiles to monitor reproductive status in a multitude of species. Knowledge of reproductive status among individuals has been used to assist in the management of captive and free-ranging populations. More recently, researchers have begun utilizing molecular and cell-based techniques to gain a more complete understanding of hormone signaling in wildlife species, and to identify potential causes of disrupted hormone signaling. In this review we examine various in vitro approaches we have used to compare estrogen receptor binding and activation by endogenous hormones and phytoestrogens in two species of rhinoceros; southern white and greater one-horned. We have found many of these techniques valuable and practical in species where access to research subjects and/or tissues is limited due to their conservation status. From cell-free, competitive binding assays to full-length receptor activation assays; each technique has strengths and weaknesses related to cost, sensitivity, complexity of the protocols, and relevance to in vivo signaling. We then present a novel approach, in which receptor activation assays are performed in primary cell lines derived from the species of interest, to minimize the artifacts of traditional heterologous expression systems. Finally, we speculate on the promise of next generation sequencing and transcriptome profiling as tools for characterizing hormone signaling in threatened and endangered species. Copyright © 2014 Elsevier Inc. All rights reserved.

Intact molecular characterization of cord factor (trehalose 6,6'-dimycolate) from nine species of mycobacteria by MALDI-TOF mass spectrometry.

PubMed

Fujita, Yukiko; Naka, Takashi; McNeil, Michael R; Yano, Ikuya

2005-10-01

Cord factor (trehalose 6,6'-dimycolate, TDM) is an unique glycolipid with a trehalose and two molecules of mycolic acids in the mycobacterial cell envelope. Since TDM consists of two molecules of very long branched-chain 3-hydroxy fatty acids, the molecular mass ranges widely and in a complex manner. To characterize the molecular structure of TDM precisely and simply, an attempt was made to determine the mycolic acid subclasses of TDM and the molecular species composition of intact TDM by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for the first time. The results showed that less than 1 microg mycolic acid methyl ester of TDM from nine representative species of mycobacteria and TDM from the same species was sufficient to obtain well-resolved mass spectra composed of pseudomolecular ions [M+Na]+. Although the mass ion distribution was extremely diverse, the molecular species of each TDM was identified clearly by constructing a molecular ion matrix consisting of the combination of two molecules of mycolic acids. The results showed a marked difference in the molecular structure of TDM among mycobacterial species and subspecies. TDM from Mycobacterium tuberculosis (H37Rv and Aoyama B) showed a distinctive mass pattern and consisted of over 60 molecular ions with alpha-, methoxy- and ketomycolate. TDM from Mycobacterium bovis BCG Tokyo 172 similarly showed over 35 molecular ions, but that from M. bovis BCG Connaught showed simpler molecular ion clusters consisting of less than 35 molecular species due to a complete lack of methoxymycolate. Mass ions due to TDM from M. bovis BCG Connaught and Mycobacterium kansasii showed a biphasic distribution, but the two major peaks of TDM from M. kansasii were shifted up two or three carbon units higher compared with M. bovis BCG Connaught. Within the rapid grower group, in TDM consisting of alpha-, keto- and wax ester mycolate from Mycobacterium phlei and Mycobacterium flavescens, the

Morphology delimits more species than molecular genetic clusters of invasive Pilosella.

PubMed

Moffat, Chandra E; Ensing, David J; Gaskin, John F; De Clerck-Floate, Rosemarie A; Pither, Jason

2015-07-01

• Accurate assessments of biodiversity are paramount for understanding ecosystem processes and adaptation to change. Invasive species often contribute substantially to local biodiversity; correctly identifying and distinguishing invaders is thus necessary to assess their potential impacts. We compared the reliability of morphology and molecular sequences to discriminate six putative species of invasive Pilosella hawkweeds (syn. Hieracium, Asteraceae), known for unreliable identifications and historical introgression. We asked (1) which morphological traits dependably discriminate putative species, (2) if genetic clusters supported morphological species, and (3) if novel hybridizations occur in the invaded range.• We assessed 33 morphometric characters for their discriminatory power using the randomForest classifier and, using AFLPs, evaluated genetic clustering with the program structure and subsequently with an AMOVA. The strength of the association between morphological and genotypic dissimilarity was assessed with a Mantel test.• Morphometric analyses delimited six species while genetic analyses defined only four clusters. Specifically, we found (1) eight morphological traits could reliably distinguish species, (2) structure suggested strong genetic differentiation but for only four putative species clusters, and (3) genetic data suggest both novel hybridizations and multiple introductions have occurred.• (1) Traditional floristic techniques may resolve more species than molecular analyses in taxonomic groups subject to introgression. (2) Even within complexes of closely related species, relatively few but highly discerning morphological characters can reliably discriminate species. (3) By clarifying patterns of morphological and genotypic variation of invasive Pilosella, we lay foundations for further ecological study and mitigation. © 2015 Botanical Society of America, Inc.

First molecular characterization of a Hepatozoon species (Apicomplexa: Hepatozoidae) infecting birds and description of a new species infecting storm petrels (Aves: Hydrobatidae).

PubMed

Merino, Santiago; Martínez, Javier; Masello, Juan F; Bedolla, Yuliana; Quillfeldt, Petra

2014-06-01

During a survey of blood parasites in a population of Leach's and black storm petrels ( Oceanodroma leucorhoa and Oceanodroma melania) in Mexico, infection by a Hepatozoon species in erythrocytes of several birds was noted. Here we describe the species as Hepatozoon peircei sp. nov. Some species of Hepatozoon described from birds have been identified as lankesterellids when DNA molecular analyses were conducted. However, a sequence of 1,774 bp of the parasite found infecting storm petrels in this study clearly show the parasite is a species of the genus Hepatozoon. This is the first Hepatozoon species infecting birds to be characterized at the molecular level and the first found infecting erythrocytes and not leucocytes.

A Review of the Composition of the Essential Oils and Biological Activities of Angelica Species.

PubMed

Sowndhararajan, Kandasamy; Deepa, Ponnuvel; Kim, Minju; Park, Se Jin; Kim, Songmun

2017-09-20

A number of Angelica species have been used in traditional systems of medicine to treat many ailments. Especially, essential oils (EOs) from the Angelica species have been used for the treatment of various health problems, including malaria, gynecological diseases, fever, anemia, and arthritis. EOs are complex mixtures of low molecular weight compounds, especially terpenoids and their oxygenated compounds. These components deliver specific fragrance and biological properties to essential oils. In this review, we summarized the chemical composition and biological activities of EOs from different species of Angelica . For this purpose, a literature search was carried out to obtain information about the EOs of Angelica species and their bioactivities from electronic databases such as PubMed, Science Direct, Wiley, Springer, ACS, Google, and other journal publications. There has been a lot of variation in the EO composition among different Angelica species. EOs from Angelica species were reported for different kinds of biological activities, such as antioxidant, anti-inflammatory, antimicrobial, immunotoxic, and insecticidal activities. The present review is an attempt to consolidate the available data for different Angelica species on the basis of major constituents in the EOs and their biological activities.

Analysis of glycerophosphocholine molecular species as derivatives of 7-[(chlorocarbonyl)-methoxy]-4-methylcoumarin.

PubMed

Wheelan, P; Zirrolli, J A; Clay, K L

1992-01-01

A method has been developed for the analysis of derivatized diradylglycerols obtained from glycerophosphocholine (GPC) of transformed murine bone marrow-derived mast cells that provided high performance liquid chromatography (HPLC) separation of GPC subclasses and molecular species separation with on-line quantitation using UV detection. In addition, the derivatized diradylglycerol species were unequivocably identified by continuous flow fast-atom bombardment mass spectrometry. GPC was initially isolated by thin-layer chromatography (TLC), the phosphocholine group was hydrolyzed, and the resultant diradylglycerol was derivatized with 7-[(chlorocarbonyl)-methoxy]-4-methylcoumarin (CMMC). After separation of the derivatized subclasses by normal phase HPLC, the individual molecular species of the alkylacyl and diacyl subclasses were quantitated and collected during a subsequent reverse phase HPLC step. With an extinction coefficient of 14,700 l mol-1 cm-1 at a wavelength detection of 320 nm, the CMMC derivatives afforded sensitive UV detection (100 pmol) and quantitation of the molecular species. Continuous flow fast-atom bombardment mass spectrometry of the alkylacyl CMMC derivatives yielded abundant [MH]+ ions and a single fragment ion formed by loss of alkylketene from the sn-2 acyl group, [MH-(R = C = O)]+. No fragmentation of the sn-1 alkyl chain was observed. Diacyl derivatives also produced abundant [MH]+ ions plus two fragment ions arising from loss of RCOOH from each of the acyl substituents and two fragment ions from the loss of alkyketene from each acyl group. Individual molecular species substituents were assigned from these ions.

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes).

PubMed

Nirchio, Mauro; Paim, Fabilene G; Milana, Valentina; Rossi, Anna R; Oliveira, Claudio

2018-01-01

Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil , a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes , commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil . Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92-93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes)

PubMed Central

Nirchio, Mauro; Paim, Fabilene G.; Milana, Valentina; Rossi, Anna R.; Oliveira, Claudio

2018-01-01

Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92–93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae. PMID:29459882

Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology.

PubMed

Nadler, Steven A; DE León, Gerardo Pérez-Ponce

2011-11-01

Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.

Lactational changes in concentration and distribution of ganglioside molecular species in human breast milk from Chinese mothers.

PubMed

Ma, Lin; Liu, Xihong; MacGibbon, Alastair K H; Rowan, Angela; McJarrow, Paul; Fong, Bertram Y

2015-11-01

Gangliosides play a critical role in human brain development and function. Human breast milk (HBM) is an important dietary source of gangliosides for the growing infant. In this study, ganglioside concentrations were measured in the breast milk from a cross-sectional sample of Chinese mothers over an 8-month lactation period. The average total ganglioside concentration increased from 13.1 mg/l during the first month to 20.9 mg/l by 8 months of lactation. The average concentration during the typically solely breast-feeding period of 1‒6 months was 18.9 mg/l. This is the first study to report the relative distribution of the individual ganglioside molecular species through lactation for any population group. The ganglioside molecular species are made up of different fatty acid moieties that influence the physical properties of these gangliosides, and hence affect their function. The GM(3) molecular species containing long-chain acyl fatty acids had the most prominent changes, increasing in both concentration and relative distribution. The equivalent long-chain acyl fatty acid GD(3) molecular species typically decreased in concentration and relative distribution. The lactational trends for both concentration and relative distribution for the very long-chain acyl fatty acid molecular species were more varied. The major GM(3) and GD(3) molecular species during lactation were d40:1 and d42:1, respectively. An understanding of ganglioside molecular species distribution in HBM is essential for accurate application of mass spectrometry methods for ganglioside quantification.

Molecular identification tools for sibling species of Scedosporium and Pseudallescheria.

PubMed

Lackner, M; Klaassen, C H; Meis, J F; van den Ende, A H G Gerrits; de Hoog, G S

2012-07-01

The aim of this study was to develop molecular identification tools for currently recognized species of Pseudallescheria and Scedosporium through the use of species-specific primers and RFLP, so as to enhance rapid differentiation of clinically relevant species. The variability of species was established in a set of 681 Internal Transcribed Spacer (ITS) and 349 ß-tubulin (BT2) sequences. Amplified Fragment Length Polymorphism profile clustering matched with BT2 results, whereas ITS grouping was less detailed. ITS was sufficient for the differentiation of most haplotypes of clinically relevant species (P. apiosperma, P. boydii, S. aurantiacum, S. dehoogii, and S. prolificans) and of environmental species (P. minutispora and Lophotrichus fimeti) when Restriction Fragment Length Polymorphism (RFLP) were applied. For the identification of P. apiosperma and P. boydii species-specific BT2 primers were needed. Pseudallescheria fusoidea, P. ellipsoidea and P. angusta remained difficult to distinguish from P. boydii.

[Molecular techniques applied in species identification of Toxocara].

PubMed

Fogt, Renata

2006-01-01

Toxocarosis is still an important and actual problem in human medicine. It can manifest as visceral (VLM), ocular (OLM) or covert (CT) larva migrans syndroms. Complicated life cycle of Toxocara, lack of easy and practical methods of species differentiation of the adult nematode and embarrassing in recognition of the infection in definitive hosts create difficulties in fighting with the infection. Although studies on human toxocarosis have been continued for over 50 years there is no conclusive answer, which of species--T. canis or T. cati constitutes a greater risk of transmission of the nematode to man. Neither blood serological examinations nor microscopic observations of the morphological features of the nematode give the satisfied answer on the question. Since the 90-ths molecular methods were developed for species identification and became useful tools being widely applied in parasitological diagnosis. This paper cover the survey of methods of DNA analyses used for identification of Toxocara species. The review may be helpful for researchers focused on Toxocara and toxocarosis as well as on detection of new species. The following techniques are described: PCR (Polymerase Chain Reaction), RFLP (Restriction Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA) and SSCP (Single Strand Conformation Polymorphism).

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae).

PubMed

Šašić, Ljiljana; Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

2016-01-01

The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods).

Enhanced understanding of predator-prey relationships using molecular methods to identify predator species, individual and sex.

PubMed

Mumma, Matthew A; Soulliere, Colleen E; Mahoney, Shane P; Waits, Lisette P

2014-01-01

Predator species identification is an important step in understanding predator-prey interactions, but predator identifications using kill site observations are often unreliable. We used molecular tools to analyse predator saliva, scat and hair from caribou calf kills in Newfoundland, Canada to identify the predator species, individual and sex. We sampled DNA from 32 carcasses using cotton swabs to collect predator saliva. We used fragment length analysis and sequencing of mitochondrial DNA to distinguish between coyote, black bear, Canada lynx and red fox and used nuclear DNA microsatellite analysis to identify individuals. We compared predator species detected using molecular tools to those assigned via field observations at each kill. We identified a predator species at 94% of carcasses using molecular methods, while observational methods assigned a predator species to 62.5% of kills. Molecular methods attributed 66.7% of kills to coyote and 33.3% to black bear, while observations assigned 40%, 45%, 10% and 5% to coyote, bear, lynx and fox, respectively. Individual identification was successful at 70% of kills where a predator species was identified. Only one individual was identified at each kill, but some individuals were found at multiple kills. Predator sex was predominantly male. We demonstrate the first large-scale evaluation of predator species, individual and sex identification using molecular techniques to extract DNA from swabs of wild prey carcasses. Our results indicate that kill site swabs (i) can be highly successful in identifying the predator species and individual responsible; and (ii) serve to inform and complement traditional methods. © 2013 John Wiley & Sons Ltd.

Identification of molecular species of acylglycerols of Philippine wild edible mushroom, Ganoderma lucidum

USDA-ARS?s Scientific Manuscript database

Wild edible mushrooms are widely consumed in many countries. We successfully cultivated four edible, medicinal Philippine mushrooms in liquid culture. Recently, we identified the molecular species of acylglycerols in the lipid extract of mushroom G. lucidum NRRL66208. One hundred and three molecular...

Molecular characterization of the species Salvinia (Salviniaceae) from the upper Paraná River floodplain.

PubMed

Machado, S A; Oliveira, A V; Fabrin, T M C; Prioli, S M A P; Prioli, A J

2016-08-12

The pteridophytes Salvinia minima, S. herzogii, and S. auriculata are among the most abundant aquatic macrophytes in the upper Paraná River floodplain. Since some species have highly similar morphological features, it is very difficult to identify members of this genus to the species level. An indication of this difficulty is a set of poorly differentiated taxa comprising S. auriculata and S. herzogii known as the 'S. auriculata complex', which is found in the Paraná River together with other Salvinia species such as S. biloba and S. molesta. Some authors have reported the existence of inter-species hybrids. Despite the complex Salvinia taxonomy, few genetic studies have been performed on purported species within the genus to resolve this complexity. The present study was conducted to determine useful molecular sequences for the discrimination of Salvinia species of the upper Paraná River floodplain. Molecular data were compared with data of other species of the genus to clarify phylogenetic relationships, employing the nucleotide sequence trnL-trnF from the chloroplast DNA. The results revealed that Salvinia populations in the upper Paraná River floodplain belong to different species and indicated that species of the S. auriculata complex may be distinguished from one another after the division of the S. minima group, corroborating results by other researchers. Although the taxonomic position of S. oblongifolia was clarified, as high closeness between S. oblongifolia and the S. auriculata complex was reported, Salvinia kinship is still not thoroughly established and further investigations in morphology and molecular diversity are required.

Unexpected diversity of Anopheles species in Eastern Zambia: implications for evaluating vector behavior and interventions using molecular tools.

PubMed

Lobo, Neil F; St Laurent, Brandyce; Sikaala, Chadwick H; Hamainza, Busiku; Chanda, Javan; Chinula, Dingani; Krishnankutty, Sindhu M; Mueller, Jonathan D; Deason, Nicholas A; Hoang, Quynh T; Boldt, Heather L; Thumloup, Julie; Stevenson, Jennifer; Seyoum, Aklilu; Collins, Frank H

2015-12-09

The understanding of malaria vector species in association with their bionomic traits is vital for targeting malaria interventions and measuring effectiveness. Many entomological studies rely on morphological identification of mosquitoes, limiting recognition to visually distinct species/species groups. Anopheles species assignments based on ribosomal DNA ITS2 and mitochondrial DNA COI were compared to morphological identifications from Luangwa and Nyimba districts in Zambia. The comparison of morphological and molecular identifications determined that interpretations of species compositions, insecticide resistance assays, host preference studies, trap efficacy, and Plasmodium infections were incorrect when using morphological identification alone. Morphological identifications recognized eight Anopheles species while 18 distinct sequence groups or species were identified from molecular analyses. Of these 18, seven could not be identified through comparison to published sequences. Twelve of 18 molecularly identified species (including unidentifiable species and species not thought to be vectors) were found by PCR to carry Plasmodium sporozoites - compared to four of eight morphological species. Up to 15% of morphologically identified Anopheles funestus mosquitoes in insecticide resistance tests were found to be other species molecularly. The comprehension of primary and secondary malaria vectors and bionomic characteristics that impact malaria transmission and intervention effectiveness are fundamental in achieving malaria elimination.

Molecular and phenotypic data supporting distinct species statuses for Scedosporium apiospermum and Pseudallescheria boydii and the proposed new species Scedosporium dehoogii.

PubMed

Gilgado, Fèlix; Cano, Josep; Gené, Josepa; Sutton, Deanna A; Guarro, Josep

2008-02-01

Based on the morphological, physiologic, and molecular (beta-tubulin gene) study of 141 isolates of the Pseudallescheria boydii species complex (including several synonyms) and relatives, the new species Scedosporium dehoogii is proposed. Scedosporium apiospermum and P. boydii are considered two different species and the new name Scedosporium boydii is proposed for the anamorph of the latter species. A summary of the key morphological and physiological features for distinguishing the species of Pseudallescheria/Scedosporium is provided.

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)

PubMed Central

Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

2016-01-01

The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

Molecular identification of python species: development and validation of a novel assay for forensic investigations.

PubMed

Ciavaglia, Sherryn A; Tobe, Shanan S; Donnellan, Stephen C; Henry, Julianne M; Linacre, Adrian M T

2015-05-01

Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Hepatozoon species (Adeleorina: Hepatozoidae) of African bufonids, with morphological description and molecular diagnosis of Hepatozoon ixoxo sp. nov. parasitising three Amietophrynus species (Anura: Bufonidae).

PubMed

Netherlands, Edward C; Cook, Courtney A; Smit, Nico J

2014-12-20

Haemogregarines comprise a large group of apicomplexan blood parasites. In 1996 all anuran haemogregarines still in the genus Haemogregarina Danilewsky, 1885 were reassigned to the genus Hepatozoon Miller, 1908. Most (11/15, 73%) African anuran Hepatozoon species have been recorded from the family Bufonidae, however, all these are recorded from only two host species, Amietophrynus mauritanicus (Schlegel, 1841) and Amietophrynus regularis (Reuss, 1833) from Northern and central Africa. To the authors' knowledge the only description of an anuran haemogregarine from South Africa is Hepatozoon theileri (Laveran, 1905), parasitising Amietia quecketti (Boulenger, 1895). Thin blood smears for morphometrics and whole blood for molecular work, were collected from 32 Amietophrynus garmani (Meek, 1897), 12 Amietophrynus gutturalis (Power, 1927), and nine Amietophrynus maculatus (Hallowell, 1854), in Ndumo Game Reserve and Kwa Nyamazane Conservancy, KwaZulu-Natal, South Africa. Smears were Giemsa-stained, screened for haemogregarines, parasite stages measured, compared to each other and to other described African bufonid haemogregarines. Parasite 18S rDNA was amplified using two apicomplexan-specific primer sets, HepF300/HepR900 and 4558/2733. Resulting sequences of the haemogregarine isolates from the three Amietophrynus species were compared with each other and to comparative haemogregarine sequences selected from GenBank. Morphological characteristics of parasite stages, in particular characteristically capped mature gamont stages, and molecular findings, supported all three haemogregarine isolates from all three Amietophrynus species to be the same, a species of Hepatozoon, and furthermore different morphologically from other previously recorded bufonid Hepatozoon species. The haemogregarine fell within a clade comprising other anuran Hepatozoon species and furthermore, within a monophyletic sub-clade along with H. theileri and are described as Hepatozoon ixoxo sp. nov

Molecular Species Delimitation and Morphology of Aquatic and Sub-Aquatic Bugs (Heteroptera) in Cameroon

PubMed Central

Le Gall, Philippe; Chen, Ping-Ping; Nieser, Nico; Guilbert, Eric; Njiokou, Flobert; Marsollier, Laurent; Guégan, Jean-François; Pluot-Sigwalt, Dominique; Eyangoh, Sara; Harry, Myriam

2016-01-01

Aquatic and semi-aquatic bugs (Heteroptera) represent a remarkable diversity and a resurging interest has been given to documenting at the species level these insects inhabiting Cameroon in Central Africa due to their potential implication in the transmission of the bacterium Mycobacterium ulcerans, the causal agent of Buruli ulcer, an emerging human disease. A survey was carried out over two years in Cameroon. Morphological analyses were done in two steps. A first step consisted in separating the specimens based on broadly shared characters into morphotypes. The specimens were then separated into two independent batches containing each the same representation of each morphotype. One batch (309 specimens) was used by taxonomy experts on aquatic bugs for species level identification and/or to reconcile nymph with their corresponding adult species. The second batch (188 specimens) was used to define species based on the COI DNA sequences (standard sequence used for “DNA barcoding”) and using the Automatic Barcode Gap Discovery (ABGD) method. The first morphological analysis step separated the specimens into 63 different morphotypes (49 adults and 14 nymphs), which were then found to belong to 54 morphological species in the infra-orders Gerromorpha and Nepomorpha based on the species-level morphological identification, and 41–45 putative molecular species according to the gap value retained in the ABGD. Integrating morphology and “DNA barcoding” reconciled all the specimens into 62 aquatic bug species in Cameroon. Generally, we obtained a good congruence between species a priori identified based on morphology from adult morphotypes and molecular putative species. Moreover, molecular identification has allowed the association of 86% of nymphs with adults. This work illustrates the importance of integrative taxonomy. PMID:27149077

Morphological and molecular characterization of Cladosporium cladosporioides species complex causing pecan tree leaf spot.

PubMed

Walker, C; Muniz, M F B; Rolim, J M; Martins, R R O; Rosenthal, V C; Maciel, C G; Mezzomo, R; Reiniger, L R S

2016-09-16

The objective of this study was to characterize species of the Cladosporium cladosporioides complex isolated from pecan trees (Carya illinoinensis) with symptoms of leaf spot, based on morphological and molecular approaches. Morphological attributes were assessed using monosporic cultures on potato dextrose agar medium, which were examined for mycelial growth, sporulation, color, and conidia and ramoconidia size. Molecular characterization comprised isolation of DNA and subsequent amplification of the translation elongation factor 1α (TEF-1α) region. Three species of the C. cladosporioides complex were identified: C. cladosporioides, Cladosporium pseudocladosporioides, and Cladosporium subuliforme. Sporulation was the most important characteristic differentiating species of this genus. However, morphological features must be considered together with molecular analysis, as certain characters are indistinguishable between species. TEF-1αcan be effectively used to identify and group isolates belonging to the C. cladosporioides complex. The present study provides an important example of a methodology to ascertain similarity between isolates of this complex causing leaf spot in pecan trees, which should facilitate future pathogenicity studies.

Portuguese Thymbra and Thymus species volatiles: chemical composition and biological activities.

PubMed

Figueiredo, A C; Barroso, J G; Pedro, L G; Salgueiro, L; Miguel, M G; Faleiro, M L

2008-01-01

Thymbra capitata and Thymus species are commonly known in Portugal as thyme and they are currently used as culinary herbs, as well as for ornamental, aromatizing and traditional medicinal purposes. The present work reports on the state of the art on the information available on the taxonomy, ethnobotany, cell and molecular biology of the Portuguese representatives of these genera and on the chemotaxonomy and antibacterial, antifungal and antioxidant activities of their essential oils and other volatile-containing extracts.

Ni-O4 species anchored on N-doped graphene-based materials as molecular entities and electrocatalytic performances for oxygen reduction reaction

NASA Astrophysics Data System (ADS)

Jang, Dawoon; Lee, Seungjun; Shin, Yunseok; Ohn, Saerom; Park, Sunghee; Lim, Donggyu; Park, Gilsoo; Park, Sungjin

2017-12-01

The generation of molecular active species on the surface of nano-materials has become promising routes to produce efficient electrocatalysts. Development of cost-effective catalysts with high performances for oxygen reduction reaction (ORR) is an important challenge for fuel cell and metal-air battery applications. In this work, we report a novel hybrid produced by room-temperature solution processes using Ni-based organometallic molecules and N-doped graphene-based materials. Chemical and structural characterizations reveal that Ni-containing species are well-dispersed on the surface of graphene network as molecular entity. The hybrid shows excellent electrocatalytic performances for ORR in basic medium with an onset potential of 0.87 V (vs. RHE), superior durability and good methanol tolerance.

Current status of the genetics and molecular taxonomy of Echinococcus species.

PubMed

McManus, D P

2013-11-01

The taxonomy of Echinococcus has long been controversial. Based mainly on differences in morphology and host-parasite specificity characteristics, 16 species and 13 subspecies were originally described. Subsequently, most of these taxa were regarded as synonyms for Echinococcus granulosus and only 4 valid species were recognised: E. granulosus; E. multilocularis; E. oligarthrus and E. vogeli. But, over the past 50 years, laboratory and field observations have revealed considerable phenotypic variability between isolates of Echinococcus, particularly those of E. granulosus, which include differences in: morphology in both larval and adult stages, development in vitro and in vivo, host infectivity and specificity, chemical composition, metabolism, proteins and enzymes, pathogenicity and antigenicity. The application of molecular tools has revealed differences in nucleic acid sequences that reflect this phenotypic variation and the genetic and phenotypic characteristics complement the previous observations made by the descriptive parasitologists many years ago. The fact that some of these variants or strains are poorly or not infective to humans has resulted in a reappraisal of the public health significance of Echinococcus in areas where such variants occur. A revised taxonomy for species in the Echinococcus genus has been proposed that is generally accepted, and is based on the new molecular data and the biological and epidemiological characteristics of host-adapted species and strains.

[Inhibition of Low Molecular Organic Acids on the Activity of Acidithiobacillus Species and Its Effect on the Removal of Heavy Metals from Contaminated Soil].

PubMed

Song, Yong-wei; Wang, He-rul; Cao, Yan-xiao; Li, Fei; Cui, Chun-hong; Zhou, Li

2016-05-15

Application of organic fertilizer can reduce the solubility and bioavailability of heavy metals in contaminated soil, but in the flooded anaerobic environment, organic fertilizer will be decomposed to produce a large number of low molecular organic acids, which can inhibit the biological activity of Acidithiobacillus species. Batch cultures studies showed that the monocarboxylic organic acids including formic acid, acetic acid, propionic acid, and butyric acid exhibited a marked toxicity to Acidithiobacillus species, as indicated by that 90% of inhibitory rate for Fe2 and So oxidation in 72 h were achieved at extremely low concentrations of 41.2 mg · L⁻¹, 78.3 mg · L⁻¹, 43.2 mg · L⁻¹, 123.4 mg · L⁻¹ and 81.9 mg 230. 4 mg · L⁻¹, 170.1 mg · L⁻¹, 123.4 mg · L⁻¹ respectively. Of these organic acids, formic acid was the most toxic one as indicated by that Fe2 and So oxidation was almost entirely inhibited at a low concentration. In addition, it was found that Acidithiobacillus ferrooxidans was more sensitive to low molecular organic acids than Acidithiobacillus thiooxidans. What's more, there was little effect on biological acidification process of heavy metal contaminated soil when organic acids were added at initial stage (Oh), but it was completely inhibited when these acids were added after 12 h of conventional biological acidification, thus decreasing the efficiency of heavy metals dissolution from soil.

Identification of the molecular species of acylglycerols containing hydroxy fatty acids in wild edible mushroom Ganoderma lucidum

USDA-ARS?s Scientific Manuscript database

Edible Philippine mushrooms including Ganoderma lucidum have many health benefits. Seventy-two molecular species of triacylglycerols and five molecular species of diacylglycerols containing hydroxy fatty acids (FA) in the lipid extract of this mushroom were identified by HPLC and MS. The mono-, di- ...

Defining species-specific immunodominant B cell epitopes for molecular serology of Chlamydia species.

PubMed

Rahman, K Shamsur; Chowdhury, Erfan U; Poudel, Anil; Ruettger, Anke; Sachse, Konrad; Kaltenboeck, Bernhard

2015-05-01

Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Defining Species-Specific Immunodominant B Cell Epitopes for Molecular Serology of Chlamydia Species

PubMed Central

Rahman, K. Shamsur; Chowdhury, Erfan U.; Poudel, Anil; Ruettger, Anke; Sachse, Konrad

2015-01-01

Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens. PMID:25761461

Isolation and identification of molecular species of phosphatidylcholine and lysophosphatidylcholine from jojoba seed meal (Simmondsia chinensis).

PubMed

Léon, Fabian; Van Boven, Maurits; de Witte, Peter; Busson, Roger; Cokelaere, Marnix

2004-03-10

A mixture of lysophosphatidylcholine (LPC) and phosphatidylcholine (PC) has been isolated by column chromatography from a jojoba meal (Simmondsia chinensis) extract. The molecular species of both classes could be separated and isolated by C18 reversed phase HPLC. The two major compounds were identified by 1D and 2D (1)H and (13)C NMR, by MS, and by GC-MS as 1-oleoyl-3-lysophosphatidylcholine and 1,2-dioleoyl-3-phosphatidylcholine. Eight other molecular species of LPC and four other molecular species of PC could be assigned by comparison of the mass spectra of the isolated compounds with the spectra of the two major compounds. Complete characterization of the individual molecular species was achieved by GC and GC-MS analysis of the fatty acyl composition from the isolated compounds. The PC/LPC proportion in the phospholipid mixture from three different samples is 1.6 +/- 0.1. LPC is considered to be an important bioactive compound; the results of this study suggest further research for the evaluation of potential health benefits of jojoba meal phospholipids.

A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex.

PubMed

Padula, Vinicius; Bahia, Juliana; Stöger, Isabella; Camacho-García, Yolanda; Malaquias, Manuel António E; Cervera, Juan Lucas; Schrödl, Michael

2016-10-01

Traditionally, species identification in nudibranch gastropods relies heavily on body color pattern. The Felimida clenchi species complex, a group of brightly colored Atlantic and Mediterranean species in the family Chromodorididae, has a history of exceptional controversy and discussion among taxonomists. The most widely accepted hypothesis is that the complex includes four species (Felimida clenchi, F. neona, F. binza and F. britoi), each with a characteristic body color pattern. In this study, we investigated the taxonomic value of coloration in the Felimida clenchi complex, using molecular phylogenetics, species-delimitation analyses (ABGD, GMYC, PTP), haplotype-network methods, and the anatomy of the reproductive system. None of our analyses recovered the traditional separation into four species. Our results indicated the existence of three species, a result inconsistent with previous taxonomic hypotheses. We distinguished an undescribed species of Felimida and redefined the concepts of F. clenchi and F. binza, both highly polychromatic species. For the first time, molecular data support the existence of extreme color polymorphism in chromatic nudibranch species, with direct implications for the taxonomy of the group and its diversity. The polychromatism observed in the F. clenchi complex apparently correlates with the regional occurrence of similar color patterns in congeneric species, suggesting different mimicry circles. This may represent a parallel in the marine environment to the mechanisms that play a major role in the diversification of color in terrestrial and fresh-water chromatic groups, such as heliconian butterflies. Copyright © 2016 Elsevier Inc. All rights reserved.

Investigation of uranium molecular species using laser ablation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curreli, Davide

2017-07-12

The goal of this project is to investigate the dynamic evolution of uranium oxide (UOx) molecular species in a rapidly cooling low-temperature plasma using a coupled experimental and modeling approach. Our purpose is to develop quantitative constraints on the UOx phase chemistry under physical conditions similar to that of a nuclear fireball at the time of debris condensation. This work is motivated by a need to better understand the factors controlling uranium chemical fractionation in post-detonation nuclear debris.

Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars (Panax ginseng).

PubMed

Jo, Ick Hyun; Kim, Young Chang; Kim, Dong Hwi; Kim, Kee Hong; Hyun, Tae Kyung; Ryu, Hojin; Bang, Kyong Hwan

2017-10-01

The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.

Identification of Pseudallescheria and Scedosporium species by three molecular methods.

PubMed

Lu, Qiaoyun; Gerrits van den Ende, A H G; Bakkers, J M J E; Sun, Jiufeng; Lackner, M; Najafzadeh, M J; Melchers, W J G; Li, Ruoyu; de Hoog, G S

2011-03-01

The major clinically relevant species in Scedosporium (teleomorph Pseudallescheria) are Pseudallescheria boydii, Scedosporium aurantiacum, Scedosporium apiospermum, and Scedosporium prolificans, while Pseudallescheria minutispora, Petriellopsis desertorum, and Scedosporium dehoogii are exceptional agents of disease. Three molecular methods targeting the partial β-tubulin gene were developed and evaluated to identify six closely related species of the S. apiospermum complex using quantitative real-time PCR (qPCR), PCR-based reverse line blot (PCR-RLB), and loop-mediated isothermal amplification (LAMP). qPCR was not specific enough for the identification of all species but had the highest sensitivity. The PCR-RLB assay was efficient for the identification of five species. LAMP distinguished all six species unambiguously. The analytical sensitivities of qPCR, PCR-RLB, and LAMP combined with MagNAPure, CTAB (cetyltrimethylammonium bromide), and FTA filter (Whatman) extraction were 50, 5 × 10(3), and 5 × 10(2) cells/μl, respectively. When LAMP was combined with a simplified DNA extraction method using an FTA filter, identification to the species level was achieved within 2 h, including DNA extraction. The FTA-LAMP assay is therefore recommended as a cost-effective, simple, and rapid method for the identification of Scedosporium species.

Identification of Pseudallescheria and Scedosporium Species by Three Molecular Methods▿

PubMed Central

Lu, Qiaoyun; Gerrits van den Ende, A. H. G.; Bakkers, J. M. J. E.; Sun, Jiufeng; Lackner, M.; Najafzadeh, M. J.; Melchers, W. J. G.; Li, Ruoyu; de Hoog, G. S.

2011-01-01

The major clinically relevant species in Scedosporium (teleomorph Pseudallescheria) are Pseudallescheria boydii, Scedosporium aurantiacum, Scedosporium apiospermum, and Scedosporium prolificans, while Pseudallescheria minutispora, Petriellopsis desertorum, and Scedosporium dehoogii are exceptional agents of disease. Three molecular methods targeting the partial β-tubulin gene were developed and evaluated to identify six closely related species of the S. apiospermum complex using quantitative real-time PCR (qPCR), PCR-based reverse line blot (PCR-RLB), and loop-mediated isothermal amplification (LAMP). qPCR was not specific enough for the identification of all species but had the highest sensitivity. The PCR-RLB assay was efficient for the identification of five species. LAMP distinguished all six species unambiguously. The analytical sensitivities of qPCR, PCR-RLB, and LAMP combined with MagNAPure, CTAB (cetyltrimethylammonium bromide), and FTA filter (Whatman) extraction were 50, 5 × 103, and 5 × 102 cells/μl, respectively. When LAMP was combined with a simplified DNA extraction method using an FTA filter, identification to the species level was achieved within 2 h, including DNA extraction. The FTA-LAMP assay is therefore recommended as a cost-effective, simple, and rapid method for the identification of Scedosporium species. PMID:21177887

Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers.

PubMed

Zhang, Defang; Xia, Tao; Yan, Maomao; Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

2014-01-01

Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids.

Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

PubMed

Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

2015-09-01

The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. Copyright © 2015 Elsevier GmbH. All rights reserved.

Molecular Diversity of Seed-borne Fusarium Species Associated with Maize in India

PubMed Central

Aiyaz, Mohammed; Divakara, Shetty Thimmappa; Mudili, Venkataramana; Moore, Geromy George; Gupta, Vijai Kumar; Yli-Mattila, Tapani; Nayaka, Siddaiah Chandra; Niranjana, Siddapura Ramachandrappa

2016-01-01

A total of 106 maize seed samples were collected from different agro-climatic regions of India. Sixty-two Fusarium isolates were recovered, 90% of which were identified as Fusarium verticillioides based on morphological and molecular characters. Use of the tef-1α gene corrected/refined the morphological species identifications of 11 isolates, and confirmed those of the remaining isolates. Genetic diversity among the Fusarium isolates involved multilocus fingerprinting profiles by Inter Simple Sequence Repeats (ISSR) UPGMA and tef-1α gene phenetic analyses; for which, we observed no significant differences among the isolates based on geographic origin or fumonisin production; most of the subdivision related to species. Genotyping was performed on the F. verticillioides isolates, using 12 primer sets from the fumonisin pathway, to elucidate the molec-ular basis of fumonisin production or non-production. One fumonisin-negative isolate, UOMMF-16, was unable to amplify nine of the 12 fumonisin cluster genes tested. We also used the CD-ELISA method to confirm fumonisin production for our 62 Fusarium isolates. Only 15 isolates were found to be fumonisin-negative. Interestingly, genotypic characterization re-vealed six isolates with various gene deletion patterns that also tested positive for the production of fumonisins via CD-ELISA. Our findings confirm the importance of molecular studies for species delimitation, and for observing genetic and phenotypic diversity, among the Fusaria. PMID:27226769

Molecular markers for identification of P. ramorum and other Phytophthora species from diseased tissue

Treesearch

Frank N. Martin; Paul W. Tooley

2006-01-01

Molecular techniques have been developed for detection and identification of P. ramorum and other Phytophthora species that are based on the mitochondrially encoded sequences. One technique uses a Phytophthora genus specific primer to determine if a Phytophthora species is present, followed by...

Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

USGS Publications Warehouse

Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

2017-01-01

To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

Molecular characterization and bio-functional property determination using SDS-PAGE and RP-HPLC of protein fractions from two Nigella species.

PubMed

Alu'datt, Muhammad H; Rababah, Taha; Alhamad, Mohammad N; Alodat, Moh'd; Al-Mahasneh, Majdi A; Gammoh, Sana; Ereifej, Khalil; Almajwal, Ali; Kubow, Stan

2017-09-01

This study aimed to investigate the molecular and bio-functional properties of protein fractions from Nigella damascena and Nigella arvensis, including the albumin, globulin, glutein-1, glutein-2 and prolamin fractions. Protein subunits were not observed in globulin and prolamin fractions. No peaks appeared in RP-HPLC chromatograms of globulin for either species. Two predominant peaks were observed in the RP-HPLC profiles of all protein fractions. Proteins separated by RP-HPLC have potential inhibitory and antioxidant activities in all fractions. Optimum ACE-inhibitory and antioxidant activities of proteins separated by RP-HPLC were observed in glutein-2 and albumin, respectively, for both species. For pepsin and combined pepsin-trypsin hydrolyses, the highest degree of hydrolysis (DH) was obtained in glutein-2 fraction of Nigella arvensis. Highest ACE-inhibitory activity of hydrolyzed protein fractions was found at 4h via pepsin hydrolysis in globulin fraction of Nigella damascena. Highest antioxidant activities of hydrolyzed protein fractions were found in glutelin-2 for both species. Copyright © 2017 Elsevier Ltd. All rights reserved.

Detecting hybridization in African schistosome species: does egg morphology complement molecular species identification?

PubMed

Boon, Nele A M; Fannes, Wouter; Rombouts, Sara; Polman, Katja; Volckaert, Filip A M; Huyse, Tine

2017-06-01

Hybrid parasites may have an increased transmission potential and higher virulence compared to their parental species. Consequently, hybrid detection is critical for disease control. Previous crossing experiments showed that hybrid schistosome eggs have distinct morphotypes. We therefore compared the performance of egg morphology with molecular markers with regard to detecting hybridization in schistosomes. We studied the morphology of 303 terminal-spined eggs, originating from 19 individuals inhabiting a hybrid zone with natural crosses between the human parasite Schistosoma haematobium and the livestock parasite Schistosoma bovis in Senegal. The egg sizes showed a high variability and ranged between 92·4 and 176·4 µm in length and between 35·7 and 93·0 µm in width. No distinct morphotypes were found and all eggs resembled, to varying extent, the typical S. haematobium egg type. However, molecular analyses on the same eggs clearly showed the presence of two distinct partial mitochondrial cox1 profiles, namely S. bovis and S. haematobium, and only a single nuclear ITS rDNA profile (S. haematobium). Therefore, in these particular crosses, egg morphology appears not a good indicator of hybrid ancestry. We conclude by discussing strengths and limitations of molecular methods to detect hybrids in the context of high-throughput screening of field samples.

Cryptic species revealed by molecular phylogenetic analysis of sequences obtained from basidiomata of Tulasnella.

PubMed

Cruz, Darío; Suárez, Juan Pablo; Kottke, Ingrid; Piepenbring, Meike

2014-01-01

Delimitation of species and the search for a proper threshold for defining phylogenetic species in fungi are under discussion. In this study, morphological and molecular data are correlated to delimit species of Tulasnella, the most important mycobionts of Orchidaceae, which suffer from poor taxonomy. Resupinate basidiomata of Tulasnella species were collected in Ecuador and Germany, and 11 specimens (seven from Ecuador, four from Germany) were assigned to traditional species concepts by use of morphological keys. The specimens were compared by micro-anatomical examination with 75 specimens of Tulasnella borrowed from fungaria to obtain better insights on variation of characters. Sequences of the ITS region (127) were obtained after cloning from the fresh basidiomata and from pure cultures. Proportional variability of ITS sequences was analyzed within and among the cultures and the specimens designated to different morphospecies. Results suggested an intragenomic variation of less than 2%, an intraspecific variation of up to 4% and an interspecific divergence of more than 9% in Tulasnella. Cryptic species in Tulasnella, mostly from Ecuador, were revealed by phylogenetic analyses with 4% intraspecific divergence as a minimum threshold for delimiting species. Conventional diagnostic morphological characters appeared insufficient for species characterization. Arguments are presented for molecular delimitation of the established species Tulasnella albida, T. asymmetrica, T. eichleriana, T. cf. pinicola, T. tomaculum and T. violea. © 2014 by The Mycological Society of America.

Molecular Identification, Antifungal Susceptibility Profile, and Biofilm Formation of Clinical and Environmental Rhodotorula Species Isolates

PubMed Central

Nunes, Jorge Meneses; Bizerra, Fernando César; Ferreira, Renata Carmona e

2013-01-01

Rhodotorula species are emergent fungal pathogens capable of causing invasive infections, primarily fungemia. They are particularly problematic in immunosuppressed patients when using a central venous catheter. In this study, we evaluated the species distribution of 51 clinical and 8 environmental Rhodotorula species isolates using the ID32C system and internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing and biofilm formation capability using a crystal violet staining assay were performed. Using ITS sequencing as the gold standard, the clinical isolates were identified as follows: 44 R. mucilaginosa isolates, 2 R. glutinis isolates, 2 R. minuta isolates, 2 R. dairenensis isolates, and 1 Rhodosporidium fluviale isolate. The environmental isolates included 7 R. mucilaginosa isolates and 1 R. slooffiae isolate. Using the ID32C system, along with a nitrate assimilation test, only 90.3% of the isolates tested were correctly identified. In the biofilm formation assay, R. mucilaginosa and R. minuta exhibited greater biofilm formation ability compared to the other Rhodotorula species; the clinical isolates of R. mucilaginosa showed greater biofilm formation compared to the environmental isolates (P = 0.04). Amphotericin B showed good in vitro activity (MIC ≤ 1 μg/ml) against planktonic cells, whereas voriconazole and posaconazole showed poor activity (MIC50/MIC90, 2/4 μg/ml). Caspofungin and fluconazole MICs were consistently high for all isolates tested (≥64 μg/ml and ≥ 4 μg/ml, respectively). In this study, we emphasized the importance of molecular methods to correctly identify Rhodotorula species isolates and non-R. mucilaginosa species in particular. The antifungal susceptibility profile reinforces amphotericin B as the antifungal drug of choice for the treatment of Rhodotorula infections. To our knowledge, this is the first study evaluating putative differences in the ability of biofilm formation among different Rhodotorula species

Molecular identification, antifungal susceptibility profile, and biofilm formation of clinical and environmental Rhodotorula species isolates.

PubMed

Nunes, Jorge Meneses; Bizerra, Fernando César; Ferreira, Renata Carmona E; Colombo, Arnaldo Lopes

2013-01-01

Rhodotorula species are emergent fungal pathogens capable of causing invasive infections, primarily fungemia. They are particularly problematic in immunosuppressed patients when using a central venous catheter. In this study, we evaluated the species distribution of 51 clinical and 8 environmental Rhodotorula species isolates using the ID32C system and internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing and biofilm formation capability using a crystal violet staining assay were performed. Using ITS sequencing as the gold standard, the clinical isolates were identified as follows: 44 R. mucilaginosa isolates, 2 R. glutinis isolates, 2 R. minuta isolates, 2 R. dairenensis isolates, and 1 Rhodosporidium fluviale isolate. The environmental isolates included 7 R. mucilaginosa isolates and 1 R. slooffiae isolate. Using the ID32C system, along with a nitrate assimilation test, only 90.3% of the isolates tested were correctly identified. In the biofilm formation assay, R. mucilaginosa and R. minuta exhibited greater biofilm formation ability compared to the other Rhodotorula species; the clinical isolates of R. mucilaginosa showed greater biofilm formation compared to the environmental isolates (P = 0.04). Amphotericin B showed good in vitro activity (MIC ≤ 1 μg/ml) against planktonic cells, whereas voriconazole and posaconazole showed poor activity (MIC(50)/MIC(90), 2/4 μg/ml). Caspofungin and fluconazole MICs were consistently high for all isolates tested (≥64 μg/ml and ≥ 4 μg/ml, respectively). In this study, we emphasized the importance of molecular methods to correctly identify Rhodotorula species isolates and non-R. mucilaginosa species in particular. The antifungal susceptibility profile reinforces amphotericin B as the antifungal drug of choice for the treatment of Rhodotorula infections. To our knowledge, this is the first study evaluating putative differences in the ability of biofilm formation among different Rhodotorula

Molecular definition and the ubiquity of species in the genus Naegleria.

PubMed

De Jonckheere, Johan F

2004-03-01

To investigate the variability within species of the genus Naegleria, the ITS1,5.8S and ITS2 rDNA were sequenced of several strains of N. lovaniensis and its Western Australian variants, N. australiensis, N. fowleri, N. andersoni, N. jamiesoni, N. tihangensis, N. pringsheimi, N. pagei, N. gruberi sensu lato and a Naegleria lineage that lost a group I intron from the SSUrDNA twintron. As a result, it is possible to define a molecular species within the Naegleria genus. In addition, one strain of each different allozyme cluster was sequenced to investigate whether they belong to described species or should be treated as distinct new species. This leads to the proposal of eleven new species. The sequencing results from those Naegleria spp. of which several strains are available indicate that these species are ubiquitous. The only exception might be the species represented by the WA variants. However, there are still many Naegleria spp. for which only one strain has been isolated, hence, it is important that the search for more isolates should be continued worldwide.

Investigating Evolutionary Questions Using Online Molecular Databases.

ERIC Educational Resources Information Center

Puterbaugh, Mary N.; Burleigh, J. Gordon

2001-01-01

Recommends using online molecular databases as teaching tools to illustrate evolutionary questions and concepts while introducing students to public molecular databases. Provides activities in which students make molecular comparisons between species. (YDS)

Effects of aging on serum levels of lipid molecular species as determined by lipidomics analysis in Japanese men and women.

PubMed

Kawanishi, Noriaki; Kato, Yuki; Yokozeki, Kyosuke; Sawada, Shuji; Sakurai, Ryota; Fujiwara, Yoshinori; Shinkai, Shoji; Goda, Nobuhito; Suzuki, Katsuhiko

2018-06-06

Aging is known to be associated with increased risk of lipid disorders related to the development of type 2 diabetes. Recent evidence revealed that change of lipid molecule species in blood is associated with the risk of type 2 diabetes. However, changes in lipid molecular species induced by aging are still unknown. We assessed the effects of age on the serum levels of lipid molecular species as determined by lipidomics analysis. Serum samples were collected from ten elderly men (71.7 ± 0.5 years old) and women (70.2 ± 1.0 years old), ten young men (23.9 ± 0.4 years old), and women (23.9 ± 0.7 years old). Serum levels of lipid molecular species were determined by liquid chromatography mass spectrometry-based lipidomics analysis. Our mass spectrometry analysis revealed increases in the levels of multiple triacylglycerol molecular species in the serum of elderly men and women. Moreover, serum levels of total ester-linked phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were increased by aging. In contrast, serum levels of specific ether-linked PC and PE molecular species were lower in elderly individuals than in young individuals. Our finding indicates that specific lipid molecular species, such as ether- and ester- linked phospholipids, may be selectively altered by aging.

Molecular and Phenotypic Data Supporting Distinct Species Statuses for Scedosporium apiospermum and Pseudallescheria boydii and the Proposed New Species Scedosporium dehoogii▿ † ‡

PubMed Central

Gilgado, Fèlix; Cano, Josep; Gené, Josepa; Sutton, Deanna A.; Guarro, Josep

2008-01-01

Based on the morphological, physiologic, and molecular (β-tubulin gene) study of 141 isolates of the Pseudallescheria boydii species complex (including several synonyms) and relatives, the new species Scedosporium dehoogii is proposed. Scedosporium apiospermum and P. boydii are considered two different species and the new name Scedosporium boydii is proposed for the anamorph of the latter species. A summary of the key morphological and physiological features for distinguishing the species of Pseudallescheria/Scedosporium is provided. PMID:18077629

Taxonomic and Molecular Identification of Mesocriconema and Criconemoides Species (Nematoda: Criconematidae)

PubMed Central

Cordero, Marco A.; Robbins, Robert T.; Szalanski, Allen L.

2012-01-01

Populations of Mesocriconema curvatum, M. kirjanovae, M. onoense, M. ornatum, M. sphaerocephala, M. surinamense, M. vadense, M. xenoplax, and Criconemoides informis from different geographical areas in the continental United States were characterized morphologically and molecularly. A new ring nematode from Washington County, Arkansas, is also described and named Mesocriconema ozarkiense n. sp., This new species is characterized by females with small flattened submedian lobes, lower than or at the same level as the labial disc, vagina straight, very well developed spermatheca without sperm, no more than one anastomoses, L=379-512 μm, V=89-93, stylet length = 49-61 μm, R=107-119, annuli with slightly crenate margins on tail portion and a simple anterior vulval lip. The molecular characterization of M. ozarkiense n. sp. using the ITS rRNA gene sequence and the phylogenesis relationship of this new species with the ring nematodes included in this study are provided. PMID:23482878

Morphological and molecular characterization of novel species of Henneguya found in the gills of farm-raised channel catfish, Ictalurus punctatus

USDA-ARS?s Scientific Manuscript database

Channel catfish Ictalurus punctatus is host to at least eight different species of myxozoan parasites in the genus Henneguya. Four of these species have been molecularly characterized; however, the life cycles of only two have been experimentally and molecularly confirmed. Some of these species can...

Studies for the Loss of Atomic and Molecular Species from IO

NASA Technical Reports Server (NTRS)

Combi, Michael R.

1999-01-01

The general objective of this project has been to advance our theoretical understanding of lo's atmosphere and how various atomic and molecular species are lost from this atmosphere and are distributed in the circumplanetary environment of Jupiter. This grant has provided support for the activities of Dr. Michael Combi at the University of Michigan to serve as a small part in collaboration with a larger project awarded to Atmospheric & Environmental Research, Inc., with primary principal investigator Dr. William H. Smyth. Dr. Combi is the Principal Investigator and Project Manager for the Michigan grant NAG5-6187. This Michigan grant has provided for a continuation of a collaboration between Drs. Smyth and Combi in related efforts beginning in 1981, and with the object to develop and apply sophisticated theoretical models to interpret and to relate a number of new and exciting observations for the atmospheric gases of the satellite. The ability to interpret and then to relate through the theoretical fabric a number of these otherwise independent observations are a central strength of this program. This comprehensive approach provides a collective power, extracting more from the sum of the parts and seeing beyond various limitations that are inherent in any one observation. Although the approach is designed to unify, the program is divided into well-defined studies for the likely dominant atmospheric gases involving species of the SO2 family (SO2, SO, O2, S and O) and for the trace atmospheric gas atomic sodium and a likely escaping molecular ion NaX(+) (where Na(X) is the atmospheric molecule and X represents one or more atoms).Attachments: IO's sodium corona and spatially cloud: a consistent flux speed distribution. and Io's plasma environment during the Galileo flyby: global three-dimensional MHD modeling with adaptive mesh refinement.

Sodium pump molecular activity and membrane lipid composition in two disparate ectotherms, and comparison with endotherms.

PubMed

Turner, Nigel; Hulbert, A J; Else, Paul L

2005-02-01

Previous research has shown that the lower sodium pump molecular activity observed in tissues of ectotherms compared to endotherms, is largely related to the lower levels of polyunsaturates and higher levels of monounsaturates found in the cell membranes of ectotherms. Marine-based ectotherms, however, have very polyunsaturated membranes, and in the current study, we measured molecular activity and membrane lipid composition in tissues of two disparate ectothermic species, the octopus (Octopus vulgaris) and the bearded dragon lizard (Pogona vitticeps), to determine whether the high level of membrane polyunsaturation generally observed in marine-based ectotherms is associated with an increased sodium pump molecular activity relative to other ectotherms. Phospholipids from all tissues of the octopus were highly polyunsaturated and contained high concentrations of the omega-3 polyunsaturate, docosahexaenoic acid (22:6 (n-3)). In contrast, phospholipids from bearded dragon tissues contained higher proportions of monounsaturates and lower proportions of polyunsaturates. Sodium pump molecular activity was only moderately elevated in tissues of the octopus compared to the bearded dragon, despite the much greater level of polyunsaturation in octopus membranes. When the current data were combined with data for the ectothermic cane toad, a significant (P = 0.003) correlation was observed between sodium pump molecular activity and the content of 22:6 (n-3) in the surrounding membrane. These results are discussed in relation to recent work which shows a similar relationship in endotherms.

New cryptic species of the 'revolutum' group of Echinostoma (Digenea: Echinostomatidae) revealed by molecular and morphological data.

PubMed

Georgieva, Simona; Selbach, Christian; Faltýnková, Anna; Soldánová, Miroslava; Sures, Bernd; Skírnisson, Karl; Kostadinova, Aneta

2013-03-13

The digenean species of Echinostoma (Echinostomatidae) with 37 collar spines that comprise the so-called 'revolutum' species complex, qualify as cryptic due to the interspecific homogeneity of characters used to differentiate species. Only five species were considered valid in the most recent revision of the group but recent molecular studies have demonstrated a higher diversity within the group. In a study of the digeneans parasitising molluscs in central and northern Europe we found that Radix auricularia, R. peregra and Stagnicola palustris were infected with larval stages of two cryptic species of the 'revolutum' complex, one resembling E. revolutum and one undescribed species, Echinostoma sp. IG. This paper provides morphological and molecular evidence for their delimitation. Totals of 2,030 R. auricularia, 357 R. peregra and 577 S. palustris were collected in seven reservoirs of the River Ruhr catchment area in Germany and a total of 573 R. peregra was collected in five lakes in Iceland. Cercariae were examined and identified live and fixed in molecular grade ethanol for DNA isolation and in hot/cold 4% formaldehyde solution for obtaining measurements from fixed materials. Partial fragments of the mitochondrial gene nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1) were amplified for 14 isolates. Detailed examination of cercarial morphology allowed us to differentiate the cercariae of the two Echinostoma spp. of the 'revolutum' species complex. A total of 14 partial nad1 sequences was generated and aligned with selected published sequences for eight species of the 'revolutum' species complex. Both NJ and BI analyses resulted in consensus trees with similar topologies in which the isolates from Europe formed strongly supported reciprocally monophyletic lineages. The analyses also provided evidence that North American isolates identified as E. revolutum represent another cryptic species of the 'revolutum' species complex. Our findings highlight

Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives.

PubMed

Zhang, Yingxiao; Iaffaldano, Brian J; Zhuang, Xiaofeng; Cardina, John; Cornish, Katrina

2017-02-02

Rubber dandelion (Taraxacum kok-saghyz, TK) is being developed as a domestic source of natural rubber to meet increasing global demand. However, the domestication of TK is complicated by its colocation with two weedy dandelion species, Taraxacum brevicorniculatum (TB) and the common dandelion (Taraxacum officinale, TO). TB is often present as a seed contaminant within TK accessions, while TO is a pandemic weed, which may have the potential to hybridize with TK. To discriminate these species at the molecular level, and facilitate gene flow studies between the potential rubber crop, TK, and its weedy relatives, we generated genomic and marker resources for these three dandelion species. Complete chloroplast genome sequences of TK (151,338 bp), TO (151,299 bp), and TB (151,282 bp) were obtained using the Illumina GAII and MiSeq platforms. Chloroplast sequences were analyzed and annotated for all the three species. Phylogenetic analysis within Asteraceae showed that TK has a closer genetic distance to TB than to TO and Taraxacum species were most closely related to lettuce (Lactuca sativa). By sequencing multiple genotypes for each species and testing variants using gel-based methods, four chloroplast Single Nucleotide Polymorphism (SNP) variants were found to be fixed between TK and TO in large populations, and between TB and TO. Additionally, Expressed Sequence Tag (EST) resources developed for TO and TK permitted the identification of five nuclear species-specific SNP markers. The availability of chloroplast genomes of these three dandelion species, as well as chloroplast and nuclear molecular markers, will provide a powerful genetic resource for germplasm differentiation and purification, and the study of potential gene flow among Taraxacum species.

Activities of E1210 and comparator agents tested by CLSI and EUCAST broth microdilution methods against Fusarium and Scedosporium species identified using molecular methods.

PubMed

Castanheira, Mariana; Duncanson, Frederick P; Diekema, Daniel J; Guarro, Josep; Jones, Ronald N; Pfaller, Michael A

2012-01-01

Fusarium (n = 67) and Scedosporium (n = 63) clinical isolates were tested by two reference broth microdilution (BMD) methods against a novel broad-spectrum (active against both yeasts and molds) antifungal, E1210, and comparator agents. E1210 inhibits the inositol acylation step in glycophosphatidylinositol (GPI) biosynthesis, resulting in defects in fungal cell wall biosynthesis. Five species complex organisms/species of Fusarium (4 isolates unspeciated) and 28 Scedosporium apiospermum, 7 Scedosporium aurantiacum, and 28 Scedosporium prolificans species were identified by molecular techniques. Comparator antifungal agents included anidulafungin, caspofungin, itraconazole, posaconazole, voriconazole, and amphotericin B. E1210 was highly active against all of the tested isolates, with minimum effective concentration (MEC)/MIC(90) values (μg/ml) for E1210, anidulafungin, caspofungin, itraconazole, posaconazole, voriconazole, and amphotericin B, respectively, for Fusarium of 0.12, >16, >16, >8, >8, 8, and 4 μg/ml. E1210 was very potent against the Scedosporium spp. tested. The E1210 MEC(90) was 0.12 μg/ml for S. apiospermum, but 1 to >8 μg/ml for other tested agents. Against S. aurantiacum, the MEC(50) for E1210 was 0.06 μg/ml versus 0.5 to >8 μg/ml for the comparators. Against S. prolificans, the MEC(90) for E1210 was only 0.12 μg/ml, compared to >4 μg/ml for amphotericin B and >8 μg/ml for itraconazole, posaconazole, and voriconazole. Both CLSI and EUCAST methods were highly concordant for E1210 and all comparator agents. The essential agreement (EA; ±2 doubling dilutions) was >93% for all comparisons, with the exception of posaconazole and F. oxysporum species complex (SC) (60%), posaconazole and S. aurantiacum (85.7%), and voriconazole and S. aurantiacum (85.7%). In conclusion, E1210 exhibited very potent and broad-spectrum antifungal activity against azole- and amphotericin B-resistant strains of Fusarium spp. and Scedosporium spp. Furthermore, in vitro

Activities of E1210 and Comparator Agents Tested by CLSI and EUCAST Broth Microdilution Methods against Fusarium and Scedosporium Species Identified Using Molecular Methods

PubMed Central

Duncanson, Frederick P.; Diekema, Daniel J.; Guarro, Josep; Jones, Ronald N.; Pfaller, Michael A.

2012-01-01

Fusarium (n = 67) and Scedosporium (n = 63) clinical isolates were tested by two reference broth microdilution (BMD) methods against a novel broad-spectrum (active against both yeasts and molds) antifungal, E1210, and comparator agents. E1210 inhibits the inositol acylation step in glycophosphatidylinositol (GPI) biosynthesis, resulting in defects in fungal cell wall biosynthesis. Five species complex organisms/species of Fusarium (4 isolates unspeciated) and 28 Scedosporium apiospermum, 7 Scedosporium aurantiacum, and 28 Scedosporium prolificans species were identified by molecular techniques. Comparator antifungal agents included anidulafungin, caspofungin, itraconazole, posaconazole, voriconazole, and amphotericin B. E1210 was highly active against all of the tested isolates, with minimum effective concentration (MEC)/MIC90 values (μg/ml) for E1210, anidulafungin, caspofungin, itraconazole, posaconazole, voriconazole, and amphotericin B, respectively, for Fusarium of 0.12, >16, >16, >8, >8, 8, and 4 μg/ml. E1210 was very potent against the Scedosporium spp. tested. The E1210 MEC90 was 0.12 μg/ml for S. apiospermum, but 1 to >8 μg/ml for other tested agents. Against S. aurantiacum, the MEC50 for E1210 was 0.06 μg/ml versus 0.5 to >8 μg/ml for the comparators. Against S. prolificans, the MEC90 for E1210 was only 0.12 μg/ml, compared to >4 μg/ml for amphotericin B and >8 μg/ml for itraconazole, posaconazole, and voriconazole. Both CLSI and EUCAST methods were highly concordant for E1210 and all comparator agents. The essential agreement (EA; ±2 doubling dilutions) was >93% for all comparisons, with the exception of posaconazole and F. oxysporum species complex (SC) (60%), posaconazole and S. aurantiacum (85.7%), and voriconazole and S. aurantiacum (85.7%). In conclusion, E1210 exhibited very potent and broad-spectrum antifungal activity against azole- and amphotericin B-resistant strains of Fusarium spp. and Scedosporium spp. Furthermore, in vitro

Molecular machines open cell membranes

NASA Astrophysics Data System (ADS)

García-López, Víctor; Chen, Fang; Nilewski, Lizanne G.; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B.; Robinson, Jacob T.; Wang, Gufeng; Pal, Robert; Tour, James M.

2017-08-01

Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.

Molecular machines open cell membranes.

PubMed

García-López, Víctor; Chen, Fang; Nilewski, Lizanne G; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B; Robinson, Jacob T; Wang, Gufeng; Pal, Robert; Tour, James M

2017-08-30

Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.

Molecular detection of candida species from hospitalized patient’s specimens.

PubMed

Camacho-Cardoso, José Luis; Martínez-Rivera, María Ángeles; Manzano-Gayosso, Patricia; Méndez-Tovar, Luis Javier; López-Martínez, Rubén; Hernández-Hernández, Francisca

To identify the most frequent Candida species in specimens from patients hospitalized in different medical centers of Mexico City, with suspected fungal infection. Specimens were grown on Sabouraud dextrose agar at 28°C for 72 h. In addition, DNA was extracted. Isolates were grown on CHROMagar Candida™, at 37°C for 48 h. The molecular identification was performed by polymerase chain reaction (PCR) using primers specific for four species. Eighty one specimens were processed and included: bronchial lavage, pleural, cerebrospinal, peritoneal, ascites and bile fluids; blood, sputum, bone marrow, oro-tracheal cannula and ganglion. By culture, 30 samples (37%) were positive, and by PCR, 41 (50.6%). By PCR, the frequency of species was: Candida albicans 82.9%, Candida tropicalis 31.7%, Candida glabrata 24.4%, and Candida parapsilosis 4.9%. In 34.1% of specimens a species mixture was detected suggesting a co-infection: Two species in five specimens (C. albicans-C tropicalis and C. albicans-C glabrata), and three species in three specimens (C. albicans-C. glabrata-C. tropicalis). The PCR is an useful tool for detection the most common Candida species causing infection in hospitalized patients, it avoids the requirement of culture weather we start from clinical specimen and it favors the early diagnosis of invasive candidiasis. Copyright: © 2017 SecretarÍa de Salud

Archigregarines of the English Channel revisited: New molecular data on Selenidium species including early described and new species and the uncertainties of phylogenetic relationships

PubMed Central

Horák, Aleš

2017-01-01

Background Gregarines represent an important transition step from free-living predatory (colpodellids s.l.) and/or photosynthetic (Chromera and Vitrella) apicomplexan lineages to the most important pathogens, obligate intracellular parasites of humans and domestic animals such as coccidians and haemosporidians (Plasmodium, Toxoplasma, Eimeria, Babesia, etc.). While dozens of genomes of other apicomplexan groups are available, gregarines are barely entering the molecular age. Among the gregarines, archigregarines possess a unique mixture of ancestral (myzocytosis) and derived (lack of apicoplast, presence of subpellicular microtubules) features. Methodology/Principal findings In this study we revisited five of the early-described species of the genus Selenidium including the type species Selenidium pendula, with special focus on surface ultrastructure and molecular data. We were also able to describe three new species within this genus. All species were characterized at morphological (light and scanning electron microscopy data) and molecular (SSU rDNA sequence data) levels. Gregarine specimens were isolated from polychaete hosts collected from the English Channel near the Station Biologique de Roscoff, France: Selenidium pendula from Scolelepis squamata, S. hollandei and S. sabellariae from Sabellaria alveolata, S. sabellae from Sabella pavonina, Selenidium fallax from Cirriformia tentaculata, S. spiralis sp. n. and S. antevariabilis sp. n. from Amphitritides gracilis, and S. opheliae sp. n. from Ophelia roscoffensis. Molecular phylogenetic analyses of these data showed archigregarines clustering into five separate clades and support previous doubts about their monophyly. Conclusions/Significance Our phylogenies using the extended gregarine sampling show that the archigregarines are indeed not monophyletic with one strongly supported clade of Selenidium sequences around the type species S. pendula. We suggest the revision of the whole archigregarine taxonomy with

Standardized molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex.

PubMed

Elfekih, Samia; Tay, Wee Tek; Gordon, Karl; Court, Leon N; De Barro, Paul J

2018-01-01

The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterization of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade, i.e. MED, MEAM1, MEAM2 and IO. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection; however, no standardized B. tabaci-specific primers are currently available which has caused inconsistencies in the species identification processes. We report three sets of polymerase chain reaction (PCR) primers developed to amplify the mtCOI region which can be used for genotyping MED, MEAM1 and IO species, and tested these primers on 91 MED, 35 MEAM1 and five IO individuals. PCR and sequencing of amplicons identified a total of 21, six and one haplotypes in MED, MEAM1 and IO respectively, of which six haplotypes were new to the B. tabaci database. These primer pairs enabled standardization and robust molecular species identification via mtCOI screening of the targeted invasive cryptic species and will improve quarantine decisions. Use of this diagnostic tool could be extended to other species within the complex. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Molecular and morphological identification of  pistachio armored scale insects (Hemiptera: Diaspididae), with description of a new species.

PubMed

Hosseininaveh, Fatemeh; Nozari, Jamasb; Kaydan, Mehmet Bora; Hosseininaveh, Vahid

2016-12-01

Members of the family Diaspididae (Hemiptera: Coccomorpha) can be devastating pests that suck parenchyma cell contents from crops and cause severe damage to pistachio trees (Pistacia vera L.). The current research collected and characterized diaspidid species from pistachio orchards in Kerman province, Iran, according to their morphological and molecular features. Lepidosaphes pistaciae Archangelskaya, Suturaspis davatchi (Balachowsky & Kaussari) and Melanaspis inopinata (Leonardi) are redescribed and a new species, Melanaspis pistaciae Hosseininaveh & Kaydan sp. n., is described. Phylogenetic trees based on molecular analysis of COI and 28S rDNA fragments placed all the species in separated clades and confirmed M. pistaciae as a new taxon which is concluded by morphological differences. Molecular analysis suggests non-monophyly of the populations of each species. Melanaspis pistaciae sp. n. has spread to most cultivated pistachio areas in Iran and has probably been misidentified as M. inopinata in the past. Further investigation of the biology of this species may lead to development of more effective approaches for controlling this pest.

Nine Human Sparganosis Cases in Thailand with Molecular Identification of Causative Parasite Species

PubMed Central

Boonyasiri, Adhiratha; Cheunsuchon, Pornsuk; Suputtamongkol, Yupin; Yamasaki, Hiroshi; Sanpool, Oranuch; Maleewong, Wanchai; Intapan, Pewpan M.

2014-01-01

Human sparganosis is one of the neglected diseases but important food-borne parasitic zoonoses. The disease is caused by larvae (spargana) of diphyllobothriidean tapeworm. Here, we describe nine cases of human sparganosis, caused by Spirometra erinaceieuropaei in a hospital in Thailand during 2001–2012. Clinical characteristics, treatment, and outcome of cases were revealed. Diagnosis and identification of causative parasite species was made by histopathological investigations followed by a polymerase chain reaction-based molecular method using formalin-fixed paraffin embedded tissues. The DNA samples were extracted from tissues and a partial fragment of cytochrome c oxidase subunit 1 (cox1) gene was amplified for the detection of parasitic DNA. Infection could be prevented by increasing activities on health communication by responsible public health agencies. PMID:24842879

Agrobacterium-assisted selenium nanoparticles: molecular aspect of antifungal activity

NASA Astrophysics Data System (ADS)

Kumar, Anil; Bera, Smritilekha; Singh, Man; Mondal, Dhananjoy

2018-03-01

Selenium nanoparticles (SeNPs) were synthesized through the bioreduction of sodium selenite (Na2SeO3) using gram-negative agrobacterium (AGBT) species. Subsequently, their physicochemical properties (pH, viscosity and surface tension) and medicinal activities as anti-dermatophyte against soil keratinophilic fungi at the molecular level were assessed. UV-visible and FTIR spectroscopic data of the biologically synthesized SeNPs were then recorded for confirming the presence of native biological materials adhered to nanoparticles, which are inherently required to enhance the stability and solubility through inhibition of the nanoparticle’s natural aggregation and agglomeration. The λ max value between 290-300 nm in the absorption spectra of the biogenic materials in different concentrations of the Na2SeO3 corroborated the presence of SeNPs in the solution. The interaction of SeNPs in solution state was further studied through the determination of pH, viscosity and surface tension values of agrobacterium-derived SeNPs in different solvents. The pH value of SeNPs dispersed in water is reported as above 7.0 and the average viscosity, and surface tensions of the SeNPs are appeared as near to the water. The particle size distribution was further determined by DLS and the highest % of particle size of the synthesized SeNPs is found in between 200-300 nm. The anti-dermatophyte activity and molecular interaction with fungi DNA molecules were assessed providing the highest anti-dermatophyte activity at 0.1 M concentration and it is observed that the quantities and qualities of fungi DNA were affected by SeNPs. Considering all the outcomes of the studies together, our findings suggest that agrobacterium-mediated synthesis of SeNPs is dependent on bacterial metabolisms but not on the concentration of Na2SeO3 and are promising selenium-derived species with potential application in the prevention of fungal infection through denaturation of fungi DNA.

Description and molecular diagnosis of a new species of Brunfelsia (Solanaceae) from the Bolivian and Argentinean Andes

PubMed Central

Filipowicz, Natalia; Nee, Michael H.; Renner, Susanne S.

2012-01-01

Abstract Brunfelsia plowmaniana N.Filipowicz & M.Nee sp. nov., a species from humid and cloud forests of the Bolivian and Argentinean Andes, is described and provided with a molecular diagnosis, using provisions available in the recently approved International Code of Nomenclature for algae, fungi and plants. Specimens belonging to the new species were previously placed in the polymorphic Brunfelsia uniflora (Pohl) D.Don, which a molecular phylogeny revealed as polyphyletic. Revision of numerous collections revealed clear morphological differences between the new species and Brunfelsia uniflora, the type locality of which is in the state of São Paulo, Brazil. PMID:22461731

Antimicrobial activities of four Tunisian Chrysanthemum species.

PubMed

Sassi, Ahlem Ben; Harzallah-Skhiri, Fethia; Bourgougnon, Nathalie; Aouni, Mahjoub

2008-02-01

Tunisian Chrysanthemum species are known to have medicinal activity and some of the species are used in traditional medicine. We have earlier shown the use of C. trifurcatum flowerheads in Tunisian traditional medicine to treat constipation. In the present study we investigated the anti microbiol activity of four Tunision Chrysanthemum species. Different parts (flowers, leaves, stems, roots, leaves and flowers and leaves and stems) of four Tunisian Chrysanthemum species, were extracted with solvents of increasing polarity to obtain aqueous and organic extracts. These extracts were tested in vitro for their antimicrobial activity against 14 bacteria and four yeasts, using agar diffusion and microdilution methods. Activity was evaluated by measuring the zones of inhibition against the tested organisms and minimum inhibitory concentrations (MIC) were determined from the lowest concentrations of extracts to inhibit the growth of microorganisms. Cytotoxity and antiviral activities against Herpes simplex virus type 1 (HSV-1), were evaluated using the neutral red incorporation method. Extracts of the 4 Chrysanthemum species showed some degree of activity against one or more of the microbial strains with MIC ranging from 0.625 to 1.25 mg/ml. Most of the extracts were well tolerated by Vero cells with CC(50) > 500 microg/ml. The petroleum ether extract of C. trifurcatum stems and leaves protected infected cells with EC(50) of 100 microg/ml. Our findings showed that some Chrysanthemum extracts exhibited antimicrobial and/or anti-HSV-1 activities. Further studies aimed to the isolation and identification of active substances from the extracts which exhibited interest activities, need to be done.

Molecular studies on the species complex of Trichosirocalus horridus in the biological control of Carduinae weeds.

USDA-ARS?s Scientific Manuscript database

The genus Trichosirocalus Colonnelli, 1979, (Coleoptera, Curculionidae, Ceutorhynchinae) includes 17 Palaearctic species mainly feeding on Plantaginaceae and Asteraceae. We studied the taxonomic status of the species complex of Trichosirocalus horridus (TH) by means of molecular markers. We used bot...

Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

PubMed Central

2012-01-01

Background Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic) and the success rate has never been explored on mesopsammic Mollusca. Results We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia) from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH). In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC), statistical parsimony, Bayesian Species Delineation (BPP) and Automatic Barcode Gap Discovery (ABGD). The secondary species hypothesis (SSH) is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’), resulting in the discovery of a radiation of (at least) 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions. Conclusions Our study confirms extensive, morphologically cryptic diversity among

Species identification and molecular typing of human Brucella isolates from Kuwait.

PubMed

Mustafa, Abu S; Habibi, Nazima; Osman, Amr; Shaheed, Faraz; Khan, Mohd W

2017-01-01

Brucellosis is a zoonotic disease of major concern in Kuwait and the Middle East. Human brucellosis can be caused by several Brucella species with varying degree of pathogenesis, and relapses are common after apparently successful therapy. The classical biochemical methods for identification of Brucella are time-consuming, cumbersome, and provide information limited to the species level only. In contrast, molecular methods are rapid and provide differentiation at intra-species level. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-8, MLVA-11 and MLVA-16 were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. 16S rRNA gene sequencing of all isolates showed 90-99% sequence identity with B. melitensis and real-time PCR with genus- and species- specific primers identified all isolates as B. melitensis. The results of ERIC-PCR suggested the existence of 75 ERIC genotypes of B. melitensis with a discriminatory index of 0.997. Cluster classification of these genotypes divided them into two clusters, A and B, diverging at ~25%. The maximum number of genotypes (n = 51) were found in cluster B5. MLVA-8 analysis identified all isolates as B. melitensis, and MLVA-8, MLVA-11 and MLVA-16 typing divided the isolates into 10, 32 and 71 MLVA types, respectively. Furthermore, the combined minimum spanning tree analysis demonstrated that, compared to MLVA types discovered all over the world, the Kuwaiti isolates were a distinct group of MLVA-11 and MLVA-16 types in the East Mediterranean Region.

Species identification and molecular typing of human Brucella isolates from Kuwait

PubMed Central

Osman, Amr; Shaheed, Faraz; Khan, Mohd W.

2017-01-01

Brucellosis is a zoonotic disease of major concern in Kuwait and the Middle East. Human brucellosis can be caused by several Brucella species with varying degree of pathogenesis, and relapses are common after apparently successful therapy. The classical biochemical methods for identification of Brucella are time-consuming, cumbersome, and provide information limited to the species level only. In contrast, molecular methods are rapid and provide differentiation at intra-species level. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-8, MLVA-11 and MLVA-16 were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. 16S rRNA gene sequencing of all isolates showed 90–99% sequence identity with B. melitensis and real-time PCR with genus- and species- specific primers identified all isolates as B. melitensis. The results of ERIC-PCR suggested the existence of 75 ERIC genotypes of B. melitensis with a discriminatory index of 0.997. Cluster classification of these genotypes divided them into two clusters, A and B, diverging at ~25%. The maximum number of genotypes (n = 51) were found in cluster B5. MLVA-8 analysis identified all isolates as B. melitensis, and MLVA-8, MLVA-11 and MLVA-16 typing divided the isolates into 10, 32 and 71 MLVA types, respectively. Furthermore, the combined minimum spanning tree analysis demonstrated that, compared to MLVA types discovered all over the world, the Kuwaiti isolates were a distinct group of MLVA-11 and MLVA-16 types in the East Mediterranean Region. PMID:28800594

Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification

PubMed Central

Smit, John; Reijnen, Bastian; Stokvis, Frank

2013-01-01

Abstract A feasibility test of molecular identification of European fruit flies (Diptera: Tephritidae) based on COI barcode sequences has been executed. A dataset containing 555 sequences of 135 ingroup species from three subfamilies and 42 genera and one single outgroup species has been analysed. 73.3% of all included species could be identified based on their COI barcode gene, based on similarity and distances. The low success rate is caused by singletons as well as some problematic groups: several species groups within the genus Terellia and especially the genus Urophora. With slightly more than 100 sequences – almost 20% of the total – this genus alone constitutes the larger part of the failure for molecular identification for this dataset. Deleting the singletons and Urophora results in a success-rate of 87.1% of all queries and 93.23% of the not discarded queries as correctly identified. Urophora is of special interest due to its economic importance as beneficial species for weed control, therefore it is desirable to have alternative markers for molecular identification. We demonstrate that the success of DNA barcoding for identification purposes strongly depends on the contents of the database used to BLAST against. Especially the necessity of including multiple specimens per species of geographically distinct populations and different ecologies for the understanding of the intra- versus interspecific variation is demonstrated. Furthermore thresholds and the distinction between true and false positives and negatives should not only be used to increase the reliability of the success of molecular identification but also to point out problematic groups, which should then be flagged in the reference database suggesting alternative methods for identification. PMID:24453563

Direct molecular mass determination of trehalose monomycolate from 11 species of mycobacteria by MALDI-TOF mass spectrometry.

PubMed

Fujita, Yukiko; Naka, Takashi; Doi, Takeshi; Yano, Ikuya

2005-05-01

Direct estimation of the molecular mass of single molecular species of trehalose 6-monomycolate (TMM), a ubiquitous cell-wall component of mycobacteria, was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. When less than 1 microg TMM was analysed by MALDI-TOF mass spectrometry, quasimolecular ions [M+Na]+ of each molecular species were demonstrated and the numbers of carbons and double bonds (or cyclopropane rings) were determined. Since the introduction of oxygen atoms such as carbonyl, methoxy and ester groups yielded the appropriate shift of mass ions, the major subclasses of mycolic acid (alpha, methoxy, keto and wax ester) were identified without resorting to hydrolytic procedures. The results showed a marked difference in the molecular species composition of TMM among mycobacterial species. Unexpectedly, differing from other mycoloyl glycolipids, TMM from Mycobacterium tuberculosis showed a distinctive mass pattern, with abundant odd-carbon-numbered monocyclopropanoic (or monoenoic) alpha-mycolates besides dicyclopropanoic mycolate, ranging from C75 to C85, odd- and even-carbon-numbered methoxymycolates ranging from C83 to C94 and even- and odd-carbon-numbered ketomycolates ranging from C83 to C90. In contrast, TMM from Mycobacterium bovis (wild strain and BCG substrains) possessed even-carbon-numbered dicyclopropanoic alpha-mycolates. BCG Connaught strain lacked methoxymycolates almost completely. These results were confirmed by MALDI-TOF mass analysis of mycolic acid methyl esters liberated by alkaline hydrolysis and methylation of the original TMM. Wax ester-mycoloyl TMM molecular species were demonstrated for the first time as an intact form in the Mycobacterium avium-intracellulare group, M. phlei and M. flavescens. The M. avium-intracellulare group possessed predominantly C85 and C87 wax ester-mycoloyl TMM, while M. phlei and the rapid growers tested contained C80, C81, C82 and C83 wax ester

Identification of the haemolytic activity of Malassezia species.

PubMed

Juntachai, Weerapong; Kummasook, Aksarakorn; Mekaprateep, Malee; Kajiwara, Susumu

2014-03-01

Malassezia species are part of the normal skin flora and are associated with a number of human and animal skin diseases. However, the mechanisms that mediate infection and host-fungal interactions are poorly understood. The haemolytic activity of several microorganisms is considered a factor that contributes to pathogenicity of the organism to humans and animals. This virulence factor was previously identified in several pathogenic fungi that cause systemic mycoses, such as Aspergillus and Candida. In this study, the haemolytic activity of six major Malassezia species, including M. furfur, M. globosa, M. pachydermatis, M. restricta, M. slooffiae and M. sympodialis, was investigated. The haemolytic activity of these species was tested on tryptone soya agar with 5% sheep blood. All the examined Malassezia species produced a halo zone of complete haemolysis. A quantitative analysis of the haemolytic activity was performed by incubating sheep erythrocytes with the extraction from culture of each Malassezia species. Interestingly, M. globosa and M. restricta showed significantly high haemolytic activity compared with the other Malassezia species. In addition, M. globosa also exhibited stable haemolytic activity after treatment at 100 °C and in the presence of some proteases, indicating that this haemolytic factor is different from those of other fungi. © 2013 Blackwell Verlag GmbH.

Assessing the viability of bacterial species in drinking water by combined cellular and molecular analyses.

PubMed

Kahlisch, Leila; Henne, Karsten; Gröbe, Lothar; Brettar, Ingrid; Höfle, Manfred G

2012-02-01

The question which bacterial species are present in water and if they are viable is essential for drinking water safety but also of general relevance in aquatic ecology. To approach this question we combined propidium iodide/SYTO9 staining ("live/dead staining" indicating membrane integrity), fluorescence-activated cell sorting (FACS) and community fingerprinting for the analysis of a set of tap water samples. Live/dead staining revealed that about half of the bacteria in the tap water had intact membranes. Molecular analysis using 16S rRNA and 16S rRNA gene-based single-strand conformation polymorphism (SSCP) fingerprints and sequencing of drinking water bacteria before and after FACS sorting revealed: (1) the DNA- and RNA-based overall community structure differed substantially, (2) the community retrieved from RNA and DNA reflected different bacterial species, classified as 53 phylotypes (with only two common phylotypes), (3) the percentage of phylotypes with intact membranes or damaged cells were comparable for RNA- and DNA-based analyses, and (4) the retrieved species were primarily of aquatic origin. The pronounced difference between phylotypes obtained from DNA extracts (dominated by Betaproteobacteria, Bacteroidetes, and Actinobacteria) and from RNA extracts (dominated by Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria) demonstrate the relevance of concomitant RNA and DNA analyses for drinking water studies. Unexpected was that a comparable fraction (about 21%) of phylotypes with membrane-injured cells was observed for DNA- and RNA-based analyses, contradicting the current understanding that RNA-based analyses represent the actively growing fraction of the bacterial community. Overall, we think that this combined approach provides an interesting tool for a concomitant phylogenetic and viability analysis of bacterial species of drinking water.

Molecular, biochemical, and morphometric characterization of Fasciola species potentially causing zoonotic disease in Egypt.

PubMed

El-Rahimy, Hoda H; Mahgoub, Abeer M A; El-Gebaly, Naglaa Saad M; Mousa, Wahid M A; Antably, Abeer S A E

2012-09-01

Fascioliasis is an important disease caused by Fasciola hepatica and Fasciola gigantica. The distributions of both species overlap in many areas of Asia and Africa including Egypt. Fifty adult Fasciola worms were collected from livers of cattle and sheep slaughtered in abattoirs, Cairo, Egypt. They were subjected to morphological and metric assessment of external features of fresh adults, morphological and metric assessment of internal anatomy of stained mounted worms, determination of electrophorezed bands of crude adult homogenates using SDS-PAGE, and molecular characterization of species-specific DNA segments using RFLP-PCR. It was found that the correlation between conventional morphology and its morphotype was statistically significant (P value = 0.00). Using SDS-PAGE, 13 bands were detected among both genotypes of Fasciola (35.7, 33.6, 32.4, 29.3, 27.5, 26, 24.4, 23, 21.45, 19, 16.75, 12.5, and 9.1 kDa).The most prevalent bands were that with a molecular weight of 29.3, 26, and 19 kDa. Bands detected were common for both species, but protein bands could not distinguish between F. hepatica and F. gigantica. The result of PCR for the amplification of the selected 28S rDNA fragment with the designed primer set yielded 618 bp long PCR products for F. hepatica and F. gigantica. Different band patterns generated after digestion of the 618 bp segment by the enzyme AvaII obtained with F. hepatica showed segments of the length 529, 62, 27 bp, while with F. gigantica 322, 269, 27 bp bands were obtained. Genotyping revealed no equivocal results. The conventional morphological parameters for species determination of Fasciola spp. endemic in Egypt were evaluated versus protein bands characterization and genotyping. It was concluded that conventional morphological and metric assessments were not useful for differentiation between F. gigantica and F. hepatica due to extensive overlap in the relative ranges. Similar conclusion was reached concerning protein band

Molecular and morphological evidence for three species of Diplostomum (Digenea: Diplostomidae), parasites of fishes and fish-eating birds in Spain.

PubMed

Pérez-del-Olmo, Ana; Georgieva, Simona; Pula, Héctor J; Kostadinova, Aneta

2014-11-12

Recent molecular studies have revealed high species diversity of Diplostomum in central and northern Europe. However, our knowledge of the distribution of Diplostomum spp. in the southern distributional range in Europe of the snail intermediate hosts (Lymnaea stagnalis and Radix spp.) is rather limited. This study aims to fill this gap in our knowledge using molecular and morphological evidence. Nineteen fish species and six fish-eating bird species were sampled opportunistically in three regions (Catalonia, Extremadura and Aragon) in Spain. All isolates of Diplostomum spp. were characterised morphologically and molecularly. Partial sequences of the barcode region of the cox1 mitochondrial gene and complete sequences of the ribosomal ITS1-5.8S-ITS2 gene cluster were used for molecular identification of the isolates. Integrated morphological and molecular analyses demonstrated the presence of three species among the larval and adult isolates of Diplostomum spp. sampled in Spain: Diplostomum spathaceum (in fish and birds), D. pseudospathaceum (in birds) and Diplostomum sp. (in fish) referred to as Clade Q sensu Georgieva et al. (Int J Parasitol, 43:57-72, 2013). We detected ten cox1 haplotypes among the isolates of D. spathaceum with only one haplotype shared with adult isolates from central and northern Europe. No specific geographic pattern of the distribution of the novel haplotypes was found. This first molecular exploration of the diversity of Diplostomum spp. in southern Europe indicates much lower species richness compared with the northern regions of Europe.

Taxonomic revision and molecular phylogenetics of the Idarnes incertus species-group (Hymenoptera, Agaonidae, Sycophaginae)

PubMed Central

Cruaud, Astrid; Genson, Gwenaëlle; Rasplus, Jean-Yves; Pereira, Rodrigo A.S.

2017-01-01

Sycophaginae is a group of non-pollinating fig wasps considered closely related to the fig pollinators (Agaoninae, Tetrapusiinae, and Kradibiinae) in the most recent phylogenetic analyses. They occur in all tropical regions and are associated with Ficus subgenera Urostigma and Sycomorus. There are six described genera of Sycophaginae, and two are native and confined to the Neotropics, namely Idarnes Walker, 1843 and Anidarnes Bouček, 1993. Genus Idarnes is divided into three morphologically distinct groups that were proven to be monophyletic by recent molecular phylogenetic analyses. In this paper we reviewed the Idarnes incertus species-group and provide detailed morphological descriptions and illustrations for the species belonging to this group. Three previously described species were redescribed: I. brasiliensis (Mayr, 1906) comb. nov., I. hansoni Bouček, 1993, and I. incertus (Ashmead, 1900). Seventeen new species are described by Farache and Rasplus: I. amacayacuensis sp. n., I. amazonicus sp. n., I. americanae sp. n., I. badiovertex sp. n., I. brevis sp. n., I. brunneus sp. n., I. comptoni sp. n., I. cremersiae sp. n., I. dimorphicus sp. n., I. flavicrus sp. n., I. flaviventris sp. n., I. gibberosus sp. n., I. gordhi sp. n., I. maximus sp. n., I. nigriventris sp. n., I. pseudoflavus sp. n. and I. ramirezi sp. n. We provided keys for the identification of the species as well as for recognising the different species-groups of Idarnes and a closely related genus (Sycophaga Westwood, 1840). Additionally, phylogenetic relationships among 13 species of the I. incertus species-group were inferred using four molecular markers and discussed in the light of Ficus taxonomy and host specificity. PMID:28168097

First molecular detection and characterization of Sarcocystis species in slaughtered cattle in North-West Tunisia.

PubMed

Amairia, Safa; Amdouni, Yosra; Rjeibi, Mohamed Ridha; Rouatbi, Mariem; Awadi, Sofia; Gharbi, Mohamed

2016-12-01

Sarcocystis spp. is one of the most prevalent foodborne parasites infecting both animals and humans. Consumption of raw or undercooked infected meat is a risk factor of human intestinal sarcocystosis. The present study aimed to estimate the prevalence of Sarcocystis species infecting slaughtered Tunisian cattle in North-West Tunisia (Béja governorate). DNA was extracted from 150 beef meat samples and a PCR-restriction fragment length polymorphism was used for identification. The overall infection prevalence of Sarcocystis spp. was 38% (57/150). Two species were identified, namely S. hominis (25%; 39/150) and S. cruzi (12%; 18/150). For both species, the highest prevalence was in Thibar locality (52.9 and 17.6% for S. hominis and S. cruzi, respectively). The molecular prevalence of S. cruzi was significantly higher in animals aged between two and eight years (19.2%; 10/52). This is the first molecular identification of Sarcocystis species in Tunisian cattle. Further studies in both human and animal Tunisian populations are needed to rank this parasitic disease among others. Copyright © 2016 Elsevier Ltd. All rights reserved.

Morphological and Molecular Characterization of a New Trichuris Species (Nematoda- Trichuridae), and Phylogenetic Relationships of Trichuris Species of Cricetid Rodents from Argentina

PubMed Central

Robles, María del Rosario; Cutillas, Cristina; Panei, Carlos Javier; Callejón, Rocío

2014-01-01

Populations of Trichuris spp. isolated from six species of sigmodontine rodents from Argentina were analyzed based on morphological characteristics and ITS2 (rDNA) region sequences. Molecular data provided an opportunity to discuss the phylogenetic relationships among the Trichuris spp. from Noth and South America (mainly from Argentina). Trichuris specimens were identified morphologically as Trichuris pardinasi, T. navonae, Trichuris sp. and Trichuris new species, described in this paper. Sequences analyzed by Maximum Parsimony, Maximum Likelihood and Bayesian inference methods showed four main clades corresponding with the four different species regardless of geographical origin and host species. These four species from sigmodontine rodents clustered together and separated from Trichuris species isolated from murine and arvicoline rodents (outgroup). Different genetic lineages observed among Trichuris species from sigmodontine rodents which supported the proposal of a new species. Moreover, host distribution showed correspondence with the different tribes within the subfamily Sigmodontinae. PMID:25393618

New cryptic species of the ‘revolutum’ group of Echinostoma (Digenea: Echinostomatidae) revealed by molecular and morphological data

PubMed Central

2013-01-01

Background The digenean species of Echinostoma (Echinostomatidae) with 37 collar spines that comprise the so-called ‘revolutum’ species complex, qualify as cryptic due to the interspecific homogeneity of characters used to differentiate species. Only five species were considered valid in the most recent revision of the group but recent molecular studies have demonstrated a higher diversity within the group. In a study of the digeneans parasitising molluscs in central and northern Europe we found that Radix auricularia, R. peregra and Stagnicola palustris were infected with larval stages of two cryptic species of the ‘revolutum’ complex, one resembling E. revolutum and one undescribed species, Echinostoma sp. IG. This paper provides morphological and molecular evidence for their delimitation. Methods Totals of 2,030 R. auricularia, 357 R. peregra and 577 S. palustris were collected in seven reservoirs of the River Ruhr catchment area in Germany and a total of 573 R. peregra was collected in five lakes in Iceland. Cercariae were examined and identified live and fixed in molecular grade ethanol for DNA isolation and in hot/cold 4% formaldehyde solution for obtaining measurements from fixed materials. Partial fragments of the mitochondrial gene nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1) were amplified for 14 isolates. Results Detailed examination of cercarial morphology allowed us to differentiate the cercariae of the two Echinostoma spp. of the ‘revolutum’ species complex. A total of 14 partial nad1 sequences was generated and aligned with selected published sequences for eight species of the ‘revolutum’ species complex. Both NJ and BI analyses resulted in consensus trees with similar topologies in which the isolates from Europe formed strongly supported reciprocally monophyletic lineages. The analyses also provided evidence that North American isolates identified as E. revolutum represent another cryptic species of the �

A proposed harmonized LPS molecular-subtyping scheme for Cronobacter species.

PubMed

Yan, Qiongqiong; Jarvis, Karen G; Chase, Hannah R; Hébert, Karine; Trach, Larisa H; Lee, Chloe; Sadowski, Jennifer; Lee, Boram; Hwang, Seongeun; Sathyamoorthy, Venugopal; Mullane, Niall; Pava-Ripoll, Monica; Iversen, Carol; Pagotto, Franco; Fanning, Séamus; Tall, Ben D

2015-09-01

Cronobacter are opportunistic pathogens, which cause infections in all age groups. To aid the characterization of Cronobacter in foods and environments a harmonized LPS identification scheme for molecular serotyping is needed. To this end, we studied 409 Cronobacter isolates representing the seven Cronobacter species using two previously reported molecular serotyping schemes, described here as Mullane-Jarvis (M-J) and Sun schemes. PCR analysis revealed many overlapping results that were obtained when independently applying the two serotyping schemes. There were complete agreements between the two PCR schemes for Cronobacter sakazakii (Csak) O:1, Csak O:3, and Csak O:7 serotypes. However, only thirty-five of 41 Csak O:4 strains, identified using the M-J scheme, were PCR-positive with the Sun scheme primers. Also the Sun scheme Csak O:5 primers failed to identify this serotype in any of the C. sakazakii strains tested, but did recognize seven Cronobacter turicensis strains, which were identified as Ctur O:3 using the M-J scheme. Similarly, the Sun scheme Csak O:6 primers recognized 30 Cronobacter malonaticus O:2 strains identified with the M-J scheme, but failed to identify this serotype in any C. sakazakii strain investigated. In this report, these findings are summarized and a harmonized molecular-serotyping scheme is proposed which is predicated on the correct identification of Cronobacter species, prior to serotype determination. In summary, fourteen serotypes were identified using the combined protocol, which consists of Csak O:1-O:4, and Csak O:7; Cmal O:1-O:2; Cdub O:1-O:2, Cmuy O:1-O:2, Cuni O:1, as well as Ctur O:1 and Ctur O:3. Published by Elsevier Ltd.

Molecular Characterization and Analysis of Antimicrobial Activity of Endophytic Fungi From Medicinal Plants in Saudi Arabia

PubMed Central

Gashgari, Rukaia; Gherbawy, Youssuf; Ameen, Fuad; Alsharari, Salam

2016-01-01

Background: Endophytic fungi, which have been reported in numerous plant species, are important components of the forest community and contribute significantly to the diversity of natural ecosystems. Objectives: The current study aimed to evaluate and characterize, at the molecular level, the diversity and antimicrobial activities of endophytic fungi from medicinal plants in Saudi Arabia. Materials and Methods: Fungi growing on plant segments were isolated and identified based on morphological and molecular characteristics. The isolates were grouped into 35 distinct operational taxonomic units, based on the sequence of the internal transcribed spacer regions in the rRNA gene. The colonization frequency and the dominant fungi percentage of these endophytic fungi were calculated. A dual culture technique was adopted to investigate the antifungal activity of these endophytes. Results: Tamarix nilotica showed the highest endophytic diversity with a relative frequency of 27.27%, followed by Cressa cretica with a relative frequency of 19.27%. The most frequently isolated species was Penicillium chrysogenum with an overall colonization rate of 98.57%. Seven out of 35 endophytic fungi exhibited strong antifungal activity to all plant fungal pathogens tested. P. chrysogenum, Fusarium oxysporum, and F. nygamai exhibited the highest inhibition against the human pathogenic bacteria Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Aspergillus sydowii, P. chrysogenum, and Eupenicillium crustaceum showed strong antimicrobial activity against Enterococcus faecalis. Conclusions: The antimicrobial activity of these endophytic microorganisms could be exploited in biotechnology, medicine, and agriculture. PMID:27099679

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species

PubMed Central

Domyan, Eric T; Kronenberg, Zev; Infante, Carlos R; Vickrey, Anna I; Stringham, Sydney A; Bruders, Rebecca; Guernsey, Michael W; Park, Sungdae; Payne, Jason; Beckstead, Robert B; Kardon, Gabrielle; Menke, Douglas B; Yandell, Mark; Shapiro, Michael D

2016-01-01

Birds display remarkable diversity in the distribution and morphology of scales and feathers on their feet, yet the genetic and developmental mechanisms governing this diversity remain unknown. Domestic pigeons have striking variation in foot feathering within a single species, providing a tractable model to investigate the molecular basis of skin appendage differences. We found that feathered feet in pigeons result from a partial transformation from hindlimb to forelimb identity mediated by cis-regulatory changes in the genes encoding the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also found that ectopic expression of Tbx5 is associated with foot feathers in chickens, suggesting similar molecular pathways underlie phenotypic convergence between these two species. These results show how changes in expression of regional patterning genes can generate localized changes in organ fate and morphology, and provide viable molecular mechanisms for diversity in hindlimb scale and feather distribution. DOI: http://dx.doi.org/10.7554/eLife.12115.001 PMID:26977633

Greek PDO saffron authentication studies using species specific molecular markers.

PubMed

Bosmali, I; Ordoudi, S A; Tsimidou, M Z; Madesis, P

2017-10-01

Saffron, the spice produced from the red stigmas of the flower of Crocus sativus L. is a frequent target of fraud and mislabeling practices that cannot be fully traced using the ISO 3632 trade standard specifications and test methods. A molecular approach is proposed herein as a promising branding strategy for the authentication of highly esteemed saffron brands such as the Greek Protected Designation of Origin (PDO) "Krokos Kozanis". Specific ISSR (inter-simple sequence repeat) markers were used to assess for the first time, the within species variability of several populations of C. sativus L. from the cultivation area of "Krokos Kozanis" as well as the potential differences with the band pattern produced by other Crocus species. Then, species-specific markers were developed taking advantage of an advanced molecular technique such as the HRM analysis coupled with universal DNA barcoding regions (trnL) (Bar-HRM) and applied to saffron admixtures with some of the most common plant adulterants (Calendula officinalis, Carthamus tinctorius, Gardenia jasminoides, Zea mays and Curcuma longa). The sensitivity of the procedure was tested for turmeric as a case study whereas HPLC-fluorescence determination of secondary metabolites was also employed for comparison. The overall results indicated that the Bar-HRM approach is quite effective in terms of specificity and sensitivity. Its effectiveness regarding the detection of turmeric was comparable to that of a conventional HPLC method (0.5% vs 1.0%, w/w). Yet, the proposed DNA-based method is much faster, cost-effective and can be used even by non-geneticists, in any laboratory having access to an HRM-capable real-time PCR instrumentation. It can be, thus, regarded as a strong analytical tool in saffron authentication studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular and Cytogenetic Characterization of Wild Musa Species

PubMed Central

Čížková, Jana; Hřibová, Eva; Christelová, Pavla; Van den Houwe, Ines; Häkkinen, Markku; Roux, Nicolas; Swennen, Rony; Doležel, Jaroslav

2015-01-01

The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region

A new species of Cacatuocotyle (Monogenea, Dactylogyridae) parasitizing Astyanax spp. (Characiformes, Characidae) from Brazil, including molecular data and a key to species identification.

PubMed

Zago, Aline Cristina; Franceschini, Lidiane; Müller, Maria Isabel; Silva, Reinaldo José da

2018-06-26

The present study describes Cacatuocotyle papilionis n. sp. (Monogenea, Dactylogyridae) from the skin of the characid fishes Astyanax lacustris (Lütken, 1875) (=Astyanax altiparanae Garutti & Britski, 2000) and Astyanax fasciatus (Cuvier, 1819) (Characiformes, Characidae) from the Southeast of Brazil, supported by morphological and molecular data. The new species differs from all congeners, mainly due to the morphology of the ventral bar (resembling a butterfly), accessory piece, and the number of rings of the male copulatory organ (MCO), comprising a coiled tube with 4.5-5.5 counterclockwise rings. The first molecular data for this monogenean genus is provided in this study, using the partial sequences of the ribosomal gene (28S), as well as providing an identification key to the species.

Activation of molecular catalysts using semiconductor quantum dots

DOEpatents

Meyer, Thomas J [Chapel Hill, NC; Sykora, Milan [Los Alamos, NM; Klimov, Victor I [Los Alamos, NM

2011-10-04

Photocatalytic materials based on coupling of semiconductor nanocrystalline quantum dots (NQD) and molecular catalysts. These materials have capability to drive or catalyze non-spontaneous chemical reactions in the presence of visible radiation, ultraviolet radiation, or both. The NQD functions in these materials as a light absorber and charge generator. Following light absorption, the NQD activates a molecular catalyst adsorbed on the surface of the NQD via transfer of one or more charges (either electrons or electron-holes) from the NQD to the molecular catalyst. The activated molecular catalyst can then drive a chemical reaction. A photoelectrolytic device that includes such photocatalytic materials is also described.

Molecular diversity of some species belonging to the genus Daphnia O. F. Müller, 1785 (Crustacea: Cladocera) in Turkey.

PubMed

Özdemir, Ebru; Altındağ, Ahmet; Kandemir, İrfan

2017-05-01

Daphnia is a freshwater zooplankton species with controversial taxonomy due to its high morphological variation linked to environmental factors and inter-specific hybridization and polyploidy in some groups. The aim of the present study is to examine molecular diversity of some Daphnia species in Turkey and to establish DNA barcodes of Turkish Daphnia species. Sequence analysis was performed using 540 bp region of cytochrome oxidase subunit I gene of mitochondrial DNA. A total of 34 haplotypes have been identified for Turkey. Daphnia pulex complex was divided into two clades with 16.1% sequence divergence according to molecular taxonomy based on Kimura 2-parameter. The clade which was molecularly diverged from Daphnia pulex with 16.1% sequence divergence was found to show 99% similarity with Daphnia cf. pulicaria (sensu Alonso 1996) instead of Daphnia pulicaria Forbes, 1893. Furthermore, this study has contributed to Turkish zoogeography by demonstrating the distribution of Daphnia species in Turkey.

EMERGING MOLECULAR AND COMPUTATIONAL APPROACHES FOR CROSS-SPECIES EXTRAPLATIONS: A WORKSHOP SUMMARY REPORT

EPA Science Inventory

Benson, W.H., R.T. Di Giulio, J.C. Cook, J. Freedman, R.L. Malek, C. Thompson and D. Versteeg. In press. Emerging Molecular and Computational Approaches for Cross-Species Extrapolations: A Workshop Summary Report (Abstract). To be presented at the SETAC Fourth World Congress, 14-...

Altitudinal distribution and advertisement call of Colostethus latinasus (Amphibia: Dendrobatidae), endemic species from eastern Panama and type species of Colostethus , with a molecular assessment of similar sympatric species.

PubMed

Ibáñez, Roberto D; Griffith, Edgardo J; Lips, Karen R; Crawford, Andrew J

2017-04-12

We conducted a molecular assessment of Colostethus-like frogs along an elevational gradient in the Serranía de Pirre, above Santa Cruz de Cana, eastern Panama, aiming to establish their species identity and to determine the altitudinal distribution of C. latinasus. Our findings confirm the view of C. latinasus as an endemic species restricted to the highlands of this mountain range, i.e., 1350-1475 m.a.s.l., considered to be type locality of this species. We described the advertisement call of C. latinasus that consists of a series of 4-18 single, short and relatively loud "peep"-like notes given in rapid succession, and its spectral and temporal features were compared with calls of congeneric species. For the first time, DNA sequences from C. latinasus were obtained, since previously reported sequences were based on misidentified specimens. This is particularly important because C. latinasus is the type species of Colostethus, a genus considered paraphyletic according to recent phylogenetic analyses based on molecular data.

Molecular evidence for species status of the endangered Hainan peacock pheasant.

PubMed

Chang, Jiang; Wang, Biao; Zhang, Yang-Yun; Liu, Ying; Liang, Wei; Wang, Ji-Chao; Shi, Hai-Tao; Su, Wen-Ba; Zhang, Zheng-Wang

2008-01-01

The Hainan peacock pheasant is an endangered taxon found only on Hainan Island of China. Due to lack of detailed taxonomic studies, whether it is a subspecies of the grey peacock pheasant (Polyplectron bicalcaratum katsumatae) or a full species (Polyplectron katsumatae) remained unclear. We used molecular markers, including the complete mitochondrial cytochrome b gene and intron G of the nuclear ovomucoid gene, to reevaluate the taxonomy of the Hainan peacock pheasant. The results showed phylogeographic monophyly and large genetic distance between the Hainan peacock pheasant and the grey peacock pheasant. Sequence differences corroborated the species-level distinction between these two peacock pheasants, which were inferred to have diverged about 1.4+/-0.3 million years ago, near the time Hainan Island became separated from mainland China. Because the population density of the Hainan peacock pheasant is very low in its tropical forest on the island and the wild population is declining, it is now becoming severely endangered and should be ranked as the rarest species in the Order Galliformes in China. Our results increase the urgency of getting more morphological data to support the classification of the Hainan peacock pheasant as a distinct species and taking more conservation action immediately to protect this endangered island species.

Molecular phylogeny of Atractus (Serpentes, Dipsadidae), with emphasis on Ecuadorian species and the description of three new taxa.

PubMed

Arteaga, Alejandro; Mebert, Konrad; Valencia, Jorge H; Cisneros-Heredia, Diego F; Peñafiel, Nicolás; Reyes-Puig, Carolina; Vieira-Fernandes, José L; Guayasamin, Juan M

2017-01-01

We present a molecular phylogeny of snake genus Atractus , with an improved taxon sampling that includes 30 of the 140 species currently recognized. The phylogenetic tree supports the existence of at least three new species in the Pacific lowlands and adjacent Andean slopes of the Ecuadorian Andes, which we describe here. A unique combination of molecular, meristic and color pattern characters support the validity of the new species. With the newly acquired data, we propose and define the Atractus iridescens species group, as well as redefine the Atractus roulei species group. The species Atractus iridescens is reported for the first time in Ecuador, whereas Atractus bocourti and Atractus medusa are removed from the herpetofauna of this country. We provide the first photographic vouchers of live specimens for Atractus multicinctus , Atractus paucidens and Atractus touzeti , along with photographs of 19 other Ecuadorian Atractus species. The current status of Atractus occidentalis and Atractus paucidens is maintained based on the discovery of new material referable to these species. With these changes, the species number reported in Ecuador increases to 27, a number that is likely to increase as material not examined in this work becomes available and included in systematic studies.

Antiplatelet Aggregation Activity of Walnut Hull Extract via Suppression of Reactive Oxygen Species Generation and Caspase Activation.

PubMed

Meshkini, Azadeh; Tahmasbi, Masoumeh

2017-06-01

Walnut hull (wal hull) is an agricultural by-product that is widely used in traditional medicine for alleviating pain and treating skin diseases, however, recently it has gained much attention in modern pharmacology due to its antioxidant properties. The current study was aimed to determine the total phenolic, flavonoid, and tannin content of Persian wal hull extract and evaluate its biological effects on platelet function. Experimental data showed that acetone extract of wal hulls has a high content of polyphenolic compounds and antioxidant properties. The analytical study of crude extract by gas chromatography-mass spectrometry demonstrated different types of high- and low-molecular-weight compounds that are basically and biologically important. Moreover, an in vitro study revealed that wal hull extract at a concentration of 50 μg/mL inhibited thrombin-induced platelet aggregation and protein secretion by 50%, without any cytotoxic effects on platelets. The examined extract suppressed reactive oxygen species generation and also caspase activation in thrombin-stimulated platelets. Identically, N-acetylcysteine inhibited the increase of reactive oxygen species level induced by thrombin in platelets, and supported a link between cellular redox status and caspase activation in activated platelets. Presumably, the antiplatelet activity of wal hull extract is related to its polyphenolic compounds and their antioxidant properties. Therefore, wal hulls can be considered as a candidate for thrombotic disorders. Copyright © 2017. Published by Elsevier B.V.

Association of Fusobacterium species in pancreatic cancer tissues with molecular features and prognosis

PubMed Central

Mitsuhashi, Kei; Nosho, Katsuhiko; Sukawa, Yasutaka; Matsunaga, Yasutaka; Ito, Miki; Kurihara, Hiroyoshi; Kanno, Shinichi; Igarashi, Hisayoshi; Naito, Takafumi; Adachi, Yasushi; Tachibana, Mami; Tanuma, Tokuma; Maguchi, Hiroyuki; Shinohara, Toshiya; Hasegawa, Tadashi; Imamura, Masafumi; Kimura, Yasutoshi; Hirata, Koichi; Maruyama, Reo; Suzuki, Hiromu; Imai, Kohzoh

2015-01-01

Recently, bacterial infection causing periodontal disease has attracted considerable attention as a risk factor for pancreatic cancer. Fusobacterium species is an oral bacterial group of the human microbiome. Some evidence suggests that Fusobacterium species promote colorectal cancer development; however, no previous studies have reported the association between Fusobacterium species and pancreatic cancer. Therefore, we examined whether Fusobacterium species exist in pancreatic cancer tissue. Using a database of 283 patients with pancreatic ductal adenocarcinoma (PDAC), we tested cancer tissue specimens for Fusobacterium species. We also tested the specimens for KRAS, NRAS, BRAF and PIK3CA mutations and measured microRNA-21 and microRNA-31. In addition, we assessed epigenetic alterations, including CpG island methylator phenotype (CIMP). Our data showed an 8.8% detection rate of Fusobacterium species in pancreatic cancers; however, tumor Fusobacterium status was not associated with any clinical and molecular features. In contrast, in multivariate Cox regression analysis, compared with the Fusobacterium species-negative group, we observed significantly higher cancer-specific mortality rates in the positive group (p = 0.023). In conclusion, Fusobacterium species were detected in pancreatic cancer tissue. Tumor Fusobacterium species status is independently associated with a worse prognosis of pancreatic cancer, suggesting that Fusobacterium species may be a prognostic biomarker of pancreatic cancer. PMID:25797243

Association of Fusobacterium species in pancreatic cancer tissues with molecular features and prognosis.

PubMed

Mitsuhashi, Kei; Nosho, Katsuhiko; Sukawa, Yasutaka; Matsunaga, Yasutaka; Ito, Miki; Kurihara, Hiroyoshi; Kanno, Shinichi; Igarashi, Hisayoshi; Naito, Takafumi; Adachi, Yasushi; Tachibana, Mami; Tanuma, Tokuma; Maguchi, Hiroyuki; Shinohara, Toshiya; Hasegawa, Tadashi; Imamura, Masafumi; Kimura, Yasutoshi; Hirata, Koichi; Maruyama, Reo; Suzuki, Hiromu; Imai, Kohzoh; Yamamoto, Hiroyuki; Shinomura, Yasuhisa

2015-03-30

Recently, bacterial infection causing periodontal disease has attracted considerable attention as a risk factor for pancreatic cancer. Fusobacterium species is an oral bacterial group of the human microbiome. Some evidence suggests that Fusobacterium species promote colorectal cancer development; however, no previous studies have reported the association between Fusobacterium species and pancreatic cancer. Therefore, we examined whether Fusobacterium species exist in pancreatic cancer tissue. Using a database of 283 patients with pancreatic ductal adenocarcinoma (PDAC), we tested cancer tissue specimens for Fusobacterium species. We also tested the specimens for KRAS, NRAS, BRAF and PIK3CA mutations and measured microRNA-21 and microRNA-31. In addition, we assessed epigenetic alterations, including CpG island methylator phenotype (CIMP). Our data showed an 8.8% detection rate of Fusobacterium species in pancreatic cancers; however, tumor Fusobacterium status was not associated with any clinical and molecular features. In contrast, in multivariate Cox regression analysis, compared with the Fusobacterium species-negative group, we observed significantly higher cancer-specific mortality rates in the positive group (p = 0.023). In conclusion, Fusobacterium species were detected in pancreatic cancer tissue. Tumor Fusobacterium species status is independently associated with a worse prognosis of pancreatic cancer, suggesting that Fusobacterium species may be a prognostic biomarker of pancreatic cancer.

Endurance exercise training and high-fat diet differentially affect composition of diacylglycerol molecular species in rat skeletal muscle.

PubMed

Kawanishi, Noriaki; Takagi, Kana; Lee, Hyeon-Cheol; Nakano, Daiki; Okuno, Toshiaki; Yokomizo, Takehiko; Machida, Shuichi

2018-06-01

Insulin resistance of peripheral muscle is implicated in the etiology of metabolic syndrome in obesity. Although accumulation of glycerolipids, such as triacylglycerol and diacylglycerol (DAG), in muscle contributes to insulin resistance in obese individuals, endurance-trained athletes also have higher glycerolipid levels but normal insulin sensitivity. We hypothesized that the difference in insulin sensitivity of skeletal muscle between athletes and obese individuals stems from changes in fatty acid composition of accumulated lipids. Here, we evaluated the effects of intense endurance exercise and high-fat diet (HFD) on the accumulation and composition of lipid molecular species in rat skeletal muscle using a lipidomic approach. Sprague-Dawley female rats were randomly assigned to three groups and received either normal diet (ND) in sedentary conditions, ND plus endurance exercise training, or HFD in sedentary conditions. Rats were fed ND or HFD between 4 and 12 wk of age. Rats in the exercise group ran on a treadmill for 120 min/day, 5 days/wk, for 8 wk. Soleus muscle lipidomic profiles were obtained using liquid chromatography/tandem mass spectrometry. Total DAG levels, particularly those of palmitoleate-containing species, were increased in muscle by exercise training. However, whereas the total DAG level in the muscle was also increased by HFD, the levels of DAG molecular species containing palmitoleate were decreased by HFD. The concentration of phosphatidylethanolamine molecular species containing palmitoleate was increased by exercise but decreased by HFD. Our results indicate that although DAG accumulation was similar levels in trained and sedentary obese rats, specific changes in molecular species containing palmitoleate were opposite.

[Study of antioxidant activity of phenolic compounds from some species of Georgian flora].

PubMed

Alaniia, M; Shalashvili, K; Sagareishvili, T; Kavtaradze, N; Sutiashvili, M

2013-09-01

The antioxidant activity of extracts obtained from different parts of Georgian flora species Hamamelis virginiana L., Astragalus caucasicus Pall., Astragalus microcephalus Willd., Vitis vinifera L., Rhododendron ponticum L., Rhododendron Ungernii Trautv., Ginkgo biloba L., Salvia officinalis L., Querqus iberica Stev., Maclura aurantiaca Nutt., Cotinus coggygria Ledeb., Fraxinus ornus L., Urtica dioica L., Rhododendron caucasicum Pall., Pueraria hirsuta Matsum., Geranium pusillum L., Astragalus Tanae Sosn., Pinus silvestris L. has been studied. Comparison with ethylentetraacetate and α-tocopherole revealed high efficacy of all extracts studied. 45 individual phenolic compounds were isolated and described by chemical examination of biologically active objects. Common sage (Salvia officinalis) extract turned out as the most active (200 %). The chemical study revealed the dominant content of condensed tannins and low molecular phenolic compounds, which may be attributed to the high antioxidant activity. Biologically active antiatherosclerotic food additive "Salbin" was developed on the basis of Common sage - Salvia officinalis L. phenolic compounds.

Method for improved selectivity in photo-activation of molecular agents

DOEpatents

Fisher, Walter G.; Wachter, Eric A.; Dees, H. Craig

1998-01-01

A method for the treatment of a particular volume of plant or animal tissue comprising the steps of treating the plant or animal tissue with at least one photo-active molecular agent, wherein the particular volume of the plant or animal tissue retains at least a portion of the at least one photo-active molecular agent, and then treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of at least one of the at least one photo-active molecular agent retained in the particular volume of the plant or animal tissue, wherein the at least one photo-active molecular agent becomes active in the particular volume of the plant or animal tissue. There is also disclosed a method for the treatment of cancer in plant or animal tissue and a method for producing at least one photo-activated molecular agent in a particular volume of a material.

Method for improved selectivity in photo-activation of molecular agents

DOEpatents

Fisher, Walter G.; Wachter, Eric A.; Dees, H. Craig

1999-01-01

A method for the treatment of a particular volume of plant or animal tissue comprising the steps of treating the plant or animal tissue with at least one photo-active molecular agent, wherein the particular volume of the plant or animal tissue retains at least a portion of the at least one photo-active molecular agent, and then treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of at least one of the at least one photo-active molecular agent retained in the particular volume of the plant or animal tissue, wherein the at least one photo-active molecular agent becomes active in the particular volume of the plant or animal tissue. There is also disclosed a method for the treatment of cancer in plant or animal tissue and a method for producing at least one photo-activated molecular agent in a particular volume of a material.

Method for improved selectivity in photo-activation of molecular agents

DOEpatents

Fisher, W.G.; Wachter, E.A.; Dees, H.C.

1998-11-03

A method for the treatment of a particular volume of plant or animal tissue comprising the steps of treating the plant or animal tissue with at least one photo-active molecular agent, wherein the particular volume of the plant or animal tissue retains at least a portion of the at least one photo-active molecular agent, and then treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of at least one of the at least one photo-active molecular agent retained in the particular volume of the plant or animal tissue, wherein the at least one photo-active molecular agent becomes active in the particular volume of the plant or animal tissue. There is also disclosed a method for the treatment of cancer in plant or animal tissue and a method for producing at least one photo-activated molecular agent in a particular volume of a material. 23 figs.

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

PubMed

Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

2012-09-01

Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

Comparative molecular species delimitation in the charismatic Nawab butterflies (Nymphalidae, Charaxinae, Polyura).

PubMed

Toussaint, Emmanuel F A; Morinière, Jérôme; Müller, Chris J; Kunte, Krushnamegh; Turlin, Bernard; Hausmann, Axel; Balke, Michael

2015-10-01

The charismatic tropical Polyura Nawab butterflies are distributed across twelve biodiversity hotspots in the Indomalayan/Australasian archipelago. In this study, we tested an array of species delimitation methods and compared the results to existing morphology-based taxonomy. We sequenced two mitochondrial and two nuclear gene fragments to reconstruct phylogenetic relationships within Polyura using both Bayesian inference and maximum likelihood. Based on this phylogenetic framework, we used the recently introduced bGMYC, BPP and PTP methods to investigate species boundaries. Based on our results, we describe two new species Polyura paulettae Toussaint sp. n. and Polyura smilesi Toussaint sp. n., propose one synonym, and five populations are raised to species status. Most of the newly recognized species are single-island endemics likely resulting from the recent highly complex geological history of the Indomalayan-Australasian archipelago. Surprisingly, we also find two newly recognized species in the Indomalayan region where additional biotic or abiotic factors have fostered speciation. Species delimitation methods were largely congruent and succeeded to cross-validate most extant morphological species. PTP and BPP seem to yield more consistent and robust estimations of species boundaries with respect to morphological characters while bGMYC delivered contrasting results depending on the different gene trees considered. Our findings demonstrate the efficiency of comparative approaches using molecular species delimitation methods on empirical data. They also pave the way for the investigation of less well-known groups to unveil patterns of species richness and catalogue Earth's concealed, therefore unappreciated diversity. Published by Elsevier Inc.

Molecular systematics and biodiversity of the Cryptotis mexicanus group (Eulipotyphla: Soricidae): two new species from Honduras supported

USGS Publications Warehouse

Baird, Amy B.; McCarthy, Timothy J.; Trujillo, Robert G.; Kang, Yuan Yuan; Esmaeiliyan, Mehdi; Valdez, Joselyn; Woodman, Neal; Bickham, John W.

2018-01-01

Small-eared shrews of the genus Cryptotis (Mammalia: Eulipotyphla: Soricidae) are widespread in the northern Neotropics. Systematic studies of these shrews over the past two decades have revealed previously undocumented morphological and species diversity, resulting in a quadrupling of the number of recognized species. Unfortunately, a small proportion of the species in the genus have been included in molecular phylogenetic studies, and evolutionary relationships within the genus are incompletely known. Traditionally, species have been assigned to four or five morphologically defined ‘species groups’, but tests of the monophyly of some of these groups show weak support and relationships amongst species groups remain somewhat speculative. The largest species group is the C. mexicanus group inhabiting Mexico and northern Central America. We studied sequences from mitochondrial cytochrome-b and 16S genes, as well as nuclear ApoB and BRCA1 genes from 22 species of Cryptotis, including 15 species in the C. mexicanus group. Our combined analysis shows that the C. goldmani subgroup is very weakly supported as monophyletic; however, the C. mexicanus group as a whole is not monophyletic. Our molecular phylogenetic analyses confirm the distinctiveness of two newly described species (C. celaque and C. mccarthyi) from isolated highlands of western Honduras and illustrate their relationship with other species formerly considered part of a widespread C. goodwini.

Functionalized active-nucleus complex sensor

DOEpatents

Pines, Alexander; Wemmer, David E.; Spence, Megan; Rubin, Seth

2003-11-25

A functionalized active-nucleus complex sensor that selectively associates with one or more target species, and a method for assaying and screening for one or a plurality of target species utilizing one or a plurality of functionalized active-nucleus complexes with at least two of the functionalized active-nucleus complexes having an attraction affinity to different corresponding target species. The functionalized active-nucleus complex has an active-nucleus and a targeting carrier. The method involves functionalizing an active-nucleus, for each functionalized active-nucleus complex, by incorporating the active-nucleus into a macromolucular or molecular complex that is capable of binding one of the target species and then bringing the macromolecular or molecular complexes into contact with the target species and detecting the occurrence of or change in a nuclear magnetic resonance signal from each of the active-nuclei in each of the functionalized active-nucleus complexes.

Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†

PubMed Central

Feng, Yaoyu; Xiao, Lihua

2011-01-01

Summary: Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination. PMID:21233509

Molecular characterization of eimeria species naturally infecting egyptian baldi chickens.

PubMed

Gadelhaq, Sahar M; Arafa, Waleed M; Aboelhadid, Shawky M

2015-01-01

Coccidiosis is a serious protozoal disease of poultry. The identification of Eimeria species has important implications for diagnosis and control as well as for epidemiology. The molecular characterization of Eimeria species infecting Egyptian baladi chickens was investigated. Eimeria species oocysts were harvested from intestines of naturally infected Egyptian baldi chickens. The morphometry characterization of oocysts along with COCCIMORPH software was done. The DNA was extracted initially by freezing and thawing then the prepared samples was subjected to commercial DNA kits. The DNA products were analyzed through conventional polymerase chain reaction by using amplified region (SCAR) marker. The PCR results confirmed the presence of 7 Eimeria species in the examined fecal samples of Egyptian baldi breed with their specific ampilicon sizes being E. acervulina (811bp), E. brunette (626bp), E. tenella (539bp), E. maxima (272bp), E. necatrix (200bp), E. mitis (327bp) and E. praecopx (354bp). A sequencing of the two most predominant species of Eimeria was done, on E. tenella and E. máxima. Analysis of the obtained sequences revealed high identities 99% between Egyptian isolates and the reference one. Similarly, E. maxima isolated from Egyptian baldi chickens showed 98% nucleotide identities with the reference strain. Only single nucleotide substitution was observed among the Egyptian E. tenella isolates (A181G) when compared to the reference one. The Egyptian isolates acquired 4 unique mutations (A68T, C164T, G190A and C227G) in compared with the reference sequence. This is the first time to identify the 7 species of Eimeria from Egyptian baladi chickens.

Molecular Characterization of Eimeria Species Naturally Infecting Egyptian Baldi Chickens

PubMed Central

GADELHAQ, Sahar M; ARAFA, Waleed M; ABOELHADID, Shawky M

2015-01-01

Background: Coccidiosis is a serious protozoal disease of poultry. The identification of Eimeria species has important implications for diagnosis and control as well as for epidemiology. The molecular characterization of Eimeria species infecting Egyptian baladi chickens was investigated. Methods: Eimeria species oocysts were harvested from intestines of naturally infected Egyptian baldi chickens. The morphometry characterization of oocysts along with COCCIMORPH software was done. The DNA was extracted initially by freezing and thawing then the prepared samples was subjected to commercial DNA kits. The DNA products were analyzed through conventional polymerase chain reaction by using amplified region (SCAR) marker. Results: The PCR results confirmed the presence of 7 Eimeria species in the examined fecal samples of Egyptian baldi breed with their specific ampilicon sizes being E. acervulina (811bp), E. brunette (626bp), E. tenella (539bp), E. maxima (272bp), E. necatrix (200bp), E. mitis (327bp) and E. praecopx (354bp). A sequencing of the two most predominant species of Eimeria was done, on E. tenella and E. máxima. Analysis of the obtained sequences revealed high identities 99% between Egyptian isolates and the reference one. Similarly, E. maxima isolated from Egyptian baldi chickens showed 98% nucleotide identities with the reference strain. Only single nucleotide substitution was observed among the Egyptian E. tenella isolates (A181G) when compared to the reference one. The Egyptian isolates acquired 4 unique mutations (A68T, C164T, G190A and C227G) in compared with the reference sequence. Conclusion: This is the first time to identify the 7 species of Eimeria from Egyptian baladi chickens. PMID:25904950

Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China.

PubMed

Laguardia, Alice; Wang, Jun; Shi, Fang-Lei; Shi, Kun; Riordan, Philip

2015-03-18

Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species' scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard (Panthera uncia) actually belonged to fox (Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats.

Widespread utility of highly informative AFLP molecular markers across divergent shark species.

PubMed

Zenger, Kyall R; Stow, Adam J; Peddemors, Victor; Briscoe, David A; Harcourt, Robert G

2006-01-01

Population numbers of many shark species are declining rapidly around the world. Despite the commercial and conservation significance, little is known on even the most fundamental aspects of their population biology. Data collection that relies on direct observation can be logistically challenging with sharks. Consequently, molecular methods are becoming increasingly important to obtain knowledge that is critical for conservation and management. Here we describe an amplified fragment length polymorphism method that can be applied universally to sharks to identify highly informative genome-wide polymorphisms from 12 primer pairs. We demonstrate the value of our method on 15 divergent shark species within the superorder Galeomorphii, including endangered species which are notorious for low levels of genetic diversity. Both the endangered sand tiger shark (Carcharodon taurus, N = 18) and the great white shark (Carcharodon carcharias, N = 7) displayed relatively high levels of allelic diversity. A total of 59 polymorphic loci (H(e) = 0.373) and 78 polymorphic loci (H(e) = 0.316) were resolved in C. taurus and C. carcharias, respectively. Results from other sharks (e.g., Orectolobus ornatus, Orectolobus sp., and Galeocerdo cuvier) produced remarkably high numbers of polymorphic loci (106, 94, and 86, respectively) from a limited sample size of only 2. A major constraint to obtaining much needed genetic data from sharks is the time-consuming process of developing molecular markers. Here we demonstrate the general utility of a technique that provides large numbers of informative loci in sharks.

Real-Time Visualization of Active Species in a Single-Site Metal–Organic Framework Photocatalyst

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Sizhuo; Pattengale, Brian; Lee, Sungsik

In this work, we report a new single-site photocatalyst (Co-Ru-UIO- 67(bpy)) based on a metal-organic framework platform with incorporated molecular photosensitizer and catalyst. We show that this catalyst not only demonstrates exceptional activity for light-driven H2 production but also can be recycled without loss of activity. Using the combination of optical transient absorption spectroscopy and in situ X-ray absorption spectroscopy, we not only captured the key CoI intermediate species formed after ultrafast charge transfer from the incorporated photosensitizer but also identified the rate-limiting step in the catalytic cycle, providing insight into the catalysis mechanism of these single-site metal-organic framework photocatalysts.

The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation

PubMed Central

Siriwut, Warut; Edgecombe, Gregory D.; Sutcharit, Chirasak; Panha, Somsak

2015-01-01

Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny. PMID:26270342

Molecular Evidence for Species-Level Distinctions in Clouded Leopards

PubMed Central

Buckley-Beason, Valerie A.; Johnson, Warren E.; Nash, Willliam G.; Stanyon, Roscoe; Menninger, Joan C.; Driscoll, Carlos A.; Howard, JoGayle; Bush, Mitch; Page, John E.; Roelke, Melody E.; Stone, Gary; Martelli, Paolo P.; Wen, Ci; Ling, Lin; Duraisingam, Ratna K.; Lam, Phan V.

2017-01-01

Summary Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats [1–5]. This secretive, mid-sized (16–23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A) [4–8]. We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 and S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainland) and N. n. diardi (Borneo; n = 3 individuals) with mtDNA (771 bp), nuclear DNA (3100 bp), and 51 microsatellite loci. Thirty-six fixed mitochondrial and nuclear nucleotide differences and 20 microsatellite loci with nonoverlapping allele-size ranges distinguished N. n. nebulosa from N. n. diardi. Along with fixed subspecies-specific chromosomal differences, this degree of differentiation is equivalent to, or greater than, comparable measures among five recognized Panthera species (lion, tiger, leopard, jaguar, and snow leopard). These distinctions increase the urgency of clouded leopard conservation efforts, and if affirmed by morphological analysis and wider sampling of N. n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi). PMID:17141620

Molecular evidence for species-level distinctions in clouded leopards.

PubMed

Buckley-Beason, Valerie A; Johnson, Warren E; Nash, Willliam G; Stanyon, Roscoe; Menninger, Joan C; Driscoll, Carlos A; Howard, JoGayle; Bush, Mitch; Page, John E; Roelke, Melody E; Stone, Gary; Martelli, Paolo P; Wen, Ci; Ling, Lin; Duraisingam, Ratna K; Lam, Phan V; O'Brien, Stephen J

2006-12-05

Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats. This secretive, mid-sized (16-23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A). We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 ans S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainland) and N. n. diardi (Borneo; n = 3 individuals) with mtDNA (771 bp), nuclear DNA (3100 bp), and 51 microsatellite loci. Thirty-six fixed mitochondrial and nuclear nucleotide differences and 20 microsatellite loci with nonoverlapping allele-size ranges distinguished N. n. nebulosa from N. n. diardi. Along with fixed subspecies-specific chromosomal differences, this degree of differentiation is equivalent to, or greater than, comparable measures among five recognized Panthera species (lion, tiger, leopard, jaguar, and snow leopard). These distinctions increase the urgency of clouded leopard conservation efforts, and if affirmed by morphological analysis and wider sampling of N. n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi).

Activating the molecular spinterface

NASA Astrophysics Data System (ADS)

Cinchetti, Mirko; Dediu, V. Alek; Hueso, Luis E.

2017-05-01

The miniaturization trend in the semiconductor industry has led to the understanding that interfacial properties are crucial for device behaviour. Spintronics has not been alien to this trend, and phenomena such as preferential spin tunnelling, the spin-to-charge conversion due to the Rashba-Edelstein effect and the spin-momentum locking at the surface of topological insulators have arisen mainly from emergent interfacial properties, rather than the bulk of the constituent materials. In this Perspective we explore inorganic/molecular interfaces by looking closely at both sides of the interface. We describe recent developments and discuss the interface as an ideal platform for creating new spin effects. Finally, we outline possible technologies that can be generated thanks to the unique active tunability of molecular spinterfaces.

Method for improved selectivity in photo-activation of molecular agents

DOEpatents

Fisher, Walter G.; Wachter, Eric A.; Dees, H. Craig

2000-01-01

An apparatus for the treatment of a particular volume of plant or animal tissue by treating the plant or animal tissue with at least one photo-active molecular agent, wherein the particular volume of the plant or animal tissue retains at least a portion of the at least one photo-active molecular agent, and then treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of at least one of the at least one photo-active molecular agent retained in the particular volume of the plant or animal tissue, wherein the at least one photo-active molecular agent becomes active in the particular volume of the plant or animal tissue.

Molecular marker to identify radiolarian species -toward establishment of paleo-environmental proxy-

NASA Astrophysics Data System (ADS)

Ishitani, Y.

2017-12-01

Marine fossilized unicellular plankton are known to have many genetically divergent species (biological species) in the single morphological species and these biological species show the species-specific environments much more precisely than that of morphological species. Among these plankton, Radiolaria are one of the best candidates for time- and environmental-indicators in the modern and past oceans, because radiolarians are the only group which represent entire water column from shallow to deep waters. However, the ecology and evolution of radiolarian were traditionally studied in paleontology and paleoceanography by morphological species. Even Radiolaria has a huge potential for novel proxy of wide and deep environments, there is no criterion to identify the biological species. The motivation for this study is setting the quantitative delimitation to establish the biological species of radiolarians based on molecular data, for leading the future ecological and paleo-environmental study. Identification of the biological species by ribosomal DNA sequences are mainly based on two ways: one is the evolutionary distance of the small subunit (SSU) rDNA, the internal transcribed spacer region of ribosomal DNA (ITS1 and 2), and the large subunit (LSU) rDNA; and the other is the secondary structure of ITS2. In the present study, all four possible genetic markers (SSU, ITS1, ITS2, and LSU rDNA) were amplified from 232 individuals of five radiolarian morphological species and applied to examine the evolutionary distance and secondary structure of rDNA. Comprehensive survey clearly shows that evolutionary distance of ITS1 rDNA and the secondary structure of ITS2 is good to identify the species. Notably, evolutionary distance of ITS1 rDNA is possible to set the common delimitation to identify the biological species, as 0.225 substitution per site. The results show that the ITS1 and ITS 2 rDNA could be the criterion for radiolarian species identification.

Molecular phylogeny of some avian species using Cytochrome b gene sequence analysis

PubMed Central

Awad, A; Khalil, S. R; Abd-Elhakim, Y. M

2015-01-01

Veritable identification and differentiation of avian species is a vital step in conservative, taxonomic, forensic, legal and other ornithological interventions. Therefore, this study involved the application of molecular approach to identify some avian species i.e. Chicken (Gallus gallus), Muskovy duck (Cairina moschata), Japanese quail (Coturnix japonica), Laughing dove (Streptopelia senegalensis), and Rock pigeon (Columba livia). Genomic DNA was extracted from blood samples and partial sequence of the mitochondrial cytochrome b gene (358 bp) was amplified and sequenced using universal primers. Sequences alignment and phylogenetic analyses were performed by CLC main workbench program. The obtained five sequences were deposited in GenBank and compared with those previously registered in GenBank. The similarity percentage was 88.60% between Gallus gallus and Coturnix japonica and 80.46% between Gallus gallus and Columba livia. The percentage of identity between the studied species and GenBank species ranged from 77.20% (Columba oenas and Anas platyrhynchos) to 100% (Gallus gallus and Gallus sonneratii, Coturnix coturnix and Coturnix japonica, Meleagris gallopavo and Columba livia). Amplification of the partial sequence of mitochondrial cytochrome b gene proved to be practical for identification of an avian species unambiguously. PMID:27175180

A Review on Phytoconstituents and Biological activities of Cuscuta species.

PubMed

Ahmad, Ateeque; Tandon, Sudeep; Xuan, Tran Dang; Nooreen, Zulfa

2017-08-01

The genus Cuscuta belonging to the Cuscutaceae family comprises of about 100-170 species spread around the world. Although several species have been studied for their phytochemical characterization and biological activities but still many species are yet unexplored till date. Cuscuta are parasitic plants generally of yellow, orange, red or rarely green color. The Cuscuta species were reported rich in flavonoid and glycosidic constituents along with alkaloids, fatty acids, fixed oil, minerals, essential oil and others phytomolecules also etc. Flavonoids and other molecules of Cuscuta species were reported for different types of biological activities such as antiproliferative activity, antioxidant activity, anti-inflammatory, hepatoprotective, antimicrobial and anxiolytic activity, while some other flavonoids have exhibited potential antiviral and anticancer especially in ovarian and breast cancer activities. This review is an attempt to compile all the available data for the 24 different of Cuscuta species on the basis of different types of phytochemical constituents and biological studies as above. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

A comparative study on immunomodulatory activity of polysaccharides from two official species of Ganoderma (Lingzhi).

PubMed

Meng, Lan-Zhen; Xie, Jing; Lv, Guang-Ping; Hu, De-Jun; Zhao, Jing; Duan, Jin-Ao; Li, Shao-Ping

2014-01-01

Two Ganoderma species, G. lucidum and G. sinense, are listed as Lingzhi in Chinese Pharmacopoeia and they are considered to have the same therapeutic effects. Polysaccharides were the main immunomodulatory and anticancer components in Ganoderma. In this study, the chemical characters and the effects of polysaccharides from G. lucidum (GLPS) and G. sinense (GSPS) on macrophage functions were investigated and compared. Chemical studies showed that GLPS and GSPS were different, displaying various molecular weight distribution and ratio of monosaccharide components. In vitro pharmacological studies showed that both GLPS and GSPS had potent effects on macrophage functions, such as promoting macrophage phagocytosis, increasing their release of nitric oxide and cytokines interleukin (IL)-1α, IL-6, IL-10, and tumor necrosis factor-α. Generally, GLPS was more powerful than GSPS. This study is helpful to elucidate the active components and pharmacological variation between the 2 Ganoderma species. The structure-activity relationship of polysaccharides from Ganoderma needs further study.

Molecular phylogeny of Atractus (Serpentes, Dipsadidae), with emphasis on Ecuadorian species and the description of three new taxa

PubMed Central

Arteaga, Alejandro; Mebert, Konrad; Valencia, Jorge H.; Cisneros-Heredia, Diego F.; Peñafiel, Nicolás; Reyes-Puig, Carolina; Vieira-Fernandes, José L.; Guayasamin, Juan M.

2017-01-01

Abstract We present a molecular phylogeny of snake genus Atractus, with an improved taxon sampling that includes 30 of the 140 species currently recognized. The phylogenetic tree supports the existence of at least three new species in the Pacific lowlands and adjacent Andean slopes of the Ecuadorian Andes, which we describe here. A unique combination of molecular, meristic and color pattern characters support the validity of the new species. With the newly acquired data, we propose and define the Atractus iridescens species group, as well as redefine the Atractus roulei species group. The species Atractus iridescens is reported for the first time in Ecuador, whereas Atractus bocourti and Atractus medusa are removed from the herpetofauna of this country. We provide the first photographic vouchers of live specimens for Atractus multicinctus, Atractus paucidens and Atractus touzeti, along with photographs of 19 other Ecuadorian Atractus species. The current status of Atractus occidentalis and Atractus paucidens is maintained based on the discovery of new material referable to these species. With these changes, the species number reported in Ecuador increases to 27, a number that is likely to increase as material not examined in this work becomes available and included in systematic studies. PMID:28769604

Cryptic Species in Tropic Sands - Interactive 3D Anatomy, Molecular Phylogeny and Evolution of Meiofaunal Pseudunelidae (Gastropoda, Acochlidia)

PubMed Central

Neusser, Timea P.; Jörger, Katharina M.; Schrödl, Michael

2011-01-01

Background Towards realistic estimations of the diversity of marine animals, tiny meiofaunal species usually are underrepresented. Since the biological species concept is hardly applicable on exotic and elusive animals, it is even more important to apply a morphospecies concept on the best level of information possible, using accurate and efficient methodology such as 3D modelling from histological sections. Molecular approaches such as sequence analyses may reveal further, cryptic species. This is the first case study on meiofaunal gastropods to test diversity estimations from traditional taxonomy against results from modern microanatomical methodology and molecular systematics. Results The examined meiofaunal Pseudunela specimens from several Indo-Pacific islands cannot be distinguished by external features. Their 3D microanatomy shows differences in the organ systems and allows for taxonomic separation in some cases. Additional molecular analyses based on partial mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA markers revealed considerable genetic structure that is largely congruent with anatomical or geographical patterns. Two new species (Pseudunela viatoris and P. marteli spp. nov.) are formally described integrating morphological and genetic analyses. Phylogenetic analysis using partial 16S rRNA, COI and the nuclear 18S rRNA markers shows a clade of Pseudunelidae species as the sister group to limnic Acochlidiidae. Within Pseudunela, two subtypes of complex excretory systems occur. A complex kidney already evolved in the ancestor of Hedylopsacea. Several habitat shifts occurred during hedylopsacean evolution. Conclusions Cryptic species occur in tropical meiofaunal Pseudunela gastropods, and likely in other meiofaunal groups with poor dispersal abilities, boosting current diversity estimations. Only a combined 3D microanatomical and molecular approach revealed actual species diversity within Pseudunela reliably. Such integrative methods are

Induction of Tca8113 tumor cell apoptosis by icotinib is associated with reactive oxygen species mediated p38-MAPK activation.

PubMed

Yang, Cailing; Yan, Jianguo; Yuan, Guoyan; Zhang, Yinghua; Lu, Derong; Ren, Mingxin; Cui, Weigang

2014-08-01

Icotinib, a selective EGFR tyrosine kinase inhibitor (EGFR-TKI), has been shown to exhibit anti-tumor activity against several tumor cell lines. However, the exact molecular mechanism of icotinib's anti-tumor effect remains unknown. This study aims to examine the zytotoxic effect of icotinib on Tca8113 cells and its potential molecular mechanism. Icotinib significantly resulted in dose-dependent cell death as determined by MTT assay, accompanied by increased levels of Bax and DNA fragmentation. Icotinib could also induce Reactive Oxygen Species (ROS) generation. Further studies confirmed that scavenging of reactive oxygen species by N-acetyl-L-cysteine (NAC), and pharmacological inhibition of MAPK reversed icotinib-induced apoptosis in Tca8113 cells. Our data provide evidence that icotinib induces apoptosis, possibly via ROS-mediated MAPK pathway in Tca8113 cells.

Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches.

PubMed

Ai, Lin; Chen, Mu-Xin; Alasaad, Samer; Elsheikha, Hany M; Li, Juan; Li, Hai-Long; Lin, Rui-Qing; Zou, Feng-Cai; Zhu, Xing-Quan; Chen, Jia-Xu

2011-06-10

Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches

PubMed Central

2011-01-01

Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp.. PMID:21658284

Spectral identification/elimination of molecular species in spacecraft glow

NASA Technical Reports Server (NTRS)

Green, B. D.; Marinelli, W. J.; Rawlins, W. T.

1985-01-01

Computer models of molecular electronic and vibrational emission intensities were developed. Known radiative emission rates (Einstein coefficients) permit the determination of relative excited state densities from spectral intensities. These codes were applied to the published spectra of glow above shuttle surface and to the Spacelab 1 results of Torr and Torr. The theoretical high-resolution spectra were convolved with the appropriate instrumental slit functions to allow accurate comparison with data. The published spacelab spectrum is complex but N2+ Meinel emission can be clearly identified in the ram spectrum. M2 First Positive emission does not correlate well with observed features, nor does the CN Red System. Spectral overlay comparisons are presented. The spectrum of glow above shuttle surfaces, in contrast to the ISO data, is not highly structured. Diatomic molecular emission was matched to the observed spectral shape. Source excitation mechanisms such as (oxygen atom)-(surface species) reaction product chemiluminescence, surface recombination, or resonance fluorescent re-emission will be discussed for each tentative assignment. These assignments are the necessary first analytical step toward mechanism identification. Different glow mechanisms will occur above surfaces under different orbital conditions.

Extreme isotopologue disequilibrium in molecular SIMS species during SHRIMP geochronology

NASA Astrophysics Data System (ADS)

Magee, Charles W., Jr.; Danišík, Martin; Mernagh, Terry

2017-12-01

The current limitation in the accuracy and precision of inter-element analysis in secondary ion mass spectrometry (SIMS) is the ability to find measurable quantities that allow relative differences in ionization and transmission efficiency of secondary ions to be normalized. In uranium-thorium-lead geochronology, the ability to make these corrections, or "calibrate" the data, results in an accuracy limit of approximately 1 %. This study looks at the ionization of uranium and thorium oxide species, which are traditionally used in U-Pb calibration, to explore the conditions under which isotopologues, or molecular species whose composition differs only in the isotopic composition of one or more atoms in the molecule, remain in or deviate from equilibrium. Isotopologue deficits of up to 0.2 (200 ‰) below ideal mixing are observed in UO2+ species during SIMS gechronological analyses using the SHRIMP IIe SIMS instrument. These are identified by bombarding natural U-bearing minerals with an 18O2- primary beam. The large anomalies are associated with repeat analyses down a single SIMS sputtering crater (Compston et al., 1984), analysis of high-uranium, radiation-damaged zircon, and analysis of baddeleyite. Analysis of zircon under routine conditions yield UO2+ isotopologue anomalies generally within a few percent of equilibrium. The conditions under which the isotopologue anomalies are observed are also conditions in which the UOx-based corrections, or calibration, for relative U vs. Pb ionization efficiencies fail. The existence of these isotopologue anomalies suggest that failure of the various UOx species to equilibrate with each other is the reason that none of them will successfully correct the U  / Pb ratio. No simple isotopologue-based correction is apparent. However, isotopologue disequilibrium appears to be a more sensitive tool for detecting high-U calibration breakdowns than Raman spectroscopy, which showed sharper peaks for ˜ 37 Ma high

Morphological and molecular analyses of Anodontinae species (Bivalvia, Unionidae) of Lake Baikal and Transbaikalia

PubMed Central

Klishko, Olga K.; Bogan, Arthur E.

2018-01-01

The diversity and taxonomy of anodontine species in Lake Baikal and Transbaikalia region has been contentious since it is based on a typological species concept, the so called “Comparatory Method”. Using this method, six Comparatory anodontine species have been described for the study area as belonging to the genus Colletopterum. This genus was separated from Anodonta based on shell characteristics and further split into two subgenera, i.e. Colletopterum sensu stricto and Colletopterum (Piscinaliana). However, many authors do not recognize this separation maintaining all Colletopterum forms within Anodonta. The current study clarifies the taxonomy and systematics of Anodontinae in this region, using a combination of molecular, morphological and anatomical data. All previously recognized Comparatory forms are here recognized as a single species, i.e. Anodonta anatina. PMID:29630628

New strategy for drug discovery by large-scale association analysis of molecular networks of different species.

PubMed

Zhang, Bo; Fu, Yingxue; Huang, Chao; Zheng, Chunli; Wu, Ziyin; Zhang, Wenjuan; Yang, Xiaoyan; Gong, Fukai; Li, Yuerong; Chen, Xiaoyu; Gao, Shuo; Chen, Xuetong; Li, Yan; Lu, Aiping; Wang, Yonghua

2016-02-25

The development of modern omics technology has not significantly improved the efficiency of drug development. Rather precise and targeted drug discovery remains unsolved. Here a large-scale cross-species molecular network association (CSMNA) approach for targeted drug screening from natural sources is presented. The algorithm integrates molecular network omics data from humans and 267 plants and microbes, establishing the biological relationships between them and extracting evolutionarily convergent chemicals. This technique allows the researcher to assess targeted drugs for specific human diseases based on specific plant or microbe pathways. In a perspective validation, connections between the plant Halliwell-Asada (HA) cycle and the human Nrf2-ARE pathway were verified and the manner by which the HA cycle molecules act on the human Nrf2-ARE pathway as antioxidants was determined. This shows the potential applicability of this approach in drug discovery. The current method integrates disparate evolutionary species into chemico-biologically coherent circuits, suggesting a new cross-species omics analysis strategy for rational drug development.

Analysis of Species-Selectivity of Human, Mouse and Rat Cytochrome P450 1A and 2B Subfamily Enzymes using Molecular Modeling, Docking and Dynamics Simulations.

PubMed

Karthikeyan, Bagavathy Shanmugam; Suvaithenamudhan, Suvaiyarasan; Akbarsha, Mohammad Abdulkader; Parthasarathy, Subbiah

2018-06-01

Cytochrome P450 (CYP) 1A and 2B subfamily enzymes are important drug metabolizing enzymes, and are highly conserved across species in terms of sequence homology. However, there are major to minor structural and macromolecular differences which provide for species-selectivity and substrate-selectivity. Therefore, species-selectivity of CYP1A and CYP2B subfamily proteins across human, mouse and rat was analyzed using molecular modeling, docking and dynamics simulations when the chiral molecules quinine and quinidine were used as ligands. The three-dimensional structures of 17 proteins belonging to CYP1A and CYP2B subfamilies of mouse and rat were predicted by adopting homology modeling using the available structures of human CYP1A and CYP2B proteins as templates. Molecular docking and dynamics simulations of quinine and quinidine with CYP1A subfamily proteins revealed the existence of species-selectivity across the three species. On the other hand, in the case of CYP2B subfamily proteins, no role for chirality of quinine and quinidine in forming complexes with CYP2B subfamily proteins of the three species was indicated. Our findings reveal the roles of active site amino acid residues of CYP1A and CYP2B subfamily proteins and provide insights into species-selectivity of these enzymes across human, mouse, and rat.

Molecular based phylogenetic species recognition in the genus Pampus (Perciformes: Stromateidae) reveals hidden diversity in the Indian Ocean.

PubMed

Divya, P R; Mohitha, C; Rahul, G Kumar; Rajool Shanis, C P; Basheer, V S; Gopalakrishnan, A

2017-04-01

Pomfrets (Genus Pampus) are commercially important fishes in the Indo Pacific region. The systematics of this genus is complicated due to morphological similarities between species. The silver pomfret from Indian waters has long been considered to be Pampus argenteus. The objective of the study was to utilize the mitochondrial COI gene to establish the molecular identity of the silver pomfret distributed in Indian waters and to resolve the phylogenetic relationships among Pampus species in the world based on sequence data in the NCBI database. Seven valid Pampus species are identified in this study. The mean genetic divergence value calculated between clades representing these species was 7.9%. The mean genetic distance between the so-called Pampus argenteus from Indian waters and sequences attributed to P. argenteus from the South China Sea, where the neotype of this species was collected, was found to be greater than 12%, strongly supporting the likelihood of the Indian species being distinct. The Indian Pampus species show very close affinity to P. cinereus, with inter species differences less than 2%. The taxonomic identity of the silver pomfret in India is also discussed here, in light of molecular and morphological evidence. Copyright © 2017 Elsevier Inc. All rights reserved.

Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota).

PubMed

Kuuskeri, Jaana; Mäkelä, Miia R; Isotalo, Jarkko; Oksanen, Ilona; Lundell, Taina

2015-10-19

The fungal genus Phlebia consists of a number of species that are significant in wood decay. Biotechnological potential of a few species for enzyme production and degradation of lignin and pollutants has been previously studied, when most of the species of this genus are unknown. Therefore, we carried out a wider study on biochemistry and systematics of Phlebia species. Isolates belonging to the genus Phlebia were subjected to four-gene sequence analysis in order to clarify their phylogenetic placement at species level and evolutionary relationships of the genus among phlebioid Polyporales. rRNA-encoding (5.8S, partial LSU) and two protein-encoding gene (gapdh, rpb2) sequences were adopted for the evolutionary analysis, and ITS sequences (ITS1+5.8S+ITS2) were aligned for in-depth species-level phylogeny. The 49 fungal isolates were cultivated on semi-solid milled spruce wood medium for 21 days in order to follow their production of extracellular lignocellulose-converting oxidoreductases and carbohydrate active enzymes. Four-gene phylogenetic analysis confirmed the polyphyletic nature of the genus Phlebia. Ten species-level subgroups were formed, and their lignocellulose-converting enzyme activity profiles coincided with the phylogenetic grouping. The highest enzyme activities for lignin modification (manganese peroxidase activity) were obtained for Phlebia radiata group, which supports our previous studies on the enzymology and gene expression of this species on lignocellulosic substrates. Our study implies that there is a species-level connection of molecular systematics (genotype) to the efficiency in production of both lignocellulose-converting carbohydrate active enzymes and oxidoreductases (enzyme phenotype) on spruce wood. Thus, we may propose a similar phylogrouping approach for prediction of lignocellulose-converting enzyme phenotypes in new fungal species or genetically and biochemically less-studied isolates of the wood-decay Polyporales.

METHYLATION INACTIVATES PENTAVALENT ARSENIC SPECIES BUT ACTIVATES TRIVALENT ARSENIC SPECIES TO POTENT GENOTOXICANTS

EPA Science Inventory

Methylation Inactivates Pentavalent Arsenic Species but Activates Trivalent Arsenic Species to Potent Genotoxicants

The sensitivity ofhumans to arsenic-induced cancer is thought to be related in part to the limited ability of humans to detoxify arsenic. Recently, methyl- ...

Determination of phosphatidylethanolamine molecular species in various food matrices by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS2).

PubMed

Zhou, Li; Zhao, Minjie; Ennahar, Saïd; Bindler, Françoise; Marchioni, Eric

2012-04-01

A liquid chromatographic-electrospray ionization-tandem mass spectrometric (LC-ESI-MS(2)) method has been developed for determination of the molecular species of phosphatidylethanolamine (PE) in four food matrices (soy, egg yolk, ox liver, and krill oil). The extraction and purification method consisted of a pressurized liquid extraction procedure for total lipid (TL) extraction, purification of phospholipids (PLs) by adsorption on a silica gel column, and separation of PL classes by semi-preparative normal-phase HPLC. Separation and identification of PE molecular species were performed by reversed-phase HPLC coupled with electrospray ionization tandem mass spectrometry (ESI-MS(2)). Methanol containing 5 mmol L(-1) ammonium formate was used as the mobile phase. A variety of PE molecular species were detected in the four food matrices. (C16:0-C18:2)PE, (C18:2-C18:2)PE, and (C16:0-C18:1)PE were the major PE molecular species in soy. Egg yolk PE contained (C16:0-C18:1)PE, (C18:0-C18:1)PE, (C18:0-C18:2)PE, and (C16:0-C18:2)PE as the major molecular species. Ox liver PE was rich in the species (C18:0-C18:1)PE, (C18:0-C20:4)PE, and (C18:0-C18:2)PE. Finally, krill oil which was particularly rich in (C16:0(alkyl)-C22:6(acyl))plasmanylethanolamine (PakE), (C16:0-C22:6)PE, and (C16:0-C20:5)PE, seemed to be an interesting potential source for supplementation of food with eicosapentaenoic acid and docosahexaenoic acid.

Mercury-resistance and mercuric reductase activity in Chromobacterium, Erwinia, and Bacillus species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trevors, J.T.

1987-06-01

Mercury resistant bacteria have been the most extensively studied of all the metal-tolerant bacteria. Mercury resistance is usually mediated by two distinctly different enzymes encoded by plasmids. Mercuric reductase reduces Hg/sup 2 +/ to metallic mercury (Hg/sup 0/). Organomercurial lyases have a molecular weight of 20,000 to 40,000, are composed of 1 or 2 subunits and require the presence of thiol. Plasmic-encoded Hg/sup 2 +/ resistance and mercuric reductase activity have not been detected in many species of bacteria. A Chromobacterium, Erwinia and Bacillus species isolated from environmental samples were capable of growth in the presence of 50 ..mu..M HgCl/submore » 2/. Cell-free extracts of the 3 organisms exhibited mercuric reductase activity that oxidized NADPH in the presence of HgCl/sub 2/. Negligible oxidation of NADPH was observed in the absence of HgCl/sub 2/. The Chromobacterium sp. did not contain any plasmid DNA. This would suggest that Hg/sup 2 +/ resistance was carried on the chromosome in Chromobacterium. A single 3 Mdal plasmid in the Bacillus sp. was refractory to curing. The Erwinia sp. contained 3 plasmids which were also refractory to curing. The location of the resistance genes is unknown in the Bacillus and Erwinia isolates.« less

Deproteinization assessment using isotopically enriched compounds to trace the coprecipitation of low-molecular-weight selenium species with proteins.

PubMed

Godin, Simon; Bouzas-Ramos, Diego; Fontagné-Dicharry, Stéphanie; Bouyssière, Brice; Bueno, Maïté

2017-08-01

Studies have shown that information related to the presence of low-molecular-weight metabolites is frequently lost after deproteinization of complex matrices, such as blood and plasma, during sample preparation. Therefore, the effect of several deproteinization reagents on low-molecular-weight selenium species has been compared by species-specific isotope labeling. Two isotopically enriched selenium tracers were used to mimic models of small inorganic anionic ( 77 Se-selenite) and organic zwitterionic ( 76 Se-selenomethionine) species. The results presented here show that the use of a methanol-acetonitrile-acetone (1:1:1 v/v/v) mixture provided approximately two times less tracer loss from plasma samples in comparison with the classic procedure using acetonitrile, which may not be optimal as it leads to important losses of low-molecular-weight selenium species. In addition, the possible interactions between selenium tracers and proteins were investigated, revealing that both coprecipitation phenomena and association with proteins were potentially responsible for selenite tracer losses during protein precipitation in blood samples. However, coprecipitation phenomena were found to be fully responsible for losses of both tracers observed in plasma samples and of the selenomethionine tracer in blood samples. This successfully applied strategy is anticipated to be useful for more extensive future studies in selenometabolomics. Copyright © 2017 Elsevier Inc. All rights reserved.

Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China

PubMed Central

LAGUARDIA, Alice; WANG, Jun; SHI, Fang-Lei; SHI, Kun; RIORDAN, Philip

2015-01-01

Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species’ scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samples. A total of 100 samples were collected in the winter of 2009 and 2011 in Taxkorgan region of Xinjiang, China. DNA was extracted successfully from 88% of samples and genetic species identification showed that more than half the scats identified in the field as snow leopard (Panthera uncia) actually belonged to fox (Vulpes vulpes). Correlation between scat characteristics and species were investigated, showing that diameter and dry weight of the scat were significantly different between the species. However it was not possible to define a precise range of values for each species because of extensive overlap between the morphological values. This preliminary study confirms that identification of snow leopard feces in the field is misleading. Research that relies upon scat samples to assess distribution or diet of the snow leopard should therefore employ molecular scatology techniques. These methods are financially accessible and employ relatively simple laboratory procedures that can give an indisputable response to species identification from scats. PMID:25855225

[A comparative analysis of Ungulata species by different molecular genetic markers (proteins, RAPD-PCR)].

PubMed

Glazko, V I; Zelenaia, L B; Iasinetskaia, N A

1997-01-01

The investigation of genetic interrelation between a number of Artiodactyla and Perissodactyla species with the use of different types of molecular-genetic markers (proteins, RAPD-PCR) were carried out. The marker-specific features of interspecific relations and their similarities on the groups of markers of both types were revealed. The distinctions between interspecies genetic relations and ones estimated from the phylogeny on the determined group of different types of markers were observed. It was supposed that these discrepancies may be related with common selection factors and involving this marker group in selection in some species.

Antimicrobial activity of some Ganoderma species from Nigeria.

PubMed

Ofodile, L N; Uma, N U; Kokubun, T; Grayer, R J; Ogundipe, O T; Simmonds, M S J

2005-04-01

The crude n-hexane:diethyl ether, chloroform:acetone and methanol extracts of four species of Ganoderma (Ganoderma colossum (Fr.) C. F. Baker, G. resinaceum Boud., G. lucidum (cf.) (Curtis) P. Karst. and G. boninense (cf.) Pat.), from Nigeria, were tested for antimicrobial activity. The three solvent extracts of all the species of Ganoderma were active against Pseudomonas syringae and Bacillus subtilis, whereas none of the extracts were active against Cladosporium herbarum. Preliminary thin layer chromatography chemical tests on these extracts of Ganoderma showed that they contained compounds that stained blue-violet and blue or green when sprayed with anisaldehyde-sulphuric acid or Dragendorff, respectively. The profile of compounds in the extracts showed some variation among the four species. (c) 2005 John Wiley & Sons, Ltd.

High and low molecular weight hyaluronic acid differentially influence macrophage activation

PubMed Central

Rayahin, Jamie E.; Buhrman, Jason S.; Zhang, Yu; Koh, Timothy J.; Gemeinhart, Richard A.

2015-01-01

Macrophages exhibit phenotypic diversity permitting wide-ranging roles in maintaining physiologic homeostasis. Hyaluronic acid, a major glycosaminoglycan of the extracellular matrix, has been shown to have differential signaling based on its molecular weight. With this in mind, the main objective of this study was to elucidate the role of hyaluronic acid molecular weight on macrophage activation and reprogramming. Changes in macrophage activation were assessed by activation state selective marker measurement, specifically quantitative real time polymerase chain reaction, and cytokine enzyme-linked immunoassays, after macrophage treatment with differing molecular weights of hyaluronic acid under four conditions: the resting state, concurrent with classical activation, and following inflammation involving either classically or alternatively activated macrophages. Regardless of initial polarization state, low molecular weight hyaluronic acid induced a classically activated-like state, confirmed by up-regulation of pro-inflammatory genes, including nos2, tnf, il12b, and cd80, and enhanced secretion of nitric oxide and TNF-α. High molecular weight hyaluronic acid promoted an alternatively activated-like state, confirmed by up regulation of pro-resolving gene transcription, including arg1, il10, and mrc1, and enhanced arginase activity. Overall, our observations suggest that macrophages undergo phenotypic changes dependent on molecular weight of hyaluronan that correspond to either (1) pro-inflammatory response for low molecular weight HA or (2) pro-resolving response for high molecular weight HA. These observations bring significant further understanding of the influence of extracellular matrix polymers, hyaluronic acid in particular, on regulating the inflammatory response of macrophages. This knowledge can be used to guide the design of HA-containing biomaterials to better utilize the natural response to HAs. PMID:26280020

Molecular Cytogenetic Analysis of One African and Five Asian Macaque Species Reveals Identical Karyotypes as in Mandrill.

PubMed

Sangpakdee, Wiwat; Tanomtong, Alongkoad; Chaveerach, Arunrat; Pinthong, Krit; Trifonov, Vladimir; Loth, Kristina; Hensel, Christiana; Liehr, Thomas; Weise, Anja; Fan, Xiaobo

2018-04-01

The question how evolution and speciation work is one of the major interests of biology. Especially, genetic including karyotypic evolution within primates is of special interest due to the close phylogenetic position of Macaca and Homo sapiens and the role as in vivo models in medical research, neuroscience, behavior, pharmacology, reproduction and Acquired Immune Deficiency Syndrome (AIDS). Karyotypes of five macaque species from South East Asia and of one macaque species as well as mandrill from Africa were analyzed by high resolution molecular cytogenetics to obtain new insights into karyotypic evolution of old world monkeys. Molecular cytogenetics applying human probes and probe sets was applied in chromosomes of Macaca arctoides, M. fascicularis, M. nemestrina, M. assamensis, M. sylvanus, M. mulatta and Mandrillus sphinx. Established two- to multicolor-fluorescence in situ hybridization (FISH) approaches were applied. Locus-specific probes, whole and partial chromosome paint probes were hybridized. Especially the FISH-banding approach multicolor-banding (MCB) as well as probes oriented towards heterochromatin turned out to be highly efficient for interspecies comparison. Karyotypes of all seven studied species could be characterized in detail. Surprisingly, no evolutionary conserved differences were found among macaques, including mandrill. Between the seven here studied and phenotypically so different species we expected several via FISH detectable karyoypic and submicroscopic changes and were surprised to find none of them on a molecular cytogenetic level. Spatial separation, may explain the speciation and different evolution for some of them, like African M. sylvanus, Mandrillus sphinx and the South Asian macaques. However, for the partially or completely overlapping habitats of the five studied South Asian macaques the species separation process can also not be deduced to karyotypic separation.

Comparison of Molecular Species Distribution of DHA-Containing Triacylglycerols in Milk and Different Infant Formulas by Liquid Chromatography-Mass Spectrometry.

PubMed

Liu, Zhiqian; Cocks, Benjamin G; Rochfort, Simone

2016-03-16

Long-chain polyunsaturated fatty acids (LC-PUFA) are an important nutritional lipid and have potential in being able to promote human health. Docosahexaenoic acid (DHA, C22:6ω3) is often added in infant formulas to meet the nutritional requirement of formula-fed infants. A comprehensive survey on DHA-containing triacylglycerol (DHA-TAG) molecular species has been conducted for seven infant formulas (IFs) sourced from Australia, Europe, and the USA as well as bovine milk and human milk. Using LC-triple quadrupole MS and LC-LTQ-orbitrap MS we were able to identify and quantify 56 DHA-TAG species in these samples; the fatty acid structure of these species was assigned using their MS(2) spectra. The species composition of DHA-TAG was found to be different between bovine milk, human milk, and IFs and also between different brands of IFs. Bovine milk and human milk contain DHA-TAG of smaller molecular size (728-952 Da), whereas five out of the seven IF samples contain species of broader mass range (from 728 to 1035 Da). Our study indicates that two types of DHA were used in the seven IF products surveyed and that there is very large difference in molecular species distribution in different IF products that may influence the fine nutritional profile and biological functions of IF products.

Molecular emission in chemically active protostellar outflows

NASA Astrophysics Data System (ADS)

Lefloch, B.

2011-12-01

Protostellar outflows play an important role in the dynamical and chemical evolution of cloud through shocks. The Herschel Space Observatory (HSO) brings new insight both on the molecular content and the physical conditions in protostellar shocks through high spectral and angular resolution studies of the emission of major gas cooling agents and hydrides. The Herschel/CHESS key-program is carrying out an in depth study of the prototypical shock region L1157-B1. Analysis of the line profiles detected allows to constrain the formation/destruction route of various molecular species, in relation with the predictions of MHD shock models. The Herschel/WISH key-program investigates the properties and origin of water emission in a broad sample of protostellar outflows and envelopes. Implications of the first results for future studies on mass-loss phenomena are discussed.

Conserved and species-specific molecular denominators in mammalian skeletal muscle aging.

PubMed

Mercken, Evi M; Capri, Miriam; Carboneau, Bethany A; Conte, Maria; Heidler, Juliana; Santoro, Aurelia; Martin-Montalvo, Alejandro; Gonzalez-Freire, Marta; Khraiwesh, Husam; González-Reyes, José A; Moaddel, Ruin; Zhang, Yongqing; Becker, Kevin G; Villalba, José M; Mattison, Julie A; Wittig, Ilka; Franceschi, Claudio; de Cabo, Rafael

2017-01-01

Aging is a complex phenomenon involving functional decline in multiple physiological systems. We undertook a comparative analysis of skeletal muscle from four different species, i.e. mice, rats, rhesus monkeys, and humans, at three different representative stages during their lifespan (young, middle, and old) to identify pathways that modulate function and healthspan. Gene expression profiling and computational analysis revealed that pathway complexity increases from mice to humans, and as mammals age, there is predominantly an upregulation of pathways in all species. Two downregulated pathways, the electron transport chain and oxidative phosphorylation, were common among all four species in response to aging. Quantitative PCR, biochemical analysis, mitochondrial DNA measurements, and electron microscopy revealed a conserved age-dependent decrease in mitochondrial content, and a reduction in oxidative phosphorylation complexes in monkeys and humans. Western blot analysis of key proteins in mitochondrial biogenesis discovered that (i) an imbalance toward mitochondrial fusion occurs in aged skeletal muscle and (ii) mitophagy is not overtly affected, presumably leading to the observed accumulation of abnormally large, damaged mitochondria with age. Select transcript expression analysis uncovered that the skeletal inflammatory profile differentially increases with age, but is most pronounced in humans, while increased oxidative stress (as assessed by protein carbonyl adducts and 4-hydroxynonenal) is common among all species. Expression studies also found that there is unique dysregulation of the nutrient sensing pathways among the different species with age. The identification of conserved pathways indicates common molecular mechanisms intrinsic to health and lifespan, whereas the recognition of species-specific pathways emphasizes the importance of human studies for devising optimal therapeutic modalities to slow the aging process.

Molecular-orbital models for the catalytic activity and selectivity of coordinatively unsaturated platinum surfaces and complexes

NASA Astrophysics Data System (ADS)

Balazs, A. C.; Johnson, K. H.

1982-01-01

Electronic structures have been calculated for 5-, 6-, and 10-atom Pt clusters, as well as for a Pt(PH 3) 4 coordination complex, using the self-consistent-field X-alpha scattered-wave (SCF-Xα-SW) molecular-orbital technique. The 10-atom cluster models the local geometry of a flat, unreconstructed Pt(100) surface, while the 5- and 6-atom clusters show features of a stepped Pt surface. Pt(PH 3) 4 resembles the chemically similar homogeneous catalyst Pt(PPh 3) 4. Common to all these coordinatively unsaturated complexes are orbitals lying near or coinciding with the highest occupied molecular orbital ("Fermi level") which show pronounced d lobes pointing directly into the vacuum. Under the hypothesis that these molecular orbitals are mainly responsible for the chemical activities of the above species, one can account for the relative similarities and differences in catalytic activity and selectivity displayed by unreconstructed Pt(100) surfaces, stepped Pt surfaces or particles, and isolated Pt(PPh 3) 4 coordination complexes. The relevance of these findings to catalyst-support interactions is also discussed. Finally, relativistic corrections to the electronic structures are calculated and their implications on catalytic properties discussed.

Molecular phylogeny and a new Iranian species of Caudospora (Sydowiellaceae, Diaporthales).

PubMed

Voglmayr, Hermann; Mehrabi, Mehdi

2018-05-02

For the first time, molecular phylogenetic data on the peculiar diaporthalean genus Caudospora are available. Macro- and microscopic morphology and phylogenetic multilocus analyses of partial nuc SSU-ITS-LSU rDNA, cal , ms204 , rpb1 , rpb2 , tef1 and tub2 sequences revealed two distinct species of Caudospora , which are described and illustrated by light and scanning electron microscopy. Caudospora iranica is described as a new species from corticated dead twigs of Quercus sp. collected in Iran. It differs from the generic type, C. taleola , mainly by coarsely verrucose ascospores. The asexual morph of C. taleola on natural substrate is described and illustrated. Caudospora taleola is neotypified, and it is recorded from Iran for the first time. Phylogenetic analyses of a multigene matrix containing a representative selection of Diaporthales from four loci (ITS, LSU rDNA, rpb2 and tef1 ) revealed a placement of Caudospora within Sydowiellaceae.

A new endogean, anophthalmous species of Parazuphium Jeannel from Northern Morocco (Coleoptera, Carabidae), with new molecular data for the tribe Zuphiini

PubMed Central

Andújar, Carmelo; Hernando, Carles; Ribera, Ignacio

2011-01-01

Abstract A new species of the genus Parazuphium (Coleoptera, Carabidae, Zuphiini), Parazuphium aguilerai sp. n., is described from the Tingitan peninsula in North Morocco. The only known specimen was found under a large deeply buried boulder, and belongs to an anophthalmous, depigmented and flattened species. This is the second species of blind Parazuphium known so far, the other being Parazuphium feloi Machado 1998 from a lava tube in the Canary Islands. Molecular data of the only known Parazuphium aguilerai sp. n. specimen are provided, and a reconstructed phylogeny based on these molecular data confirms its inclusion inside Zuphiini within Harpalinae. Identification keys to the Mediterranean and Macaronesian species of Parazuphium are provided. PMID:21747680

Molecular dynamics simulation of the diffusion of uranium species in clay pores.

PubMed

Liu, Xiao-yu; Wang, Lu-hua; Zheng, Zhong; Kang, Ming-liang; Li, Chun; Liu, Chun-li

2013-01-15

Molecular dynamics simulations were carried out to investigate the diffusive behavior of aqueous uranium species in montmorillonite pores. Three uranium species (UO(2)(2+), UO(2)CO(3), UO(2)(CO(3))(2)(2-)) were confirmed in both the adsorbed and diffuse layers. UO(2)(CO(3))(3)(4-) was neglected in the subsequent analysis due to its scare occurrence. The species-based diffusion coefficients in montmorillonite pores were then calculated, and compared with the water mobility and their diffusivity in aqueous solution/feldspar nanosized fractures. Three factors were considered that affected the diffusive behavior of the uranium species: the mobility of water, the self-diffusion coefficient of the aqueous species, and the electrostatic forces between the negatively charged surface and charged molecules. The mobility of U species in the adsorbed layer decreased in the following sequence: UO(2)(2+)>UO(2)CO(3)>UO(2)(CO(3))(2)(2-). In the diffuse layer, we obtained the highest diffusion coefficient for UO(2)(CO(3))(2)(2-) with the value of 5.48×10(-10) m(2) s(-1), which was faster than UO(2)(2+). For these two charged species, the influence of electrostatic forces on the diffusion of solutes in the diffuse layer is overwhelming, whereas the influence of self-diffusion and water mobility is minor. Our study demonstrated that the negatively charged uranyl carbonate complex must be addressed in the safety assessment of potential radioactive waste disposal systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular Genetic Equipment for Improved Inventory and Monitoring of Species of Conservation Concern on Department of Defense Lands

DTIC Science & Technology

2015-11-18

University of Idaho was tasked with designing methods to monitor species of concern on DoD lands as part of four DoD grants. With the funds granted we were...Approved for Public Release; Distribution Unlimited Final Report: Molecular Genetic Equipment for Improved Inventory and Monitoring of Species of...Monitoring of Species of Conservation Concern on Department of Defense Lands Report Title The Laboratory for Ecological, Evolutionary and Conservation

Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC.

PubMed

Dellicour, Simon; Flot, Jean-François

2015-11-01

Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Molecular Characterization of Cryptosporidium Species and Giardia duodenalis from Symptomatic Cambodian Children.

PubMed

Moore, Catrin E; Elwin, Kristin; Phot, Nget; Seng, Chanthou; Mao, Saroeun; Suy, Kuong; Kumar, Varun; Nader, Johanna; Bousfield, Rachel; Perera, Sanuki; Bailey, J Wendi; Beeching, Nicholas J; Day, Nicholas P J; Parry, Christopher M; Chalmers, Rachel M

2016-07-01

In a prospective study, 498 single faecal samples from children aged under 16 years attending an outpatient clinic in the Angkor Hospital for Children, northwest Cambodia, were examined for Cryptosporidium oocysts and Giardia cysts using microscopy and molecular assays. Cryptosporidium oocysts were detected in 2.2% (11/498) of samples using microscopy and in 7.7% (38/498) with molecular tests. Giardia duodenalis cysts were detected in 18.9% (94/498) by microscopy and 27.7% (138/498) by molecular tests; 82% of the positive samples (by either method) were from children aged 1-10 years. Cryptosporidium hominis was the most common species of Cryptosporidium, detected in 13 (34.2%) samples, followed by Cryptosporidium meleagridis in 9 (23.7%), Cryptosporidium parvum in 8 (21.1%), Cryptosporidium canis in 5 (13.2%), and Cryptosporidium suis and Cryptosporidium ubiquitum in one sample each. Cryptosporidium hominis and C. parvum positive samples were subtyped by sequencing the GP60 gene: C. hominis IaA16R6 and C. parvum IIeA7G1 were the most abundant subtypes. Giardia duodenalis was typed using a multiplex real-time PCR targeting assemblages A and B. Assemblage B (106; 76.8% of all Giardia positive samples) was most common followed by A (12.3%) and mixed infections (5.1%). Risk factors associated with Cryptosporidium were malnutrition (AOR 9.63, 95% CI 1.67-55.46), chronic medical diagnoses (AOR 4.51, 95% CI 1.79-11.34) and the presence of birds in the household (AOR 2.99, 95% CI 1.16-7.73); specifically C. hominis (p = 0.03) and C. meleagridis (p<0.001) were associated with the presence of birds. The use of soap was protective against Giardia infection (OR 0.74, 95% CI 0.58-0.95). This is the first report to describe the different Cryptosporidium species and subtypes and Giardia duodenalis assemblages in Cambodian children. The variety of Cryptosporidium species detected indicates both anthroponotic and zoonotic transmission in this population. Interventions to improve

Molecular and morphological identification of mealybug species (Hemiptera: Pseudococcidae) in Brazilian vineyards.

PubMed

Pacheco da Silva, Vitor C; Bertin, Aline; Blin, Aurélie; Germain, Jean-François; Bernardi, Daniel; Rignol, Guylène; Botton, Marcos; Malausa, Thibaut

2014-01-01

Mealybugs (Hemiptera: Pseudococcidae) are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Brazil, by morphological and molecular characterization. Our secondary aim was to develop a rapid identification kit based on species-specific Polymerase Chain Reactions, to facilitate the routine identification of the most common pest species. We surveyed 40 sites infested with mealybugs and identified 17 species: Dysmicoccus brevipes (Cockerell), Dysmicoccus sylvarum Williams and Granara de Willink, Dysmicoccus texensis (Tinsley), Ferrisia cristinae Kaydan and Gullan, Ferrisia meridionalis Williams, Ferrisia terani Williams and Granara de Willink, Phenacoccus baccharidis Williams, Phenacoccus parvus Morrison, Phenacoccus solenopsis Tinsley, Planococcus citri (Risso), Pseudococcus viburni (Signoret), Pseudococcus cryptus Hempel, four taxa closely related each of to Pseudococcus viburni, Pseudococcus sociabilis Hambleton, Pseudococcus maritimus (Ehrhorn) and Pseudococcus meridionalis Prado, and one specimen from the genus Pseudococcus Westwood. The PCR method developed effectively identified five mealybug species of economic interest on grape in Brazil: D. brevipes, Pl. citri, Ps. viburni, Ph. solenopsis and Planococcus ficus (Signoret). Nevertheless, it is not possible to assure that this procedure is reliable for taxa that have not been sampled already and might be very closely related to the target species.

A simplified protocol for molecular identification of Eimeria species in field samples.

PubMed

Haug, Anita; Thebo, Per; Mattsson, Jens G

2007-05-15

This study aimed to find a fast, sensitive and efficient protocol for molecular identification of chicken Eimeria spp. in field samples. Various methods for each of the three steps of the protocol were evaluated: oocyst wall rupturing methods, DNA extraction methods, and identification of species-specific DNA sequences by PCR. We then compared and evaluated five complete protocols. Three series of oocyst suspensions of known number of oocysts from Eimeria mitis, Eimeria praecox, Eimeria maxima and Eimeria tenella were prepared and ground using glass beads or mini-pestle. DNA was extracted from ruptured oocysts using commercial systems (GeneReleaser, Qiagen Stoolkit and Prepman) or phenol-chloroform DNA extraction, followed by identification of species-specific ITS-1 sequences by optimised single species PCR assays. The Stoolkit and Prepman protocols showed insufficient repeatability, and the former was also expensive and relatively time-consuming. In contrast, both the GeneReleaser protocol and phenol-chloroform protocols were robust and sensitive, detecting less than 0.4 oocysts of each species per PCR. Finally, we evaluated our new protocol on 68 coccidia positive field samples. Our data suggests that rupturing the oocysts by mini-pestle grinding, preparing the DNA with GeneReleaser, followed by optimised single species PCR assays, makes a robust and sensitive procedure for identifying chicken Eimeria species in field samples. Importantly, it also provides minimal hands-on-time in the pre-PCR process, lower contamination risk and no handling of toxic chemicals.

Molecular and Morphological Identification of Mealybug Species (Hemiptera: Pseudococcidae) in Brazilian Vineyards

PubMed Central

Pacheco da Silva, Vitor C.; Bertin, Aline; Blin, Aurélie; Germain, Jean-François; Bernardi, Daniel; Rignol, Guylène; Botton, Marcos; Malausa, Thibaut

2014-01-01

Mealybugs (Hemiptera: Pseudococcidae) are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Brazil, by morphological and molecular characterization. Our secondary aim was to develop a rapid identification kit based on species-specific Polymerase Chain Reactions, to facilitate the routine identification of the most common pest species. We surveyed 40 sites infested with mealybugs and identified 17 species: Dysmicoccus brevipes (Cockerell), Dysmicoccus sylvarum Williams and Granara de Willink, Dysmicoccus texensis (Tinsley), Ferrisia cristinae Kaydan and Gullan, Ferrisia meridionalis Williams, Ferrisia terani Williams and Granara de Willink, Phenacoccus baccharidis Williams, Phenacoccus parvus Morrison, Phenacoccus solenopsis Tinsley, Planococcus citri (Risso), Pseudococcus viburni (Signoret), Pseudococcus cryptus Hempel, four taxa closely related each of to Pseudococcus viburni, Pseudococcus sociabilis Hambleton, Pseudococcus maritimus (Ehrhorn) and Pseudococcus meridionalis Prado, and one specimen from the genus Pseudococcus Westwood. The PCR method developed effectively identified five mealybug species of economic interest on grape in Brazil: D. brevipes, Pl. citri, Ps. viburni, Ph. solenopsis and Planococcus ficus (Signoret). Nevertheless, it is not possible to assure that this procedure is reliable for taxa that have not been sampled already and might be very closely related to the target species. PMID:25062012

Characteristics of an Electron Cyclotron Resonance Plasma Source for the Production of Active Nitrogen Species in III-V Nitride Epitaxy

NASA Technical Reports Server (NTRS)

Meyyappan, Meyya; Arnold, James O. (Technical Monitor)

1997-01-01

A simple analysis is provided to determine the characteristics of an electron cyclotron resonance (ECR) plasma source for the generation of active nitrogen species in the molecular beam epitaxy of III-V nitrides. The effects of reactor geometry, pressure, power, and flow rate on the dissociation efficiency and ion flux are presented. Pulsing the input power is proposed to reduce the ion flux.

DNA barcodes and molecular diagnostics to distinguish an introduced and native Laricobius (Coleoptera: Derodontidae) species in eastern North America

Treesearch

G.A. Davis; N.P. Havill; Z.N. Adelman; A. Caccone; L.T. Kok; S.M. Salom

2011-01-01

Molecular diagnostics based on DNA barcodes can be powerful identification tools in the absence of distinctive morphological characters for distinguishing between closely related species. A specific example is distinguishing the endemic species Laricobius rubidus from Laricobius nigrinus, a biological control agent of hemlock...

Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitation and insights into chromosome evolution.

PubMed

Koehler, Samantha; Cabral, Juliano S; Whitten, W Mark; Williams, Norris H; Singer, Rodrigo B; Neubig, Kurt M; Guerra, Marcelo; Souza, Anete P; Amaral, Maria do Carmo E

2008-10-01

Species' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species' identification. Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes. Six of 21 currently accepted species were recovered. The results also support recognition of the 'C. pumila' clade as a single species. Molecular phylogenetic relationships within the 'C. acicularis-C. madida' and 'C. ferdinandiana-C. neowiedii' species' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands. The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic

Molecular Phylogeny of the Neotropical Genus Christensonella (Orchidaceae, Maxillariinae): Species Delimitation and Insights into Chromosome Evolution

PubMed Central

Koehler, Samantha; Cabral, Juliano S.; Whitten, W. Mark; Williams, Norris H.; Singer, Rodrigo B.; Neubig, Kurt M.; Guerra, Marcelo; Souza, Anete P.; Amaral, Maria do Carmo E.

2008-01-01

Background and Aims Species' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species' identification. Methods Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes. Key Results Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands. Conclusions The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent

The Economics of Saving Endangered Species: A Teaching Activity.

ERIC Educational Resources Information Center

Schug, Mark C.; Shaw, Jane S.

1997-01-01

Argues that well-intentioned government policies, such as the Endangered Species Act, can actually cause harm to endangered species by creating disincentives to preserving the habitat for endangered species. Maintains that the use of incentives can lead to voluntary species protection. Includes instructions for an in-class teaching activity. (MJP)

Morphological and molecular evidence for the occurrence of three Hippocampus species (Teleostei: Syngnathidae) in Brazil.

PubMed

Silveira, Rosana Beatriz; Siccha-Ramirez, Raquel; Silva, José Rodrigo Santos; Oliveira, Claudio

2014-09-16

For many decades only two species of seahorses were recognized from Brazil: Hippocampus reidi Ginsburg, 1933, the long snout seahorse, and H. erectus Perry, 1810, the lined seahorse. The presence of a possible third species, recognized in 2002, brought about the need for a broad revision of the genus in Brazilian waters. A total of 335 specimens of seahorses, obtained from Brazilian and other collections, representing the three putative species from Brazil were analyzed: H. reidi, the species of greatest abundance and occurs in estuaries and the sea; H. erectus, which occurs only in the sea, and Hippocampus patagonicus was also determined to be present based on multiple specimens. Our morphometric / numerical and molecular analysis showed that the species currently identified as H. erectus in Brazil is actually H. patagonicus Piacentino & Luzatto, 2004. The existence of a possible third species, was instead based on the true H. erectus, as confirmed in the present study by the study of classical systematic and mitochondrial analysis. Thus, we recognize three species of seahorses in Brazil: H. erectus, H. reidi and H. patagonicus.

Molecular Insights into the Ctenophore Genus Beroe in Europe: New Species, Spreading Invaders.

PubMed

Johansson, Mattias L; Shiganova, Tamara A; Ringvold, Halldis; Stupnikova, Alexandra N; Heath, Daniel D; MacIsaac, Hugh J

2018-06-07

The genus Beroe Browne, 1756 (Ctenophora, Beroidae) occurs worldwide, with 25 currently-described species. Because the genus is poorly studied, the definitive number of species is uncertain. Recently, a possible new Beroe species was suggested based on internal transcribed spacer 1 (ITS1) sequences from samples collected in Svalbard, Norway. Another species, Beroe ovata, was introduced to Europe from North America, initially in the Black Sea and subsequently (and possibly secondarily) into the Mediterranean and Baltic Seas. In areas where ctenophores have been introduced, they have often had significant detrimental ecological effects. The potential for other cryptic and/or undescribed Beroe species, and history of spread of some species in the genus, give reason for additional study. When alive, morphological hallmarks may be challenging to spot and photograph owing to the animals' transparency and near-constant motion. We sampled and analyzed 109 putative Beroe specimens from Europe, using morphological and molecular approaches. DNA analyses were conducted using cytochrome oxidase 1 and internal transcribed spacer sequences, and together with published sequences from GenBank, phylogenetic relationships of the genus were explored. Our study suggests the presence of at least five genetic lineages of Beroe in Europe, of which three could be assigned to known species: Beroe gracilis Künne 1939; Beroe cucumis Fabricius, 1780 and Beroe ovata sensu Mayer, 1912. The other two lineages (here provisionally named Beroe "norvegica" and Beroe "anatoliensis") did not clearly coincide with any known species, and might therefore reflect new species, but confirmation of this requires further study.

Method for improved selectivity in photo-activation and detection of molecular diagnostic agents

DOEpatents

Wachter, Eric A.; Fisher, Walter G.; Dees, H. Craig

1998-01-01

A method for the imaging of a particular volume of plant or animal tissue, wherein the plant or animal tissue contains at least one photo-active molecular agent. The method includes the steps of treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of the photo-active molecular agent contained in the particular volume of the plant or animal tissue, photo-activating at least one of the at least one photo-active molecular agent in the particular volume of the plant or animal tissue, thereby producing at least one photo-activated molecular agent, wherein the at least one photo-activated molecular agent emits energy, detecting the energy emitted by the at least one photo-activated molecular agent, and producing a detected energy signal which is characteristic of the particular volume of plant or animal tissue. The present invention is also a method for the imaging of a particular volume of material, wherein the material contains at least one photo-active molecular agent.

Method for improved selectivity in photo-activation and detection of molecular diagnostic agents

DOEpatents

Wachter, E.A.; Fisher, W.G.; Dees, H.C.

1998-11-10

A method for the imaging of a particular volume of plant or animal tissue, wherein the plant or animal tissue contains at least one photo-active molecular agent. The method includes the steps of treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of the photo-active molecular agent contained in the particular volume of the plant or animal tissue, photo-activating at least one of the at least one photo-active molecular agent in the particular volume of the plant or animal tissue, thereby producing at least one photo-activated molecular agent, wherein the at least one photo-activated molecular agent emits energy, detecting the energy emitted by the at least one photo-activated molecular agent, and producing a detected energy signal which is characteristic of the particular volume of plant or animal tissue. The present invention is also a method for the imaging of a particular volume of material, wherein the material contains at least one photo-active molecular agent. 13 figs.

Methods for improved selectivity in photo-activation and detection of molecular diagnostic agents

DOEpatents

Wachter, Eric A [Oak Ridge, TN; Fisher, Walter G [Knoxville, TN; Dees, H Craig [Knoxville, TN

2008-03-18

A method for the imaging of a particular volume of plant or animal tissue, wherein the plant or animal tissue contains at least one photo-active molecular agent. The method comprises the steps of treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of the photo-active molecular agent contained in the particular volume of the plant or animal tissue, photo-activating at least one of the at least one photo-active molecular agent in the particular volume of the plant or animal tissue, thereby producing at least one photo-activated molecular agent, wherein the at least one photo-activated molecular agent emits energy, detecting the energy emitted by the at least one photo-activated molecular agent, and producing a detected energy signal which is characteristic of the particular volume of plant or animal tissue. The present invention also provides a method for the imaging of a particular volume of material, wherein the material contains at least one photo-active molecular agent.

Morphological and molecular features of some freshwater prawn species under genus Macrobrachium Spence Bate, 1868 (Crustacea: Decapoda: Palaemonidae) from Myanmar.

PubMed

Mar, Win; Kang, Peng-Fei; Mao, Bin; Wang, Yu-Feng

2018-02-28

Myanmar is abundant in lakes and rivers, yet only a few investigations on the fauna of shrimps and prawns have been conducted and no molecular characteristics of prawn species have been described. This study reveals the morphologically identification of five freshwater prawn species under the genus Macrobrachium, including M. cavernicola, M. australiense, M. johnsoni, M. josephi and Macrobrachium sp.WMY-2017. As there was no previous record and information concerning with M. australiense, M. johnsoni, M. josephi and Macrobrachium sp. WMY-2017, they were regarded as the first record from Myanmar. A fragment of Mitochondrial Cytochrome Oxidase I Gene (COI) was amplified successfully from three studied species: M. australiense, M. josephi, and Macrobrachium sp.WMY-2017. The interspecific divergences of studied species varied from 0.01 to 0.15. The phylogenetic tree based on COI fragment sequences showed that M. australiense was closely related to M. rosenbergii, while Macrobrachium sp. WMY-2017 was closest to M. josephi. The results of molecular phylogeny has clarified the relationship within the genus Macrobrachium and represents the first step toward understanding the pattern of speciation base on molecular approach in Myanmar.

A new species of the genus Aulacorthum (Hemiptera: Aphididae) from the Korean Peninsula and its discrimination from a closely-related species using morphological and molecular characters.

PubMed

Lee, Wonhoon; Kim, Hyojoong; Havelka, Jan; Lee, Seunghwan

2011-04-01

Aulacorthum sp. collected on Artemisia princeps and Artemisia stolonifera (Asteraceae) in the Korean Peninsula was compared with the eight Aulacorthum species using molecular and morphological characters. In the sequence analysis, the genetic divergences of two mitochondrial genes, COI and CytB, between Aulacorthum sp. and the congeneric species were higher than those among the congeneric species. In the morphometric analysis, principal components analysis using 13 morphological characters reveals that Aulacorthum sp. is distinguished from the congeneric species, especially Aulacorthum albimagnoliae, which is morphologically most similar to Aulacorthum sp.. Based on these results, we propose a new species, Aulacorthum (Aulacorthum) artemisiphaga Lee, Havelka, and Lee sp. nov., with a description of apterous and alate viviparous females and an identification key to species in the genus Aulacorthum in the Korean Peninsula based on apterous viviparous females.

Clinical significance, antimicrobial susceptibility and molecular identification of Nocardia species isolated from children with cystic fibrosis.

PubMed

Betrán, Ana; Villuendas, M Cruz; Rezusta, Antonio; Pereira, Javier; Revillo, M José; Rodríguez-Nava, Verónica

2016-01-01

Nocardia is an opportunistic pathogen that causes respiratory infections in immunocompromised patients. The aim of this study was to analyze the epidemiology, clinical significance and antimicrobial susceptibility of Nocardia species isolated from eight children with cystic fibrosis. The isolated species were identified as Nocardia farcinica, Nocardia transvalensis, Nocardia pneumoniae, Nocardia veterana and Nocardia wallacei. N. farcinica was isolated in three patients and all of them presented lung affectation with a chronic colonization and pneumonia. N. farcinica showed resistance against gentamicin, tobramycin, cefotaxime, but was susceptible to trimethoprim-sulfamethoxazole and amikacin. N. transvalensis, which was isolated from two patients, showed an association with chronic colonization. N. transvalensis was resistant to tobramycin and amikacin, but susceptible to ciprofloxacin, trimethoprim-sulfamethoxazole and cefotaxime. N. veterana, N. pneumoniae and N. wallacei were isolated from three different patients and appeared in transitory lung colonization. N. veterana and N. pneumoniae were susceptible to imipenem, trimethoprim-sulfamethoxazole, amikacin, tobramycin, and cefotaxime. N. wallacei was resistant to amikacin, tobramycin, imipenem, and trimethoprim-sulfamethoxazole and susceptible to ciprofloxacin and cefotaxime. All the isolates were identified up to species level by 16S rRNA gene sequencing. The presence of Nocardia in the sputum of patients with cystic fibrosis is not always an indication of an active infection; therefore, the need for a treatment should be evaluated on an individual basis. The detection of multidrug-resistant species needs molecular identification and susceptibility testing, and should be performed for all Nocardia infections. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Studies for the Loss of Atomic and Molecular Species from Io

NASA Technical Reports Server (NTRS)

Smyth, William H.

1997-01-01

The general objective of this project is to advance our theoretical understanding of Io's atmosphere by studying how various atomic and molecular species are lost from this atmosphere and are distributed near the satellite and in the circumplanetary environment of Jupiter. The project is divided into well-defined studies described for the likely dominant atmospheric gases involving species of the SO2 family (SO2, SO, 02, 0, S) and for the trace atmospheric gas atomic sodium. The relative abundance of the members of the S02 family and Na (and its parent Na(x)) at the satellite exobase and their relative spatial densities beyond in the extended corona of lo are not well known but will depend upon a number of factors including the upward transport rate of gases from below, the velocity distribution and corresponding escape rate of gases at the exobase, and the operative magnetospheric/solar-photon driven chemistry for the different gases. This question of relative abundance will be studied in this project.

Experimental and Numerical Analysis of Narrowband Coherent Rayleigh-Brillouin Scattering in Atomic and Molecular Species (Pre Print)

DTIC Science & Technology

2012-02-01

use of polar gas species. While current simplified models have adequately predicted CRS and CRBS line shapes for a wide variety of cases, multiple ...published simplified models are presented for argon, molecular nitrogen, and methane at 300 & 500 K and 1 atm. The simplified models require uncertain gas... models are presented for argon, molecular nitrogen, and methane at 300 & 500 K and 1 atm. The simplified models require uncertain gas properties

Molecular characterization of cryptic and sympatric lymnaeid species from the Galba/Fossaria group in Mendoza Province, Northern Patagonia, Argentina

PubMed Central

2013-01-01

Background Freshwater lymnaeid snails can act as the intermediate hosts for trematode parasites such as the liver fluke Fasciola hepatica, that cause significant economic and biomedical burden worldwide, particularly through bovine fascioliasis. Transmission potential is tightly coupled to local compatibility with snail hosts, so accurate identification of lymnaeid species is crucial for understanding disease risk, especially when invasive species are encountered. Mendoza Province, in Argentina, is a center of livestock production and also an area of endemic fascioliasis transmission. However, the distribution of lymnaeid species in the region is not well known. Methods This study examined lymnaeid snails from seven localities in the Department of Malarguë, Mendoza Province, using morphological and molecular analyses and also describing ecological variables associated with snail presence. Results While morphological characters identified two species of lymnaeid, Galba truncatula and G. viatrix, molecular data revealed a third, cryptic species, G. neotropica, which was sympatric with G. viatrix. G. truncatula was exclusively found in high altitude (>1900 meters above sea level [masl]) sites, whereas mixed G. neotropica/G. viatrix localities were at middle elevations (1300–1900 masl), and G. viatrix was found alone at the lowest altitude sites (<1300 masl). Phylogenetic analysis using two mitochondrial markers revealed G. neotropica and G. viatrix to be closely related, and given their morphological similarities, their validities as separate taxonomic entities should be questioned. Conclusions This study highlights the need of a robust taxonomic framework for the identification of lymnaeid snails, incorporating molecular, morphological and ecological variables while avoiding nomenclature redundancy. As the three species observed here, including one alien invasive species, are considered hosts of varying susceptibility to Fasciola parasites, and given the economic

Alcohol dehydrogenase activities and ethanol tolerance in Anastrepha (Diptera, Tephritidae) fruit-fly species and their hybrids

PubMed Central

2009-01-01

The ADH (alcohol dehydrogenase) system is one of the earliest known models of molecular evolution, and is still the most studied in Drosophila. Herein, we studied this model in the genus Anastrepha (Diptera, Tephritidae). Due to the remarkable advantages it presents, it is possible to cross species with different Adh genotypes and with different phenotype traits related to ethanol tolerance. The two species studied here each have a different number of Adh gene copies, whereby crosses generate polymorphisms in gene number and in composition of the genetic background. We measured certain traits related to ethanol metabolism and tolerance. ADH specific enzyme activity presented gene by environment interactions, and the larval protein content showed an additive pattern of inheritance, whilst ADH enzyme activity per larva presented a complex behavior that may be explained by epistatic effects. Regression models suggest that there are heritable factors acting on ethanol tolerance, which may be related to enzymatic activity of the ADHs and to larval mass, although a pronounced environmental effect on ethanol tolerance was also observed. By using these data, we speculated on the mechanisms of ethanol tolerance and its inheritance as well as of associated traits. PMID:21637665

Antifungal activity of low molecular weight chitosan against clinical isolates of Candida spp.

PubMed

Alburquenque, Claudio; Bucarey, Sergio A; Neira-Carrillo, Andrónico; Urzúa, Blanca; Hermosilla, Germán; Tapia, Cecilia V

2010-12-01

Chitosan is a natural polymer derived from chitin, a structural component of fungi, insects and shrimp, which exerts antimicrobial effects against bacteria and fungi. The aim of this study was to investigate the in vitro antifungal activity of low molecular weight chitosan (LMWC), and the potential synergy between chitosan and a currently used antifungal drug, fluconazole. The in vitro minimal inhibitory concentrations (MICs) of chitosan and fluconazole against 105 clinical Candida isolates were measured by the broth microdilution method. LMWC exhibited a significant antifungal activity, inhibiting over 89.9% of the clinical isolates examined (68.6% of which was completely inhibited). The species included several fluconazole-resistant strains and less susceptible species such as C. glabrata, which was inhibited at a concentration of 4.8 mg/l LMWC. Although some strains were susceptible at pH 7.0, a greater antifungal activity of LMWC was observed at pH 4.0. There was no evidence of a synergistic effect of the combination of LMWC and fluconazole at pH 7.0. This is the first report in which the antifungal activity of LMWC was investigated with clinical Candida strains. The use of LMWC as an antifungal compound opens new therapeutic perspectives, as the low toxicity of LMWC in humans supports its use in new applications in an environment of pH 4.0-4.5, such as a topical agent for vulvovaginal candidiasis.

Molecular and antimicrobial susceptibility profiling of atypical Streptococcus species from porcine clinical specimens.

PubMed

Moreno, Luisa Z; Matajira, Carlos E C; Gomes, Vasco T M; Silva, Ana Paula S; Mesquita, Renan E; Christ, Ana Paula G; Sato, Maria Inês Z; Moreno, Andrea M

2016-10-01

The Streptococcus species present broad phenotypic variation, making identification difficult using only traditional microbiological methods. Even though Streptococcus suis is the most important species for the worldwide swine industry, other Streptococcus species appear to be able to cause disease in swine and could represent a higher underestimated risk for porcine health. The aim of this study was to identify Streptococcus-like isolates by MALDI-TOF MS and 16S rRNA sequencing and further molecular and antibiotic susceptibility characterization of the atypical Streptococcus species capable of causing disease in swine. Fifty presumptive Streptococcus isolates from diseased pigs isolated from different Brazilian States between 2002 and 2014 were evaluated. Among the studied isolates, 26% were identified as Streptococcus hyovaginalis, 24% as Streptococcus plurianimalium, 12% as Streptococcus alactolyticus, 10% as Streptococcus hyointestinalis, and the remaining isolates belonged to Streptococcus henryi (6%), Streptococcus thoraltensis (6%), Streptococcus gallolyticus (6%), Streptococcus gallinaceus (4%), Streptococcus sanguinis (4%), and Streptococcus mitis (2%). The Streptococcus isolates were successfully identified by spectral cluster analysis and 16S rRNA sequencing with 96% of concordance between the techniques. The SE-AFLP analysis also supported Streptococcus species distinction and enabled further observation of higher genetic heterogeneity intra-species. The identified Streptococcus species presented variable MIC values to β-lactams, enrofloxacin and florfenicol, and high resistance rates to tetracyclines and macrolides, which appear to be directly related to the industry's antimicrobial usage and resistance selection. Copyright © 2016 Elsevier B.V. All rights reserved.

Accurate calibration of a molecular beam time-of-flight mass spectrometer for on-line analysis of high molecular weight species.

PubMed

Apicella, B; Wang, X; Passaro, M; Ciajolo, A; Russo, C

2016-10-15

Time-of-Flight (TOF) Mass Spectrometry is a powerful analytical technique, provided that an accurate calibration by standard molecules in the same m/z range of the analytes is performed. Calibration in a very large m/z range is a difficult task, particularly in studies focusing on the detection of high molecular weight clusters of different molecules or high molecular weight species. External calibration is the most common procedure used for TOF mass spectrometric analysis in the gas phase and, generally, the only available standards are made up of mixtures of noble gases, covering a small mass range for calibration, up to m/z 136 (higher mass isotope of xenon). In this work, an accurate calibration of a Molecular Beam Time-of Flight Mass Spectrometer (MB-TOFMS) is presented, based on the use of water clusters up to m/z 3000. The advantages of calibrating a MB-TOFMS with water clusters for the detection of analytes with masses above those of the traditional calibrants such as noble gases were quantitatively shown by statistical calculations. A comparison of the water cluster and noble gases calibration procedures in attributing the masses to a test mixture extending up to m/z 800 is also reported. In the case of the analysis of combustion products, another important feature of water cluster calibration was shown, that is the possibility of using them as "internal standard" directly formed from the combustion water, under suitable experimental conditions. The water clusters calibration of a MB-TOFMS gives rise to a ten-fold reduction in error compared to the traditional calibration with noble gases. The consequent improvement in mass accuracy in the calibration of a MB-TOFMS has important implications in various fields where detection of high molecular mass species is required. In combustion products analysis, it is also possible to obtain a new calibration spectrum before the acquisition of each spectrum, only modifying some operative conditions. Copyright © 2016

Synthesis, molecular modeling studies and evaluation of antifungal activity of a novel series of thiazole derivatives.

PubMed

Lino, Cleudiomar Inácio; Gonçalves de Souza, Igor; Borelli, Beatriz Martins; Silvério Matos, Thelma Tirone; Santos Teixeira, Iasmin Natália; Ramos, Jonas Pereira; Maria de Souza Fagundes, Elaine; de Oliveira Fernandes, Philipe; Maltarollo, Vinícius Gonçalves; Johann, Susana; de Oliveira, Renata Barbosa

2018-05-10

In the search for new antifungal agents, a novel series of fifteen hydrazine-thiazole derivatives was synthesized and assayed in vitro against six clinically important Candida and Cryptococcus species and Paracoccidioides brasiliensis. Eight compounds showed promising antifungal activity with minimum inhibitory concentration (MIC) values ranging from 0.45 to 31.2 μM, some of them being equally or more active than the drug fluconazole and amphotericin B. Active compounds were additionally tested for toxicity against human embryonic kidney (HEK-293) cells and none of them exhibited significant cytotoxicity, indicating high selectivity. Molecular modeling studies results corroborated experimental SAR results, suggesting their use in the design of new antifungal agents. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Molecular instability induced by aluminum stress in Plantago species.

PubMed

Correia, Sofia; Matos, Manuela; Ferreira, Vanessa; Martins, Neusa; Gonçalves, Sandra; Romano, Anabela; Pinto-Carnide, Olinda

2014-08-01

Aluminum (Al) is one of the most abundant metals on earth's crust and Al toxicity represents one of the major factors that limit plant growth and productivity in acid soils (with a pH≤5.0). In this study the mutagenic/genotoxic effects of Al were evaluated in roots and leaves of two Plantago, species, Plantago almogravensis and Plantago lagopus, using ISSRs markers. Both species were exposed to 400 μM Al during 7 and 21 days. Ten ISSR primers produced polymorphic bands. In P. almogravensis, a total of 257 and 258 bands in roots and 255 and 265 bands in leaves were produced in the presence and absence of Al, respectively. In P. lagopus were produced 279 and 278 a total bands in roots and 275 and 274 bands in leaves, under the same conditions. The changes in ISSR profiles after Al treatment were considered as gain and/or loss of bands compared with the controls. The results suggest that changes in genomic template stability (GTS) could be detected with ISSR profiles. This molecular marker proved to be a good tool to detect the effects of Al on DNA profiles. It seems that Al did not interfere significantly with DNA integrity in both species but generated less ISSR stability in P. almogravensis than in P. lagopus. The results confirm the tolerance of P. almogravensis and suggest the same behavior of P. lagopus. Although further studies are required for confirmation the Al tolerance behavior of P. lagopus, a potential application for phytoremediation can be also considered due its wide distribution. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular mechanism of the Syk activation switch.

PubMed

Tsang, Emily; Giannetti, Anthony M; Shaw, David; Dinh, Marie; Tse, Joyce K Y; Gandhi, Shaan; Ho, Hoangdung; Wang, Sandra; Papp, Eva; Bradshaw, J Michael

2008-11-21

Many immune signaling pathways require activation of the Syk tyrosine kinase to link ligation of surface receptors to changes in gene expression. Despite the central role of Syk in these pathways, the Syk activation process remains poorly understood. In this work we quantitatively characterized the molecular mechanism of Syk activation in vitro using a real time fluorescence kinase assay, mutagenesis, and other biochemical techniques. We found that dephosphorylated full-length Syk demonstrates a low initial rate of substrate phosphorylation that increases during the kinase reaction due to autophosphorylation. The initial rate of Syk activity was strongly increased by either pre-autophosphorylation or binding of phosphorylated immune tyrosine activation motif peptides, and each of these factors independently fully activated Syk. Deletion mutagenesis was used to identify regions of Syk important for regulation, and residues 340-356 of the SH2 kinase linker region were identified to be important for suppression of activity before activation. Comparison of the activation processes of Syk and Zap-70 revealed that Syk is more readily activated by autophosphorylation than Zap-70, although both kinases are rapidly activated by Src family kinases. We also studied Syk activity in B cell lysates and found endogenous Syk is also activated by phosphorylation and immune tyrosine activation motif binding. Together these experiments show that Syk functions as an "OR-gate" type of molecular switch. This mechanism of switch-like activation helps explain how Syk is both rapidly activated after receptor binding but also sustains activity over time to facilitate longer term changes in gene expression.

In-Depth Lipidomic Analysis of Molecular Species of Triacylglycerides, Diacylglycerides, Glycerophospholipids, and Sphingolipids of Buttermilk by GC-MS/FID, HPLC-ELSD, and UPLC-QToF-MS

PubMed Central

Castro-Gómez, Pilar; Montero, Olimpio; Fontecha, Javier

2017-01-01

Buttermilk, a byproduct of butter manufacturing, has gained considerable attention due to its high concentration of polar lipids as phospho- and sphingolipids from the milk fat globule membrane (MFGM). These polar lipids (PLs) are essential components of all cellular membranes and exert a variety of indispensable metabolic, neurological, and intracellular signaling processes. Despite its importance, there are few research studies that report a comprehensive characterization of the lipid molecular species of MFGM that could contribute to a better understanding of their putative healthful activities. In this study, procedures such as pressurized liquid extraction of polar and nonpolar lipids and their fractionation by flash chromatography have been carried out. The obtained fractions were submitted to an exhaustive characterization from a lipidomic point of view. The characterization includes new data about the identification and quantification of triacylglycerides (TAG), diacylglycerides (DAG), and phospho- and sphingolipids using different chromatographic techniques. The fatty acid profile was comparable to that of the milk fat but with a highly diverse composition of fatty acids. Molecular species have also been determined by using ultra-high performance liquid chromatography/quadruple-time-of-flight mass spectrometry (UPLC/QToF-MS). The TAG (16:0/16:0/6:0) and TAG (16:0/16:0/8:0) were the predominant saturated TAG species and TAG (14:0/18:1/16:0) and TAG (16:0/16:0/18:1) presented the highest content of monounsaturated TAG species. Furthermore; over 30 molecular species of phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylinositol (PI) could be identified within PL, with PC (16:0/18:1) being the most abundant species. Whereas C16:0 was found to be the preferred FA in TAGs, it was C18:1 in PLs. Several ganglioside species have also been characterized with d18:1 ceramide moiety and secondary acyl chains ranging from C

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-Rich DNA, and nuclear DNA analyses

USGS Publications Warehouse

Freeman, S.; Pham, M.; Rodriguez, R.J.

1993-01-01

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-rich DNA, and nuclear DNA analyses. Experimental Mycology 17, 309-322. Isolates of Colletotrichum were grouped into 10 separate species based on arbitrarily primed PCR (ap-PCR), A + T-rich DNA (AT-DNA) and nuclear DNA banding patterns. In general, the grouping of Colletotrichum isolates by these molecular approaches corresponded to that done by classical taxonomic identification, however, some exceptions were observed. PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of the 10 species. HaeIII digestion patterns of AT-DNA also distinguished between species of Colletotrichum by generating species-specific band patterns. In addition, hybridization of the repetitive DNA element (GcpR1) to genomic DNA identified a unique set of Pst 1-digested nuclear DNA fragments in each of the 10 species of Colletotrichum tested. Multiple isolates of C. acutatum, C. coccodes, C. fragariae, C. lindemuthianum, C. magna, C. orbiculare, C. graminicola from maize, and C. graminicola from sorghum showed 86-100% intraspecies similarity based on ap-PCR and AT-DNA analyses. Interspecies similarity determined by ap-PCR and AT-DNA analyses varied between 0 and 33%. Three distinct banding patterns were detected in isolates of C. gloeosporioides from strawberry. Similarly, three different banding patterns were observed among isolates of C. musae from diseased banana.

Effect of Sulfation and Molecular Weight on Anticoagulant Activity of Dextran.

PubMed

Drozd, N N; Logvinova, Yu S; Torlopov, M A; Udoratina, E V

2017-02-01

Sulfation (to 2.8) of dextrans with molecular weight of 150 and 20 kDa was followed by the appearance of anticoagulant activity that increased with decreasing their molecular weight and did not depend on antithrombin, plasma inhibitor of serine proteases of the blood coagulation system. Antithrombin activity of dextran sulfate with a molecular weight of 20 kDa reached 12.6-15.3 U/mg. Dextran sulfates with molecular weights of 20 and 150 kDa did not potentiate ADP-induced human platelet aggregation.

Discrepancy between species borders at morphological and molecular levels in the genus Cochliopodium (Amoebozoa, Himatismenida), with the description of Cochliopodium plurinucleolum n. sp.

PubMed

Geisen, Stefan; Kudryavtsev, Alexander; Bonkowski, Michael; Smirnov, Alexey

2014-05-01

Amoebae of the genus Cochliopodium are characterized by a tectum that is a layer of scales covering the dorsal surface of the cell. A combination of scale structure, morphological features and, nowadays, molecular information allows species discrimination. Here we describe a soil species Cochliopodium plurinucleolum n. sp. that besides strong genetic divergence from all currently described species of Cochliopodium differs morphologically by the presence of several peripheral nucleoli in the nucleus. Further, we unambiguously show that the Golgi attachment associated with a dictyosome in Cochliopodium is a cytoplasmic microtubule organizing center (MTOC). Last, we provide detailed morphological and molecular information on the sister clade of C. plurinucleolum, containing C. minus, C. minutoidum, C. pentatrifurcatum and C. megatetrastylus. These species share nearly identical sequences of both, small subunit ribosomal RNA and partial Cox1 genes, and nearly identical structure of the scales. Scales of C. pentatrifurcatum differ, however, strongly from scales of the others while sequences of C. pentatrifurcatum and C. minus are nearly identical. These discrepancies urge for future sampling efforts to disentangle species characteristics within Cochliopdium and to investigate morphological and molecular patterns that allow reliable species differentiation. Copyright © 2014 Elsevier GmbH. All rights reserved.

Studies for the loss of atomic and molecular species from Io

NASA Technical Reports Server (NTRS)

Combi, Michael R.

1994-01-01

The general objective of this project is to advance theoretical understanding of Io's atmosphere and how various atomic and molecular species are lost from this atmosphere and are distributed in the circumplanetary environment of Jupiter. The major task for the University of Michigan portion of this work is the generalization of the Io sodium cloud model to simulate the ion-precursor of sodium that is the apparent source of the fast sodium jet observed by Schneider et al. (1991). The goal is a quantitative test of the molecular ion hypothesis with a model that is comparable to a general sodium cloud model published previously. A detailed comparison of observations with such a model will help to probe the feasibility of such a source and to examine the rates and scale lengths associated with the decay of the ion precursor so as to possibly uncover the identity of the parent ion. Another important task to be performed at Michigan is more support of AER in the general area of modeling the Na and SO2-family clouds.

A Scalable Approach for Discovering Conserved Active Subnetworks across Species

PubMed Central

Verfaillie, Catherine M.; Hu, Wei-Shou; Myers, Chad L.

2010-01-01

Overlaying differential changes in gene expression on protein interaction networks has proven to be a useful approach to interpreting the cell's dynamic response to a changing environment. Despite successes in finding active subnetworks in the context of a single species, the idea of overlaying lists of differentially expressed genes on networks has not yet been extended to support the analysis of multiple species' interaction networks. To address this problem, we designed a scalable, cross-species network search algorithm, neXus (Network - cross(X)-species - Search), that discovers conserved, active subnetworks based on parallel differential expression studies in multiple species. Our approach leverages functional linkage networks, which provide more comprehensive coverage of functional relationships than physical interaction networks by combining heterogeneous types of genomic data. We applied our cross-species approach to identify conserved modules that are differentially active in stem cells relative to differentiated cells based on parallel gene expression studies and functional linkage networks from mouse and human. We find hundreds of conserved active subnetworks enriched for stem cell-associated functions such as cell cycle, DNA repair, and chromatin modification processes. Using a variation of this approach, we also find a number of species-specific networks, which likely reflect mechanisms of stem cell function that have diverged between mouse and human. We assess the statistical significance of the subnetworks by comparing them with subnetworks discovered on random permutations of the differential expression data. We also describe several case examples that illustrate the utility of comparative analysis of active subnetworks. PMID:21170309

Low-energy electron interaction with retusin extracted from Maackia amurensis: towards a molecular mechanism of the biological activity of flavonoids.

PubMed

Pshenichnyuk, Stanislav A; Elkin, Yury N; Kulesh, Nadezda I; Lazneva, Eleonora F; Komolov, Alexei S

2015-07-14

The antioxidant isoflavone retusin efficiently attaches low-energy electrons in vacuo, generating fragment species via dissociative electron attachment (DEA), as has been shown by DEA spectroscopy. According to in silico results obtained by means of density functional theory, retusin is able to attach solvated electrons and could be decomposed under reductive conditions in vivo, for instance, near the mitochondrial electron transport chain, analogous to gas-phase DEA. The most intense decay channels of retusin temporary negative ions were found to be associated with the elimination of H atoms and H2 molecules. Doubly dehydrogenated fragment anions were predicted to possess a quinone structure. It is thought that molecular hydrogen, known for its selective antioxidant properties, can be efficiently generated via electron attachment to retusin in mitochondria and may be responsible for its antioxidant activity. The second abundant species, i.e., quinone bearing an excess negative charge, can serve as an electron carrier and can return the captured electron back to the respiration cycle. The number of OH substituents and their relative positions are crucial for the present molecular mechanism, which can explain the radical scavenging activity of polyphenolic compounds.

Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples.

PubMed

Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David; Šlapeta, Jan

2017-09-01

Fasciolosis, due to Fasciola hepatica and Fasciola gigantica, is a re-emerging zoonotic parasitic disease of worldwide importance. Human and animal infections are commonly diagnosed by the traditional sedimentation and faecal egg-counting technique. However, this technique is time-consuming and prone to sensitivity errors when a large number of samples must be processed or if the operator lacks sufficient experience. Additionally, diagnosis can only be made once the 12-week pre-patent period has passed. Recently, a commercially available coprological antigen ELISA has enabled detection of F. hepatica prior to the completion of the pre-patent period, providing earlier diagnosis and increased throughput, although species differentiation is not possible in areas of parasite sympatry. Real-time PCR offers the combined benefits of highly sensitive species differentiation for medium to large sample sizes. However, no molecular diagnostic workflow currently exists for the identification of Fasciola spp. in faecal samples. A new molecular diagnostic workflow for the highly-sensitive detection and quantification of Fasciola spp. in faecal samples was developed. The technique involves sedimenting and pelleting the samples prior to DNA isolation in order to concentrate the eggs, followed by disruption by bead-beating in a benchtop homogeniser to ensure access to DNA. Although both the new molecular workflow and the traditional sedimentation technique were sensitive and specific, the new molecular workflow enabled faster sample throughput in medium to large epidemiological studies, and provided the additional benefit of speciation. Further, good correlation (R2 = 0.74-0.76) was observed between the real-time PCR values and the faecal egg count (FEC) using the new molecular workflow for all herds and sampling periods. Finally, no effect of storage in 70% ethanol was detected on sedimentation and DNA isolation outcomes; enabling transport of samples from endemic to non

Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples

PubMed Central

Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David

2017-01-01

Background Fasciolosis, due to Fasciola hepatica and Fasciola gigantica, is a re-emerging zoonotic parasitic disease of worldwide importance. Human and animal infections are commonly diagnosed by the traditional sedimentation and faecal egg-counting technique. However, this technique is time-consuming and prone to sensitivity errors when a large number of samples must be processed or if the operator lacks sufficient experience. Additionally, diagnosis can only be made once the 12-week pre-patent period has passed. Recently, a commercially available coprological antigen ELISA has enabled detection of F. hepatica prior to the completion of the pre-patent period, providing earlier diagnosis and increased throughput, although species differentiation is not possible in areas of parasite sympatry. Real-time PCR offers the combined benefits of highly sensitive species differentiation for medium to large sample sizes. However, no molecular diagnostic workflow currently exists for the identification of Fasciola spp. in faecal samples. Methodology/Principal findings A new molecular diagnostic workflow for the highly-sensitive detection and quantification of Fasciola spp. in faecal samples was developed. The technique involves sedimenting and pelleting the samples prior to DNA isolation in order to concentrate the eggs, followed by disruption by bead-beating in a benchtop homogeniser to ensure access to DNA. Although both the new molecular workflow and the traditional sedimentation technique were sensitive and specific, the new molecular workflow enabled faster sample throughput in medium to large epidemiological studies, and provided the additional benefit of speciation. Further, good correlation (R2 = 0.74–0.76) was observed between the real-time PCR values and the faecal egg count (FEC) using the new molecular workflow for all herds and sampling periods. Finally, no effect of storage in 70% ethanol was detected on sedimentation and DNA isolation outcomes; enabling

Identification of Acinetobacter species: is Bruker biotyper MALDI-TOF mass spectrometry a good alternative to molecular techniques?

PubMed

Alvarez-Buylla, Adela; Culebras, Esther; Picazo, Juan J

2012-03-01

Acinetobacter spp. has become a leading cause of nosocomial infection in recent years. Phenotypic similarities between the species in the genus have made it difficult to identify them clearly using routine diagnostic methods. Consequently, more relevant species have been grouped together as Acinetobacter calcoaceticus-Acinetobacter baumannii complex (A. baumannii, A. calcoaceticus, Acinetobacter genospecies 3 and A. genospecies 13TU). However, there are other species that may also have clinical significance. The aims of this study were to establish the usefulness of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Acinetobacter species by comparison with two molecular techniques, as well as determine the role of species other than A. baumannii play in nosocomial infections.The study sample comprised 109 clinical isolates of Acinetobacter. They were all identified using MALDI-TOF MS. Thirty-one isolates of these were also tested using comparator amplification of bla(OXA51-like) and sequencing of the rpoB gene. Different score values in MALDI-TOF MS revealed 87 A. baumannii, 19 A. genospecies 3, 1 Acinetobacter junii, 1 Acinetobacter baylyi and 1 Acinetobacter tjernbergiae. Amplification of bla(OXA-51)(-like) showed products in 85 isolates. Sequencing of the rpoB gene allowed us to identify all the 31 isolates analyzed: 16 were consistent with the results of spectrometry and 15 were not. This work showed that molecular techniques are still needed to identify the different species of clinical interest within the genus Acinetobacter. Although, MALDI-TOF MS could be useful to identify A. baumannii but not other species in the genus. Copyright © 2012 Elsevier B.V. All rights reserved.

Comparison of compounds of three Rubus species and their antioxidant activity.

PubMed

Caidan, Rezeng; Cairang, Limao; Pengcuo, Jiumei; Tong, Li

2015-12-01

Rubus amabilis, Rubus niveus Thunb., and Rubus sachalinensis are three Rubus species that are alternatively found in Manubzhithang, a Tibetan medicine, in different areas of China. The current study analyzed HPLC/UV chromatograms and it compared compounds of these three Rubus species in contrast to reference substances such as 2,6-dimethoxy-4-hydroxyphenol-1-O-β-D-glucopyranoside, procyanidin B4, and isovitexin-7-O-glucoside. The three Rubus species produced similar peaks in chromatograms. The antioxidant activity of the three Rubus species was determined using an assay for DPPH free radical scavenging activity. Results indicated that the three Rubus species extracts had almost the same level of free radical scavenging activity. Thus, findings indicated the rationality of substituting these species for one another as an ingredient in Manubzhithang.

Quantification of the molecular species of tetraacylglycerols in lesquerella (Physaria fendleri) Oil by HPLC and MS

USDA-ARS?s Scientific Manuscript database

Thirteen molecular species of tetraacylglycerols in the seed oil of Physaria fendleri were recently identified. We report here the quantification of these tetraacylglycerols using HPLC with evaporative light scattering detector and the MS of the HPLC fractions. Ion signal intensities of MS1 from th...

Ratios of the molecular species of triacylglycerols in lesquerella (Physaria fendleri) oil estimated by mass spectrometry

USDA-ARS?s Scientific Manuscript database

The ratios of regioisomers of 72 molecular species of triacylglycerols (TAG) in lesquerella oil were estimated using the electrospray ionization mass spectrometry of the lithium adducts of TAG in the HPLC fractions of lesquerella oil. The ratios of ion signal intensities (or relative abundances) of ...

Molecular prevalence of Cryptosporidium species among household cats and pet shop kittens in Japan.

PubMed

Ito, Yoichi; Itoh, Naoyuki; Iijima, Yuko; Kimura, Yuya

2017-01-01

To address the lack of up-to-date published data, the present study evaluates the PCR-based prevalence of Cryptosporidium species infection and molecular characteristics of isolates among household cats and pet shop kittens in Japan. A total of 357 and 329 fresh faecal samples were collected from household cats and pet shop kittens, respectively, with or without clinical signs of infection. A nested PCR assay targeting the 18S rRNA gene was employed for the detection of Cryptosporidium species. After specific DNA fragments (approximately 826 base pairs) were confirmed, the amplicons were sequenced to determine species. Seven (2.0%) household cats and one (0.3%) pet shop kitten tested positive for the presence of Cryptosporidium species. In household cats, there was a significant difference in prevalence between cats aged <1 year (4.6%) and those aged ⩾1 year (0.4%). No significantly different prevalence was observed with regard to faecal condition in either household cats or pet shop kittens. A total of eight Cryptosporidium species isolates, seven from household cats and one from a pet shop kitten, were identified as Cryptosporidium felis . The present study demonstrates the risk of zoonotic transmission of Cryptosporidium species from household cats and pet shop kittens to humans is low in Japan.

Proteinase activity of prevotella species associated with oral purulent infection.

PubMed

Yanagisawa, Maki; Kuriyama, Tomoari; Williams, David W; Nakagawa, Kiyomasa; Karasawa, Tadahiro

2006-05-01

Prevotella intermedia and Prevotella nigrescens are often regarded as principal causes of acute dentoalveolar infection; however, other species within the genus are also known to be associated with such infection. The aim of this study was to determine the in vitro proteolytic activity of these different Prevotella species that have been implicated with dentoalveolar infection. A total of 234 strains were obtained from pus specimens from dentoalveolar infection and from the plaque of healthy volunteers. Prevotella loescheii, Prevotella oralis, Prevotella melaninogenica, Prevotella buccae, and Prevotella denticola were all shown to have a proteolytic activity (8.5-10.5 x 10(-8) A-units) lower than that of P. intermedia and P. nigrescens (21.1-23.5 x 10(-8) A-units). In the case of P. loescheii, P. melaninogenica, and P. intermedia, the level of proteolytic activity for clinical strains was significantly (P < 0.05) higher than that recorded for commensal strains. Proteolytic activity for all species of Prevotella examined was inhibited by N-ethylmaleimide and phenymethylsulfonyl fluoride. This study suggests that Prevotella species associated with oral purulent infection produce cysteine and serine proteinases and that in certain species of Prevotella, the strains involved in infection exhibit higher proteolytic activity when compared with strains from healthy sites.

Taxonomic review of the species of Mugil (Teleostei: Perciformes: Mugilidae) from the Atlantic South Caribbean and South America, with integration of morphological, cytogenetic and molecular data.

PubMed

Menezes, Naércio A; Nirchio, Mauro; De Oliveira, Cláudio; Siccharamirez, Raquel

2015-01-10

Analysis of morphological, molecular and cytological data helped to define and more precisely characterize the species of Mugil from the Atlantic coasts of South Caribbean and South America, allowing a correction of prior misidentifications and distributional ranges. A new species from Venezuela is described and all the species from the area are redescribed. It is demonstrated that the apparent similarity in morphological traits, which contradicted the results from recent molecular studies, is the result of the misuse of traditional morphological characters, and thus both the molecular and cytological data instead are congruent with the morphological differences that are found among mullet species. The presence of Mugil hospes Jordan & Culver in the western south Atlantic is refuted based on the comparison of type material of this species with specimens from this area that also indicated a very significant morphological difference, what on the other hand justifies the recognition of these specimens as Mugil brevirostris (Ribeiro). The distribution of Mugil incilis Hancock is restricted and the similarities among the species formerly depicted in a prior dendrogram is modified following the inclusion of recently obtained molecular data for Mugil curvidens Valenciennes.

Species-Specific Activation of TLR4 by Hypoacylated Endotoxins Governed by Residues 82 and 122 of MD-2

PubMed Central

Oblak, Alja; Jerala, Roman

2014-01-01

The Toll-like receptor 4/MD-2 receptor complex recognizes endotoxin, a Gram-negative bacterial cell envelope component. Recognition of the most potent hexaacylated form of endotoxin is mediated by the sixth acyl chain that protrudes from the MD-2 hydrophobic pocket and bridges TLR4/MD-2 to the neighboring TLR4 ectodomain, driving receptor dimerization via hydrophobic interactions. In hypoacylated endotoxins all acyl chains could be accommodated within the binding pocket of the human hMD-2. Nevertheless, tetra- and pentaacylated endotoxins activate the TLR4/MD-2 receptor of several species. We observed that amino acid residues 82 and 122, located at the entrance to the endotoxin binding site of MD-2, have major influence on the species-specific endotoxin recognition. We show that substitution of hMD-2 residue V82 with an amino acid residue with a bulkier hydrophobic side chain enables activation of TLR4/MD-2 by pentaacylated and tetraacylated endotoxins. Interaction of the lipid A phosphate group with the amino acid residue 122 of MD-2 facilitates the appropriate positioning of the hypoacylated endotoxin. Moreover, mouse TLR4 contributes to the agonistic effect of pentaacylated msbB endotoxin. We propose a molecular model that explains how the molecular differences between the murine or equine MD-2, which both have sufficiently large hydrophobic pockets to accommodate all five or four acyl chains, influence the positioning of endotoxin so that one of the acyl chains remains outside the pocket and enables hydrophobic interactions with TLR4, leading to receptor activation. PMID:25203747

Species-specific activation of TLR4 by hypoacylated endotoxins governed by residues 82 and 122 of MD-2.

PubMed

Oblak, Alja; Jerala, Roman

2014-01-01

The Toll-like receptor 4/MD-2 receptor complex recognizes endotoxin, a Gram-negative bacterial cell envelope component. Recognition of the most potent hexaacylated form of endotoxin is mediated by the sixth acyl chain that protrudes from the MD-2 hydrophobic pocket and bridges TLR4/MD-2 to the neighboring TLR4 ectodomain, driving receptor dimerization via hydrophobic interactions. In hypoacylated endotoxins all acyl chains could be accommodated within the binding pocket of the human hMD-2. Nevertheless, tetra- and pentaacylated endotoxins activate the TLR4/MD-2 receptor of several species. We observed that amino acid residues 82 and 122, located at the entrance to the endotoxin binding site of MD-2, have major influence on the species-specific endotoxin recognition. We show that substitution of hMD-2 residue V82 with an amino acid residue with a bulkier hydrophobic side chain enables activation of TLR4/MD-2 by pentaacylated and tetraacylated endotoxins. Interaction of the lipid A phosphate group with the amino acid residue 122 of MD-2 facilitates the appropriate positioning of the hypoacylated endotoxin. Moreover, mouse TLR4 contributes to the agonistic effect of pentaacylated msbB endotoxin. We propose a molecular model that explains how the molecular differences between the murine or equine MD-2, which both have sufficiently large hydrophobic pockets to accommodate all five or four acyl chains, influence the positioning of endotoxin so that one of the acyl chains remains outside the pocket and enables hydrophobic interactions with TLR4, leading to receptor activation.

Molecular mechanisms of mucocutaneous immunity against Candida and Staphylococcus species.

PubMed

Maródi, László; Cypowyj, Sophie; Tóth, Beáta; Chernyshova, Liudmyla; Puel, Anne; Casanova, Jean-Laurent

2012-11-01

Signal transducer and activator of transcription (STAT) proteins are key components of the innate and adaptive immune responses to pathogenic microorganisms. Recent research on primary immunodeficiency disorders and the identification of patients carrying germline mutations in STAT1, STAT3, and STAT5B have highlighted the role of human STATs in host defense against various viruses, bacteria, and fungi. Mutations in STAT1 and STAT3 disrupt various cytokine pathways that control mucocutaneous immunity against Candida species, especially Candida albicans, and Staphylococcus species, especially Staphylococcus aureus. Here we consider inborn errors of immunity arising from mutations in either STAT1 or STAT3 that affect mucocutaneous immunity to Candida and Staphylococcus species. Copyright © 2012 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

Spectral molecular line surveys of active galaxies

NASA Astrophysics Data System (ADS)

Villicana Pedraza, Ilhuiyolitzin

The enormous mass of molecular gas and dust found in the nuclei of active galaxies has a major role in feeding the activity (either starburst or AGN) and therefore in the galactic evolution. Thus, observations of the molecular can provide clues to identify and analyze the type of activity in very deeply obscured galactic nuclei. Indeed, studies of the chemical composition in starburst galaxies via wide band spectral has shown the potential of molecular spectroscopy to trace the physical and chemical propierties of their central ISM material. In this work we present the analysis of the emission of molecules such as HCN, CCH, CN,CS,HCO+, HNC, CH3OH, among others obtained from the survey of spectra of the 3 near seyfert galaxies observed with the APEX Telescope. We have also found that one of the molecules is not at LTE conditions- H3O+ molecule. Whether radiatively pumped or maser enhanced, the emission of H3O+ is emerging from a different region from most other molecules (distributed in two molecular lobes seen as the two velocity components). H3O+ emission peaks close to the systemic velocity of the system, particularly clear in NGC 253, which suggest the emission to be centrally peaked towards the nuclear engine, It is common in the same kind of galaxies? In adition, preliminar conclusions show isotopic ratio 12C/13C in starburst galaxies is higher than nuclei of the Milky Way indicating that interestelar matter in starburst nuclei is less processed than in the nucleus of the Milky Way .There are two possible explanations for this effect in starburst, nucleosynthesis differences due stellar population history and acretion of matter from halo.

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.

PubMed

Patalano, Solenn; Vlasova, Anna; Wyatt, Chris; Ewels, Philip; Camara, Francisco; Ferreira, Pedro G; Asher, Claire L; Jurkowski, Tomasz P; Segonds-Pichon, Anne; Bachman, Martin; González-Navarrete, Irene; Minoche, André E; Krueger, Felix; Lowy, Ernesto; Marcet-Houben, Marina; Rodriguez-Ales, Jose Luis; Nascimento, Fabio S; Balasubramanian, Shankar; Gabaldon, Toni; Tarver, James E; Andrews, Simon; Himmelbauer, Heinz; Hughes, William O H; Guigó, Roderic; Reik, Wolf; Sumner, Seirian

2015-11-10

Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

PubMed Central

Patalano, Solenn; Vlasova, Anna; Wyatt, Chris; Ewels, Philip; Camara, Francisco; Ferreira, Pedro G.; Asher, Claire L.; Jurkowski, Tomasz P.; Segonds-Pichon, Anne; Bachman, Martin; González-Navarrete, Irene; Minoche, André E.; Krueger, Felix; Lowy, Ernesto; Marcet-Houben, Marina; Rodriguez-Ales, Jose Luis; Nascimento, Fabio S.; Balasubramanian, Shankar; Gabaldon, Toni; Tarver, James E.; Andrews, Simon; Himmelbauer, Heinz; Hughes, William O. H.; Guigó, Roderic; Reik, Wolf; Sumner, Seirian

2015-01-01

Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity. PMID:26483466

Mucorales species activation of a serum leukotactic factor.

PubMed Central

Marx, R S; Forsyth, K R; Hentz, S K

1982-01-01

Previous studies have suggested that the focal accumulation of phagocytic leukocytes is an important feature of the host response in mucormycosis. To ascertain the basis for this influx of inflammatory cells, we evaluated the effect of members of the order Mucorales, including species from the genera Rhizopus, Absidia, and Mucor, on the chemotactic activity of normal human serum for neutrophils and monocytes. Both hyphae and spores produced concentration-dependent chemotaxigenesis in serum to a maximum level equivalent to that produced by zymosan activation of serum. Chemotactic activity was similar for live and heat-killed hyphae. No leukotactic activity was demonstrated in the absence of serum. The pretreatment of serum with anti-C3 antibody, heating at 56 degrees C, or 0.01 M EDTA abolished the activity. The pretreatment of serum with 0.01 M ethylene glycol-bis(beta-aminoethyl ether)-N,N-tetraacetic acid did not abolish the activity. These data provide evidence that the leukotactic activity of Mucorales species is generated through the alternative complement pathway. PMID:6759409

Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

PubMed

Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-lin; Du, Guan-hua

2016-05-01

A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives. © 2015 John Wiley & Sons A/S.

Molecular prevalence of Cryptosporidium species among household cats and pet shop kittens in Japan

PubMed Central

Ito, Yoichi; Itoh, Naoyuki; Iijima, Yuko; Kimura, Yuya

2017-01-01

Objectives To address the lack of up-to-date published data, the present study evaluates the PCR-based prevalence of Cryptosporidium species infection and molecular characteristics of isolates among household cats and pet shop kittens in Japan. Methods A total of 357 and 329 fresh faecal samples were collected from household cats and pet shop kittens, respectively, with or without clinical signs of infection. A nested PCR assay targeting the 18S rRNA gene was employed for the detection of Cryptosporidium species. After specific DNA fragments (approximately 826 base pairs) were confirmed, the amplicons were sequenced to determine species. Results Seven (2.0%) household cats and one (0.3%) pet shop kitten tested positive for the presence of Cryptosporidium species. In household cats, there was a significant difference in prevalence between cats aged <1 year (4.6%) and those aged ⩾1 year (0.4%). No significantly different prevalence was observed with regard to faecal condition in either household cats or pet shop kittens. A total of eight Cryptosporidium species isolates, seven from household cats and one from a pet shop kitten, were identified as Cryptosporidium felis. Conclusions and relevance The present study demonstrates the risk of zoonotic transmission of Cryptosporidium species from household cats and pet shop kittens to humans is low in Japan. PMID:28955478

Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning.

PubMed

Fu, J J; Mei, Z Q; Tania, M; Yang, L Q; Cheng, J L; Khan, M A

2015-05-25

The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.

Immunostimulative Activity of Low Molecular Weight Chitosans in RAW264.7 Macrophages

PubMed Central

Wu, Ning; Wen, Zheng-Shun; Xiang, Xing-Wei; Huang, Yan-Na; Gao, Yang; Qu, You-Le

2015-01-01

Chitosan and its derivatives such as low molecular weight chitosans (LMWCs) have been reported to exert many biological activities, such as antioxidant and antitumor effects. However, complex and molecular weight dependent effects of chitosan remain controversial and the mechanisms that mediate these complex effects are still poorly defined. This study was carried out to investigate the immunostimulative effect of different molecular weight chitosan in RAW264.7 macrophages. Our data suggested that two LMWCs (molecular weight of 3 kDa and 50 kDa) both possessed immunostimulative activity, which was dependent on dose and, at the higher doses, also on the molecular weight. LMWCs could significantly enhance the the pinocytic activity, and induce the production of tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), interferon-γ (IFN-γ), nitric oxide (NO) and inducible nitric oxide synthase (iNOS) in a molecular weight and concentration-dependent manner. LMWCs were further showed to promote the expression of the genes including iNOS, TNF-α. Taken together, our findings suggested that LMWCs elicited significantly immunomodulatory response through up-regulating mRNA expression of proinflammatory cytokines and activated RAW264.7 macrophage in a molecular weight- and concentration-dependent manner. PMID:26437419

Constituents of ophiuroidea. 1. Isolation and structure of three ganglioside molecular species from the brittle star Ophiocoma scolopendrina.

PubMed

Inagaki, M; Shibai, M; Isobe, R; Higuchi, R

2001-12-01

Three ganglioside molecular species, OSG-0 (1), OSG-1 (2), and OSG-2 (3) have been obtained from the polar lipid fraction of the chloroform/methanol extract of the brittle star Ophiocoma scolopendrina. The structures of these gangliosides have been determined on the basis of chemical and spectroscopic evidence as 1-O-[(N-glycolyl-alpha-D-neuraminosyl)-(2-->6)-beta-D-glucopyranosyl]-ceramide (1), 1-O-[8-O-sulfo-(N-acetyl-alpha-D-neuraminosyl)-(2-->6)-beta-D-glucopyranosyll-ceramide (2) and 1-O-[(N-glycolyl-alpha-D-neuraminosyl)-(2-->8)-(N-acetyl- and N-glycolyl-alpha-D-neuraminosyl)-(2-->6)-beta-D-glucopyranosyl]-ceramide (3). The ceramide moieties were composed of heterogeneous unsubstituted fatty acid, 2-hydroxy fatty acid and phytosphingosine units. Compounds 2 and 3 represent new ganglioside molecular species.

Two new species of Cichlidogyrus (Monogenea: Dactylogyridae) parasitizing the gills of African cichlid fishes (Perciformes) from Senegal: morphometric and molecular characterization.

PubMed

Rehulková, Eva; Mendlová, Monika; Simková, Andrea

2013-04-01

Two new species of Cichlidogyrus are described from the gills of three species of African cichlids collected from the Gambia River basin in the Niokolo-Koba National Park, Senegal: Cichlidogyrus dracolemma n. sp. from Hemichromis letourneuxi and Cichlidogyrus nageus n. sp. from Sarotherodon galilaeus and Tilapia guineensis. The new species are recognized on the basis of morphological differences in the male copulatory organs (MCOs) and apparent differences in the SSU rDNA and ITS1 sequence data. C. dracolemma n. sp. resembles specimens of Cichlidogyrus from Hemichromis bimaculatus, probably misidentified as Cichlidogyrus bychowskii by Paperna in 1965, in having morphologically similar types of haptoral sclerites and MCO. The new species is characterized by possessing an MCO with a kite-shaped termination of the accessory piece and a vagina distally surrounded by a circular superficial sclerotization of the body surface. Molecular phylogenetic analyses showed a strongly supported clade including C. dracolemma n. sp. and two species collected from Hemichromis fasciatus, namely Cichlidogyrus longicirrus Paperna, 1965 and Cichlidogyrus falcifer Dossou and Birgi, 1984. Based on both morphology and molecular phylogeny, C. nageus n. sp. appears to be closely related to Cichlidogyrus acerbus Dossou, 1982 obtained from S. galilaeus. Morphologically, C. nageus n. sp. is readily separated from all known congeners by the characteristic pestle shaped termination of the accessory piece of the MCO. Molecular phylogenetic reconstruction showed that C. dracolemma n. sp. and C. nageus n. sp. cluster with the Cichlidogyrus species possessing the same haptoral configuration and host preferences (on subfamily and tribe level, respectively).

Molecular Links between Caloric Restriction and Sir2/SIRT1 Activation

PubMed Central

2014-01-01

Ageing is the most significant risk factor for a range of prevalent diseases, including cancer, cardiovascular disease, and diabetes. Accordingly, interventions are needed for delaying or preventing disorders associated with the ageing process, i.e., promotion of healthy ageing. Calorie restriction is the only nongenetic and the most robust approach to slow the process of ageing in evolutionarily divergent species, ranging from yeasts, worms, and flies to mammals. Although it has been known for more than 80 years that calorie restriction increases lifespan, a mechanistic understanding of this phenomenon remains elusive. Yeast silent information regulator 2 (Sir2), the founding member of the sirtuin family of protein deacetylases, and its mammalian homologue Sir2-like protein 1 (SIRT1), have been suggested to promote survival and longevity of organisms. SIRT1 exerts protective effects against a number of age-associated disorders. Caloric restriction increases both Sir2 and SIRT1 activity. This review focuses on the mechanistic insights between caloric restriction and Sir2/SIRT1 activation. A number of molecular links, including nicotinamide adenine dinucleotide, nicotinamide, biotin, and related metabolites, are suggested to be the most important conduits mediating caloric restriction-induced Sir2/SIRT1 activation and lifespan extension. PMID:25349818

Molecular and morphological data reveal three new cryptic species of Chiasmocleis (Mehely 1904) (Anura, Microhylidae) endemic to the Atlantic Forest, Brazil

PubMed Central

Forlani, Mauricio C.; Cruz, Carlos A.G.; Zaher, Hussam

2017-01-01

Three new cryptic species of Chiasmocleis from the Atlantic Forest of Brazil are described. Two of these species occur in the northeastern states of Sergipe and Bahia, whereas the third species is found in the southeastern state of São Paulo. The new species can be distinguished from other congeneric species by the molecular data, as evidenced in the phylogeny, and by a combination of morphological characters including: size, foot webbing, dermal spines, and coloration patterns. Chiasmocleis species differ in osteological traits, therefore we also provide an osteological description of each new species and comparsions with data reported for other species in the genus. PMID:28243531

Structural characteristics of the molecular species of tetraacylglycerols in lesquerella (Physaria fendleri) oil elucidated by mass spectrometry

USDA-ARS?s Scientific Manuscript database

The structure and ratios of regioisomers of the molecular species of tetraacylglycerols affect their physical properties. They were elucidated by ESI mass spectrometry of the lithium adducts of tetraacylglycerols from the HPLC fractions of lesquerella oil. The contents of acyl and acylacyl chains at...

Active transport improves the precision of linear long distance molecular signalling

NASA Astrophysics Data System (ADS)

Godec, Aljaž; Metzler, Ralf

2016-09-01

Molecular signalling in living cells occurs at low copy numbers and is thereby inherently limited by the noise imposed by thermal diffusion. The precision at which biochemical receptors can count signalling molecules is intimately related to the noise correlation time. In addition to passive thermal diffusion, messenger RNA and vesicle-engulfed signalling molecules can transiently bind to molecular motors and are actively transported across biological cells. Active transport is most beneficial when trafficking occurs over large distances, for instance up to the order of 1 metre in neurons. Here we explain how intermittent active transport allows for faster equilibration upon a change in concentration triggered by biochemical stimuli. Moreover, we show how intermittent active excursions induce qualitative changes in the noise in effectively one-dimensional systems such as dendrites. Thereby they allow for significantly improved signalling precision in the sense of a smaller relative deviation in the concentration read-out by the receptor. On the basis of linear response theory we derive the exact mean field precision limit for counting actively transported molecules. We explain how intermittent active excursions disrupt the recurrence in the molecular motion, thereby facilitating improved signalling accuracy. Our results provide a deeper understanding of how recurrence affects molecular signalling precision in biological cells and novel medical-diagnostic devices.

Active molecular plasmonics: tuning surface plasmon resonances by exploiting molecular dimensions

NASA Astrophysics Data System (ADS)

Chen, Kai; Leong, Eunice Sok Ping; Rukavina, Michael; Nagao, Tadaaki; Liu, Yan Jun; Zheng, Yuebing

2015-06-01

Molecular plasmonics explores and exploits the molecule-plasmon interactions on metal nanostructures to harness light at the nanoscale for nanophotonic spectroscopy and devices. With the functional molecules and polymers that change their structural, electrical, and/or optical properties in response to external stimuli such as electric fields and light, one can dynamically tune the plasmonic properties for enhanced or new applications, leading to a new research area known as active molecular plasmonics (AMP). Recent progress in molecular design, tailored synthesis, and self-assembly has enabled a variety of scenarios of plasmonic tuning for a broad range of AMP applications. Dimension (i.e., zero-, two-, and threedimensional) of the molecules on metal nanostructures has proved to be an effective indicator for defining the specific scenarios. In this review article, we focus on structuring the field of AMP based on the dimension of molecules and discussing the state of the art of AMP. Our perspective on the upcoming challenges and opportunities in the emerging field of AMP is also included.

Use of Molecular Models for Active Learning in Biochemistry Lecture Courses

ERIC Educational Resources Information Center

Hageman, James H.

2010-01-01

The pedagogical value of having biochemistry and organic chemistry students build and manipulate physical models of chemical species is well established in the literature. Nevertheless, for the most part, the use of molecular models is generally limited to several laboratory exercises or to demonstrations in the classroom setting. A simple…

Molecular Survey on Brucellosis in Rodents and Shrews - Natural Reservoirs of Novel Brucella Species in Germany?

PubMed

Hammerl, J A; Ulrich, R G; Imholt, C; Scholz, H C; Jacob, J; Kratzmann, N; Nöckler, K; Al Dahouk, S

2017-04-01

Brucellosis is a widespread zoonotic disease introduced from animal reservoirs to humans. In Germany, bovine and ovine/caprine brucellosis were eradicated more than a decade ago and mandatory measures in livestock have been implemented to keep the officially brucellosis-free status. In contrast, surveillance of wildlife is still challenging, and reliable data on the prevalence of brucellae in small mammal populations do not exist. To assess the epidemiology of Brucella spp. in rodents and shrews, a molecular survey was carried out. A total of 537 rodents and shrews were trapped in four federal states located throughout Germany and investigated for the presence of Brucella. Using a two-step molecular assay based on the detection of the Brucella-specific bcsp31 and IS711 sequences in tissue samples, 14.2% (n = 76) of the tested animals were positive. These originated mainly from western and south-western Germany, where preliminary analyses indicate population density-dependent Brucella prevalence in voles (Myodes glareolus) and mice (Apodemus spp.). recA typing revealed a close relationship to a potentially novel Brucella species recently isolated from red foxes (Vulpes vulpes) in Austria. The molecular detection of brucellae in various rodent taxa and for the first time in shrew species shows that these animals may be naturally infected or at least have a history of exposure to Brucella spp. © 2015 Blackwell Verlag GmbH.

Species diversity and molecular analysis of Staphylococcus in confectioneries of a developing country, Iran.

PubMed

Hoveida, Laleh; Ataei, Behrooz; Amirmozafari, Nour; Noormohammadi, Zahra

2018-06-01

Confectionery is one of the potential sources of contamination and transmission of gastrointestinal infections to humans. Staphylococcus species, and particularly the coagulase-positive ones, have the remarkable capability to produce high amounts of enterotoxin in food. In the present study, the frequency and diversity of Staphylococcus in confectioneries in Iran were assessed by using a combination of conventional and molecular methods. A total of 55 confection samples were collected from 30 confectioneries of Isfahan. They were analyzed for the presence of Staphylococcus using standard protocols for isolation and characterization of the isolates. The conventional tests were used for primary identification and the sequence analysis of 16S rRNA was used for the species identification. A total of 47 out of 55 samples were gram-positive cocci (85.45%). They belonged to 39 Staphylococcus spp., 7 Macrococcus spp., and one Micrococcus spp. The most prevalent 11 various Staphylococcus species were S. aureus 30.8 %, S. warneri 20.5% and S. succinus 17.9. Identification and characterization of Staphylococcus species can be important for epidemiological investigations and assessment of virulence factors such as enterotoxin production and development of specific management practices to prevent staphylococcal food poisoning.

Molecular detection of Lactobacillus species in the neovagina of male-to-female transsexual women

PubMed Central

Petricevic, Ljubomir; Kaufmann, Ulrike; Domig, Konrad J.; Kraler, Manuel; Marschalek, Julian; Kneifel, Wolfgang; Kiss, Herbert

2014-01-01

There is a general opinion that penile skin lined neovagina of transsexual women is not able to support the growth of lactobacilli. This study was undertaken to prove if lactobacilli strains could survive in neovagina and to characterise the most dominant Lactobacillus species. Sixty three male-to-female transsexual women without abnormal vaginal discharge, clinical signs of infection were recruited on an ongoing basis from among transsexual outpatients in an academic research institution and tertiary care centre. Neovaginal smears were taken for molecular Lactobacillus spp. profiling by denaturing gradient gel electrophoresis (PCR–DGGE). Lactobacillus species were detected from 47/63 transsexual women (75%). The 279 Lactobacillus signals detected by PCR-DGGE technique belonged to 13 different species. Lactobacilli of the L. delbrueckii group (L. gasseri, L. crispatus, L. johnsonii, L. iners, L. jensenii) were predominant. More than 90% of women harboured a combination of two or more neovaginal Lactobacillus species. In this study we report the frequent occurrence of lactobacilli from neovagina of transsexual women. Both, frequency and composition were similar to the normal lactic acid bacterial microflora in both women of reproductive age and postmenopausal women. PMID:24434849

Molecular signatures of transgenerational response to ocean acidification in a species of reef fish

NASA Astrophysics Data System (ADS)

Schunter, Celia; Welch, Megan J.; Ryu, Taewoo; Zhang, Huoming; Berumen, Michael L.; Nilsson, Göran E.; Munday, Philip L.; Ravasi, Timothy

2016-11-01

The impact of ocean acidification on marine ecosystems will depend on species capacity to adapt. Recent studies show that the behaviour of reef fishes is impaired at projected CO 2 levels; however, individual variation exists that might promote adaptation. Here, we show a clear signature of parental sensitivity to high CO 2 in the brain molecular phenotype of juvenile spiny damselfish, Acanthochromis polyacanthus, primarily driven by circadian rhythm genes. Offspring of CO 2-tolerant and CO 2-sensitive parents were reared at near-future CO 2 (754 μatm) or present-day control levels (414 μatm). By integrating 33 brain transcriptomes and proteomes with a de novo assembled genome we investigate the molecular responses of the fish brain to increased CO 2 and the expression of parental tolerance to high CO 2 in the offspring molecular phenotype. Exposure to high CO 2 resulted in differential regulation of 173 and 62 genes and 109 and 68 proteins in the tolerant and sensitive groups, respectively. Importantly, the majority of differences between offspring of tolerant and sensitive parents occurred in high CO 2 conditions. This transgenerational molecular signature suggests that individual variation in CO 2 sensitivity could facilitate adaptation of fish populations to ocean acidification.

Molecular phylogeny of the Trechus brucki group, with description of two new species from the Pyreneo-Cantabrian area (France, Spain) (Coleoptera, Carabidae, Trechinae)

PubMed Central

Faille, Arnaud; Bourdeau, Charles; Fresneda, Javier

2012-01-01

Abstract A molecular phylogeny of the species from the Trechus brucki clade (previously Trechus uhagoni group)based on fragments of four mitochondrial genes and one nuclear gene is given. We describe Trechus (Trechus) bouilloni sp. n. from the western pre–Pyrenees: Sierras de Urbasa–Andía, Navarra, Spain. The species was collected in mesovoid shallow substratum (mss), a subterranean environment. Molecular as well as morphological evidences demonstrate that the new species belongs to the Trechus brucki clade. A narrow endemic species of high altitude in western French Pyrenees merged with Trechus brucki Fairmaire, 1862a, Trechus bruckoides sp. n., is described. A lectotype is designated for Trechus brucki and Trechus planiusculus Fairmaire, 1862b (junior synonym of Trechus brucki). The species group is redefined based on molecular and morphological characters, and renamed as the brucki group, as Trechus brucki was the first described species of the clade. A unique synapomorphy of the male genitalia, a characteristic secondary sclerotization of the sperm duct, which is shared by all the species of the brucki group sensu novo, is described and illustrated. The Trechus brucki group sensu novo is composed of Trechus beusti (Schaufuss, 1863), Trechus bouilloni sp. n., Trechus brucki, Trechus bruckoides sp. n., Trechus grenieri Pandellé, 1867, T. uhagoni uhagoni Crotch, 1869, T. uhagoni ruteri Colas, 1935 and Trechus pieltaini Jeannel, 1920. We discuss the taxonomy of the group and provide illustrations of structures showing the differences between the species, along with distribution data and biogeographical comments. PMID:22977341

High-resolution molecular line observations of active galaxies

NASA Astrophysics Data System (ADS)

García-Burillo, S.; Combes, F.; Usero, A.; Graciá-Carpio, J.

2008-10-01

The study of the content, distribution and kinematics of interstellar gas is a key to understand the origin and maintenance of both starburst and nuclear (AGN) activity in galaxies. The processes involved in AGN fueling encompass a wide range of scales, both spatial and temporal, which have to be studied. Probing the gas flow from the outer disk down to the central engine of an AGN host, requires the use of specific tracers of the interstellar medium adapted to follow the change of phase of the gas as a function of radius. Current mm-interferometers can provide a sharp view of the distribution and kinematics of molecular gas in the circumnuclear disks of galaxies through extensive CO line mapping. As such, CO maps are an essential tool to study AGN feeding mechanisms in the local universe. This is the scientific driver of the NUclei of GAlaxies (NUGA) survey, whose latest results are here reviewed. On the other hand, the use of specific molecular tracers of the dense gas phase can probe the feedback influence of activity on the chemistry and energy balance/redistribution in the interstellar medium of nearby galaxies. Millimeter interferometers are able to unveil the strong chemical differentiation present in the molecular gas disks of nearby starbursts and AGNs. Nearby active galaxies can be used as local templates to address the study of more distant galaxies where both star formation and AGN activity are deeply embedded.

Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers

PubMed Central

Steenkeste, Nicolas; Incardona, Sandra; Chy, Sophy; Duval, Linda; Ekala, Marie-Thérèse; Lim, Pharath; Hewitt, Sean; Sochantha, Tho; Socheat, Doung; Rogier, Christophe; Mercereau-Puijalon, Odile; Fandeur, Thierry; Ariey, Frédéric

2009-01-01

Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the molecular methods. Dot18S and

Distribution of Cytokinin-active Ribonucleosides in Wheat Germ tRNA Species 1

PubMed Central

Struxness, Leslie A.; Armstrong, Donald J.; Gillam, Ian; Tener, Gordon M.; Burrows, William J.; Skoog, Folke

1979-01-01

The distribution of cytokinin activity in wheat (Triticum aestivum) germ tRNA fractionated by BD-cellulose and RPC-5 chromatography has been examined. As in other organisms, the cytokinin moieties in wheat germ tRNA appear to be restricted to tRNA species that would be expected to respond to codons beginning with U. Only a few of the wheat germ tRNA species in this coding group actually contain cytokinin modifications. Cytokinin activity was associated with isoaccepting tRNASer species and with a minor tRNALeu species from wheat germ. All other wheat germ tRNA species corresponding to codons beginning with U were devoid of cytokinin activity in the tobacco callus bioassay. PMID:16660688

Molecular phylogenetic and dating analysis of pierid butterfly species using complete mitochondrial genomes.

PubMed

Cao, Y; Hao, J S; Sun, X Y; Zheng, B; Yang, Q

2016-12-02

Pieridae is a butterfly family whose evolutionary history is poorly understood. Due to the difficulties in identifying morphological synapomorphies within the group and the scarcity of the fossil records, only a few studies on higher phylogeny of Pieridae have been reported to date. In this study, we describe the complete mitochondrial genomes of four pierid butterfly species (Aporia martineti, Aporia hippia, Aporia bieti, and Mesapia peloria), in order to better characterize the pierid butterfly mitogenomes and perform the phylogenetic analyses using all available mitogenomic sequence data (13PCGs, rRNAs, and tRNAs) from the 18 pierid butterfly species comprising the three main subfamilies (Dismorphiinae, Coliadinae and Pierinae). Our analysis shows that the four new mitogenomes share similar features with other known pierid mitogenomes in gene order and organization. Phylogenetic analyses by maximum likelihood and Bayesian inference show that the pierid higher-level relationship is: Dismorphiinae + (Coliadinae + Pierinae), which corroborates the results of some previous molecular and morphological studies. However, we found that the Hebomoia and Anthocharis make a sister group, supporting the traditional tribe Anthocharidini; in addition, the Mesapia peloria was shown to be clustered within the Aporia group, suggesting that the genus Mesapia should be reduced to the taxonomic status of subgenus. Our molecular dating analysis indicates that the family Pieridae began to diverge during the Late Cretaceous about 92 million years ago (mya), while the subfamily Pierinae diverged from the Coliadinae at about 86 mya (Late Cretaceous).

Statistical Analysis of the Processes Controlling Choline and Ethanolamine Glycerophospholipid Molecular Species Composition

PubMed Central

Kiebish, Michael A.; Yang, Kui; Han, Xianlin; Gross, Richard W.; Chuang, Jeffrey

2012-01-01

The regulation and maintenance of the cellular lipidome through biosynthetic, remodeling, and catabolic mechanisms are critical for biological homeostasis during development, health and disease. These complex mechanisms control the architectures of lipid molecular species, which have diverse yet highly regulated fatty acid chains at both the sn1 and sn2 positions. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) serve as the predominant biophysical scaffolds in membranes, acting as reservoirs for potent lipid signals and regulating numerous enzymatic processes. Here we report the first rigorous computational dissection of the mechanisms influencing PC and PE molecular architectures from high-throughput shotgun lipidomic data. Using novel statistical approaches, we have analyzed multidimensional mass spectrometry-based shotgun lipidomic data from developmental mouse heart and mature mouse heart, lung, brain, and liver tissues. We show that in PC and PE, sn1 and sn2 positions are largely independent, though for low abundance species regulatory processes may interact with both the sn1 and sn2 chain simultaneously, leading to cooperative effects. Chains with similar biochemical properties appear to be remodeled similarly. We also see that sn2 positions are more regulated than sn1, and that PC exhibits stronger cooperative effects than PE. A key aspect of our work is a novel statistically rigorous approach to determine cooperativity based on a modified Fisher's exact test using Markov Chain Monte Carlo sampling. This computational approach provides a novel tool for developing mechanistic insight into lipidomic regulation. PMID:22662143

Molecular studies of Planetary Nebulae

NASA Astrophysics Data System (ADS)

Zhang, Yong

2017-10-01

Circumstellar envelopes (CEs) around evolved stars are an active site for the production of molecules. After evolving through the Asymptotic Giant Branch (AGB), proto-planetary nebula (PPN), to planetary nebula (PN) phases, CEs ultimately merge with the interstellar medium (ISM). The study of molecules in PNe, therefore, is essential to understanding the transition from stellar to interstellar materials. So far, over 20 molecular species have been discovered in PNe. The molecular composition of PNe is rather different from those of AGB and PPNe, suggesting that the molecules synthesized in PN progenitors have been heavily processed by strong ultraviolet radiation from the central star. Intriguingly, fullerenes and complex organic compounds having aromatic and aliphatic structures can be rapidly formed and largely survive during the PPN/PN evolution. The similar molecular compositions in PNe and diffuse clouds as well as the detection of C60 + in the ISM reinforce the view that the mass-loss from PNe can significantly enrich the ISM with molecular species, some of which may be responsible for the diffuse interstellar bands. In this contribution, I briefly summarize some recent observations of molecules in PNe, with emphasis on their implications on circumstellar chemistry.

16S rRNA partial gene sequencing for the differentiation and molecular subtyping of Listeria species.

PubMed

Hellberg, Rosalee S; Martin, Keely G; Keys, Ashley L; Haney, Christopher J; Shen, Yuelian; Smiley, R Derike

2013-12-01

Use of 16S rRNA partial gene sequencing within the regulatory workflow could greatly reduce the time and labor needed for confirmation and subtyping of Listeria monocytogenes. The goal of this study was to build a 16S rRNA partial gene reference library for Listeria spp. and investigate the potential for 16S rRNA molecular subtyping. A total of 86 isolates of Listeria representing L. innocua, L. seeligeri, L. welshimeri, and L. monocytogenes were obtained for use in building the custom library. Seven non-Listeria species and three additional strains of Listeria were obtained for use in exclusivity and food spiking tests. Isolates were sequenced for the partial 16S rRNA gene using the MicroSeq ID 500 Bacterial Identification Kit (Applied Biosystems). High-quality sequences were obtained for 84 of the custom library isolates and 23 unique 16S sequence types were discovered for use in molecular subtyping. All of the exclusivity strains were negative for Listeria and the three Listeria strains used in food spiking were consistently recovered and correctly identified at the species level. The spiking results also allowed for differentiation beyond the species level, as 87% of replicates for one strain and 100% of replicates for the other two strains consistently matched the same 16S type. Copyright © 2013 Elsevier Ltd. All rights reserved.

Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).

PubMed

Vélez-Zuazo, Ximena; Agnarsson, Ingi

2011-02-01

Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively

Evolutionary history of tall fescue morphotypes inferred from molecular phylogenetics of the Lolium-Festuca species complex

PubMed Central

2010-01-01

the Festuca genus to include representatives of each tall fescue morphotype, and to use low copy nuclear gene-derived sequences to identify putative progenitors of the polyploid species. The demonstration of distinct tall fescue lineages has implications for both taxonomy and molecular breeding strategies, and may facilitate the generation of morphotype and/or sub-genome-specific molecular markers. PMID:20937141

Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae).

PubMed

Alwan, Nisreen; Esmaeili, Hamid-Reza; Krupp, Friedhelm

2016-01-01

Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area's geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103) and the two adjacent divergence regions (D1-D2) of the nuclear 28S rRNA genes (n = 65). Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations.

Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae)

PubMed Central

Alwan, Nisreen; Esmaeili, Hamid-Reza; Krupp, Friedhelm

2016-01-01

Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area’s geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103) and the two adjacent divergence regions (D1-D2) of the nuclear 28S rRNA genes (n = 65). Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations. PMID:27309854

Application of DNA barcoding in biodiversity studies of shallow-water octocorals: molecular proxies agree with morphological estimates of species richness in Palau

NASA Astrophysics Data System (ADS)

McFadden, C. S.; Brown, A. S.; Brayton, C.; Hunt, C. B.; van Ofwegen, L. P.

2014-06-01

The application of DNA barcoding to anthozoan cnidarians has been hindered by their slow rates of mitochondrial gene evolution and the failure to identify alternative molecular markers that distinguish species reliably. Among octocorals, however, multilocus barcodes can distinguish up to 70 % of morphospecies, thereby facilitating the identification of species that are ecologically important but still very poorly known taxonomically. We tested the ability of these imperfect DNA barcodes to estimate species richness in a biodiversity survey of the shallow-water octocoral fauna of Palau using multilocus ( COI, mtMutS, 28S rDNA) sequences obtained from 305 specimens representing 38 genera of octocorals. Numbers and identities of species were estimated independently (1) by a taxonomic expert using morphological criteria and (2) by assigning sequences to molecular operational taxonomic units (MOTUs) using predefined genetic distance thresholds. Estimated numbers of MOTUs ranged from 73 to 128 depending on the barcode and distance threshold applied, bracketing the estimated number of 118 morphospecies. Concordance between morphospecies identifications and MOTUs ranged from 71 to 75 % and differed little among barcodes. For the speciose and ecologically dominant genus Sinularia, however, we were able to identify 95 % of specimens correctly simply by comparing mtMutS sequences and in situ photographs of colonies to an existing vouchered database. Because we lack a clear understanding of species boundaries in most of these taxa, numbers of morphospecies and MOTUs are both estimates of the true species diversity, and we cannot currently determine which is more accurate. Our results suggest, however, that the two methods provide comparable estimates of species richness for shallow-water Indo-Pacific octocorals. Use of molecular barcodes in biodiversity surveys will facilitate comparisons of species richness and composition among localities and over time, data that do not

Molecular Identification and Prevalence of Malassezia Species in Pityriasis Versicolor Patients From Kashan, Iran

PubMed Central

Talaee, Rezvan; Katiraee, Farzad; Ghaderi, Maryam; Erami, Mahzad; Kazemi Alavi, Azam; Nazeri, Mehdi

2014-01-01

Background: Malassezia species are lipophilic yeasts found on the skin surface of humans and other warm-blooded vertebrates. It is associated with various human diseases, especially pityriasis versicolor, which is a chronic superficial skin disorder. Objectives: The aim of the present study was to identify Malassezia species isolated from patients’ samples affected by pityriasis versicolor, using molecular methods in Kashan, Iran. Patients and Methods: A total of 140 subjects, suspected of having pityriasis versicolor from Kashan, were clinically diagnosed and then confirmed by direct microscopic examination. The scraped skin specimens were inoculated in modified Dixon’s medium. DNA was extracted from the colonies and PCR amplification was carried out for the 26s rDNA region. PCR products were used to further restriction fragment length polymorphism by CfoI enzyme. Results: Direct examination was positive in 93.3% of suspected pityriasis versicolor lesions. No statistically significant difference was observed in the frequency of Malassezia species between women and men. The highest prevalence of tinea versicolor was seen in patients 21–30 years-of-age. No difference could be seen in the frequency of Malassezia species depending on the age of the patients. In total, 65% of patients with pityriasis versicolor had hyperhidrosis. The most commonly isolated Malassezia species in the pityriasis versicolor lesions were; Malassezia globosa (66%), M. furfur (26%), M. restricta (3%), M. sympodialis (3%), and M. slooffiae (2%). Malassezia species were mainly isolated from the neck and chest. Conclusions: This study showed M. globosa to be the most common Malassezia species isolated from Malassezia skin disorders in Kashan, Iran. The PCR-RFLP method was useful in the rapid identification of the Malassezia species. By using these methods, the detection and identification of individual Malassezia species from clinical samples was substantially easier. PMID:25485051

First Molecular Characterization of Leishmania Species Causing Visceral Leishmaniasis among Children in Yemen

PubMed Central

Mahdy, Mohammed A. K.; Al-Mekhlafi, Abdulsalam M.; Abdul-Ghani, Rashad; Saif-Ali, Reyadh; Al-Mekhlafi, Hesham M.; Al-Eryani, Samira M.; Lim, Yvonne A. L.; Mahmud, Rohela

2016-01-01

Visceral leishmaniasis (VL) is a debilitating, often fatal disease caused by Leishmania donovani complex; however, it is a neglected tropical disease. L. donovani complex comprises two closely related species, L. donovani that is mostly anthroponotic and L. infantum that is zoonotic. Differentiation between these two species is critical due to the differences in their epidemiology and pathology. However, they cannot be differentiated morphologically, and their speciation using isoenzyme-based methods poses a difficult task and may be unreliable. Molecular characterization is now the most reliable method to differentiate between them and to determine their phylogenetic relationships. The present study aims to characterize Leishmania species isolated from bone marrows of Yemeni pediatric patients using sequence analysis of the ribosomal internal transcribed spacer-1 (ITS1) gene. Out of 41 isolates from Giemsa-stained bone marrow smears, 25 isolates were successfully amplified by nested polymerase chain reaction and sequenced in both directions. Phylogenetic analysis using neighbor joining method placed all study isolates in one cluster with L. donovani complex (99% bootstrap). The analysis of ITS1 for microsatellite repeat numbers identified L. infantum in 11 isolates and L. donovani in 14 isolates. These data suggest the possibility of both anthroponotic and zoonotic transmission of VL-causing Leishmania species in Yemen. Exploring the possible animal reservoir hosts is therefore needed for effective control to be achieved. PMID:26966902

Molecular typing of environmental Cryptococcus neoformans/C. gattii species complex isolates from Manaus, Amazonas, Brazil.

PubMed

Alves, Gleica Soyan Barbosa; Freire, Ana Karla Lima; Bentes, Amaury Dos Santos; Pinheiro, José Felipe de Souza; de Souza, João Vicente Braga; Wanke, Bodo; Matsuura, Takeshi; Jackisch-Matsuura, Ani Beatriz

2016-08-01

Cryptococcus neoformans and Cryptococcus gattii are the main causative agents of cryptococcosis, a systemic fungal disease that affects internal organs and skin, and which is acquired by inhalation of spores or encapsulated yeasts. It is currently known that the C. neoformans/C. gattii species complex has a worldwide distribution, however, some molecular types seem to prevail in certain regions. Few environmental studies of Cryptococcus have been conducted in the Brazilian Amazon. This is the first ecological study of the pathogenic fungi C. neoformans/C. gattii species complex in the urban area of Manaus, Amazonas, Brazil. A total of 506 samples from pigeon droppings (n = 191), captive bird droppings (n = 60) and tree hollows (n = 255) were collected from June 2012 to January 2014 at schools and public buildings, squares, pet shops, households, the zoo and the bus station. Samples were plated on niger seed agar (NSA) medium supplemented with chloramphenicol and incubated at 25°C for 5 days. Dark-brown colonies were isolated and tested for thermotolerance at 37°C, cycloheximide resistance and growth on canavanine-glycine-bromothymol blue agar. Molecular typing was done by PCR-RFLP. Susceptibility to the antifungal drugs amphotericin B, fluconazole, itraconazole and ketoconazole was tested using Etest(®) strips. In total, 13 positive samples were obtained: one tree hollow (C. gattiiVGII), nine pigeon droppings (C. neoformansVNI) and three captive bird droppings (C. neoformansVNI). The environmental cryptococcal isolates found in this study were of the same molecular types as those responsible for infections in Manaus. © 2016 Blackwell Verlag GmbH.

Molecular identification and phylogenetic analysis of human Trichostrongylus species from an endemic area of Iran.

PubMed

Sharifdini, Meysam; Derakhshani, Sedigheh; Alizadeh, Safar Ali; Ghanbarzadeh, Laleh; Mirjalali, Hamed; Mobedi, Iraj; Saraei, Mehrzad

2017-12-01

Human infections with Trichostrongylus species have been reported in most parts of Iran. The aim of this study was the identification, molecular characterization and phylogenetic analysis of human Trichostrongylus species based on ITS2 region of ribosomal DNA from Guilan Province, northern Iran. Stool samples were collected from rural inhabitants and examined by formalin-ether concentration and agar plate culture techniques. After anthelmintic treatment, male adult worms were collected from five infected cases. Genomic DNA was extracted from one male worm of each species in every treated individual and one filariform larva isolated from each case. PCR amplification of ITS2-rDNA region was performed and the products were sequenced. Among 1508 individuals, 46 (3.05%) were found infected with Trichostrongylus species using parasitological methods. Male worms of T. colubriformis, T. vitrinus and T. longispicularis were expelled from five patients after treatment. Out of 41 filariform larvae, 40 were T. colubriformis, and the other one was T. axei. Phylogenetic analysis showed that each species was placed together with reference sequences submitted to GenBank database. Intra-species similarity for all species obtained in the current study was 100%. T. colubriformis was found to be probably the most common species in this region of Iran. For the first time, the authors of the present study report the occurrence of natural human infection by T. longispicularis in the world. Therefore, the number of Trichostrongylus species infecting human in Iran now increased to ten. Copyright © 2017. Published by Elsevier B.V.

Molecular Analysis of the In Situ Growth Rates of Subsurface Geobacter Species

PubMed Central

Giloteaux, Ludovic; Barlett, Melissa; Chavan, Milind A.; Smith, Jessica A.; Williams, Kenneth H.; Wilkins, Michael; Long, Philip; Lovley, Derek R.

2013-01-01

Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole-genome microarray analyses of a subsurface isolate of Geobacter uraniireducens, grown under a variety of conditions, identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, was further evaluated with quantitative reverse transcription-PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r2 = 0.90) with specific growth rates. Therefore, expression patterns of rpsC were used to estimate specific growth rates of Geobacter species during an in situ uranium bioremediation field experiment in which acetate was added to the groundwater to promote dissimilatory metal reduction. Initially, increased availability of acetate in the groundwater resulted in higher expression of Geobacter rpsC, and the increase in the number of Geobacter cells estimated with fluorescent in situ hybridization compared well with specific growth rates estimated from levels of in situ rpsC expression. However, in later phases, cell number increases were substantially lower than predicted from rpsC transcript abundance. This change coincided with a bloom of protozoa and increased attachment of Geobacter species to solid phases. These results suggest that monitoring rpsC expression may better reflect the actual rate that Geobacter species are metabolizing and growing during in situ uranium bioremediation than changes in cell abundance. PMID:23275510

Effect of phospholipids and their molecular species on cholesterol solubility and nucleation in human and model biles.

PubMed Central

Halpern, Z; Moshkowitz, M; Laufer, H; Peled, Y; Gilat, T

1993-01-01

Much research in the pathophysiology of gall stones has been devoted to various molecular species of bile salts. Recent findings have shown the importance of phospholipids in biliary pathophysiology. In the present study the addition of increasing doses of egg lecithin to human and model biles progressively prolonged the nucleation time. Concurrently biliary cholesterol was shifted from the vesicular to the non-vesicular carrier(s) while the cholesterol/phospholipid ratio of the remaining vesicles was progressively lowered. Model bile solutions of identical lipid concentration were prepared using phosphatidylcholine, phosphatidylserine, and phosphatidylethanolamine as the only phospholipid. With phosphatidylethanolamine most of the cholesterol was shifted to the vesicular carrier while phosphatidylserine shifted most of the cholesterol to the non-vesicular carrier(s). With phosphatidylcholine the cholesterol was distributed in both carriers. Phosphatidyl choline species composed of various acyl fatty acids in the sn-1 and sn-2 positions were used as the sole phospholipid in otherwise identical model bile solutions. With palmitic acid in the sn-1 position and arachidonic acid in the sn-2 position most of the cholesterol was found in the non-vesicular carrier. When stearic acid was used in sn-2 position instead of arachidonic acid most of the cholesterol was found in the vesicular carrier. These and other variations in phospholipid molecular species shifted cholesterol among its carriers and also modified the nucleation time of model biles. Most of these effects were also found upon addition of the various phospholipid species to human biles. These findings show the importance of phospholipid species in biliary pathophysiology and may be useful when trying to manipulate cholesterol carriers and solubility in bile. PMID:8432440

Antioxidant, Antimicrobial and Antiproliferative Activities of Five Lichen Species

PubMed Central

Mitrović, Tatjana; Stamenković, Slaviša; Cvetković, Vladimir; Tošić, Svetlana; Stanković, Milan; Radojević, Ivana; Stefanović, Olgica; Čomić, Ljiljana; Đačić, Dragana; Ćurčić, Milena; Marković, Snežana

2011-01-01

The antioxidative, antimicrobial and antiproliferative potentials of the methanol extracts of the lichen species Parmelia sulcata, Flavoparmelia caperata, Evernia prunastri, Hypogymnia physodes and Cladonia foliacea were evaluated. The total phenolic content of the tested extracts varied from 78.12 to 141.59 mg of gallic acid equivalent (GA)/g of extract and the total flavonoid content from 20.14 to 44.43 mg of rutin equivalent (Ru)/g of extract. The antioxidant capacities of the lichen extracts were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals scavenging. Hypogymnia physodes with the highest phenolic content showed the strongest DPPH radical scavenging effect. Further, the antimicrobial potential of the lichen extracts was determined by a microdilution method on 29 microorganisms, including 15 strains of bacteria, 10 species of filamentous fungi and 4 yeast species. A high antimicrobial activity of all the tested extracts was observed with more potent inhibitory effects on the growth of Gram (+) bacteria. The highest antimicrobial activity among lichens was demonstrated by Hypogymnia physodes and Cladonia foliacea. Finally, the antiproliferative activity of the lichen extracts was explored on the colon cancer adenocarcinoma cell line HCT-116 by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) viability assay and acridine orange/ethidium bromide staining. The methanol extracts of Hypogymnia physodes and Cladonia foliacea showed a better cytotoxic activity than the other extracts. All lichen species showed the ability to induce apoptosis of HCT-116 cells. PMID:21954369

Chemical Probes for Molecular Imaging and Detection of Hydrogen Sulfide and Reactive Sulfur Species in Biological Systems

PubMed Central

2014-01-01

Hydrogen sulfide (H2S), a gaseous species produced by both bacteria and higher eukaryotic organisms, including mammalian vertebrates, has attracted attention in recent years for its contributions to human health and disease. H2S has been proposed as a cytoprotectant and gasotransmitter in many tissue types, including mediating vascular tone in blood vessels as well as neuromodulation in the brain. The molecular mechanisms dictating how H2S affects cellular signaling and other physiological events remain insufficiently understood. Furthermore, the involvement of H2S in metal-binding interactions and formation of related RSS such as sulfane sulfur may contribute to other distinct signaling pathways. Owing to its widespread biological roles and unique chemical properties, H2S is an appealing target for chemical biology approaches to elucidate its production, trafficking, and downstream function. In this context, reaction-based fluorescent probes offer a versatile set of screening tools to visualize H2S pools in living systems. Three main strategies used in molecular probe development for H2S detection include azide and nitro group reduction, nucleophilic attack, and CuS precipitation. Each of these approaches exploit the strong nucleophilicity and reducing potency of H2S to achieve selectivity over other biothiols. In addition, a variety of methods have been developed for the detection of other reactive sulfur species (RSS), including sulfite and bisulfite, as well as sulfane sulfur species and related modifications such as S-nitrosothiols. Access to this growing chemical toolbox of new molecular probes for H2S and related RSS sets the stage for applying these developing technologies to probe reactive sulfur biology in living systems. PMID:25474627

A new species of Andean toad (Bufonidae, Osornophryne) discovered using molecular and morphological data, with a taxonomic key for the genus

PubMed Central

Páez-Moscoso, Diego J.; Guayasamin, Juan M.; Yánez-Muñoz, Mario

2011-01-01

Abstract Combining a molecular phylogeny and morphological data, we discovered a new species of Osornophryne from the Amazonian slope of the Ecuadorian Andes. Morphologically, the new taxon is distinguished from all others species in Osornophryne by having the Toes IV and V longer than Toes I–III, a short and rounded snout with a small rostral papilla, and conical pustules on flanks. The new species previously was confused with Osornophryne guacamayo. A taxonomic key is provided for all known species of Osornophryne. PMID:21852930

A marine algicidal Thalassospira and its active substance against the harmful algal bloom species Karenia mikimotoi.

PubMed

Lu, Xiuhua; Zhou, Bin; Xu, Lili; Liu, Lin; Wang, Gangyuan; Liu, Xiaodong; Tang, Xuexi

2016-06-01

The aim of the present study was to obtain a marine bacterium active against Karenia mikimotoi from the East China Sea and to characterize its extracellular algicidal substances. Using preparative high-performance liquid chromatography (prep-HPLC) and electrospray ionization/quadrupole-time of flight mass spectrometer coupled with a high-performance liquid chromatography (LC/MS-Q-TOF) system, we purified the alga-lysing substance produced by strain ZR-2 and determined its molecular structure. Based on morphology and l6S ribosomal DNA (rDNA) sequence analysis, the ZR-2 strain was highly homologous to Thalassospira species. Algicidal activity against K. mikimotoi was detected in the cell-free filtrate but not in bacterial cells. The alga-lysing substance produced by ZR-2 was ethanol-soluble and thermostable, with a retention time of 6.3 min and a measured elemental composition of C7H5O2 ([M-H](-) ion at m/z 121.0295). The alga-lysing substance produced by ZR-2 was determined to be benzoic acid. Compared with the negative control, both purified ZR-2 bacteria-free filtrate and standard benzoic acid promoted K. mikimotoi cell disruption and induced K. mikimotoi cell content leakage. Our study is the first to report benzoic acid activity against K. mikimotoi as well as production of benzoic acid by a Thalassospira species.

Morphological and molecular data confirm the transfer of homostylous species in the typically distylous genus Galianthe (Rubiaceae), and the description of the new species Galianthe vasquezii from Peru and Colombia.

PubMed

Florentín, Javier Elias; Cabaña Fader, Andrea Alejandra; Salas, Roberto Manuel; Janssens, Steven; Dessein, Steven; Cabral, Elsa Leonor

2017-01-01

Galianthe (Rubiaceae) is a neotropical genus comprising 50 species divided into two subgenera, Galianthe subgen. Galianthe, with 39 species and Galianthe subgen. Ebelia , with 11 species. The diagnostic features of the genus are: usually erect habit with xylopodium, distylous flowers arranged in lax thyrsoid inflorescences, bifid stigmas, 2-carpellate and longitudinally dehiscent fruits, with dehiscent valves or indehiscent mericarps, plump seeds or complanate with a wing-like strophiole, and pollen with double reticulum, rarely with a simple reticulum. This study focused on two species that were originally described under Diodia due to the occurrence of fruits indehiscent mericarps: Diodia palustris and D. spicata . In the present study, classical taxonomy is combined with molecular analyses. As a result, we propose that both Diodia species belong to Galianthe subgen. Ebelia . The molecular position within Galianthe , based on ITS and ETS sequences, has been supported by the following morphological characters: thyrsoid, spiciform or cymoidal inflorescences, bifid stigmas, pollen grains with a double reticulum, and indehiscent mericarps. However, both species, unlike the remainder of the genus Galianthe , have homostylous flowers, so the presence of this type of flower significantly modifies the generic concept. In this framework, a third homostylous species, Galianthe vasquezii , from the Andean region is also described. Until now, this species remained cryptic under specimens of Galianthe palustris It differs however from the latter by having longer calyx lobes, the presence of dispersed trichomes inside the corolla lobes (vs. glabrous), fruits that are acropetally dehiscent (vs. basipetally dehiscent), and its Andean geographical distribution (vs. Paranaense). Additionally, a lectotype has been chosen for Diodia palustris , Borreria pterophora has been placed under synonymy of Galianthe palustris , and Galianthe boliviana is reported for the first time from Peru

Degradation of Lignin by Cyathus Species

PubMed Central

Abbott, Thomas P.; Wicklow, Donald T.

1984-01-01

The ability of 12 Cyathus species to degrade 14C-labeled lignin in kenaf was studied. The sum of 14C released into solution plus 14C released into the gas phase over a 32-day fermentation period was used to determine average daily rates of lignin biodegradation. Cyathus pallidus. C. africanus, and C. berkeleyanus delignified kenaf most rapidly. C. canna showed the greatest preference for lignin degradation over other plant components, and its rate of lignin degradation was only slightly lower than the three most active species. The apparent ability of fungi to metabolize low-molecular-weight lignin breakdown products correlated well with their overall delignification rates. C. stercoreus metabolized degradation products of lignin from wheat straw better than those from kenaf lignin, based on the amount of low-molecular-weight products left in solution. PMID:16346497

Molecular characterization and physical localization of highly repetitive DNA sequences from Brazilian Alstroemeria species.

PubMed

Kuipers, A G J; Kamstra, S A; de Jeu, M J; Visser, R G F

2002-01-01

Highly repetitive DNA sequences were isolated from genomic DNA libraries of Alstroemeria psittacina and A. inodora. Among the repetitive sequences that were isolated, tandem repeats as well as dispersed repeats could be discerned. The tandem repeats belonged to a family of interlinked Sau3A subfragments with sizes varying from 68-127 bp, and constituted a larger HinfI repeat of approximately 400 bp. Southern hybridization showed a similar molecular organization of the tandem repeats in each of the Brazilian Alstroemeria species tested. None of the repeats hybridized with DNA from Chilean Alstroemeria species, which indicates that they are specific for the Brazilian species. In-situ localization studies revealed the tandem repeats to be localized in clusters on the chromosomes of A. inodora and A. psittacina: distal hybridization sites were found on chromosome arms 2PS, 6PL, 7PS, 7PL and 8PL, interstitial sites on chromosome arms 2PL, 3PL, 4PL and 5PL. The applicability of the tandem repeats for cytogenetic analysis of interspecific hybrids and their role in heterochromatin organization are discussed.

Phylogenetic survey of soluble saxitoxin-binding activity in pursuit of the function and molecular evolution of saxiphilin, a relative of transferrin.

PubMed Central

Llewellyn, L E; Bell, P M; Moczydlowski, E G

1997-01-01

Saxiphilin is a soluble protein of unknown function which binds the neurotoxin, saxitoxin (STX), with high affinity. Molecular characterization of saxiphilin from the North American bullfrog, Rana catesbeiana, has previously shown that it is a member of the transferrin family. In this study we surveyed various animal species to investigate the phylogenetic distribution of saxiphilin, as detected by the presence of soluble [3H]STX binding activity in plasma, haemolymph or tissue extracts. We found that saxiphilin activity is readily detectable in a wide variety of arthropods, fish, amphibians, and reptiles. The pharmacological characteristics of [3H]STX binding activity in phylogenetically diverse species indicates that a protein homologous to bullfrog saxiphilin is likely to be constitutively expressed in many ectothermic animals. The results suggest that the saxiphilin gene is evolutionarily as old as an ancestral gene encoding bilobed transferrin, an Fe(2+)-binding and transport protein which has been identified in several arthropods and all the vertebrates which have been studied. PMID:9225480

Phytochemical profiling of five medicinally active constituents across 14 Eutrema species.

PubMed

Hao, Guoqian; Wang, Qian; Liu, Bingbing; Liu, Jianquan

2016-04-01

Wasabi or Japanese horseradish (Eutrema japonicum) is both a traditional condiment and a medicinally important plant with diverse uses. Its medicinally active constituents appear to include five isothiocyanates, but their spatial variations in naturally occurring congeners are unknown. Thus, in this study we measured concentrations of these five active constituents in 20 populations of 14 species of Eutrema and one related species, Yinshania sinuata. Three to five of these constituents were detected in each of the examined species, at concentrations that varied greatly between sampled species and populations of the same species. However, two species, Eutrema tenue and Eutrema deltoideum, had higher total concentrations of the five isothiocyanates and substantially higher concentrations of one or two, than the widely cultivated E. japonicum. Thus, both of these species could be important wild resources for artificial cultivation, in addition to the currently widely cultivated E. japonicum. Copyright © 2016 Elsevier B.V. All rights reserved.

[Incomplete congruence between morphobiological characters and sex-specific molecular markers in Pacific salmons: 1. Analysis of discrepancy in five species of the genus Oncorhynchus].

PubMed

Brykov, Vl A; Kukhlevskiĭ, A D; Podlesnykh, A V

2010-07-01

The congruence between molecular markers, identifying the presence of the Y chromosome, and secondary sexual characters was examined in Asian populations of five Pacific salmon species: pink salmon (Oncorhynchus gorbuscha), chum salmon (O. keta), sockeye salmon (O. nerka), chinook salmon (O. tschawytsha), and sima (O. masou). It was demonstrated that in all species examined, the presence or absence of sex-specific molecular markers was to a considerable degree congruent with secondary sexual characters, but in some cases, an incongruence was found. These findings suggested that the mechanism underlying this phenomenon was similar or identical in all species examined. Possible genetic and physiological explanations of this phenomenon are discussed.

Species and hybrid identification of sturgeon caviar: a new molecular approach to detect illegal trade.

PubMed

Boscari, E; Barmintseva, A; Pujolar, J M; Doukakis, P; Mugue, N; Congiu, L

2014-05-01

Overexploitation of wild populations due to the high economic value of caviar has driven sturgeons to near extinction. The high prices commanded by caviar on world markets have made it a magnet for illegal and fraudulent caviar trade, often involving low-value farmed caviar being sold as top-quality caviar. We present a new molecular approach for the identification of pure sturgeon species and hybrids that are among the most commercialized species in Europe and North America. Our test is based on the discovery of species-specific single nucleotide polymorphisms (SNPs) in the ribosomal protein S7, supplemented with the Vimentin gene and the mitochondrial D-loop. Test validations performed in 702 specimens of target and nontarget sturgeon species demonstrated a 100% identification success for Acipenser naccarii, A. fulvescens, A. stellatus, A. sinensis and A. transmontanus. In addition to species identification, our approach allows the identification of Bester and AL hybrids, two of the most economically important hybrids in the world, with 80% and 100% success, respectively. Moreover, the approach has the potential to identify many other existing sturgeon hybrids. The development of a standardized sturgeon identification tool will directly benefit trade law enforcement, providing the tools to monitor and regulate the legal trade of caviar and protect sturgeon stocks from illicit producers and traders, hence contributing to safeguarding this group of heavily threatened species. © 2013 John Wiley & Sons Ltd.

Enzyme activities in plasma, kidney, liver, and muscle of five avian species

USGS Publications Warehouse

Franson, J.C.; Murray, H.C.; Bunck, C.

1985-01-01

Activities of alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), creatine phosphokinase (CPK), and lactate dehydrogenase (LDH) were determined in plasma, kidney, liver, and muscle from five species of captive birds. Few differences occurred in plasma activities between sexes but considerable differences occurred between species. All five enzymes were detected in each of the tissues sampled. Relative enzyme activities in liver, kidney, and muscle were similar for each species. CPK activity was much higher in muscle than in liver or kidney and, of the five enzymes studied, may be the best indicator of muscle damage. Most of the other enzymes were more evenly distributed among the three tissues, and no organ-specific enzyme could be identified for liver or kidney. Because of interspecific variations in plasma enzyme activities, it is important to establish baseline values for each species to ensure accurate interpretation of results.

Molecular cytogenetic characterisation and phylogenetic analysis of the seven cultivated Vigna species (Fabaceae).

PubMed

She, C-W; Jiang, X-H; Ou, L-J; Liu, J; Long, K-L; Zhang, L-H; Duan, W-T; Zhao, W; Hu, J-C

2015-01-01

The genomic organisation of the seven cultivated Vigna species, V. unguiculata, V. subterranea, V. angularis, V. umbellata, V. radiata, V. mungo and V. aconitifolia, was determined using sequential combined PI and DAPI (CPD) staining and dual-colour fluorescence in situ hybridisation (FISH) with 5S and 45S rDNA probes. For phylogenetic analyses, comparative genomic in situ hybridisation (cGISH) onto somatic chromosomes and sequence analysis of the internal transcribed spacer (ITS) of 45S rDNA were used. Quantitative karyotypes were established using chromosome measurements, fluorochrome bands and rDNA FISH signals. All species had symmetrical karyotypes composed of only metacentric or metacentric and submetacentric chromosomes. Distinct heterochromatin differentiation was revealed by CPD staining and DAPI counterstaining after FISH. The rDNA sites among all species differed in their number, location and size. cGISH of V. umbellata genomic DNA to the chromosomes of all species produced strong signals in all centromeric regions of V. umbellata and V. angularis, weak signals in all pericentromeric regions of V. aconitifolia, and CPD-banded proximal regions of V. mungo var. mungo. Molecular phylogenetic trees showed that V. angularis and V. umbellata were the closest relatives, and V. mungo and V. aconitifolia were relatively closely related; these species formed a group that was separated from another group comprising V. radiata, V. unguiculata ssp. sesquipedalis and V. subterranea. This result was consistent with the phylogenetic relationships inferred from the heterochromatin and cGISH patterns; thus, fluorochrome banding and cGISH are efficient tools for the phylogenetic analysis of Vigna species. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Molecular characterization of Babesia species in wild animals and their ticks in Turkey.

PubMed

Orkun, Ömer; Karaer, Zafer

2017-11-01

To date, no study has investigated Babesia ecology in wild boars, hares or foxes in Turkey. This study aimed to determine and characterize Babesia spp. in wild animals and their ticks. We identified a novel Babesia genotype and four known Babesia species in wild animals and their ticks. We detected Babesia spp. molecularly in hares for the first time. In addition, we identified B. vulpes in foxes for the first time in Turkey. The presence of B. rossi, B. crassa and B. occultans was also revealed in ticks collected from wild boars and hares. This is only the second report of B. rossi in ticks outside of Africa and suggests that B. rossi is circulating in ticks in Turkey. Therefore B. rossi poses a significant threat to domestic dogs. Here we demonstrate the role of wild animals in the life cycle of Babesia species in Turkey and contribute to Babesia ecological and taxonomic information. Copyright © 2017 Elsevier B.V. All rights reserved.

Diversity and enzyme activity of Penicillium species associated with macroalgae in Jeju Island.

PubMed

Park, Myung Soo; Lee, Seobihn; Oh, Seung-Yoon; Cho, Ga Youn; Lim, Young Woon

2016-10-01

A total of 28 strains of 19 Penicillium species were isolated in a survey of extracellular enzyme-producing fungi from macroalgae along the coast of Jeju Island of Korea. Penicillium species were identified based on morphological and β-tubulin sequence analyses. In addition, the halo-tolerance and enzyme activity of all strains were evaluated. The diversity of Penicillium strains isolated from brown algae was higher than the diversity of strains isolated from green and red algae. The commonly isolated species were Penicillium antarcticum, P. bialowiezense, P. brevicompactum, P. crustosum, P. oxalicum, P. rubens, P. sumatrense, and P. terrigenum. While many strains showed endoglucanase, β-glucosidase, and protease activity, no alginase activity was detected. There was a positive correlation between halo-tolerance and endoglucanase activity within Penicillium species. Among 19 Penicillium species, three species-P. kongii, P. olsonii, and P. viticola-have not been previously recorded in Korea.

Quantitation of phosphatidic acid and lysophosphatidic acid molecular species using hydrophilic interaction liquid chromatography coupled to electrospray ionization high resolution mass spectrometry.

PubMed

Triebl, Alexander; Trötzmüller, Martin; Eberl, Anita; Hanel, Pia; Hartler, Jürgen; Köfeler, Harald C

2014-06-20

A method for a highly selective and sensitive identification and quantitation of lysophosphatidic acid (LPA) and phosphatidic acid (PA) molecular species was developed using hydrophilic interaction liquid chromatography (HILIC) followed by negative-ion electrospray ionization high resolution mass spectrometry. Different extraction methods for the polar LPA and PA species were compared and a modified Bligh & Dyer extraction by addition of 0.1M hydrochloric acid resulted in a ≈1.2-fold increase of recovery for the 7 PA and a more than 15-fold increase for the 6 LPA molecular species of a commercially available natural mix compared to conventional Bligh & Dyer extraction. This modified Bligh & Dyer extraction did not show any artifacts resulting from hydrolysis of natural abundant phospholipids. The developed HILIC method is able to separate all PA and LPA species from major polar membrane lipid classes which might have suppressive effects on the minor abundant lipid classes of interest. The elemental compositions of intact lipid species are provided by the high mass resolution of 100,000 and high mass accuracy below 3ppm of the Orbitrap instrument. Additionally, tandem mass spectra were generated in a parallel data dependent acquisition mode in the linear ion trap to provide structural information at molecular level. Limits of quantitation were identified at 45fmol on column and the dynamic range reaches 20pmol on column, covering the range of natural abundance well. By applying the developed method to mouse brain it can be shown that phosphatidic acid contains less unsaturated fatty acids with PA 34:1 and PA 36:1 as the major species. In contrast, for LPA species a high content of polyunsaturated fatty acids (LPA 20:4 and LPA 22:6) was quantified. Copyright © 2014 Elsevier B.V. All rights reserved.

Neuroprotective Effects of Reactive Oxygen Species Mediated by BDNF-Independent Activation of TrkB

PubMed Central

Huang, Yang Zhong; McNamara, James O.

2012-01-01

Reactive oxygen species (ROS) have diverse biological consequences in the mammalian CNS, but the molecular targets mediating these pleiotropic effects are incompletely understood. Like ROS, the neurotrophin receptor, TrkB receptor tyrosine kinase, has diverse effects in the developing and mature mammalian brain. Our discovery that zinc can transactivate TrkB, together with the finding that ROS can trigger zinc release from cytosolic zinc binding proteins, led us to hypothesize that ROS can transactivate TrkB in CNS neurons by a zinc-dependent mechanism. We found that both exogenous H2O2 and endogenous ROS activate TrkB signaling by a Src family kinase-dependent but brain-derived neurotrophic factor-independent mechanism in cultured rat cortical neurons. Exogenous H2O2 enhances cytosolic zinc content in a metallothionein-3 (MT-3)-requiring manner. Both exogenous H2O2 and endogenous ROS mediated transactivation of TrkB requires intracellular zinc and MT-3. The ROS-triggered transactivation of TrkB exerts neuroprotective effects, because inhibition of TrkB kinase activity or uncoupling Shc signaling from TrkB exacerbates neuronal cell death induced by H2O2. Thus, we propose a molecular signaling event whereby ROS induce release of zinc from cytosolic MT-3, the increased cytosolic zinc transactivates TrkB, and the enhanced Shc signaling downstream from TrkB promotes prosurvival effects. We suggest that such neuroprotective effects mediated by ROS are operative in diverse acute and chronic neurological disorders. PMID:23115189

Molecular Evidence of Different Rickettsia Species in Villeta, Colombia.

PubMed

Faccini-Martínez, Álvaro A; Ramírez-Hernández, Alejandro; Forero-Becerra, Elkin; Cortés-Vecino, Jesús A; Escandón, Patricia; Rodas, Juan D; Palomar, Ana M; Portillo, Aránzazu; Oteo, José A; Hidalgo, Marylin

2016-02-01

The aim of this work was to detect and identify Rickettsia species in ticks collected in rural areas of Villeta, Colombia. Tick specimens were collected from domestic animals and walls of houses in five rural villages of Villeta town and from humans in Naranjal village (same town). Moreover, a flea collected from the same area was also processed. DNA was extracted and tested by conventional, semi-nested, and nested PCR reactions targeting rickettsial genes. In the ticks collected from humans from Naranjal village, a nymph of Amblyomma cajennense sensu lato was amplified using primers for ompA and sequenced (100% identity with "Candidatus Rickettsia amblyommii"). Last, three amplicons from the Ctenocephalides felis flea, corresponding to gltA, ompB, and 16S rRNA genes, showed high identity with R. felis (98.5%, 97.3%, and 99.2%, respectively) and "Candidatus Rickettsia asemboensis" (99.7% and 100%, respectively). To our knowledge, these results correspond to the first molecular detection in Colombia of "Candidatus Rickettsia amblyommii" and "Ca. Rickettsia asemboensis" in fleas.

Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers.

PubMed

Coutinho, João Paulo; Carvalho, Ana; Martín, Antonio; Lima-Brito, José

2018-04-01

Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.

Relationships of the Woody Medicago Species (Section Dendrotelis) Assessed by Molecular Cytogenetic Analyses

PubMed Central

Rosato, Marcela; Castro, Mercedes; Rosselló, Josep A.

2008-01-01

Background and Aims The organization of rDNA genes in the woody medic species from the agronomically important Medicago section Dendrotelis was analysed to gain insight into their taxonomic relationships, to assess the levels of infraspecific variation concerning ribosomal loci in a restricted and fragmented insular species (M. citrina) and to assess the nature of its polyploidy. Methods Fluorescence in situ hybridization (FISH) was used for physical mapping of 5S and 45S ribosomal DNA genes in the three species of section Dendrotelis (M. arborea, M. citrina, M. strasseri) and the related M. marina from section Medicago. Genomic in situ hybridization (GISH) was used to assess the genomic relationships of the polyploid M. citrina with the putatively related species from section Dendrotelis. Key Results The diploid (2n = 16) M. marina has a single 45S and two 5S rDNA loci, a pattern usually detected in previous studies of Medicago diploid species. However, polyploid species from section Dendrotelis depart from expectations. The tetraploid species (2n = 32) M. arborea and M. strasseri have one 45S rDNA locus and two 5S rDNA loci, whereas in the hexaploid (2n = 48) M. citrina four 45S rDNA and five 5S rDNA loci have been detected. No single chromosome of M. citrina was uniformly labelled after using genomic probes from M. arborea and M. strasseri. Instead, cross-hybridization signals in M. citrina were restricted to terminal chromosome arms and NOR regions. Conclusions FISH results support the close taxonomic interrelationship between M. arborea and M. strasseri. In these tetraploid species, NOR loci have experienced a diploidization event through physical loss of sequences, a cytogenetic feature so far not reported in other species of the genus. The high number of rDNA loci and GISH results support the specific status for the hexaploid M. citrina, and it is suggested that this species is not an autopolyploid derivative of M. arborea or M. strasseri. Further, molecular

Defining the molecular structure of teixobactin analogues and understanding their role in antibacterial activities.

PubMed

Parmar, Anish; Prior, Stephen H; Iyer, Abhishek; Vincent, Charlotte S; Van Lysebetten, Dorien; Breukink, Eefjan; Madder, Annemieke; Taylor, Edward J; Singh, Ishwar

2017-02-07

The discovery of the highly potent antibiotic teixobactin, which kills the bacteria without any detectable resistance, has stimulated interest in its structure-activity relationship. However, a molecular structure-activity relationship has not been established so far for teixobactin. Moreover, the importance of the individual amino acids in terms of their l/d configuration and their contribution to the molecular structure and biological activity are still unknown. For the first time, we have defined the molecular structure of seven teixobactin analogues through the variation of the d/l configuration of its key residues, namely N-Me-d-Phe, d-Gln, d-allo-Ile and d-Thr. Furthermore, we have established the role of the individual d amino acids and correlated this with the molecular structure and biological activity. Through extensive NMR and structural calculations, including molecular dynamics simulations, we have revealed the residues for maintaining a reasonably unstructured teixobactin which is imperative for biological activity.

Prevalence and molecular characterization of Cryptosporidium species in cattle and buffalo calves in Mumbai region of India.

PubMed

Hingole, A C; Gudewar, J G; Pednekar, R P; Gatne, M L

2017-03-01

Faecal samples of cattle and buffaloes of Mumbai region collected between November 2012 to June 2013 were analysed by conventional and molecular tools to note the prevalence of cryptosporidiosis and species involved in the infection. Conventional analysis viz., direct faecal smear examination, faecal smear examination after normal saline sedimentation, Sheather's floatation and Sheather's floatation sedimentation smear methods demonstrated oocysts of Cryptosporidium in 141 (36.06 %) of 391 samples with higher occurrence in buffaloes (36.99 %) than cattle (34.48 %). Diarrhoeic loose faeces showed higher prevalence (42.07 %) than apparently normal faeces (31.72 %) irrespective of the host species. When data were arranged as per age groups viz., calves of 0-1 month, 1-2 months, 2-3 months and adults, the highest prevalence was noted in the youngest group (47.12 %) declining gradually with the advancing age with lowest (6.25 %) in adults indicating inverse correlation between prevalence rate and age of the host. These differences were statistically significant in case of buffaloes. Cryptosporidium andersoni was tentatively identified by morphometric analysis. By employing molecular tools like nested PCR, PCR-RFLP and sequence analysis of few samples showed good correlation in the identification of species of Cryptosporidium involved in the infection and demonstrated occurrence of C. parvum , C. ryanae and C. bovis. Thus all the four commonly occurring bovine species of Cryptosporidium were encountered in the study area which appears to be a first record reporting the occurrence of Cryptosporidium with species level identification in large ruminants from Western region of India. Additionally, the public health significance of C. parvum was also discussed in light of epidemiological factors pertaining to the region.

Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lu-Cun; Friend, C. M.; Fushimi, Rebecca

The activation of molecular O 2as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O 2activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O 2dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O 2dissociationmore » is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O 2dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction.« less

Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lu-Cun; Friend, C. M.; Fushimi, Rebecca

2016-01-01

The activation of molecular O 2as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O 2activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O 2dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O 2dissociationmore » is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O 2dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction.« less

Experimental Investigation of Molecular Species Formation in Metal Plasmas During Laser Ablation

NASA Astrophysics Data System (ADS)

Radousky, H.; Crowhurst, J.; Rose, T.; Armstrong, M.; Stavrou, E.; Zaug, J.; Weisz, D.; Azer, M.; Finko, M.; Curreli, D.

2016-10-01

Atomic and molecular spectra on metal plasmas generated by laser ablation have been measured using single, nominally 6-7 ns pulses at 1064 nm, and with energies less than 50 mJ. The primary goal for these studies is to constrain the physical and chemical mechanisms that control the distribution of radionuclides in fallout after a nuclear detonation. In this work, laser emission spectroscopy was used to obtain in situdata for vapor phase molecular species as they form in a controlled oxygen atmosphere for a variety of metals such as Fe, Al, as well as preliminary results for U. In particular, the ablation plumes created from these metals have been imaged with a resolution of 10 ns, and it is possible to observe the expansion of the plume out to 0.5 us. These data serve as one set of inputs for a semi-empirical model to describe the chemical fractionation of uranium during fallout formation. Prepared by LLNL under Contract DE-AC52-07NA27344. This project was sponsored by the Department of the Defense, Defense Threat Reduction Agency, under Grant Number HDTRA1-16-1-0020.

Ratios of regioisomers of the molecular species of triacylglycerols in lesquerella (Physaria fendleri) oil estimated by mass spectrometry

USDA-ARS?s Scientific Manuscript database

The ratios of regioisomers of 74 molecular species of triacylglycerols (TAG) in lesquerella oil were estimated using HPLC and the electrospray ionization mass spectrometry of the lithium adducts of TAG in the HPLC fractions of lequerella oil. The ratios of relative abundances of the fragment ions fr...

Coarse-grained molecular dynamics simulation of activated penetrant transport in glassy polymers.

PubMed

Zhang, Kai; Meng, Dong; Müller-Plathe, Florian; Kumar, Sanat K

2018-01-17

Membrane separations of gas mixtures strive to maximize the permeability of a desired species while keeping out undesired ones. Permeability vs. selectivity data from many polymer membranes for a given gas pair with diameters d A and d B are typically collected in a "Robeson plot"', and are bound from above by a line with a slope λ = (d B /d A ) 2 - 1. A microscopic understanding of this relationship, especially λ, is still missing. We perform molecular dynamics simulations of penetrant diffusion using three different coarse-grained polymer models over a wide range of penetrant sizes, temperatures, and monomer densities. The empirically relevant λ = (d B /d A ) 2 - 1 is only found for polymers that are either supercooled liquids with caged segmental dynamics or glasses and when the penetrant size is approximately half the Kuhn length of the chains, for which the penetrant diffusion is an activated process.

Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

PubMed

Brabec, Jan; Kostadinova, Aneta; Scholz, Tomáš; Littlewood, D Timothy J

2015-06-19

The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology. Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared. We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida. Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and

Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species

PubMed Central

Buyyarapu, Ramesh; Kantety, Ramesh V.; Yu, John Z.; Saha, Sukumar; Sharma, Govind C.

2011-01-01

New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum   EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

Exponential growth for self-reproduction in a catalytic reaction network: relevance of a minority molecular species and crowdedness

NASA Astrophysics Data System (ADS)

Kamimura, Atsushi; Kaneko, Kunihiko

2018-03-01

Explanation of exponential growth in self-reproduction is an important step toward elucidation of the origins of life because optimization of the growth potential across rounds of selection is necessary for Darwinian evolution. To produce another copy with approximately the same composition, the exponential growth rates for all components have to be equal. How such balanced growth is achieved, however, is not a trivial question, because this kind of growth requires orchestrated replication of the components in stochastic and nonlinear catalytic reactions. By considering a mutually catalyzing reaction in two- and three-dimensional lattices, as represented by a cellular automaton model, we show that self-reproduction with exponential growth is possible only when the replication and degradation of one molecular species is much slower than those of the others, i.e., when there is a minority molecule. Here, the synergetic effect of molecular discreteness and crowding is necessary to produce the exponential growth. Otherwise, the growth curves show superexponential growth because of nonlinearity of the catalytic reactions or subexponential growth due to replication inhibition by overcrowding of molecules. Our study emphasizes that the minority molecular species in a catalytic reaction network is necessary for exponential growth at the primitive stage of life.

Allergens/Antigens, toxins and polyketides of important Aspergillus species.

PubMed

Bhetariya, Preetida J; Madan, Taruna; Basir, Seemi Farhat; Varma, Anupam; Usha, Sarma P

2011-04-01

The medical, agricultural and biotechnological importance of the primitive eukaryotic microorganisms, the Fungi was recognized way back in 1920. Among various groups of fungi, the Aspergillus species are studied in great detail using advances in genomics and proteomics to unravel biological and molecular mechanisms in these fungi. Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Aspergillus nidulans and Aspergillus terreus are some of the important species relevant to human, agricultural and biotechnological applications. The potential of Aspergillus species to produce highly diversified complex biomolecules such as multifunctional proteins (allergens, antigens, enzymes) and polyketides is fascinating and demands greater insight into the understanding of these fungal species for application to human health. Recently a regulator gene for secondary metabolites, LaeA has been identified. Gene mining based on LaeA has facilitated new metabolites with antimicrobial activity such as emericellamides and antitumor activity such as terrequinone A from A. nidulans. Immunoproteomic approach was reported for identification of few novel allergens for A. fumigatus. In this context, the review is focused on recent developments in allergens, antigens, structural and functional diversity of the polyketide synthases that produce polyketides of pharmaceutical and biological importance. Possible antifungal drug targets for development of effective antifungal drugs and new strategies for development of molecular diagnostics are considered.

High-molecular weight Aβ oligomers and protofibrils are the predominant Aβ species in the native soluble protein fraction of the AD brain.

PubMed

Upadhaya, Ajeet Rijal; Lungrin, Irina; Yamaguchi, Haruyasu; Fändrich, Marcus; Thal, Dietmar Rudolf

2012-02-01

Alzheimer's disease (AD) is characterized by the aggregation and deposition of amyloid β protein (Aβ) in the brain. Soluble Aβ oligomers are thought to be toxic. To investigate the predominant species of Aβ protein that may play a role in AD pathogenesis, we performed biochemical analysis of AD and control brains. Sucrose buffer-soluble brain lysates were characterized in native form using blue native (BN)-PAGE and also in denatured form using SDS-PAGE followed by Western blot analysis. BN-PAGE analysis revealed a high-molecular weight smear (>1000 kD) of Aβ(42) -positive material in the AD brain, whereas low-molecular weight and monomeric Aβ species were not detected. SDS-PAGE analysis, on the other hand, allowed the detection of prominent Aβ monomer and dimer bands in AD cases but not in controls. Immunoelectron microscopy of immunoprecipitated oligomers and protofibrils/fibrils showed spherical and protofibrillar Aβ-positive material, thereby confirming the presence of high-molecular weight Aβ (hiMWAβ) aggregates in the AD brain. In vitro analysis of synthetic Aβ(40) - and Aβ(42) preparations revealed Aβ fibrils, protofibrils, and hiMWAβ oligomers that were detectable at the electron microscopic level and after BN-PAGE. Further, BN-PAGE analysis exhibited a monomer band and less prominent low-molecular weight Aβ (loMWAβ) oligomers. In contrast, SDS-PAGE showed large amounts of loMWAβ but no hiMWAβ(40) and strikingly reduced levels of hiMWAβ(42) . These results indicate that hiMWAβ aggregates, particularly Aβ(42) species, are most prevalent in the soluble fraction of the AD brain. Thus, soluble hiMWAβ aggregates may play an important role in the pathogenesis of AD either independently or as a reservoir for release of loMWAβ oligomers. © 2011 The Authors Journal of Cellular and Molecular Medicine © 2011 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

Inhibition of O-linked N-acetylglucosamine transferase activity in PC12 cells - A molecular mechanism of organophosphate flame retardants developmental neurotoxicity.

PubMed

Gu, Yuxin; Yang, Yu; Wan, Bin; Li, Minjie; Guo, Liang-Hong

2018-06-01

Organophosphate flame retardants (OPFRs), as alternatives of brominated flame retardants, can cause neurodevelopmental effects similar to organophosphate pesticides. However, the molecular mechanisms underlying the toxicity remain elusive. O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) regulates numerous neural processes through the O-GlcNAcylation modification of nuclear and cytoplasmic proteins. In this study, we aimed to investigate the molecular mechanisms accounting for the developmental neurotoxicity of OPFRs by identifying potential targets of OPFRs and the attendant effects. Twelve OPFRs were evaluated for inhibition of OGT activity using an electrochemical biosensor. Their potency differed with substituent groups. The alkyl group substituted OPFRs had no inhibitory effect. Instead, the six OPFRs substituted with aromatic or chlorinated alkyl groups inhibited OGT activity significantly, with tri-m-cresyl phosphate (TCrP) being the strongest. The six OPFRs (0-100 μM exposure) also inhibited OGT activity in PC12 cells and decreased protein O-GlcNAcylation level. Inhibition of OGT by OPFRs might be involved in the subsequent toxic effects, including intracellular reactive oxygen species (ROS), calcium level, as well as cell proliferation and autophagy. Molecular docking of the OGT/OPFR complexes provided rationales for the difference in their structure-dependent inhibition potency. Our findings may provide a new biological target of OPFRs in their neurotoxicological actions, which might be a major molecular mechanism of OPFRs developmental neurotoxicity. Copyright © 2018 Elsevier Inc. All rights reserved.

Recent insights into the molecular mechanisms of the NLRP3 inflammasome activation

PubMed Central

Próchnicki, Tomasz; Mangan, Matthew S.; Latz, Eicke

2016-01-01

Inflammasomes are high-molecular-weight protein complexes that are formed in the cytosolic compartment in response to danger- or pathogen-associated molecular patterns. These complexes enable activation of an inflammatory protease caspase-1, leading to a cell death process called pyroptosis and to proteolytic cleavage and release of pro-inflammatory cytokines interleukin (IL)-1β and IL-18. Along with caspase-1, inflammasome components include an adaptor protein, ASC, and a sensor protein, which triggers the inflammasome assembly in response to a danger signal. The inflammasome sensor proteins are pattern recognition receptors belonging either to the NOD-like receptor (NLR) or to the AIM2-like receptor family. While the molecular agonists that induce inflammasome formation by AIM2 and by several other NLRs have been identified, it is not well understood how the NLR family member NLRP3 is activated. Given that NLRP3 activation is relevant to a range of human pathological conditions, significant attempts are being made to elucidate the molecular mechanism of this process. In this review, we summarize the current knowledge on the molecular events that lead to activation of the NLRP3 inflammasome in response to a range of K + efflux-inducing danger signals. We also comment on the reported involvement of cytosolic Ca 2+ fluxes on NLRP3 activation. We outline the recent advances in research on the physiological and pharmacological mechanisms of regulation of NLRP3 responses, and we point to several open questions regarding the current model of NLRP3 activation. PMID:27508077

Molecular-Flow Properties of RIB Type Vapor-Transport Systems Using a Fast-Valve

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alton, Gerald D; Bilheux, Hassina Z; Zhang, Y.

2014-01-01

The advent of the fast-valve device, described previously, permits measurement of molecular-flow times of chemically active or inactive gaseous species through radioactive ion beam (RIB) target ion source systems, independent of size, geometry and materials of construction. Thus, decay losses of short-half-life RIBs can be determined for a given target/vapor-transport system in advance of on-line operation, thereby ascertaining the feasibility of the system design for successful processing of a given isotope. In this article, molecular-flow-time theory and experimentally measured molecular-flow time data are given for serial- and parallel-coupled Ta metal RIB vapor-transport systems similar to those used at ISOL basedmore » RIB facilities. In addition, the effect of source type on the molecular-flow time properties of a given system is addressed, and a chemical passivation method for negating surface adsorption enthalpies for chemically active gaseous species on Ta surfaces is demonstrated.« less

Peptidase activity in various species of dairy thermophilic lactobacilli.

PubMed

Gatti, M; Fornasari, M E; Lazzi, C; Mucchetti, G; Neviani, E

2004-01-01

The aim of the present work was to evaluate the enzymatic potential manifested by aminopeptidase activity of different thermophilic Lactobacillus biotypes and to measure the influence of cell growth phase on enzyme expression. The activities were evaluated by the hydrolysis of beta-naphthylamide substrates for both whole and mechanically disrupted cells of L. helveticus, L. delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis strains, collected from both the exponential and the stationary growth phase. In general, activities were higher for cells in the exponential rather than in the stationary phase and the disrupted cells showed higher activities than the whole cells. The highest activity expressed by all strains corresponded to X-prolyl-dipeptidyl aminopeptidase while a moderate activity was observed towards Arg-betaNa, Lys-betaNa and Leu-betaNa. The lowest activity was observed for Pro-betaNa. It may be inferred that the cell structure and the cell physiology are crucial to define the level of efficiency of expression for aminopeptidase activity. The two species may be characterized by a different enzymatic system that hydrolyses N-terminal leucine. The differences of peptidase activities in L. helveticus and L. delbrueckii species acquires an importance to comprehend their role in the biochemical events occurring in cheese ripening.

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation. II - Structures and thermodynamics of the activated complex species

NASA Technical Reports Server (NTRS)

Collins, Jack R.; Loew, Gilda H.; Luke, Brian T.; White, David H.

1988-01-01

Molecular orbital calculations are used to study amino acid activation by anhydride formation in neutral phosphates and in tetrahedral silicate and aluminate sites on clay edges. The results agree with previous ab initio studies of Luke et al. (1984) on the reactant species. Relative heats of formation of the anhydrides indicate the extent of anhydride formation to be the greatest for Al and the least for phosphate, which is the same order as the stability of hydrolysis.

Evaluation of molecular species of prostate-specific antigen complexed with immunoglobulin M in prostate cancer and benign prostatic hyperplasia.

PubMed

Goč, Sanja; Janković, Miroslava

2013-01-01

This study was aimed at defining molecular species of prostate-specific antigen (PSA) in immune complexes with immunoglobulin M (IgM). Having in mind the oligoreactivity of IgM and its preference for carbohydrate antigens, there is the possibility that it can selectively recognize known PSA glycoisoforms. PSA-IgM complexes and free PSA fractions were separated from the sera of subjects with prostate cancer (PCa) and benign prostatic hyperplasia (BPH) by gel filtration and subjected to on-chip immunoaffinity and ion-exchange chromatography. PSA-immunoreactive species were detected using surface-enhanced laser desorption/ionization time of flight mass spectrometry. The obtained spectra were analyzed for protein and glycan composition. The general pattern of the molecular species of PCa PSA and BPH PSA found in complexes with IgM was similar. It comprised major peaks at 17 kDa and minor peaks at 28 kDa, corresponding to the entire mature glycosylated PSA. The main difference was the presence of incompletely glycosylated 26.8 kDa species, having putative paucimannosidic structures, observed in PCa PSA-IgM, but not in BPH PSA-IgM. Characteristic PCa PSA-IgM glycoforms pose the question of the possible role of glycosylation as a framework for immune surveillance and may be of interest in light of recent data indicating mannose-containing glycans as cancer biomarker.

Molecular, morphological and acoustic assessment of the genus Ophryophryne (Anura, Megophryidae) from Langbian Plateau, southern Vietnam, with description of a new species

PubMed Central

Jr., Nikolay A. Poyarkov; Duong, Tang Van; Orlov, Nikolai L.; Gogoleva, Svetlana S.; Vassilieva, Anna B.; Nguyen, Luan Thanh; Nguyen, Vu Dang Hoang; Nguyen, Sang Ngoc; Che, Jing; Mahony, Stephen

2017-01-01

Abstract Asian Mountain Toads (Ophryophryne) are a poorly known genus of mostly small-sized anurans from southeastern China and Indochina. To shed light on the systematics within this group, the most comprehensive mitochondrial DNA phylogeny for the genus to date is presented, and the taxonomy and biogeography of this group is discussed. Complimented with extensive morphological data (including associated statistical analyses), molecular data indicates that the Langbian Plateau, in the southern Annamite Mountains, Vietnam, is one of the diversity centres of this genus where three often sympatric species of Ophryophryne are found, O. gerti, O. synoria and an undescribed species. To help resolve outstanding taxonomic confusion evident in literature (reviewed herein), an expanded redescription of O. gerti is provided based on the examination of type material, and the distributions of both O. gerti and O. synoria are considerably revised based on new locality records. We provide the first descriptions of male mating calls for all three species, permitting a detailed bioacoustics comparison of the species. We describe the new species from highlands of the northern and eastern Langbian Plateau, and distinguish it from its congeners by a combination of morphological, molecular and acoustic characters. The new species represents one of the smallest known members of the genus Ophryophryne. At present, the new species is known from montane evergreen forest between 700–2200 m a.s.l. We suggest the species should be considered Data Deficient following IUCN’s Red List categories. PMID:28769667

Molecular, morphological and acoustic assessment of the genus Ophryophryne (Anura, Megophryidae) from Langbian Plateau, southern Vietnam, with description of a new species.

PubMed

Poyarkov, Nikolay A; Duong, Tang Van; Orlov, Nikolai L; Gogoleva, Svetlana S; Vassilieva, Anna B; Nguyen, Luan Thanh; Nguyen, Vu Dang Hoang; Nguyen, Sang Ngoc; Che, Jing; Mahony, Stephen

2017-01-01

Asian Mountain Toads ( Ophryophryne ) are a poorly known genus of mostly small-sized anurans from southeastern China and Indochina. To shed light on the systematics within this group, the most comprehensive mitochondrial DNA phylogeny for the genus to date is presented, and the taxonomy and biogeography of this group is discussed. Complimented with extensive morphological data (including associated statistical analyses), molecular data indicates that the Langbian Plateau, in the southern Annamite Mountains, Vietnam, is one of the diversity centres of this genus where three often sympatric species of Ophryophryne are found, O. gerti , O. synoria and an undescribed species. To help resolve outstanding taxonomic confusion evident in literature (reviewed herein), an expanded redescription of O. gerti is provided based on the examination of type material, and the distributions of both O. gerti and O. synoria are considerably revised based on new locality records. We provide the first descriptions of male mating calls for all three species, permitting a detailed bioacoustics comparison of the species. We describe the new species from highlands of the northern and eastern Langbian Plateau, and distinguish it from its congeners by a combination of morphological, molecular and acoustic characters. The new species represents one of the smallest known members of the genus Ophryophryne . At present, the new species is known from montane evergreen forest between 700-2200 m a.s.l. We suggest the species should be considered Data Deficient following IUCN's Red List categories.

Exoenzyme activity and possibility identification of Candida dubliniensis among Candida albicans species isolated from vaginal candidiasis.

PubMed

Jafari, Maryam; Salari, Samira; Pakshir, Keyvan; Zomorodian, Kamiar

2017-09-01

Vulvovaginal candidiasis (VVC) or vaginal candidiasis is a common fungal infection of the genitals causing inflammation, irritation, itching, and vaginal discharge. Common yeast infections are caused by the yeast species C. albicans. However, there are other species of Candida such as C. dubliniensis which are considered as the causative agents of this infection. Hydrolytic enzymes such as proteinase and coagulase are known as virulence factors. The aim of this study was the molecular confirmation and differentiation of C. dubliniensis among C. albicans strains isolated from women with vulvovaginal candidiasis by PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) and the evaluation of proteinase and coagulase activities. A total of 100 C. albicans strains isolated from women with vulvovaginal candidiasis referred to Shiraz medical clinics were enrolled in the study. All the isolates were primarily identified by conventional methods. PCR-RFLP method was used for the confirmation and identification of C. albicans and C. dubliniensis. Moreover, in vitro proteinase and coagulase activities of these isolates were evaluated using bovine serum albumin media and classical rabbit plasma tube test. As a result, PCR-RFLP identified 100% of the isolates as C. albicans, and no C. dubliniensis could be identified in this study. 84% of the isolates showed proteinase activity, whereas coagulase activity was only detected in 5% of the isolates. This study reveals that C. dubliniensis plays no role in vaginal candidiasis in Iranian patients. Proteinase production could be an essential virulence factor in C. albicans pathogenicity, but coagulase activity has less potential in this matter. Copyright © 2017 Elsevier Ltd. All rights reserved.

"Invented Invaders": An Engaging Activity to Teach Characteristics Control of Invasive Species

ERIC Educational Resources Information Center

Lampert, Evan

2015-01-01

Invasive species, defined as exotic species that reach pest status, are major threats to global biodiversity. Although invasive species can belong to any taxonomic group, general characteristics such as rapid growth and reproduction are shared by many invasive species. "Invented Invaders" is a collaborative activity in which students…

[The low-molecular weight antioxidants of microorganisms].

PubMed

Skorokhod, I O; Kurdysh, I K

2014-01-01

Support of optimum redox-homeostasis in the cells of microorganisms plays a substantial role in the processes of DNA synthesis, respiration, providing of immune and protective reactions, activity of enzymes, etc. The changes of the redox-status can be accompanied by the increase of the level of reactive oxygen species (ROS) which predetermine the damage of biologically active molecules. Adjusting of ROS concentrations is a very important process in development of microorganisms. Low-molecular antioxidants are effective inhibitors of free-radical processes. The authors of the review present the description of oxidants and consider the ways of origin and consequences of their influence on the living cells. An accent is done on phenomenological description of low-molecular antioxidants. The basic mechanisms of their action are considered. Special attention is given to the question of synergism between these protectors. The detailed study of mechanisms of functioning of low-molecular antioxidants in the cells of microorganisms will allow using these living objects in different spheres of human activity.

Physiological and molecular characterization of Si uptake in wild rice species.

PubMed

Mitani-Ueno, Namiki; Ogai, Hisao; Yamaji, Naoki; Ma, Jian Feng

2014-07-01

Cultivated rice (Oryza sativa) accumulates high concentration of silicon (Si), which is required for its high and sustainable production. High Si accumulation in cultivated rice is achieved by a high expression of both influx (Lsi1) and efflux (Lsi2) Si transporters in roots. Herein, we physiologically investigated Si uptake, isolated and functionally characterized Si transporters in six wild rice species with different genome types. Si uptake by the roots was lower in Oryza rufipogon, Oryza barthii (AA genome), Oryza australiensis (EE genome) and Oryza punctata (BB genome), but similar in Oryza glumaepatula and Oryza meridionalis (AA genome) compared with the cultivated rice (cv. Nipponbare). However, all wild rice species and the cultivated rice showed similar concentration of Si in the shoots when grown in a field. All species with AA genome showed the same amino acid sequence of both Lsi1 and Lsi2 as O. sativa, whereas species with EE and BB genome showed several nucleotide differences in both Lsi1 and Lsi2. However, proteins encoded by these genes also showed transport activity for Si in Xenopus oocyte. The mRNA expression of Lsi1 in all wild rice species was lower than that in the cultivated rice, whereas the expression of Lsi2 was lower in O. rufipogon and O. barthii but similar in other species. Similar cellular localization of Lsi1 and Lsi2 was observed in all wild rice as the cultivated rice. These results indicate that superior Si uptake, the important trait for rice growth, is basically conserved in wild and cultivated rice species. © 2013 Scandinavian Plant Physiology Society.

Phytochemistry and biological activities of Phlomis species.

PubMed

Limem-Ben Amor, Ilef; Boubaker, Jihed; Ben Sgaier, Mohamed; Skandrani, Ines; Bhouri, Wissem; Neffati, Aicha; Kilani, Soumaya; Bouhlel, Ines; Ghedira, Kamel; Chekir-Ghedira, Leila

2009-09-07

The genus Phlomis L. belongs to the Lamiaceae family and encompasses 100 species native to Turkey, North Africa, Europe and Asia. It is a popular herbal tea enjoyed for its taste and aroma. Phlomis species are used to treat various conditions such as diabetes, gastric ulcer, hemorrhoids, inflammation, and wounds. This review aims to summarize recent research on the phytochemistry and pharmacological properties of the genus Phlomis, with particular emphasis on its ethnobotanical uses. The essential oil of Phomis is composed of four chemotypes dominated by monoterpenes (alpha-pinene, limonene and linalool), sesquiterpenes (germacrene D and beta-caryophyllene), aliphalic compounds (9,12,15-octadecatrienoic acid methyl ester), fatty acids (hexadecanoic acid) and other components (trans-phytol, 9,12,15-octadecatrien-1-ol). Flavonoids, iridoids and phenylethyl alcohol constitute the main compounds isolated from Phlomis extracts. The pharmacological activities of some Phlomis species have been investigated. They are described according to antidiabetic, antinociceptive, antiulcerogenic, protection of the vascular system, anti-inflammatory, antiallergic, anticancer, antimicrobial and antioxidant properties.

Medulloblastoma, WNT-activated/SHH-activated: clinical impact of molecular analysis and histogenetic evaluation.

PubMed

Cambruzzi, Eduardo

2018-05-01

Medulloblastoma (MDB) is a small cell poorly differentiated embryonal tumor of the cerebellum, which more frequently compromises children. Overall prognosis is favorable, but dependent of stage, histopathological pattern and molecular group. Approximately 30% of the affected patients will die from the disease. WHO 2016 Classification of Tumors of the Central Nervous System (CNS) has been classified MDB into four principal groups: WNT-activated MDB, SHH-activated MDB, group 3 MDB, and group 4 MDB. WNT-activated MDB is associated to monosomy 6, CTNNB1, DDX3X and TP53 mutations, beta-catenin nuclear immunoexpression, and a better prognosis than SHH-activated MDB. WNT-activated tumors account approximately for 10% of cases of MDBs, and are thought to arise from cells in the dorsal brain stem/lower rhombic lip progenitor cells. SHH-activated MDB more frequently arises in the lateral hemispheres of the cerebellum, and clinical outcome in this group is variable. TP53-mutant SHHactivated MDB usually shows the large cell/anaplastic pattern, and can be related to MYCN amplification, GLI2 amplification and 17p loss. TP53-wildtype SHH-activated MDB is more commonly of desmoplastic/nodular morphology, and can be related to PTCH1 deletion and 10q loss. Gene expression and methylation profiling is the gold standard for defining molecular groups of MDB. In immunohistochemistry assays, anti-GAB1 antibody expression is positive in tumors showing SHH pathway activation or PTCH mutation, while positive immunoexpression for YAP1 antibody can be only found in WNT-activated and SHH-activated MDB.

Molecular Determinants of the Thickened Matrix in a Dual-Species Pseudomonas aeruginosa and Enterococcus faecalis Biofilm

PubMed Central

Lee, Keehoon; Lee, Kang-Mu; Kim, Donggeun

2017-01-01

ABSTRACT Biofilms are microbial communities that inhabit various surfaces and are surrounded by extracellular matrices (ECMs). Clinical microbiologists have shown that the majority of chronic infections are caused by biofilms, following the introduction of the first biofilm infection model by J. W. Costerton and colleagues (J. Lam, R. Chan, K. Lam, and J. W. Costerton, Infect Immun 28:546–556, 1980). However, treatments for chronic biofilm infections are still limited to surgical removal of the infected sites. Pseudomonas aeruginosa and Enterococcus faecalis are two frequently identified bacterial species in biofilm infections; nevertheless, the interactions between these two species, especially during biofilm growth, are not clearly understood. In this study, we observed phenotypic changes in a dual-species biofilm of P. aeruginosa and E. faecalis, including a dramatic increase in biofilm matrix thickness. For clear elucidation of the spatial distribution of the dual-species biofilm, P. aeruginosa and E. faecalis were labeled with red and green fluorescence, respectively. E. faecalis was located at the lower part of the dual-species biofilm, while P. aeruginosa developed a structured biofilm on the upper part. Mutants with altered exopolysaccharide (EPS) productions were constructed in order to determine the molecular basis for the synergistic effect of the dual-species biofilm. Increased biofilm matrix thickness was associated with EPSs, not extracellular DNA. In particular, Pel and Psl contributed to interspecies and intraspecies interactions, respectively, in the dual-species P. aeruginosa and E. faecalis biofilm. Accordingly, targeting Pel and Psl might be an effective part of eradicating P. aeruginosa polymicrobial biofilms. IMPORTANCE Chronic infection is a serious problem in the medical field. Scientists have observed that chronic infections are closely associated with biofilms, and the vast majority of infection-causing biofilms are polymicrobial. Many

Molecular Determinants of the Thickened Matrix in a Dual-Species Pseudomonas aeruginosa and Enterococcus faecalis Biofilm.

PubMed

Lee, Keehoon; Lee, Kang-Mu; Kim, Donggeun; Yoon, Sang Sun

2017-11-01

Biofilms are microbial communities that inhabit various surfaces and are surrounded by extracellular matrices (ECMs). Clinical microbiologists have shown that the majority of chronic infections are caused by biofilms, following the introduction of the first biofilm infection model by J. W. Costerton and colleagues (J. Lam, R. Chan, K. Lam, and J. W. Costerton, Infect Immun 28:546-556, 1980). However, treatments for chronic biofilm infections are still limited to surgical removal of the infected sites. Pseudomonas aeruginosa and Enterococcus faecalis are two frequently identified bacterial species in biofilm infections; nevertheless, the interactions between these two species, especially during biofilm growth, are not clearly understood. In this study, we observed phenotypic changes in a dual-species biofilm of P. aeruginosa and E. faecalis , including a dramatic increase in biofilm matrix thickness. For clear elucidation of the spatial distribution of the dual-species biofilm, P. aeruginosa and E. faecalis were labeled with red and green fluorescence, respectively. E. faecalis was located at the lower part of the dual-species biofilm, while P. aeruginosa developed a structured biofilm on the upper part. Mutants with altered exopolysaccharide (EPS) productions were constructed in order to determine the molecular basis for the synergistic effect of the dual-species biofilm. Increased biofilm matrix thickness was associated with EPSs, not extracellular DNA. In particular, Pel and Psl contributed to interspecies and intraspecies interactions, respectively, in the dual-species P. aeruginosa and E. faecalis biofilm. Accordingly, targeting Pel and Psl might be an effective part of eradicating P. aeruginosa polymicrobial biofilms. IMPORTANCE Chronic infection is a serious problem in the medical field. Scientists have observed that chronic infections are closely associated with biofilms, and the vast majority of infection-causing biofilms are polymicrobial. Many studies

A new species of Alopoglossus lizard (Squamata, Gymnophthalmidae) from the tropical Andes, with a molecular phylogeny of the genus

PubMed Central

Torres-Carvajal, Omar; Lobos, Simón E.

2014-01-01

Abstract We describe a new species of Alopoglossus from the Pacific slopes of the Andes in northern Ecuador based on morphological and molecular evidence. The new species differs most significantly from all other congeners in having a double longitudinal row of widened gular scales, lanceolate dorsal scales in transverse rows, 29–32 dorsal scales in a transverse row at midbody, and 4 longitudinal rows of ventrals at midbody. It is most similar in morphology to A. festae, the only species of Alopoglossus currently recognized in western Ecuador. We analyze the phylogenetic relationships among species of Alopoglossus based on the mitochondrial gene ND4. Cis-Andean [east of the Andes] and Trans-Andean [west of the Andes] species are nested in two separate clades, suggesting that the uplift of these mountains had an important effect in the diversification of Alopoglossus. In addition, we present an updated key to the species of Alopoglossus. PMID:24899852

Activities of arginine and ornithine decarboxylases in various plant species.

PubMed

Birecka, H; Bitonti, A J; McCann, P P

1985-10-01

In extracts from the youngest leaves of Avena sativa, Hordeum vulgare, Zea Mays, Pisum sativum, Phaseolus vulgaris, Lactuca sativa, and four pyrrolizidine alkaloid-bearing species of Heliotropium, the activities of ornithine decarboxylase, close to V(max), ranged between traces and 1.5 nanomoles per hour per gram fresh weight when based on putrescine formed during incubation with labeled ornithine. The arginine decarboxylase activities in the same extracts ranged between 8 and 8000 nanomoles per hour per gram fresh weight being lowest in the borages and highest in oat and barley. alpha-Difluoromethylornithine and alpha-difluoromethylarginine inhibited ornithine and arginine decarboxylases, respectively, in all species. Agmatine, putrescine, spermidine, and spermine were found in all, diaminopropane in eight, and cadaverine in three species.No correlation was observed between arginine or ornithine decarboxylase level and the levels of total polyamines. The in vitro decarboxylase activities found in the borages cannot explain the high accumulation of putrescine-derived pyrrolizidines in their youngest leaves if the pyrrolizidines are produced in situ from arginine and/or ornithine as precursors; other possibilities are discussed.In assays of ornithine decarboxylase, an interference of decarboxylation not due to this enzyme was observed in extracts from all species. In arginine decarboxylase assays, the interfering decarboxylation as well as the interference of arginase were apparent in two species. Addition of aminoguanidine was needed to suppress oxidative degradation of putrescine and agmatine during incubation of extracts from pea, bean, lettuce, Heliotropium angiospermum, and Heliotropium indicum.

Molecular insights into species phylogeny, biogeography, and morphological stasis in the ancient spider genus Hypochilus (Araneae: Hypochilidae).

PubMed

Hedin, M C

2001-02-01

The spider genus Hypochilus is currently restricted to cool, moist microhabitats in three widely separated montane regions of North America, providing an opportunity to study both deep (i.e., continental level) and shallow (within montane region) biogeographic history. Members of the genus also retain many plesiomorphic morphological characteristics, inviting the study of comparative rates of morphological evolution. In this paper, Hypochilus phylogeny and associated evolutionary problems are addressed using both new molecular (28S nDNA and CO1 mtDNA) and previously published (K. M. Catley, 1994, Am. Mus. Nov. 3088, 1-27) morphological data. Although the molecular data provide limited resolution of root placement within Hypochilus, most analyses are at least consistent with morphology-supported montane relationships of (Rockies (California, Appalachian)). The monophyly of Hypochilus species distributed in the California mountains is ambiguous, with several analyses indicating that this fauna may be paraphyletic with respect to a monophyletic Appalachian lineage. The montane regions differ in consistent ways in depths of both mitochondrial and nuclear phylogenetic divergence. Molecular clock analyses, in combination with arthropod-based mtDNA rate calibrations, suggest that the regional faunas are of different ages and that speciation in all faunas likely occurred prior to the Pleistocene. Limited intraspecific sampling reveals extraordinarily high levels of mtDNA cytochrome oxidase sequence divergence. These extreme divergences are most consistent with morphological stasis at the species level, despite preliminary evidence that Hypochilus taxa are characterized by fragmented population structures. Copyright 2001 Academic Press.

Antifungal activity of some essential oils against toxigenic Aspergillus species.

PubMed

Alizadeh, Alireza; Zamani, Elham; Sharaifi, Rohollah; Javan-Nikkhah, Mohammad; Nazari, Somayeh

2010-01-01

Increasing attentions have been paid on the application of essential oils and plant extracts for control of postharvest pathogens due to their natural origin and less appearance of resistance in fungi pathogens. Some Aspergillus species are toxigenic and responsible for many cases of food and feed contamination. Some Toxins that produce with some Aspergillus species are known to be potent hepatocarcinogens in animals and humans. The present work evaluated the parameters of antifungal activity of the essential oils of Zataria multiflora, Thymus migricus, Satureja hortensis, Foeniculum vulgare, Carum capticum and thiabendazol fungicide on survival and growth of different species of Aspergillus. Aerial part and seeds of plant species were collected then dried and its essential oils isolated by means of hydrodistillation. Antifungal activity was evaluated in vitro by poisonous medium technique with PDA medium at six concentrations. Results showed that all essential oils could inhibit the growth of Aspergillus species. The essential oil with the best effect and lowest EC50 and MIC (Minimum Inhibitory Concentration) was Z. multiflora (223 microl/l and 650 microl/l, respectively). The chemical composition of the Z. multiflora essential oil was analyzed by GC-MS.

Genome differentiation in a species pair of coregonine fishes: an extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications

PubMed Central

2013-01-01

Background Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments. The nature of divergences between co-occurring sympatric species, factors contributing to reproductive isolation and modes of genome evolution is a much debated topic in evolutionary biology addressed by various experimental tools. To the best of our knowledge, nobody approached this field using molecular cytogenetics. We examined chromosomes and genomes of one postglacial species pair, sympatric European winter-spawning Coregonus albula and the local endemic dwarf-sized spring-spawning C. fontanae, both originating in Lake Stechlin. We have employed molecular cytogenetic tools to identify the genomic differences between the two species of the sympatric pair on the sub-chromosomal level of resolution. Results Fluorescence in situ hybridization (FISH) experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) between C. albula and C. fontanae genomes. In C. fontanae, up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C. albula only 8–10 chromosomes possessed these genes. To determine mechanisms how such extensive genome alternation might have arisen, a PCR screening for retrotransposons from genomic DNA of both species was performed. The amplified retrotransposon Rex1 was used as a probe for FISH mapping onto chromosomes of both species. These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region of one or two acrocentric chromosomes in both species. Conclusion We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis. We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently affecting recombination rates

Molecular identification of Nocardia species using the sodA gene: Identificación molecular de especies de Nocardia utilizando el gen sodA.

PubMed

Sánchez-Herrera, K; Sandoval, H; Mouniee, D; Ramírez-Durán, N; Bergeron, E; Boiron, P; Sánchez-Saucedo, N; Rodríguez-Nava, V

2017-09-01

Currently for bacterial identification and classification the rrs gene encoding 16S rRNA is used as a reference method for the analysis of strains of the genus Nocardia. However, it does not have enough polymorphism to differentiate them at the species level. This fact makes it necessary to search for molecular targets that can provide better identification. The sod A gene (encoding the enzyme superoxide dismutase) has had good results in identifying species of other Actinomycetes. In this study the sod A gene is proposed for the identification and differentiation at the species level of the genus Nocardia. We used 41 type species of various collections; a 386 bp fragment of the sod A gene was amplified and sequenced, and a phylogenetic analysis was performed comparing the genes rrs (1171 bp), hsp 65 (401 bp), sec A1 (494 bp), gyr B (1195 bp) and rpo B (401 bp). The sequences were aligned using the Clustal X program. Evolutionary trees according to the neighbour-joining method were created with the programs Phylo_win and MEGA 6. The specific variability of the sod A genus of the genus Nocardia was analysed. A high phylogenetic resolution, significant genetic variability, and specificity and reliability were observed for the differentiation of the isolates at the species level. The polymorphism observed in the sod A gene sequence contains variable regions that allow the discrimination of closely related Nocardia species. The clear specificity, despite its small size, proves to be of great advantage for use in taxonomic studies and clinical diagnosis of the genus Nocardia.

Unravelling the Biodiversity and Molecular Phylogeny of Needle Nematodes of the Genus Longidorus (Nematoda: Longidoridae) in Olive and a Description of Six New Species

PubMed Central

Archidona-Yuste, Antonio; Navas-Cortés, Juan A.; Cantalapiedra-Navarrete, Carolina; Palomares-Rius, Juan E.; Castillo, Pablo

2016-01-01

The genus Longidorus includes a remarkable group of invertebrate animals of the phylum Nematoda comprising polyphagous root-ectoparasites of numerous plants including several agricultural crops and trees. Damage is caused by direct feeding on root cells as well as by transmitting nepoviruses that cause disease on those crops. Thus, correct identification of Longidorus species is essential to establish appropriate control measures. We provide the first detailed information on the diversity and distribution of Longidorus species infesting wild and cultivated olive soils in a wide-region in southern Spain that included 159 locations from which 449 sampling sites were analyzed. The present study doubles the known biodiversity of Longidorus species identified in olives by including six new species (Longidorus indalus sp. nov., Longidorus macrodorus sp. nov., Longidorus onubensis sp. nov., Longidorus silvestris sp. nov., Longidorus vallensis sp. nov., and Longidorus wicuolea sp. nov.), two new records for wild and cultivate olives (L. alvegus and L. vineacola), and two additional new records for wild olive (L. intermedius and L. lusitanicus). We also found evidence of some geographic species associations to western (viz. L. alvegus, L. intermedius, L. lusitanicus, L. onubensis sp. nov., L. vineacola, L. vinearum, L. wicuolea sp. nov.) and eastern distributions (viz. L. indalus sp. nov.), while only L. magnus was detected in both areas. We developed a comparative study by considering morphological and morphometrical features together with molecular data from nuclear ribosomal RNA genes (D2–D3 expansion segments of 28S, ITS1, and partial 18S). Results of molecular and phylogenetic analyses confirmed the morphological hypotheses and allowed the delimitation and discrimination of six new species of the genus described herein and four known species. Phylogenetic analyses of Longidorus spp. based on three molecular markers resulted in a general consensus of these species

Unravelling the Biodiversity and Molecular Phylogeny of Needle Nematodes of the Genus Longidorus (Nematoda: Longidoridae) in Olive and a Description of Six New Species.

PubMed

Archidona-Yuste, Antonio; Navas-Cortés, Juan A; Cantalapiedra-Navarrete, Carolina; Palomares-Rius, Juan E; Castillo, Pablo

2016-01-01

The genus Longidorus includes a remarkable group of invertebrate animals of the phylum Nematoda comprising polyphagous root-ectoparasites of numerous plants including several agricultural crops and trees. Damage is caused by direct feeding on root cells as well as by transmitting nepoviruses that cause disease on those crops. Thus, correct identification of Longidorus species is essential to establish appropriate control measures. We provide the first detailed information on the diversity and distribution of Longidorus species infesting wild and cultivated olive soils in a wide-region in southern Spain that included 159 locations from which 449 sampling sites were analyzed. The present study doubles the known biodiversity of Longidorus species identified in olives by including six new species (Longidorus indalus sp. nov., Longidorus macrodorus sp. nov., Longidorus onubensis sp. nov., Longidorus silvestris sp. nov., Longidorus vallensis sp. nov., and Longidorus wicuolea sp. nov.), two new records for wild and cultivate olives (L. alvegus and L. vineacola), and two additional new records for wild olive (L. intermedius and L. lusitanicus). We also found evidence of some geographic species associations to western (viz. L. alvegus, L. intermedius, L. lusitanicus, L. onubensis sp. nov., L. vineacola, L. vinearum, L. wicuolea sp. nov.) and eastern distributions (viz. L. indalus sp. nov.), while only L. magnus was detected in both areas. We developed a comparative study by considering morphological and morphometrical features together with molecular data from nuclear ribosomal RNA genes (D2-D3 expansion segments of 28S, ITS1, and partial 18S). Results of molecular and phylogenetic analyses confirmed the morphological hypotheses and allowed the delimitation and discrimination of six new species of the genus described herein and four known species. Phylogenetic analyses of Longidorus spp. based on three molecular markers resulted in a general consensus of these species

Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera).

PubMed

Gómez, Africa; Serra, Manuel; Carvalho, Gary R; Lunt, David H

2002-07-01

Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

Natural Korean Medicine Dang-Gui: Biosynthesis, Effective Extraction and Formulations of Major Active Pyranocoumarins, Their Molecular Action Mechanism in Cancer, and Other Biological Activities.

PubMed

Reddy, Chinreddy Subramanyam; Kim, Seong Cheol; Hur, Mok; Kim, Yeon Bok; Park, Chun Geon; Lee, Woo Moon; Jang, Jae Ki; Koo, Sung Cheol

2017-12-07

Angelica gigas Nakai (AGN) is a crucial oriental medicinal herb that grows especially in Korea and the Far-East countries. It contains chemically active compounds like pyranocoumarins, polyacetylenes and essential oils, which might be useful for treatment of several chronic diseases. It has been used for centuries as a traditional medicine in Southeast Asia, but in Western countries is used as a functional food and a major ingredient of several herbal products. The genus Angelica is also known as 'female ginseng' due to its critical therapeutic role in female afflictions, such as gynecological problems. However, it is well-documented that the AGN pyranocoumarins may play vital beneficial roles against cancer, neurodisorders, inflammation, osteoporosis, amnesia, allergies, depression, fungi, diabetes, ischemia, dermatitis, reactive oxygen species (ROS) and androgen. Though numerous studies revealed the role of AGN pyranocoumarins as therapeutic agents, none of the reviews have published their molecular mechanism of action. To the best of our knowledge, this would be the first review that aims to appraise the biosynthesis of AGN's major active pyranocoumarins, discuss effective extraction and formulation methods, and detail the molecular action mechanism of decursin (D), decursinol angelate (DA) and decursinol (DOH) in chronic diseases, which would further help extension of research in this area.

The species flocks of East African cichlid fishes: recent advances in molecular phylogenetics and population genetics

NASA Astrophysics Data System (ADS)

Salzburger, Walter; Meyer, Axel

With more than 3,000 species, the fish family Cichlidae is one of the most species-rich families of vertebrates. Cichlids occur in southern and central America, Africa, Madagascar, and India. The hotspot of their biodiversity is East Africa, where they form adaptive radiations composed of hundreds of endemic species in several lakes of various sizes and ages. The unparalleled species richness of East African cichlids has been something of a conundrum for evolutionary biologists and ecologists, since it has been in doubt whether these hundreds of species arose by allopatric speciation or whether it is necessary to invoke somewhat less traditional models of speciation, such as micro-allopatric, peripatric, or even sympatric speciation or evolution through sexual selection mediated by female choice. Ernst Mayr's analyses of these evolutionary uniquely diverse species assemblages have contributed to a more direct approach to this problem and have led to a deeper understanding of the patterns and processes that caused the formation of these huge groups of species. We review here recent molecular data on population differentiation and phylogenetics, which have helped to unravel, to some extent, the patterns and processes that led to the formation and ecological maintenance of cichlid species flocks. It is becoming apparent that sexually selected traits do play an important role in speciation in micro-allopatric or even sympatric settings. Species richness seems to be roughly correlated with the surface area, but not the age, of the lakes. We observe that the oldest lineages of a species flock of cichlids are often less species-rich and live in the open water or deepwater habitats. While the species flocks of the Lake Malawai and the Lake Victoria areas were shown to be monophyletic, the cichlid assemblage of Lake Tanganyika seems to consist of several independent species flocks. Cichlids emerge as an evolutionary model system in which many fundamental questions in

Description of three new species of Hepatozoon (Apicomplexa, Hepatozoidae) from Rattlesnakes (Crotalus durissus terrificus) based on molecular, morphometric and morphologic characters.

PubMed

O'Dwyer, Lucia Helena; Moço, Tatiana Cristina; Paduan, Karina dos Santos; Spenassatto, Carine; da Silva, Reinaldo José; Ribolla, Paulo Eduardo Martins

2013-10-01

Hepatozoon spp. are commonly found infecting snakes. Since the latter are parasitized by diverse forms and data in the literature show divergence, we studied Hepatozoon spp. diversity on Crotalus durissus terrificus snakes using both molecular and morphological approaches. Naturally infected animals were employed. Blood was collected, blood smears were prepared and an aliquot was stored at -20°C for DNA extraction. Five specimens of C. durissus terrificus were selected, each of them infected with one gamont type. Morphological and morphometric analyses of the found gamonts led to their grouping into three populations. For molecular characterization, seven oligonucleotide pairs that amplify distinct regions of rDNA gene were tested by adopting the PCR technique. Only the oligonucleotide pairs HepF300/Hep900 and HEMO1/HEMO2 were efficient in amplifying and distinguishing different isolates of Hepatozoon spp. from snakes. The better results were obtained when both oligonucleotide pairs were used in association. Based on the molecular and morphologic differences, three new species were proposed: Hepatozoon cuestensis sp. nov.; Hepatozoon cevapii sp. nov. and Hepatozoon massardii sp. nov. This is the first description of new Hepatozoon species from snakes, based on molecular characterization and morphological data, in South America. Copyright © 2013 Elsevier Inc. All rights reserved.

Two New Species of Liuixalus (Rhacophoridae, Anura): Evidence from Morphological and Molecular Analyses

PubMed Central

Jiang, Ke; Cai, Bo; Xie, Feng; Jiang, Jianping; Murphy, Robert W.; Li, Jia-Tang; Wang, Yuezhao

2015-01-01

Due to small body sizes, superficial similarities in morphologies, and obscure activity behaviors, the phylogeny and taxonomy of species in the genus Liuixalus were very troublesome. Some species might comprise a complex of cryptic species. To investigate the species of group, we constructed the matrilineal genealogy of the genus using 16s rRNA mitochondrial DNA sequences. Analyses recovered six well supported matrilines that involved L. romeri, L. ocellatus, L. hainanus, L. calcarius, Liuixalus shiwandashan sp. nov. and Liuixalus jinxiuensis sp. nov., though the historical relationships among them remained unresolved. Currently, Liuixalus included 4 species, distributed eastwards from northern Vietnam to Hong Kong, China. Based on genealogical and morphological distinctiveness, we described Liuixalus jinxiuensis sp. nov. from the type locality Mt. Dayao, Jinxiu, China and Liuixalus shiwandashan sp. nov. from the type locality Mt. Shiwanda, China. A combination of morphological measurements, genetic, bioacoustic and osteological analysis was served to diagnose the new taxa. PMID:26305377

Two New Species of Liuixalus (Rhacophoridae, Anura): Evidence from Morphological and Molecular Analyses.

PubMed

Qin, Shaobo; Mo, Yunming; Jiang, Ke; Cai, Bo; Xie, Feng; Jiang, Jianping; Murphy, Robert W; Li, Jia-Tang; Wang, Yuezhao

2015-01-01

Due to small body sizes, superficial similarities in morphologies, and obscure activity behaviors, the phylogeny and taxonomy of species in the genus Liuixalus were very troublesome. Some species might comprise a complex of cryptic species. To investigate the species of group, we constructed the matrilineal genealogy of the genus using 16s rRNA mitochondrial DNA sequences. Analyses recovered six well supported matrilines that involved L. romeri, L. ocellatus, L. hainanus, L. calcarius, Liuixalus shiwandashan sp. nov. and Liuixalus jinxiuensis sp. nov., though the historical relationships among them remained unresolved. Currently, Liuixalus included 4 species, distributed eastwards from northern Vietnam to Hong Kong, China. Based on genealogical and morphological distinctiveness, we described Liuixalus jinxiuensis sp. nov. from the type locality Mt. Dayao, Jinxiu, China and Liuixalus shiwandashan sp. nov. from the type locality Mt. Shiwanda, China. A combination of morphological measurements, genetic, bioacoustic and osteological analysis was served to diagnose the new taxa.

Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae).

PubMed

Dow, Rory A; Hämäläinen, Matti; Stokvis, Frank R

2015-10-23

Species of Devadatta from Borneo are studied using both morphological and molecular methods. As well as D. podolestoides Laidlaw, four new species are recognised from the island: D. aran spec. nov. (holotype ♂, from Pulong Tau National Park, Miri division, Sarawak, Malaysia, deposited in RMNH), D. clavicauda spec. nov. (holotype ♂, from Bukit Mina, Bukit Mina Wildlife Corridor, Sarawak Planted Forest Project, Bintulu division, Sarawak, Malaysia, deposited in RMNH), D. somoh spec. nov. (holotype ♂, from the Sungai Kahei area, Ulu Balui, Kapit division, Sarawak, Malaysia, deposited in RMNH) and D. tanduk spec. nov. (holotype ♂, from Poring Hot Springs, Kinabalu National Park, West Coast division, Sabah, Malaysia, deposited in RMNH). The Philippine taxon D. basilanensis Laidlaw is considered a good species rather than a subspecies of D. podolestoides. The Bornean species plus D. basilanensis are provisionally considered to form a species group, the podolestoides-group, within Devadatta. The species of the podolestoides-group are so similar in morphology and colouration that they are close to truly cryptic species. Two species appear to exhibit character displacement where their ranges overlap with other Devadatta species. A molecular analysis using four markers (COI, 16S, ITS and 28S) is presented. This analysis includes specimens of all species from the podolestoides-group and two Devadatta species from mainland Asia.

Molecular cloning of doublesex genes of four cladocera (water flea) species.

PubMed

Toyota, Kenji; Kato, Yasuhiko; Sato, Masaru; Sugiura, Naomi; Miyagawa, Shinichi; Miyakawa, Hitoshi; Watanabe, Hajime; Oda, Shigeto; Ogino, Yukiko; Hiruta, Chizue; Mizutani, Takeshi; Tatarazako, Norihisa; Paland, Susanne; Jackson, Craig; Colbourne, John K; Iguchi, Taisen

2013-04-10

The gene doublesex (dsx) is known as a key factor regulating genetic sex determination in many organisms. We previously identified two dsx genes (DapmaDsx1 and DapmaDsx2) from a freshwater branchiopod crustacean, Daphnia magna, which are expressed in males but not in females. D. magna produces males by parthenogenesis in response to environmental cues (environmental sex determination) and we showed that DapmaDsx1 expression during embryonic stages is responsible for the male trait development. The D. magna dsx genes are thought to have arisen by a cladoceran-specific duplication; therefore, to investigate evolutionary conservation of sex specific expression of dsx genes and to further assess their functions in the environmental sex determination, we searched for dsx homologs in four closely related cladoceran species. We identified homologs of both dsx genes from, D. pulex, D. galeata, and Ceriodaphnia dubia, yet only a single dsx gene was found from Moina macrocopa. The deduced amino acid sequences of all 9 dsx homologs contained the DM and oligomerization domains, which are characteristic for all arthropod DSX family members. Molecular phylogenetic analysis suggested that the dsx gene duplication likely occurred prior to the divergence of these cladoceran species, because that of the giant tiger prawn Penaeus monodon is rooted ancestrally to both DSX1 and DSX2 of cladocerans. Therefore, this result also suggested that M. macrocopa lost dsx2 gene secondarily. Furthermore, all dsx genes identified in this study showed male-biased expression levels, yet only half of the putative 5' upstream regulatory elements are preserved in D. magna and D. pulex. The all dsx genes of five cladoceran species examined had similar amino acid structure containing highly conserved DM and oligomerization domains, and exhibited sexually dimorphic expression patterns, suggesting that these genes may have similar functions for environmental sex determination in cladocerans.

Genetic variability and molecular identification of Brazilian Biomphalaria species (Mollusca: Planorbidae).

PubMed

Carvalho, S; Caldeira, R L; Simpson, A J; Vidigal, T H

2001-01-01

Freshwater snails belonging to the genus Biomphalaria are intermediate hosts of the trematode Schistosoma mansoni in the Neotropical region and Africa. In Brazil, one subspecies and ten species of Biomphalaria have been identified: B. glabrata, B. tenagophila, B. straminea, B. occidentalis, B. peregrina, B. kuhniana, B. schrammi, B. amazonica, B. oligoza, B. intermedia and B.t. guaibensis. However, only the first three species are found naturally infected with S. mansoni. The classical identification of these planorbids is based on comparison of morphological characteristics of the shell and male and female reproductive organs, which is greatly complicated by the extensive intra-specific variation. Several molecular techniques have been used in studies on the identification, genetic structure as well as phylogenetic relationships between these groups of organisms. Using the randomly amplified polymorphic DNAs (RAPD) analysis we demonstrated that B. glabrata exhibits a remarkable degree of intra-specific polymorphism. Thus, the genetics of the snail host may be more important to the epidemiology of schistosomiasis than those of the parasite itself. Using the simple sequence repeat anchored polymerase chain reaction (SSR-PCR) in intra-populational and intra-specific studies we have demonstrated that snails belonging to the B. straminea complex (B. straminea, B. kuhniana and B. intermedia) clearly presented higher heterogeneity. Using the low stringency polymerase chain reaction (LS-PCR) technique we were able to separate B. glabrata from B. tenagophila and B. tenagophila from B. occidentalis. To separate all Brazilian Biomphalaria species we used the restriction fragment length polymorphism (PCR-RFLP) of the internal transcribed spacer region (ITS) of the DNA gene. The method also proved to be efficient for the specific identification of DNA extracted from snail eggs. Recently we have sequenced the ITS2 region for phylogenetic studies of all Biomphalaria snails from

Molecular cloning of doublesex genes of four cladocera (water flea) species

PubMed Central

2013-01-01

Background The gene doublesex (dsx) is known as a key factor regulating genetic sex determination in many organisms. We previously identified two dsx genes (DapmaDsx1 and DapmaDsx2) from a freshwater branchiopod crustacean, Daphnia magna, which are expressed in males but not in females. D. magna produces males by parthenogenesis in response to environmental cues (environmental sex determination) and we showed that DapmaDsx1 expression during embryonic stages is responsible for the male trait development. The D. magna dsx genes are thought to have arisen by a cladoceran-specific duplication; therefore, to investigate evolutionary conservation of sex specific expression of dsx genes and to further assess their functions in the environmental sex determination, we searched for dsx homologs in four closely related cladoceran species. Results We identified homologs of both dsx genes from, D. pulex, D. galeata, and Ceriodaphnia dubia, yet only a single dsx gene was found from Moina macrocopa. The deduced amino acid sequences of all 9 dsx homologs contained the DM and oligomerization domains, which are characteristic for all arthropod DSX family members. Molecular phylogenetic analysis suggested that the dsx gene duplication likely occurred prior to the divergence of these cladoceran species, because that of the giant tiger prawn Penaeus monodon is rooted ancestrally to both DSX1 and DSX2 of cladocerans. Therefore, this result also suggested that M. macrocopa lost dsx2 gene secondarily. Furthermore, all dsx genes identified in this study showed male-biased expression levels, yet only half of the putative 5’ upstream regulatory elements are preserved in D. magna and D. pulex. Conclusions The all dsx genes of five cladoceran species examined had similar amino acid structure containing highly conserved DM and oligomerization domains, and exhibited sexually dimorphic expression patterns, suggesting that these genes may have similar functions for environmental sex

Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution.

PubMed

Melkikh, Alexey V; Khrennikov, Andrei

2017-11-01

A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Integrative taxonomy: Combining morphological, molecular and chemical data for species delineation in the parthenogenetic Trhypochthonius tectorum complex (Acari, Oribatida, Trhypochthoniidae)

PubMed Central

2011-01-01

Background There is a long-standing controversial about how parthenogenetic species can be defined in absence of a generally accepted species concept for this reproductive mode. An integrative approach was suggested, combining molecular and morphological data to identify distinct monophyletic entities. Using this approach, speciation of parthenogenetic lineages was recently demonstrated for groups of bdelloid rotifers and oribatid mites. Trhypochthonius tectorum, an oribatid mite from the entirely parthenogenetic desmonomatan family Trhypochthoniidae, is traditionally treated as a single species in Central Europe. However, two new morphological lineages were recently proposed for some Austrian populations of T. tectorum, and were described as novel subspecies (T. silvestris europaeus) or form (T. japonicus forma occidentalis). We used the morphological and morphometrical data which led to this separation, and added mitochondrial and nuclear DNA sequences and the chemical composition of complex exocrine oil gland secretions to test this taxonomical hypothesis. This is the first attempt to combine these three types of data for integrative taxonomical investigations of oribatid mites. Results We show that the previous European species T. tectorum represents a species complex consisting of three distinct lineages in Austria (T.tectorum, T. silvestris europaeus and T. japonicus forma occidentalis), each clearly separated by morphology, oil gland secretion profiles and mitochondrial cox1 sequences. This diversification happened in the last ten million years. In contrast to these results, no variation among the lineages was found in the nuclear 18S rDNA. Conclusions Our approach combined morphological, molecular and chemical data to investigate diversity and species delineation in a parthenogenetic oribatid mite species complex. To date, hypotheses of a general oribatid mite phylogeny are manifold, and mostly based on single-method approaches. Probably, the integrative

Molecular and morphological systematics of Doto Oken, 1851 (Gastropoda: Heterobranchia), with descriptions of five new species and a new genus.

PubMed

Shipman, Carissa; Gosliner, Terrence

2015-06-16

The nudibranch family Dotidae has been an extremely challenging group to study taxonomically due to their small body size, lack of distinct internal morphological differences and similar color patterns. This integrative systematic study of the Dotidae encompasses 29 individuals from the north Atlantic and Mediterranean, and 11 from the Indo-Pacific. Two mitochondrial genes, 16S, COI, and a nuclear gene, H3, were sequenced for 31 specimens and Bayesian and RAxML concatenated analyses were run. Dotidae is monophyletic and possesses strong geographic structure. Co-evolution between some of the north Atlantic taxa and their hydroid prey is apparent, thus supporting the hypothesis that speciation may be correlated with prey diversification. This study also supports the notion that the hydroid prey is a reliable indicator for distinguishing between cryptic species. Doto coronata Gmelin, the type species for the genus Doto, is re-described and a neotype, collected near Goes, Netherlands, is designated. From the molecular data, D. millbayana, D. dunnei, D. koenneckeri, D. maculata Lemche within the Doto coronata species complex, are confirmed to be distinct from D. coronata. Based on molecular data, specimens previously identified as D. coronata from South Africa are determined to represent a new species. It is described here and named Doto africoronata n. sp. Kabeiro n. gen. is introduced for the clade of elongate individuals from the Indo-Pacific, which diverges by 11.6% or greater in 16S from short-bodied Doto species. These elongate species are sister to all the short-bodied species and possess an enlarged pericardium, elongate cerata, a reproductive system with a pocketed prostate (penial gland), and an external tube-like digestive gland, which are absent in short-bodied Doto. Species of Kabeiro described here are: Kabeiro christianae n. sp., Kabeiro rubroreticulata n. sp., and Kabeiro phasmida n. sp. from the Philippines. The Indo-Pacific short-bodied species, Doto

Redox-signals and macrophage biology (for the upcoming issue of molecular aspects of medicine on signaling by reactive oxygen species).

PubMed

Weigert, Andreas; von Knethen, Andreas; Fuhrmann, Dominik; Dehne, Nathalie; Brüne, Bernhard

2018-01-11

Macrophages are known for their versatile role in biology. They sense and clear structures that contain exogenous or endogenous pathogen-associated molecular patterns. This process is tightly linked to the production of a mixture of potentially harmful oxidants and cytokines. Their inherent destructive behavior is directed against foreign material or structures of 'altered self', which explains the role of macrophages during innate immune reactions and inflammation. However, there is also another side of macrophages when they turn into a tissue regenerative, pro-resolving, and healing phenotype. Phenotype changes of macrophages are termed macrophage polarization, representing a continuum between classical and alternative activation. Macrophages as the dominating producers of superoxide/hydrogen peroxide and nitric oxide are not only prone to oxidative modifications but also to more subtle signaling properties of redox-active molecules conveying redox regulation. We review basic concepts of the enzymatic nitric oxide and superoxide production within macrophages, refer to their unique chemical reactions and outline biological consequences not only for macrophage biology but also for their communication with cells in the microenvironment. These considerations link hypoxia to the NO system, addressing feedforward as well as feedback circuits. Moreover, we summarize the role of redox-signaling affecting epigenetics and reflect the central role of mitochondrial-derived oxygen species in inflammation. To better understand the diverse functions of macrophages during initiation as well as resolution of inflammation and to decode their versatile roles during innate and adaptive immunity with the entire spectrum of cell protective towards cell destructive activities we need to appreciate the signaling properties of redox-active species. Herein we discuss macrophage responses in terms of nitric oxide and superoxide formation with the modulating impact of hypoxia. Copyright �

Molecular phylogenetic relationships of the Liolaemus rothi complex and a new species of lizard from Auca Mahuida Volcano (Squamata: Liolaemini).

PubMed

Avila, Luciano Javier; Olave, Melisa; Perez, Cristian Hernan Fulvio; Perez, Daniel Roberto; Morando, Mariana

2013-01-21

A new species of lizard of the genus Liolaemus from Neuquén Province, western Argentina, is described. The new species is a member of the Liolaemus rothi species complex, and mitochondrial and nuclear molecular data show it as sister taxon of the clade composed of (L. hermannunezi (L. tromen + L. loboi)), differing in size, squamation, coloration, and sexual dimorphism from the other species of this group. Liolaemus sitesi sp. nov. has a dark body coloration with series of notched blotches on the dorsum, with bright spots, and a very iridescent yellow-green coloration in natural light. Liolaemus sitesi sp. nov. is found only in the Auca Mahuida volcano and is terrestrial, dwelling on the stony slopes with sandy soil between 1300 m and the volcano summit.

Screening Active Compounds from Garcinia Species Native to China Reveals Novel Compounds Targeting the STAT/JAK Signaling Pathway

PubMed Central

Xu, Linfeng; Lao, Yuanzhi; Zhao, Yanhui; Qin, Jian; Fu, Wenwei; Zhang, Yingjia; Xu, Hongxi

2015-01-01

Natural compounds from medicinal plants are important resources for drug development. In a panel of human tumor cells, we screened a library of the natural products from Garcinia species which have anticancer potential to identify new potential therapeutic leads and discovered that caged xanthones were highly effective at suppressing multiple cancer cell lines. Their anticancer activities mainly depended on apoptosis pathways. For compounds in sensitive cancer line, their mechanisms of mode of action were evaluated. 33-Hydroxyepigambogic acid and 35-hydroxyepigambogic acid exhibited about 1 μM IC50 values against JAK2/JAK3 kinases and less than 1 μM IC50 values against NCI-H1650 cell which autocrined IL-6. Thus these two compounds provided a new antitumor molecular scaffold. Our report describes 33-hydroxyepigambogic acid and 35-hydroxyepigambogic acid that inhibited NCI-H1650 cell growth by suppressing constitutive STAT3 activation via direct inhibition of JAK kinase activity. PMID:26090459

The genus Syllis Savigny in Lamarck, 1818 (Annelida, Syllidae) from Australia. Molecular analysis and re-description of some poorly-known species.

PubMed

Álvarez-Campos, Patricia; Riesgo, Ana; Hutchings, Pat; San Martín, Guillermo

2015-12-03

The taxonomy and phylogenetic relationships within Syllis Savigny in Lamarck, 1818, the type genus of the family Syllidae, are still a matter of debate because the group does not show clear synapomorphies and because of the lack of molecular data for many of the species. In order to help understand some of the phylogenetic relationships within the genus Syllis, we have performed a morphological revision of part of the material collected during decades by the Australian Museum staff, and provide molecular data for species not sequenced before. In particular, seven poorly known Australian species of the genus Syllis Savigny in Lamarck, 1818 have been re-described in detail and sequenced to analyze their phylogenetic position: Syllis broomensis n. comb., S. crassicirrata (Treadwell, 1925) n. comb., Syllis cruzi Núñez & San Martín, 1991, S. edensis (Hartmann-Schröder, 1989), Syllis gracilis Grube, 1840, Syllis picta (Kinberg, 1866) n. comb., and S. setoensis (Imajima, 1966). The results obtained indicate the paraphyly of Typosyllis and a possible new organization of Syllis, which contains at least four well-supported clades.

Molecular Diagnosis of Pathogenic Sporothrix Species

PubMed Central

Rodrigues, Anderson Messias; de Hoog, G. Sybren; de Camargo, Zoilo Pires

2015-01-01

Background Sporotrichosis is a chronic (sub)cutaneous infection caused by thermodimorphic fungi in the order, Ophiostomatales. These fungi are characterized by major differences in routes of transmission, host predilections, species virulence, and susceptibilities to antifungals. Sporothrix species emerge in the form of outbreaks. Large zoonoses and sapronoses are ongoing in Brazil and China, respectively. Current diagnostic methods based on morphology and physiology are inaccurate due to closely related phenotypes with overlapping components between pathogenic and non-pathogenic Sporothrix. There is a critical need for new diagnostic tools that are specific, sensitive, and cost-effective. Methodology We developed a panel of novel markers, based on calmodulin (CAL) gene sequences, for the large-scale diagnosis and epidemiology of clinically relevant members of the Sporothrix genus, and its relative, Ophiostoma. We identified specific PCR-based markers for S. brasiliensis, S. schenckii, S. globosa, S. mexicana, S. pallida, and O. stenoceras. We employed a murine model of disseminated sporotrichosis to optimize a PCR assay for detecting Sporothrix in clinical specimens. Results Primer-BLAST searches revealed candidate sequences that were conserved within a single species. Species-specific primers showed no significant homology with human, mouse, or microorganisms outside the Sporothrix genus. The detection limit was 10–100 fg of DNA in a single round of PCR for identifying S. brasiliensis, S. schenckii, S. globosa, S. mexicana, and S. pallida. A simple, direct PCR assay, with conidia as a source of DNA, was effective for rapid, low-cost genotyping. Samples from a murine model of disseminated sporotrichosis confirmed the feasibility of detecting S. brasiliensis and S. schenckii DNA in spleen, liver, lungs, heart, brain, kidney, tail, and feces of infected animals. Conclusions This PCR-based method could successfully detect and identify a single species in samples

Chemiluminescent activation of the antiviral activity of hypericin: a molecular flashlight.

PubMed Central

Carpenter, S; Fehr, M J; Kraus, G A; Petrich, J W

1994-01-01

Hypericin is a naturally occurring photosensitizer that displays potent antiviral activity in the presence of light. The absence of light in many regions of the body may preclude the use of hypericin and other photosensitizers as therapeutic compounds for the treatment of viral infections in vivo. The chemiluminescent oxidation of luciferin by the luciferase from the North American firefly Photinus pyralis was found to generate sufficiently intense and long-lived emission to induce antiviral activity of hypericin. Light-induced virucidal activity of hypericin was demonstrated against equine infectious anemia virus, a lentivirus structurally, genetically, and antigenically related to the human immunodeficiency virus. The implications for exploiting chemiluminescence as a "molecular flashlight" for effecting photodynamic therapy against virus-infected cells and tumor cells are discussed. PMID:7991618

Metabolic alterations by clofibric acid in the formation of molecular species of phosphatidylcholine in rat liver.

PubMed

Mizuguchi, H; Kudo, N; Kawashima, Y

2001-10-01

The mechanism by which p-chlorophenoxyisobutyric acid (clofibric acid) induces striking changes in the proportion of the molecular species of phosphatidylcholine (PC) in rat liver was studied. Treatment of rats with clofibric acid strikingly increased the content of 1-palmitoyl-2-oleoyl (16:0-18:1) PC, but decreased the contents of 1-palmitoyl-2-docosahexaenoyl (16:0-22:6), 1-stearoyl-2-arachidonoyl (18:0-20:4), and 1-stearoyl-2-linoleoyl (18:0-18:2) PC; the drug did not change the content of 1-palmitoyl-2-arachidonoyl (16:0-20:4) PC. The mechanism underlying these changes has been investigated with regard to the in vivo formation of the molecular species of PC by: (i) de novo synthesis, (ii) reacylation, and (iii) methylation of phosphatidylethanolamine (PE). We found that (i) the incorporation of [3H]glycerol, which was injected intravenously, into 16:0-18:1 diacylglycerol (DG) and 16:0-18:1 PC was increased markedly by clofibric acid feeding without changing the substrate specificity of CDP-choline:DG cholinephosphotransferase, (ii) the in vivo formation of 16:0-18:1 and 16:0-20:4 PC from 1-16:0-[3H]glycerophosphocholine (GPC), which was injected intraportally, was increased markedly by clofibric acid feeding, and (iii) the incorporation of [14C]ethanolamine, which was injected intravenously into 16:0-22:6, 18:0-22:6, and 18:0-20:4 PC, was decreased by clofibric acid feeding; the extent of the decrease in 16:0-20:4 PC was less than that of 18:0-20:4 PC. It was concluded, therefore, that (i) clofibric acid selectively increased the content and proportion of 16:0-18:1 PC by enhancing both the CDP-choline pathway and the remodeling of the pre-existing PC molecule, and (ii) the drug kept the content of 16:0-20:4 PC unchanged by stimulating the remodeling of the pre-existing PC molecule, whereas the formation of other more long chain, polyunsaturated molecular species, such as 16:0-22:6, 18:0-22:6, and 18:0-20:4, was decreased owing to the suppression of PE

Molecular characterization of Trichinella species from wild animals in Israel.

PubMed

Erster, Oran; Roth, Asael; King, Roni; Markovics, Alex

2016-11-15

Trichinellosis is a worldwide disease caused by nematode worms of the genus Trichinella, frequently diagnosed in Israel. However, the identity of the Israeli isolates have not been studied. Here we describe the molecular characterization of 58 isolates collected from jackals (Canis aureus), wild boar (Sus scrofa), foxes (Vulpes vulpes) and a wolf (Canis lupus) in central and northern Israel. Isolates were analyzed using the multiplex PCR analysis encompassing expansion segment V (ESV) and internal sequence 1 (ITS-1) markers, which identified 52 of the 58 samples. Out of the six unidentified samples, four were successfully identified using extended PCR assays for ESV and ITS-1, developed in this study. Our analysis identified 44 isolates as T. britovi, 8 as T. spiralis, four mixed infections, and two isolates were not identified. Clonal analysis of the ITS-1 sequences from six isolates confirmed the initial identification of four mixed infections. These results show that the prevalent species in Israel are T. britovi and T. spiralis, with nearly 7% (4 of 58) incidence of mixed infection. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular Identification and Antifungal Susceptibility Pattern of Non-albicans Candida Species Isolated from Vulvovaginal Candidiasis

PubMed Central

Nejat, Ziba Abbasi; Farahyar, Shirin; Falahati, Mehraban; Khozani, Mahtab Ashrafi; Hosseini, Aga Fateme; Faiazy, Azamsadat; Ekhtiari, Masoome; Hashemi-Hafshenjani, Saeideh

2018-01-01

Background: Vulvovaginal candidiasis (VVC) is an important health problem caused by Candida spp. The aim of this study was molecular identification, phylogenetic analysis, and evaluation of antifungal susceptibility of non-albicans Candida isolates from VVC. Methods: Vaginal secretion samples were collected from 550 vaginitis patients at Sayyad Shirazi Medical and Educational Center of Gorgan (Golestan Province, Iran) from May to October 2015. Samples were analyzed using conventional mycological and molecular approaches. Clinical isolates were analyzed with specific PCR using CGL primers, and the internal transcribed spacer region and the D1-D2 domain of the large-subunit rRNA gene were amplified and sequenced. Susceptibility to amphotericin B, fluconazole, itraconazole, and clotrimazole was determined by the guidelines of the Clinical and Laboratory Standard Institute. Results: In total, 35 non-albicans Candida isolates were identified from VVC patients. The isolates included 27 strains of Candida glabrata (77.1%), 5 Candida krusei (Pichia kudriavzevii; 14.3%), 2 Candida kefyr (Kluyveromyces marxianus; 5.7%), and 1 Candida lusitaniae (Clavispora lusitaniae; 2.9%). The fungicides itraconazole and amphotericin B were effective against all species. One isolate of C. glabrata showed resistance to fluconazole and clotrimazole, and 26 isolates of C. glabrata indicated dose-dependent susceptibility to fluconazole. C. lusitaniae was susceptible in a dose-dependent manner to fluconazole and resistant to clotrimazole. Conclusions: Non-albicans Candida spp. are common agents of vulvovaginitis, and C. glabrata is the most common species in the tested patients. PMID:28688376

Revision of the genus Dinotoperla Tillyard, 1921 (Plecoptera: Gripopterygidae) using morphological characters and molecular data: Establishes two new genera, three new species and updates the larval taxonomy.

PubMed

Mynott, Julia H; Suter, Phillip J; Theischinger, Gunther

2017-01-23

The larval taxonomy of Australian stoneflies (Plecoptera) shows a large disparity in knowledge when compared to the adult taxonomy with many species having undescribed larval forms. The importance of stoneflies as an indicator group for monitoring aquatic ecosystems means knowledge of the larval taxonomy and the ability to identify species is essential. This study combined morphology and mitochondrial gene sequences to associate the adult and larval life-stages for species of Dinotoperla Tillyard. Morphological identification of adult males was recognised for 17 of the 35 Dinotoperla species and combining molecular data with morphology confirmed eight new adult-larval life stage associations. Further, molecular data supported the larval taxonomy for five morphospecies which remain unassociated. The combination of molecular and morphological methods enabled the larval morphology to be reassessed for the genus Dinotoperla and this has led to the establishment of two new genera, Odontoperla, gen. nov. and Oedemaperla, gen. nov., and the new species Dinotoperla aryballoi, sp. nov, D. tasmaniensis, sp. nov. and Oedemaperla shackletoni, sp. nov. as well as the new or updated descriptions of the larvae of 31 species and a comprehensive dichotomous key to these larvae.

Active mechanics in living oocytes reveal molecular-scale force kinetics

NASA Astrophysics Data System (ADS)

Ahmed, Wylie; Fodor, Etienne; Almonacid, Maria; Bussonnier, Matthias; Verlhac, Marie-Helene; Gov, Nir; Visco, Paolo; van Wijland, Frederic; Betz, Timo

Unlike traditional materials, living cells actively generate forces at the molecular scale that change their structure and mechanical properties. This nonequilibrium activity is essential for cellular function, and drives processes such as cell division. Single molecule studies have uncovered the detailed force kinetics of isolated motor proteins in-vitro, however their behavior in-vivo has been elusive due to the complex environment inside the cell. Here, we quantify active forces and intracellular mechanics in living oocytes using in-vivo optical trapping and laser interferometry of endogenous vesicles. We integrate an experimental and theoretical framework to connect mesoscopic measurements of nonequilibrium properties to the underlying molecular- scale force kinetics. Our results show that force generation by myosin-V drives the cytoplasmic-skeleton out-of-equilibrium (at frequencies below 300 Hz) and actively softens the environment. In vivo myosin-V activity generates a force of F ~ 0 . 4 pN, with a power-stroke of length Δx ~ 20 nm and duration τ ~ 300 μs, that drives vesicle motion at vv ~ 320 nm/s. This framework is widely applicable to characterize living cells and other soft active materials.

Intrinsically disordered proteins as molecular shields†

PubMed Central

Chakrabortee, Sohini; Tripathi, Rashmi; Watson, Matthew; Kaminski Schierle, Gabriele S.; Kurniawan, Davy P.; Kaminski, Clemens F.; Wise, Michael J.; Tunnacliffe, Alan

2017-01-01

The broad family of LEA proteins are intrinsically disordered proteins (IDPs) with several potential roles in desiccation tolerance, or anhydrobiosis, one of which is to limit desiccation-induced aggregation of cellular proteins. We show here that this activity, termed molecular shield function, is distinct from that of a classical molecular chaperone, such as HSP70 – while HSP70 reduces aggregation of citrate synthase (CS) on heating, two LEA proteins, a nematode group 3 protein, AavLEA1, and a plant group 1 protein, Em, do not; conversely, the LEA proteins reduce CS aggregation on desiccation, while HSP70 lacks this ability. There are also differences in interaction with client proteins – HSP70 can be co-immunoprecipitated with a polyglutamine-containing client, consistent with tight complex formation, whereas the LEA proteins can not, although a loose interaction is observed by Förster resonance energy transfer. In a further exploration of molecular shield function, we demonstrate that synthetic polysaccharides, like LEA proteins, are able to reduce desiccation-induced aggregation of a water-soluble proteome, consistent with a steric interference model of anti-aggregation activity. If molecular shields operate by reducing intermolecular cohesion rates, they should not protect against intramolecular protein damage. This was tested using the monomeric red fluorescent protein, mCherry, which does not undergo aggregation on drying, but the absorbance and emission spectra of its intrinsic fluorophore are dramatically reduced, indicative of intramolecular conformational changes. As expected, these changes are not prevented by AavLEA1, except for a slight protection at high molar ratios, and an AavLEA1-mCherry fusion protein is damaged to the same extent as mCherry alone. A recent hypothesis proposed that proteomes from desiccation-tolerant species contain a higher degree of disorder than intolerant examples, and that this might provide greater intrinsic stability

Intrinsically disordered proteins as molecular shields.

PubMed

Chakrabortee, Sohini; Tripathi, Rashmi; Watson, Matthew; Schierle, Gabriele S Kaminski; Kurniawan, Davy P; Kaminski, Clemens F; Wise, Michael J; Tunnacliffe, Alan

2012-01-01

The broad family of LEA proteins are intrinsically disordered proteins (IDPs) with several potential roles in desiccation tolerance, or anhydrobiosis, one of which is to limit desiccation-induced aggregation of cellular proteins. We show here that this activity, termed molecular shield function, is distinct from that of a classical molecular chaperone, such as HSP70 - while HSP70 reduces aggregation of citrate synthase (CS) on heating, two LEA proteins, a nematode group 3 protein, AavLEA1, and a plant group 1 protein, Em, do not; conversely, the LEA proteins reduce CS aggregation on desiccation, while HSP70 lacks this ability. There are also differences in interaction with client proteins - HSP70 can be co-immunoprecipitated with a polyglutamine-containing client, consistent with tight complex formation, whereas the LEA proteins can not, although a loose interaction is observed by Förster resonance energy transfer. In a further exploration of molecular shield function, we demonstrate that synthetic polysaccharides, like LEA proteins, are able to reduce desiccation-induced aggregation of a water-soluble proteome, consistent with a steric interference model of anti-aggregation activity. If molecular shields operate by reducing intermolecular cohesion rates, they should not protect against intramolecular protein damage. This was tested using the monomeric red fluorescent protein, mCherry, which does not undergo aggregation on drying, but the absorbance and emission spectra of its intrinsic fluorophore are dramatically reduced, indicative of intramolecular conformational changes. As expected, these changes are not prevented by AavLEA1, except for a slight protection at high molar ratios, and an AavLEA1-mCherry fusion protein is damaged to the same extent as mCherry alone. A recent hypothesis proposed that proteomes from desiccation-tolerant species contain a higher degree of disorder than intolerant examples, and that this might provide greater intrinsic stability

Contrasting activity patterns of two related octopus species, Octopus macropus and Octopus vulgaris.

PubMed

Meisel, Daniela V; Byrne, Ruth A; Kuba, Michael; Mather, Jennifer; Ploberger, Werner; Reschenhofer, Erhard

2006-08-01

Octopus macropus and Octopus vulgaris have overlapping habitats and are exposed to similar temporal changes. Whereas the former species is described as nocturnal in the field, there are conflicting reports about the activity time of the latter one. To compare activity patterns, the authors tested both species in the laboratory. Octopuses were exposed to a light-dark cycle and held under constant dim light for 7 days each. O. macropus showed nocturnal and light-cued activity. According to casual observations, O. vulgaris started out nocturnal but had switched to mostly diurnal when the experiment began. Individual variation of its activity was found. The different activity patterns of O. macropus and O. vulgaris might reflect their lifestyles, the latter species being more generalist. ((c) 2006 APA, all rights reserved).

Availability of surface boron species in improved oxygen reduction activity of Pt catalysts: A first-principles study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Libo; Zhou, Gang, E-mail: gzhou@mail.buct.edu.cn

2016-04-14

The oxidation process of boron (B) species on the Pt(111) surface and the beneficial effects of boron oxides on the oxygen reduction activity are investigated by first-principles calculations. The single-atom B anchored on the Pt surface has a great attraction for the oxygen species in the immediate environment. With the dissociation of molecular oxygen, a series of boron oxides is formed in succession, both indicating exothermic oxidation reactions. After BO{sub 2} is formed, the subsequent O atom immediately participates in the oxygen reduction reaction. The calculated O adsorption energy is appreciably decreased as compared to Pt catalysts, and more approximatemore » to the optimal value of the volcano plot, from which is clear that O hydrogenation kinetics is improved. The modulation mechanism is mainly based on the electron-deficient nature of stable boron oxides, which normally reduces available electronic states of surface Pt atoms that bind the O by facilitating more electron transfer. This modification strategy from the exterior opens the new way, different from the alloying, to efficient electrocatalyst design for PEMFCs.« less

Cytogenetic and Molecular Data Demonstrate that the Bryconinae (Ostariophysi, Bryconidae) Species from Southeastern Brazil Form a Phylogenetic and Phylogeographic Unit

PubMed Central

Travenzoli, Natália Martins; Silva, Priscilla Caroline; Santos, Udson; Zanuncio, José Cola; Oliveira, Claudio; Dergam, Jorge Abdala

2015-01-01

Brycon spp. occur in Neotropical watersheds to the west and east of the Andes, and as they are sensitive to anthropogenic changes, many these species are endangered in southeastern Brazil. Coastal rivers in southeastern Brazil are characterized by the presence of relatively few freshwater fish species and high endemism of this fauna. The objective of this study was to examine whether Brycon spp. occurring in the coastal basins of southeastern Brazil are monophyletic, using cytogenetic data, mitochondrial, and nuclear molecular markers. All the species showed a diploid number of 50 chromosomes, a conserved number within the subfamily Bryconinae. However, the karyotypic formulas were unique to most species, including Brycon devillei (26m+22sm+2st), Brycon ferox (26m+12sm+12st), Brycon insignis (22m+20sm+8st), Brycon opalinus, and Brycon vermelha (24m+20sm+6st), indicating the prevalence of pericentric and paracentric inversions in the chromosomal evolution of these species. All of them had nucleolar organizer regions in the first pair of subtelocentric chromosomes and no equilocal distribution of heterochromatin in the first pair of chromosomes of the karyotype. These two features, not seen in any other Brycon spp. examined to date, indicate that Bryconinae species from the Brazilian southeastern coastal basins, including the monotypic genus Henochilus, are monophyletic. Also, this is the first study that reports NOR location and C-banding patterns as synapomorphies for a Neotropical fish species group. The monophyly was also supported by a phylogenetic analysis of 16S rDNA (16S), cytochrome oxidase subunit I (COI), alpha-myosin (MYH6) genes and S72 intron molecular data. Our results partially corroborate the “Brycon acuminatus” group proposed by Howes in 1982: our proposed clade keeps B. devillei, B. ferox, and B. insignis; but it also includes B. opalinus, B. vermelha, and H. weatlandii whereas it excludes B. nattereri. The phylogeographic unit formed by

Molecular basis of sodium butyrate-dependent proapoptotic activity in cancer cells.

PubMed

Pajak, B; Orzechowski, A; Gajkowska, B

2007-01-01

This review outlines the molecular events that accompany the antitumor action of sodium butyrate (NaBt). Butyrate, a low-molecular weight four-carbon chain volatile fatty acid (VFA) has been previously shown to withdraw cells from cell cycle or to promote cell differentiation, and finally to induce programmed cell death. Recent advances in molecular biology indicate, that this product of large bowel microbial fermentation of dietary fiber, might evoke the above-mentioned effects by indirect action on genes. NaBt was shown to inhibit histone deacetylase activity, allowing DNA binding of several transcription factors. Higher genomic activity leads to the higher expression of proapoptotic genes, higher level of their protein products and elevated sensitivity to death ligand-induced apoptosis. Cancer cells might be arrested in G1 phase of cell cycle in a p21-dependent manner. Proapoptotic activity of NaBt includes higher expression of membrane death receptors (DR4/5), higher level and activation of Smad3 protein in TGF-beta-dependent apoptotic pathway, lower level of antiapoptotic proteins (cFLIP, XIAP) and activation ofproapoptotic tBid protein. Thus, both intrinsic and extrinsic apoptotic pathways are stimulated to ampify the apoptotic signals. These effects are specific for tumor but not for regular cells. Unique properties of NaBt make this agent a promising metabolic inhibitor to retard tumorigenesis to suppress tumor growth.

Polysaccharides and their depolymerized fragments from Costaria costata: Molecular weight and sulfation-dependent anticoagulant and FGF/FGFR signal activating activities.

PubMed

Hou, Ningning; Zhang, Meng; Xu, Yingjie; Sun, Zhongmin; Wang, Jing; Zhang, Lijuan; Zhang, Quanbin

2017-12-01

Crude polysaccharides from Costaria costata were extracted by hot water and further fractionated by anion exchange chromatography into three polysaccharide fractions. Three low molecular weight fragments were then prepared by degradation of the polysaccharides with hydrogen peroxide and ascorbic acid. The structural features of the polysaccharides and their low molecular weight fragments were elucidated for the first time based on the HGPC, FT-IR, NMR, MS, monosaccharide composition, and other chemical analyses. Their anticoagulant and FGF-1, -2, -7, -8, -9, -10/FGFR1c signaling activation activities in BaF3 cells were also examined. Our studies showed that the polysaccharides were sulfated at different positions of galactose and fucose residues. The APTT-, PT- and TT-based anticoagulant assay results indicated that a high molecular weight and a higher degree of sulfation were essential for their anticoagulant activities. In contrast, not only the polysaccharides but also the depolymerized fragments showed significant FGF/FGFR signal activating activities in a FGF-, molecular weight-, and sulfation-dependent manner. The results presented in current study demonstrated the potential use of the polysaccharides and their fragments as anticoagulants and FGF signal regulators. Copyright © 2017 Elsevier B.V. All rights reserved.

Antioxidant activity of fractions from oregano essential oils obtained by molecular distillation.

PubMed

Olmedo, Ruben; Nepote, Valeria; Grosso, Nelson Ruben

2014-08-01

The objective of this study was to determine the antioxidant activity of fractions separated from oregano essential oil by short-path molecular distillation. Two residue (R1 and R2) and two distillate (D1 and D2) fractions were prepared by molecular distillation. The major components were: carvacrol, terpinen-4-ol and γ-terpinene in R1 and R2; and γ-terpinene, α-terpineol and sabinene in D1 and D2. Free-radical scavenging activity was observed in all fractions and was highest in R2 (77.2%). D1 and D2 showed a smaller amount of volatile oxidation compounds produced from sunflower oil stored at 60°C for 14days. The greatest antioxidant activity was observed in D1 and D2. The thermal stability of oregano essential oil and its fractions was also analysed. R1 and R2 presented an increased carvacrol concentration and thermal stability. The short-path molecular distillation fractions can be used to prepare fractions from oregano essential oil with a higher antioxidant activity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular Identification of Malassezia Species in Patients with Malassezia folliculitis in Sfax, Tunisia.

PubMed

Cheikhrouhou, F; Guidara, R; Masmoudi, A; Trabelsi, H; Neji, S; Sellami, H; Makni, F; Ayadi, A

2017-06-01

Malassezia folliculitis is caused by the invasion of hair follicles by large numbers of Malassezia cells. Several Malassezia researches still use cultures, morphology and biochemical techniques. The aim of this study was to identify Malassezia species isolated from patients diagnosed with folliculitis, at the Parasitology and Mycology Laboratory of Sfax University Hospital, and to explore the genetic diversity of Malassezia by using PCR-RFLP and PCR-sequencing targeting the rDNA region of the Malassezia genome. Specimens were taken from 27 patients with Malassezia folliculitis. For the molecular identification, PCR amplification of the 26S rDNAD1/D2 region was carried out using the Malup and Maldown primers and three restriction enzymes (BanI, MspI and HeaII) for RFLP analysis. The nucleotide sequences of each isolate were compared to those in the NCBI GenBank by using BLASTIN algorithm. Three species of Malassezia yeasts were identified among the 31 Malassezia strains isolated: M. globosa (83.9%), M. sympodialis (12. 9%) and M. furfur (3.2%). The sequence analysis of M. globosa showed six genotypes. There is a high genotypic variability of M. globosa colonizing patients with folliculitis.

Decreased hepatic contents of coenzyme A molecular species in mice after subchronic mild social defeat stress.

PubMed

Kubota, Yoshifumi; Goto, Tatsuhiko; Hagiya, Yuki; Chohnan, Shigeru; Toyoda, Atsushi

2016-01-01

Social stress may precipitate psychiatric disorders such as depression, which is related to the occurrence of the metabolic syndrome, including obesity and type 2 diabetes. We have evaluated the effects of social stress on central and peripheral metabolism using a model of depression in mice. In the present study, we focused on coenzyme A (CoA) molecular species [i.e. non-esterified CoA (CoASH), acetyl-CoA and malonyl-CoA] which play important roles in numerous metabolic pathways, and we analyzed changes in expression of these molecules in the hypothalamus and liver of adult male mice (C57BL/6J) subjected to 10 days of subchronic mild social defeat stress (sCSDS) with ICR mice as aggressors. Mice (n = 12) exposed to showed hyperphagia- and polydipsia-like symptoms and increased body weight gain compared with control mice which were not affected by exposure to ICR mice (n = 12). To elucidate the underlying metabolic features in the sCSDS model, acetyl-CoA, malonyl-CoA and CoASH tissue levels were analyzed using the acyl-CoA cycling method. The levels of hypothalamic malonyl-CoA, which decreases feeding behavior, were not influenced by sCSDS. However, sCSDS reduced levels of acetyl-CoA, malonyl-CoA and total CoA (sum of the three CoA molecular species) in the liver. Hence, hyperphagia-like symptoms in sCSDS mice evidently occurred independently of hypothalamic malonyl-CoA, but might consequently lead to down-regulation of hepatic CoA via altered expression of nudix hydrolase 7. Future studies should investigate the molecular mechanism(s) underlying the down-regulation of liver CoA pools in sCSDS mice.

A Review on the Medicinal Plant Dalbergia odorifera Species: Phytochemistry and Biological Activity

PubMed Central

2017-01-01

The crucial medicinal plant Dalbergia odorifera T. Chen species belongs to genus Dalbergia, with interesting secondary metabolites, consisting of main classes of flavonoid, phenol, and sesquiterpene derivatives, as well as several arylbenzofurans, quinones, and fatty acids. Biological studies were carried out on extracts, fractions, and compounds from this species involved in cytotoxic assays; antibacterial, antioxidative, anti-inflammatory, antithrombotic, antiplatelet, antiosteosarcoma, antiosteoporosis, antiangiogenesis, and prostaglandin biosynthetic enzyme inhibition activities; vasorelaxant activities; alpha-glucosidase inhibitory activities; and many other effects. In terms of the valuable resources for natural new drugs development, D. odorifera species are widely used as medicinal drugs in many countries for treatment of cardiovascular diseases, cancer, diabetes, blood disorders, ischemia, swelling, necrosis, or rheumatic pain. Although natural products from this plant have been increasingly playing an important role in drug discovery programs, there is no supportive evidence to provide a general insight into phytochemical studies on D. odorifera species and biological activities of extracts, fractions, and isolated compounds. To a certain extent, this review deals with an overview of almost naturally occurring compounds from this species, along with extensive coverage of their biological evaluations. PMID:29348771

Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

PubMed

Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

2016-09-01

A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

Protease-inhibiting, molecular modeling and antimicrobial activities of extracts and constituents from Helichrysum foetidum and Helichrysum mechowianum (compositae).

PubMed

Malolo, Fanny-Aimée Essombe; Bissoue Nouga, Achille; Kakam, Antoine; Franke, Katrin; Ngah, Lidwine; Flausino, Otavio; Mpondo Mpondo, Emmanuel; Ntie-Kang, Fidele; Ndom, Jean Claude; Bolzani, Vanderlan da Silva; Wessjohann, Ludger

2015-01-01

Helichrysum species are used extensively for stress-related ailments and as dressings for wounds normally encountered in circumcision rites, bruises, cuts and sores. It has been reported that Helichysum species are used to relief abdominal pain, heart burn, cough, cold, wounds, female sterility, menstrual pain. From the extracts of Helichrysum foetidum (L.) Moench, six known compounds were isolated and identified. They were 7, 4'-dihydroxy-5-methoxy-flavanone (1), 6'-methoxy-2',4, 4'-trihydroxychalcone (2), 6'-methoxy-2',4-dihydroxychalcone -4'-O-β-D-glucoside (3), apigenin (4), apigenin-7-O-β-D-glucoside (5), kaur-16-en-18-oic acid (6) while two known compounds 3,5,7-trihydroxy-8-methoxyflavone (12), 4,5-dicaffeoyl quinic acid (13) together with a mixture of phytosterol were isolated from the methanol extract of Helichrysum mechowianum Klatt. All the compounds were characterized by spectroscopic and mass spectrometric methods, and by comparison with literature data. Both extracts and all the isolates were screened for the protease inhibition, antibacterial and antifungal activities. In addition, the phytochemical profiles of both species were investigated by ESI-MS experiments. These results showed that the protease inhibition assay of H. foetidum could be mainly attributed to the constituents of flavonoids glycosides (3, 5) while the compound (13) from H. mechowianum contributes to the stomach protecting effects. In addition, among the antibacterial and antifungal activities of all the isolates, compound (6) was found to possess a potent inhibitor effect against the tested microorganisms. The heterogeneity of the genus is also reflected in its phytochemical diversity. The differential bioactivities and determined constituents support the traditional use of the species. Molecular modelling was carried out by computing selected descriptors related to drug absorption, distribution, metabolism, excretion and toxicity (ADMET). Graphical abstractCompounds isolated

A new species of Alsodes (Anura: Alsodidae) from Altos de Cantillana, central Chile.

PubMed

Charrier, Andrés; Correa, Claudio; Castro, Camila; Méndez, Marco A

2015-02-05

Based on morphological and molecular evidence (mitochondrial and nuclear sequences) we describe a new species of spiny-chest frog, Alsodes cantillanensis, from central Chile (around 34°S). The type locality, Quebrada Infiernillo, is located in the Coastal Range at approximately 65 km from Santiago (Metropolitan Region), the capital of Chile. The distribution of the new species is included entirely in that of A. nodosus (32-36°S approximately), which was identified as the sister taxon according to molecular phylogenetic analyses. Moreover, both species are sympatric in the type locality. The new species was found in a Nothofagus macrocarpa relict forest potentially threatened by gold mining activities. We identify other threats for its conservation and some biological data needed for understanding the evolution of this species. This discovery reveals the scarce knowledge about biogeography, evolution and ecology of spiny-chest frogs from central Chile. 

The Mediterranean red alga Asparagopsis taxiformis has antifungal activity against Aspergillus species.

PubMed

Genovese, Giuseppa; Leitner, Sandra; Minicante, Simona A; Lass-Flörl, Cornelia

2013-09-01

The red algae Asparagopsis taxiformis collected from the Straits of Messina (Italy) were screened for antifungal activity against Aspergillus species. EUCAST methodology was applied and extracts showed antifungal activity against A. fumigatus, A. terreus and A. flavus. The lowest minimum inhibitory concentrations observed were <0.15 mg ml(-1) and the highest were >5 mg ml(-1) for Aspergillus spp. tested. Agar diffusion assays confirmed antifungal activity of A. taxiformis extracts in Aspergillus species. © 2013 Blackwell Verlag GmbH.

Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh

PubMed Central

Begum, Rabeya; Alam, Sheikh Shamimul; Menzel, Gerhard; Schmidt, Thomas

2009-01-01

Background and Aims Dendrobium species show tremendous morphological diversity and have broad geographical distribution. As repetitive sequence analysis is a useful tool to investigate the evolution of chromosomes and genomes, the aim of the present study was the characterization of repetitive sequences from Dendrobium moschatum for comparative molecular and cytogenetic studies in the related species Dendrobium aphyllum, Dendrobium aggregatum and representatives from other orchid genera. Methods In order to isolate highly repetitive sequences, a c0t-1 DNA plasmid library was established. Repeats were sequenced and used as probes for Southern hybridization. Sequence divergence was analysed using bioinformatic tools. Repetitive sequences were localized along orchid chromosomes by fluorescence in situ hybridization (FISH). Key Results Characterization of the c0t-1 library resulted in the detection of repetitive sequences including the (GA)n dinucleotide DmoO11, numerous Arabidopsis-like telomeric repeats and the highly amplified dispersed repeat DmoF14. The DmoF14 repeat is conserved in six Dendrobium species but diversified in representative species of three other orchid genera. FISH analyses showed the genome-wide distribution of DmoF14 in D. moschatum, D. aphyllum and D. aggregatum. Hybridization with the telomeric repeats demonstrated Arabidopsis-like telomeres at the chromosome ends of Dendrobium species. However, FISH using the telomeric probe revealed two pairs of chromosomes with strong intercalary signals in D. aphyllum. FISH showed the terminal position of 5S and 18S–5·8S–25S rRNA genes and a characteristic number of rDNA sites in the three Dendrobium species. Conclusions The repeated sequences isolated from D. moschatum c0t-1 DNA constitute major DNA families of the D. moschatum, D. aphyllum and D. aggregatum genomes with DmoF14 representing an ancient component of orchid genomes. Large intercalary telomere-like arrays suggest chromosomal

Morphological, molecular and biological evidence reveal two cryptic species in Mecinus janthinus Germar (Coleoptera, Curculionidae), a successful biological control agent of Dalmatian toadflax, Linaria dalmatica (Lamiales, Plantaginaceae)

Treesearch

Ivo Tosevski; Roberto Caldara; Jelena Jovic; Gerardo Hernandez-Vera; Cosimo Baviera; Andre Gassmann; Brent C. Emerson

2011-01-01

A combined morphological, molecular and biological study shows that the weevil species presently named Mecinus janthinus is actually composed of two different cryptic species: M. janthinus Germar, 1821 and M. janthiniformis Tosevski & Caldara sp.n. These species are morphologically distinguishable from each other by a few very subtle morphological characters. On...

The activity of Rubisco's molecular chaperone, Rubisco activase, in leaf extracts

USDA-ARS?s Scientific Manuscript database

Rubisco frequently undergoes unproductive interactions with its sugar-phosphate substrate that stabilize active sites in an inactive conformation. Restoring catalytic competence to these sites requires the “molecular chiropractic” activity of Rubisco activase (activase). To make the study of activas...

Whole Blood Cholinesterase Activity in 20 Species of Wild Birds.

PubMed

Horowitz, Igal H; Yanco, Esty G; Landau, Shmulik; Nadler-Valency, Rona; Anglister, Nili; Bueller-Rosenzweig, Ariela; Apelbom-Halbersberg, Tal; Cuneah, Olga; Hanji, Vera; Bellaiche, Michel

2016-06-01

Clinical signs of organophosphate and carbamate intoxication in wild birds can be mistaken for those of other diseases, thus potentially delaying diagnosis and implementation of life-saving treatment. The objective of this study was to determine the reference interval for blood cholinesterase activity in 20 different wild avian species from 7 different orders, thereby compiling a reference database for wildlife veterinarians. Blood was collected from birds not suspected of having organophosphate or carbamate toxicosis, and the modified Michel method, which determines the change in blood pH that directly correlates with cholinesterase activity, was used to measure blood cholinesterase levels. Results of change in blood pH values ranged from 0.11 for the white-tailed eagle ( Haliaeetus albicilla ) to 0.90 for the honey buzzard ( Pernis apivorus ). The results showed that even within the same family, interspecies differences in normal cholinesterase blood activity were not uncommon. The findings emphasized the importance of determining reference intervals for avian blood cholinesterase activity at the species level.

Molecular catalytic coal liquid conversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stock, L.M.; Yang, Shiyong

1995-12-31

This research, which is relevant to the development of new catalytic systems for the improvement of the quality of coal liquids by the addition of dihydrogen, is divided into two tasks. Task 1 centers on the activation of dihydrogen by molecular basic reagents such as hydroxide ion to convert it into a reactive adduct (OH{center_dot}H{sub 2}){sup {minus}} that can reduce organic molecules. Such species should be robust withstanding severe conditions and chemical poisons. Task 2 is focused on an entirely different approach that exploits molecular catalysts, derived from organometallic compounds that are capable of reducing monocyclic aromatic compounds under verymore » mild conditions. Accomplishments and conclusions are discussed.« less

Using Active Learning in a Studio Classroom to Teach Molecular Biology

ERIC Educational Resources Information Center

Nogaj, Luiza A.

2013-01-01

This article describes the conversion of a lecture-based molecular biology course into an active learning environment in a studio classroom. Specific assignments and activities are provided as examples. The goal of these activities is to involve students in collaborative learning, teach them how to participate in the learning process, and give…

Ecological niche comparison and molecular phylogeny segregate the invasive moss species Campylopus introflexus (Leucobryaceae, Bryophyta) from its closest relatives.

PubMed

Gama, Renato; Aguirre-Gutiérrez, Jesús; Stech, Michael

2017-10-01

The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer , has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus . Analyses of an extended ITS dataset displayed statistically supported incongruence between ITS1 and ITS2. ITS1 separates the New World clade of C. pilifer from a clade comprising C. introflexus and the Old World C. pilifer . Ancestral state reconstruction showed that this topology is morphologically supported by differences in the height of the dorsal costal lamellae in leaf cross-section (despite some overlap). ITS2, in contrast, supports the current morphological species concept, i.e., separating C. introflexus from C. pilifer , which is morphologically supported by the orientation of the hyaline hair point at leaf apex as well as costal lamellae height. Re-analysis of published and newly generated plastid atpB-rbcL spacer sequences supported the three ITS lineages. Ecological niche modeling proved a useful approach and showed that all three molecular lineages occupy distinct environmental spaces that are similar, but undoubtedly not equivalent. In line with the ITS1 topology, the C. pilifer lineage from the New World occupies the most distinct environmental niche, whereas the niches of Old World C. pilifer and C. introflexus are very similar. Taking the inferences from ecological niche comparisons, phylogenetics, and morphology together, we conclude that all three molecular lineages represent different taxa that should be recognized as independent species, viz. C. introflexus , C. pilifer (Old World clade), and the reinstated C. lamellatus Mont. (New World clade).

Activities of Arginine and Ornithine Decarboxylases in Various Plant Species 1

PubMed Central

Birecka, Helena; Bitonti, Alan J.; McCann, Peter P.

1985-01-01

In extracts from the youngest leaves of Avena sativa, Hordeum vulgare, Zea Mays, Pisum sativum, Phaseolus vulgaris, Lactuca sativa, and four pyrrolizidine alkaloid-bearing species of Heliotropium, the activities of ornithine decarboxylase, close to Vmax, ranged between traces and 1.5 nanomoles per hour per gram fresh weight when based on putrescine formed during incubation with labeled ornithine. The arginine decarboxylase activities in the same extracts ranged between 8 and 8000 nanomoles per hour per gram fresh weight being lowest in the borages and highest in oat and barley. α-Difluoromethylornithine and α-difluoromethylarginine inhibited ornithine and arginine decarboxylases, respectively, in all species. Agmatine, putrescine, spermidine, and spermine were found in all, diaminopropane in eight, and cadaverine in three species. No correlation was observed between arginine or ornithine decarboxylase level and the levels of total polyamines. The in vitro decarboxylase activities found in the borages cannot explain the high accumulation of putrescine-derived pyrrolizidines in their youngest leaves if the pyrrolizidines are produced in situ from arginine and/or ornithine as precursors; other possibilities are discussed. In assays of ornithine decarboxylase, an interference of decarboxylation not due to this enzyme was observed in extracts from all species. In arginine decarboxylase assays, the interfering decarboxylation as well as the interference of arginase were apparent in two species. Addition of aminoguanidine was needed to suppress oxidative degradation of putrescine and agmatine during incubation of extracts from pea, bean, lettuce, Heliotropium angiospermum, and Heliotropium indicum. PMID:16664442

The scavenging of free radical and oxygen species activities and hydration capacity of collagen hydrolysates from walleye pollock ( Theragra chalcogramma) skin

NASA Astrophysics Data System (ADS)

Zhuang, Yongliang; Li, Bafang; Zhao, Xue

2009-06-01

Fish skin collagen hydrolysates (FSCH) were prepared from walleye pollock ( Theragra chalcogramma) using a mixture of enzymes, namely trypsin and flavourzyme. The degree of hydrolysis of the skin collagen was 27.3%. FSCH was mainly composed of low-molecular-weight peptides and the relative proportion of <1000Da fraction was 70.6%. Free radical and oxygen species scavenging activities of FSCH were investigated in four model systems, including diphenylpicrylhy-drazyl radical (DPPH), superoxide anion radical, hydroxyl radical and hydrogen peroxide model, and compared with that of a native antioxidant, reduced glutathione (GSH). FSCH was also evaluated by water-absorbing and water-holding capacity. The results showed that FSCH was able to scavenge free radical and oxygen species significantly and to enhance water-absorbing and water-holding capacity remarkably. Therefore, FSCH may have potential applications in the medicine and food industries.

Characterization of the Sweet Taste Receptor Tas1r2 from an Old World Monkey Species Rhesus Monkey and Species-Dependent Activation of the Monomeric Receptor by an Intense Sweetener Perillartine

PubMed Central

Cai, Chenggu; Jiang, Hua; Li, Lei; Liu, Tianming; Song, Xuejie; Liu, Bo

2016-01-01

Sweet state is a basic physiological sensation of humans and other mammals which is mediated by the broadly acting sweet taste receptor-the heterodimer of Tas1r2 (taste receptor type 1 member 2) and Tas1r3 (taste receptor type 1 member 3). Various sweeteners interact with either Tas1r2 or Tas1r3 and then activate the receptor. In this study, we cloned, expressed and functionally characterized the taste receptor Tas1r2 from a species of Old World monkeys, the rhesus monkey. Paired with the human TAS1R3, it was shown that the rhesus monkey Tas1r2 could respond to natural sugars, amino acids and their derivates. Furthermore, similar to human TAS1R2, rhesus monkey Tas1r2 could respond to artificial sweeteners and sweet-tasting proteins. However, the responses induced by rhesus monkey Tas1r2 could not be inhibited by the sweet inhibitor amiloride. Moreover, we found a species-dependent activation of the Tas1r2 monomeric receptors of human, rhesus monkey and squirrel monkey but not mouse by an intense sweetener perillartine. Molecular modeling and sequence analysis indicate that the receptor has the conserved domains and ligand-specific interactive residues, which have been identified in the characterized sweet taste receptors up to now. This is the first report of the functional characterization of sweet taste receptors from an Old World monkey species. PMID:27479072

Characterization of the Sweet Taste Receptor Tas1r2 from an Old World Monkey Species Rhesus Monkey and Species-Dependent Activation of the Monomeric Receptor by an Intense Sweetener Perillartine.

PubMed

Cai, Chenggu; Jiang, Hua; Li, Lei; Liu, Tianming; Song, Xuejie; Liu, Bo

2016-01-01

Sweet state is a basic physiological sensation of humans and other mammals which is mediated by the broadly acting sweet taste receptor-the heterodimer of Tas1r2 (taste receptor type 1 member 2) and Tas1r3 (taste receptor type 1 member 3). Various sweeteners interact with either Tas1r2 or Tas1r3 and then activate the receptor. In this study, we cloned, expressed and functionally characterized the taste receptor Tas1r2 from a species of Old World monkeys, the rhesus monkey. Paired with the human TAS1R3, it was shown that the rhesus monkey Tas1r2 could respond to natural sugars, amino acids and their derivates. Furthermore, similar to human TAS1R2, rhesus monkey Tas1r2 could respond to artificial sweeteners and sweet-tasting proteins. However, the responses induced by rhesus monkey Tas1r2 could not be inhibited by the sweet inhibitor amiloride. Moreover, we found a species-dependent activation of the Tas1r2 monomeric receptors of human, rhesus monkey and squirrel monkey but not mouse by an intense sweetener perillartine. Molecular modeling and sequence analysis indicate that the receptor has the conserved domains and ligand-specific interactive residues, which have been identified in the characterized sweet taste receptors up to now. This is the first report of the functional characterization of sweet taste receptors from an Old World monkey species.

Multicenter evaluation of molecular and culture-dependent diagnostics for Shigella species and Entero-invasive Escherichia coli in the Netherlands.

PubMed

van den Beld, Maaike J C; Friedrich, Alexander W; van Zanten, Evert; Reubsaet, Frans A G; Kooistra-Smid, Mirjam A M D; Rossen, John W A

2016-12-01

An inter-laboratory collaborative trial for the evaluation of diagnostics for detection and identification of Shigella species and Entero-invasive Escherichia coli (EIEC) was performed. Sixteen Medical Microbiological Laboratories (MMLs) participated. MMLs were interviewed about their diagnostic methods and a sample panel, consisting of DNA-extracts and spiked stool samples with different concentrations of Shigella flexneri, was provided to each MML. The results of the trial showed an enormous variety in culture-dependent and molecular diagnostic techniques currently used among MMLs. Despite the various molecular procedures, 15 out of 16 MMLs were able to detect Shigella species or EIEC in all the samples provided, showing that the diversity of methods has no effect on the qualitative detection of Shigella flexneri. In contrast to semi quantitative analysis, the minimum and maximum values per sample differed by approximately five threshold cycles (Ct-value) between the MMLs included in the study. This indicates that defining a uniform Ct-value cut-off for notification to health authorities is not advisable. Copyright © 2016 Elsevier B.V. All rights reserved.

Active porous transition towards spatiotemporal control of molecular flow in a crystal membrane

NASA Astrophysics Data System (ADS)

Takasaki, Yuichi; Takamizawa, Satoshi

2015-11-01

Fluidic control is an essential technology widely found in processes such as flood control in land irrigation and cell metabolism in biological tissues. In any fluidic control system, valve function is the key mechanism used to actively regulate flow and miniaturization of fluidic regulation with precise workability will be particularly vital in the development of microfluidic control. The concept of crystal engineering is alternative to processing technology in microstructure construction, as the ultimate microfluidic devices must provide molecular level control. Consequently, microporous crystals can instantly be converted to microfluidic devices if introduced in an active transformability of porous structure and geometry. Here we show that the introduction of a stress-induced martensitic transition mechanism converts a microporous molecular crystal into an active fluidic device with spatiotemporal molecular flow controllability through mechanical reorientation of subnanometre channels.