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Sample records for active molecular species

  1. Characterization of Metarhizium species and varieties based on molecular analysis, heat tolerance and cold activity

    USGS Publications Warehouse

    Fernandes, E.K.K.; Keyser, C.A.; Chong, J.P.; Rangel, D.E.N.; Miller, M.P.; Roberts, D.W.

    2010-01-01

    Aims: The genetic relationships and conidial tolerances to high and low temperatures were determined for isolates of several Metarhizium species and varieties. Methods and Results: Molecular-based techniques [AFLP and rDNA (ITS1, ITS2 and 5??8S) gene sequencing] were used to characterize morphologically identified Metarhizium spp. isolates from a wide range of sources. Conidial suspensions of isolates were exposed to wet heat (45 ?? 0??2??C) and plated on potato dextrose agar plus yeast extract (PDAY) medium. After 8-h exposure, the isolates divided clearly into two groups: (i) all isolates of Metarhizium anisopliae var. anisopliae (Ma-an) and Metarhizium from the flavoviride complex (Mf) had virtually zero conidial relative germination (RG), (ii) Metarhizium anisopliae var. acridum (Ma-ac) isolates demonstrated high heat tolerance (c. 70-100% RG). Conidial suspensions also were plated on PDAY and incubated at 5??C for 15 days, during which time RGs for Ma-an and Ma-ac isolates were virtually zero, whereas the two Mf were highly cold active (100% RG). Conclusions: Heat and cold exposures can be used as rapid tools to tentatively identify some important Metarhizium species and varieties. Significance and Impact of the Study: Identification of Metarhizium spp. currently relies primarily on DNA-based methods; we suggest a simple temperature-based screen to quickly obtain tentative identification of isolates as to species or species complexes. ?? 2009 The Society for Applied Microbiology.

  2. Molecular Epidemiology of Fonsecaea Species

    PubMed Central

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A.; Klaassen, Corne H.W.; Bonifaz, Alexandro; van den Ende, A.H.G. Gerrits; Menken, Steph B.J.

    2011-01-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, β-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration. PMID:21392438

  3. Molecular epidemiology of Fonsecaea species.

    PubMed

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A; Klaassen, Corne H W; Bonifaz, Alexandro; Gerrits van den Ende, A H G; Menken, Steph B J; de Hoog, G Sybren

    2011-03-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, beta-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration.

  4. [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.

  5. Copper-catalyzed activation of molecular oxygen for oxidative destruction of acetaminophen: The mechanism and superoxide-mediated cycling of copper species.

    PubMed

    Zhang, Yunfei; Fan, Jinhong; Yang, Bo; Huang, Wutao; Ma, Luming

    2017-01-01

    In this study, the commercial zero-valent copper (ZVC) was investigated to activate the molecular oxygen (O2) for the degradation of acetaminophen (ACT). 50 mg/L ACT could be completely decomposed within 4 h in the ZVC/air system at initial pH 3.0. The H2O2, hydroxyl radical (OH) and superoxide anion radical (O2(-)) were identified as the main reactive oxygen species (ROSs) generated in the above reaction; however, only OH caused the decomposition and mineralization of ACT in the copper-catalyzed O2 activation process. In addition, the in-situ generated Cu(+) from ZVC dissolution not only activated O2 to produce H2O2, but also initiated the decomposition of H2O2 to generate OH. Meanwhile, the H2O2 could also be partly decomposed into O2(-), which served as a mediator for copper cycling by reduction of Cu(2+) to Cu(+) in the ZVC/air system. Therefore, OH could be continuously generated; and then ACT was effectively degraded. Additionally, the effect of solution pH and the dosage of ZVC were also investigated. As a result, this study indicated the key behavior of the O2(-) during Cu-catalyzed activation of O2, which further improved the understanding of O2 activation mechanism by zero-valent metals.

  6. Molecular Determinants of Species-Specific Agonist and Antagonist Activity of A Substituted Flavone towards the Aryl Hydrocarbon Receptor*

    PubMed Central

    Henry, E. C.; Gasiewicz, T. A.

    2008-01-01

    The aryl hydrocarbon receptor (AhR) mediates the toxicity of dioxins and related xenobiotics. Other chemicals also bind the AhR to elicit either agonist or antagonist responses. Here we used site-directed mutagenesis within the ligand binding domain of murine AhR to probe for specific residues that might interact differentially with the antagonist 3’-methoxy-4’-nitroflavone (MNF) compared with the prototypical agonist TCDD. Reduced 3 H-TCDD binding, dioxin-response element (DRE) binding, and transcriptional activity were observed for several point mutants. One mutation, R355I, changed the response to MNF from antagonist to agonist. Notably, Ile is the residue found in the guinea pig AhR, towards which MNF has partial agonist activity in contrast to its strong antagonist activity in mouse. A similar reversal of response to MNF was observed in chimeric AhRs in which the C-terminal region of mAhR was replaced with the guinea pig C-terminal region. These data demonstrate that different amino acids can be important in binding of different AhR ligands and can mediate distinct responses. The ultimate response of the AhR also depends on how other portions of the receptor protein are functionally coupled to the initial ligand binding event. PMID:18294953

  7. In Vitro Activities of Tigecycline and Eight Other Antimicrobials against Different Nocardia Species Identified by Molecular Methods▿

    PubMed Central

    Cercenado, Emilia; Marín, Mercedes; Sánchez-Martínez, Mónica; Cuevas, Oscar; Martínez-Alarcón, José; Bouza, Emilio

    2007-01-01

    The in vitro activities of tigecycline and other antimicrobials against 51 isolates of Nocardia spp. were evaluated. MIC90s and MIC ranges were as follows: tigecycline, 4 and ≤0.06 to 8 mg/liter, respectively; minocycline, 2 and ≤0.06 to 2 mg/liter, respectively; linezolid, 1 and ≤0.06 to 2 mg/liter, respectively; moxifloxacin, 2 and ≤0.06 to >64 mg/liter, respectively; ertapenem, 32 and ≤0.06->64 mg/liter, respectively; imipenem, 2 and ≤0.06 to >64 mg/liter, respectively; meropenem, 8 and ≤0.06 to >64 mg/liter, respectively; amikacin, 1 and ≤0.06 to 32 mg/liter, respectively; and trimethoprim-sulfamethoxazole, 1/19 and ≤0.5/9.5 to >2/38 mg/liter, respectively. PMID:17194827

  8. How to Predict Molecular Interactions between Species?

    PubMed Central

    Schulze, Sylvie; Schleicher, Jana; Guthke, Reinhard; Linde, Jörg

    2016-01-01

    Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory networks. Often, our knowledge of these networks is incomplete. Network inference predicts gene regulatory interactions based on transcriptome data. An emerging application of high-throughput transcriptome studies are dual transcriptomics experiments. Here, the transcriptome of two or more interacting species is measured simultaneously. Based on a dual RNA-seq data set of murine dendritic cells infected with the fungal pathogen Candida albicans, the software tool NetGenerator was applied to predict an inter-species gene regulatory network. To promote further investigations of molecular inter-species interactions, we recently discussed dual RNA-seq experiments for host-pathogen interactions and extended the applied tool NetGenerator (Schulze et al., 2015). The updated version of NetGenerator makes use of measurement variances in the algorithmic procedure and accepts gene expression time series data with missing values. Additionally, we tested multiple modeling scenarios regarding the stimuli functions of the gene regulatory network. Here, we summarize the work by Schulze et al. (2015) and put it into a broader context. We review various studies making use of the dual transcriptomics approach to investigate the molecular basis of interacting species. Besides the application to host-pathogen interactions, dual transcriptomics data are also utilized to study mutualistic and commensalistic interactions. Furthermore, we give a short introduction into additional approaches for the prediction of gene regulatory networks and discuss their application to dual transcriptomics data. We

  9. Collagen degrading activity associated with Mycobacterium species

    PubMed Central

    Masso, F; Paez, A; Varela, E; d Diaz; Zenteno, E; Montano, L

    1999-01-01

    BACKGROUND—The mechanism of Mycobacterium tuberculosis penetration into tissues is poorly understood but it is reasonable to assume that there is a contribution from proteases capable of disrupting the extracellular matrix of the pulmonary epithelium and the blood vessels. A study was undertaken to identify and characterise collagen degrading activity of M tuberculosis.
METHODS—Culture filtrate protein extract (CFPE) was obtained from reference mycobacterial strains and mycobacteria isolated from patients with tuberculosis. The collagen degrading activity of CFPE was determined according to the method of Johnson-Wint using 3H-type I collagen. The enzyme was identified by the Birkedal-Hansen and Taylor method and its molecular mass determined by SDS-PAGE and Sephacryl S-300 gel filtration chromatography using an electroelution purified enzyme.
RESULTS—CFPE from Mycobacterium tuberculosis strain H37Rv showed collagenolytic activity that was four times higher than that of the avirulent strain H37Ra. The 75 kDa enzyme responsible was divalent cation dependent. Other mycobacterial species and those isolated from patients with tuberculosis also had collagen degrading activity.
CONCLUSIONS—Mycobacterium species possess a metalloprotease with collagen degrading activity. The highest enzymatic activity was found in the virulent reference strain H37Rv.

 PMID:10212111

  10. Molecular species identification boosts bat diversity

    PubMed Central

    Mayer, Frieder; Dietz, Christian; Kiefer, Andreas

    2007-01-01

    The lack of obvious morphological differences between species impedes the identification of species in many groups of organisms. Meanwhile, DNA-based approaches are increasingly used to survey biological diversity. In this study we show that sequencing the mitochondrial protein-coding gene NADH dehydrogenase, subunit 1 (nd1) from 534 bats of the Western Palaearctic region corroborates the promise of DNA barcodes in two major respects. First, species described with classical taxonomic tools can be genetically identified with only a few exceptions. Second, substantial sequence divergence suggests an unexpected high number of undiscovered species. PMID:17295921

  11. Composition of cardiolipin molecular species in Escherichia coli.

    PubMed Central

    Yokota, K; Kanamoto, R; Kito, M

    1980-01-01

    The composition of the molecular species of acidic phospholipids in Escherichia coli B during the late exponential growth phase at 37 degrees C was determined. Two phosphatidyl groups of cardiolipin, the 3-(3-sn-phosphatidyl) and 1-(3-sn-phosphatidyl) moieties of cardiolipin, were isolated by limited hydrolysis with phospholipase C. No significant difference in the composition of the molecular species was found between the 3-(3-sn-phosphatidyl) and 1-(3-sn-phosphatidyl) moieties. On the other hand, the composition of the molecular species of phosphatidylglycerol was different from that of cardiolipin. Phosphatidylglycerol contained more of the 1-palmitoyl 2-cis-9,10-methylenehexadecanoyl and 1-palmitoyl 2-cis-11,12-methyleneoctadecanoyl species than did cardiolipin. The difference in the composition of the molecular species between cardiolipin and phosphatidylglycerol may depend on the difference in the turnover rates of both phospholipids. PMID:6988400

  12. Molecular characterization of Eimeria species in macropods.

    PubMed

    Yang, Rongchang; Fenwick, Stan; Potter, Abbey; Elliot, Aileen; Power, Michelle; Beveridge, Ian; Ryan, Una

    2012-10-01

    A total of 597 faecal samples were collected from western grey kangaroos (Macropus fuliginosus), Euros (M. robustus), red kangaroos (M. rufus) in Western Australia and Eastern Grey Kangaroos (M. giganteus) from Victoria and screened for the presence of Eimeria by PCR at the 18S ribosomal RNA (rRNA) locus. The overall prevalence was 24.3% (145/597). At the 18S rRNA locus, sequences were obtained for 25 of the 145 positives. Phylogenetic analysis indicated that all the macropod-derived Eimeria species grouped in a separate marsupial clade that included Eimeria trichosuri from brushtail possums. At least 6 different clades were identified within the marsupial isolates and many of the genotypes identified are likely to be valid species, however morphological and biological data need to be collected to match sequences to previously characterized Eimeria species or identify if they are new species.

  13. 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

  14. Molecular Differentiation of Seven Malassezia Species

    PubMed Central

    Gupta, Aditya K.; Kohli, Yatika; Summerbell, Richard C.

    2000-01-01

    A system based on PCR and restriction endonuclease analysis was developed to distinguish the seven currently recognized Malassezia species. Seventy-eight strains, including authentic culture collection strains and routine clinical isolates, were investigated for variation in the ribosomal DNA repeat units. Two genomic regions, namely, the large subunit of the ribosomal gene and the internal transcribed spacer (ITS) region, were amplified by PCR, and products were digested with restriction endonucleases. The patterns generated were useful in identification of five out of seven Malassezia species. M. sympodialis was readily distinguishable in that its ITS region yielded a 700-bp amplified fragment, whereas the other six species yielded an 800-bp fragment. M. globosa and M. restricta were very similar in the regions studied and could be distinguished only by performing a hot start-touchdown PCR on primers for the β-tubulin gene. Primers based on the conserved areas of the Candida cylindracea lipase gene, which were used in an attempt to amplify Malassezia lipases, yielded an amplification product after annealing at 55°C only with M. pachydermatis. This specific amplification may facilitate the rapid identification of this organism. PMID:10790115

  15. Characterization of Capsicum species using anatomical and molecular data.

    PubMed

    Dias, G B; Gomes, V M; Moraes, T M S; Zottich, U P; Rabelo, G R; Carvalho, A O; Moulin, M; Gonçalves, L S A; Rodrigues, R; Da Cunha, M

    2013-02-28

    Capsicum species are frequently described in terms of genetic divergence, considering morphological, agronomic, and molecular databases. However, descriptions of genetic differences based on anatomical characters are rare. We examined the anatomy and the micromorphology of vegetative and reproductive organs of several Capsicum species. Four Capsicum accessions representing the species C. annuum var. annuum, C. baccatum var. pendulum, C. chinense, and C. frutescens were cultivated in a greenhouse; leaves, fruits and seeds were sampled and their organ structure analyzed by light and scanning electronic microscopy. Molecular accession characterization was made using ISSR markers. Polymorphism was observed among tector trichomes and also in fruit color and shape. High variability among accessions was detected by ISSR markers. Despite the species studied present a wide morphological and molecular variability that was not reflected by anatomical features.

  16. Molecular and phytochemical investigation of Angelica dahurica and Aneelica pubescentis essential oils and their biological activity against Aedes aegypti, Stephanitis pyrioides and Colletotrichum species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Water distilled essential oils from the roots of Angelica dahurica and Angelica pubescentis were investigated for their antifungal activity against plant pathogens Colletotrichum acutatum, C. fragariae, and C. gloeosporioides as well as insecticidal activity against the yellow fever mosquito, Aedes ...

  17. Molecular characteristics versus biological activity

    USGS Publications Warehouse

    Applegate, Vernon C.; Smith, Manning A.; Willeford, Bennett R.

    1967-01-01

    The molecular characteristics of mononitrophenols containing halogens not only play a key role in their biological activity but provide a novel example of selective toxicity among vertebrate animals. It has been reported that efforts to control the parasitic sea lamprey in the Great Lakes are directed at present to the applications of a selective toxicant to streams inhabited by lamprey larvae. Since 1961, the larvicide that has been used almost exclusively in the control program has been 3-trifluoromethyl-4-nitrophenol (TFM). However, this is only one of about 15 closely related compounds, all halogen-containing mononitrophenols, that display a selectively toxic action upon lampreys. Although not all of the halogenated mononitrophenols are selectively toxic to lampreys (in fact, fewer than half of those tested), no other group of related compounds has displayed any useful larvicidal activity except for the substituted nitrosalicylanilides.

  18. Low molecular weight species in humic and fulvic fractions

    USGS Publications Warehouse

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

  19. Molecular and phytochemical investigation of Angelica dahurica and Angelica pubescentis essential oils and their biological activity against Aedes aegypti, Stephanitis pyrioides, and Colletotrichum species.

    PubMed

    Tabanca, Nurhayat; Gao, Zengping; Demirci, Betul; Techen, Natascha; Wedge, David E; Ali, Abbas; Sampson, Blair J; Werle, Chris; Bernier, Ulrich R; Khan, Ikhlas A; Baser, Kemal Husnu Can

    2014-09-03

    In this study, Angelica dahurica and Angelica pubescentis root essential oils were investigated as pest management perspectives, and root samples were also analyzed genetically using the nuclear ribosomal internal transcribed spacer (ITS) region as a DNA barcode marker. A. pubescentis root essential oil demonstrated weak antifungal activity against Colletotrichum acutatum, Colletotrichum fragariae, and Colletotrichum gloeosporioides, whereas A. dahurica root essential oil did not show antifungal activity. Conversely, A. dahurica root essential oil demonstrated better biting deterrent and insecticidal activity against yellow fever mosquito, Aedes aegypti, and azalea lace bugs, Stephanitis pyrioides, than A. pubescentis root oil. The major compounds in the A. dahurica oil were found as α-pinene (46.3%), sabinene (9.3%), myrcene (5.5%), 1-dodecanol (5.2%), and terpinen-4-ol (4.9%). α-Pinene (37.6%), p-cymene (11.6%), limonene (8.7%), and cryptone (6.7%) were the major compounds found in the A. pubescentis oil. In mosquito bioassays, 1-dodecanol and 1-tridecanol showed antibiting deterrent activity similar to the positive control DEET (N,N-diethyl-3-methylbenzamide) at 25 nmol/cm(2) against Ae. aegypti, whereas only 1-tridecanol showed repellent activity in human-based cloth patch bioassay with minimum effective dosages (MED) of 0.086 ± 0.089 mg/cm(2) (DEET = 0.007 ± 0.003 mg/cm(2)). In larval bioassays, 1-tridecanol was more toxic with an LC50 value of 2.1 ppm than 1-dodecanol having an LC50 value of 5.2 ppm against 1-day-old Ae. aegypti larvae. 1-Dodecanol and 1-tridecanol could be useful for the natural mosquito control agents.

  20. Molecular species delimitation in the genus Eumerus (Diptera: Syrphidae).

    PubMed

    Chroni, A; Djan, M; Vidaković, D Obreht; Petanidou, T; Vujić, A

    2017-02-01

    Eumerus is one of the most diverse genera of hoverfly worldwide. Species delimitation within genus is considered to be difficult due to: (a) lack of an efficient key; (b) non-defined taxonomical status of a large number of species; and (c) blurred nomenclature. Here, we present the first molecular study to delimit species of the genus by using a fragment of the mitochondrial cytochrome-c oxidase subunit I gene (COI) gene. We assessed 75 specimens assigned to 28 taxa originating from two biogeographic zones: 22 from the western Palaearctic and six from the Afrotropical region. Two datasets were generated based on different sequence lengths to explore the significance of availability of more polymorphic sites for species delimitation; dataset A with a total length of 647 bp and dataset B with 746 bp. Various tree inference approaches and Poisson tree processes models were applied to evaluate the putative 'taxonomical' vs. 'molecular' taxa clusters. All analyses resulted in high taxonomic resolution and clear species delimitation for both the dataset lengths. Furthermore, we revealed a high number of mitochondrial haplotypes and high intraspecific variability. We report two major monophyletic clades, and seven 'molecular' groups of taxa formed, which are congruent with morphology-based taxonomy. Our results support the use of the mitochondrial COI gene in species diagnosis of Eumerus.

  1. Molecular Mechanisms of Anthracycline Activity

    NASA Astrophysics Data System (ADS)

    Beretta, Giovanni Luca; Zunino, Franco

    On the basis of evidence that anthracyclines are DNA intercalating agents and DNA is the primary target, a large number of analogs and related intercalators have been developed. However, doxorubicin and closely related anthracyclines still remain among the most effective antitumor agents. Multiple mechanisms have been proposed to explain their efficacy. They include inhibition of DNA-dependent functions, free radical formation, and membrane interactions. The primary mechanism of action is now ascribed to drug interference with the function of DNA topoisomerase II. The stabilization of the topoisomerase-mediated cleavable complex results in a specific type of DNA damage (i.e., double-strand protein-associated DNA breaks). The drug-stabilized cleavable complex is a potentially reversible molecular event and its persistence, as a consequence of strong DNA binding, may be recognized as an apoptotic stimulus. Indirect evidence supports the notion that the bioreductive processes of the quinone moiety generating the semiquinone radical with concomitant production of reactive oxygen species may contribute to the drug effects. The cellular defense mechanisms and response to genotoxic/cytotoxic stress appear to be critical determinants of the tumor sensitivity to anthracyclines.

  2. Texas Endangered Species Activity Book.

    ERIC Educational Resources Information Center

    Jackson, Kathleen Marie; Campbell, Linda

    This publication is the result of the Texas Parks and Wildlife Division's (TPWD's) commitment to education and the fertile partnerships formed between TPWD biologists and educators. This activity book brings together the expertise and practical knowledge of a classroom teacher with the technical knowledge and skills of a TPWD biologist and artist.…

  3. Molecular Systematic Comparison of North American Lygus Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Lygus is widely distributed in North America and Eurasia. The tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), is one of the most serious pest species within this genus. This pest has over 300 known host plants. We employed various molecular markers to investigate both inter- a...

  4. Improved Molecular Technique for the Differentiation of Neotropical Anopheline Species

    PubMed Central

    Matson, Ryan; Rios, Carlos Tong; Chavez, Cesar Banda; Gilman, Robert H.; Florin, David; Sifuentes, Victor Lopez; Greffa, Roldan Cardenas; Yori, Pablo Peñataro; Fernandez, Roberto; Portocarrero, Daniel Velasquez; Vinetz, Joseph M.; Kosek, Margaret

    2008-01-01

    We evaluated a PCR-RFLP of the ribosomal internal transcribed spacer 2 region (ITS2) to distinguish species of Anopheles commonly reported in the Amazon and validated this method using reared F1 offspring. The following species of Anopheles were used for molecular analysis: An. (Nys.) benarrochi, An. (Nys.) darlingi, An. (Nys.) nuneztovari, An. (Nys.) konderi, An. (Nys.) rangeli, and An. (Nys.) triannulatus sensu lato (s.l.). In addition, three species of the subgenus Anopheles, An. (Ano.) forattini, An. (Ano.) mattogrossensis, and An. (Ano.) peryassui were included for testing. Each of the nine species tested yielded diagnostic banding patterns. The PCR-RFLP method was successful in identifying all life stages including exuviae with small fractions of the sample. The assay is rapid and can be applied as an unbiased confirmatory method for identification of morphologic variants, disputed samples, imperfectly preserved specimens, and life stages from which taxonomic keys do not allow for definitive species determination. PMID:18337348

  5. A single molecular marker to distinguish between species of Dioscorea.

    PubMed

    Techen, Natascha; Parveen, Iffat; Khan, Ikhlas A

    2017-03-01

    Yams are species of the genus Dioscorea (family Dioscoreaceae), which consists of approximately 630 species. The majority of the world production of yams occurs in Africa with 58.8 million t annually, but they are also produced in the Americas and Asia. The saponins in yams have been reported to possess various properties to improve health. The tuber and aerial parts of various species often share morphological similarities, which can cause problems in the proper identification of sample material. For example, the rootstocks and aerial parts of Dioscorea villosa L. share similarities with Dioscorea polystachia Turcz. Dioscorea bulbifera L. may be mistaken for Dioscorea alata L. owing to similar morphologies. Various molecular analyses have been published to help with the identification of species and varieties within the genus Dioscorea. The multi-loci or single-locus analysis has resulted in varying success, some with only a limited discrimination rate. In the present study, a single nuclear genomic region, biparentally inherited, was analyzed for its usefulness as a molecular marker for species identification and discrimination between D. bulbifera, D. villosa, D. nipponica, D. alata, D. caucasica, and D. deltoidea samples. The results of this study show that the LFY genomic region can be useful as a molecular marker to distinguish between samples.

  6. Corroborating molecular species discovery: Four new pine-feeding species of Chionaspis (Hemiptera, Diaspididae)

    PubMed Central

    Vea, Isabelle M.; Gwiazdowski, Rodger A.; Normark, Benjamin B.

    2013-01-01

    Abstract The genus Chionaspis (Hemiptera, Diaspididae) includes two North American species of armored scale insects feeding on Pinaceae: Chionaspis heterophyllae Cooley, and Chionaspis pinifoliae (Fitch). Despite the economic impact of conifer-feeding Chionaspis on horticulture, the species diversity in this group has only recently been systematically investigated using samples from across the group’s geographic and host range. This paper provides morphological recognition characters for four new species that were recently hypothesized to exist on the basis of molecular evidence. The new species, here described, are Chionaspis brachycephalon Vea sp. n., Chionaspis caudata Vea sp. n., Chionaspis sonorae Vea sp. n. and Chionaspis torreyanae Vea sp. n.  One of the new species, Chionaspis caudata Vea, has a gland spine at the apex of the pygidium, between the median lobes, unlike any other species of Chionaspis. An identification key to the species of Chionaspis feeding on pine in North America is provided. PMID:23717184

  7. Molecular approaches to identify cryptic species and polymorphic species within a complex community of fig wasps.

    PubMed

    Xiao, Jin-Hua; Wang, Ning-Xin; Li, Yan-Wei; Murphy, Robert W; Wan, Dong-Guang; Niu, Li-Ming; Hu, Hao-Yuan; Fu, Yue-Guan; Huang, Da-Wei

    2010-11-29

    Cryptic and polymorphic species can complicate traditional taxonomic research and both of these concerns are common in fig wasp communities. Species identification is very difficult, despite great effort and the ecological importance of fig wasps. Herein, we try to identify all chalcidoid wasp species hosted by one species of fig, using both morphological and molecular methods. We compare the efficiency of four different DNA regions and find that ITS2 is highly effective for species identification, while mitochondrial COI and Cytb regions appear less reliable, possibly due to the interference signals from either nuclear copies of mtDNA, i.e. NUMTs, or the effects of Wolbachia infections. The analyses suggest that combining multiple markers is the best choice for inferring species identifications as any one marker may be unsuitable in a given case.

  8. Analysis of lidar systems for profiling aurorally excited molecular species.

    PubMed

    Collins, R L; Lummerzheim, D; Smith, R W

    1997-08-20

    We report a detailed analysis of lidar systems that profile aurorally excited molecular species in the upper mesosphere and lower thermosphere ( ~80 -300 km). Current profiling of this region is performed with incoherent scatter radars that determine the total electron and ion concentrations but not the individual species. Studies of the aeronomy of the thermosphere requires knowledge of the species present and their relative populations in the different vibrational and rotational states. We review the spectroscopy of nitrogen to determine an optimized lidar system. We combine these results with current auroral observations and models to determine the performance of an actual lidar system. The study shows that such systems can provide high-resolution (1 km, 100 s) measurements of these species with current laser technology.

  9. Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation.

    PubMed

    Richards, Z T; Miller, D J; Wallace, C C

    2013-12-01

    To better understand the underlying causes of rarity and extinction risk in Acropora (staghorn coral), we contrast the minimum divergence ages and nucleotide diversity of an array of species with different range sizes and levels of threat. Time-calibrated Bayesian analyses based upon concatenated nuclear and mitochondrial sequence data implied contemporary range size and vulnerability are linked to species age. However, contrary to previous hypotheses that suggest geographically restricted Acropora species evolved in the Plio-Pleistocene, the molecular phylogeny depicts some Indo-Australian species have greater antiquity, diverging in the Miocene. Species age is not related to range size as a simple positive linear function and interpreting the precise tempo of evolution in this genus is greatly complicated by morphological homoplasy and a sparse fossil record. Our phylogenetic reconstructions provide new examples of how morphology conceals cryptic evolutionary relationships in this keystone genus, and offers limited support for the species groupings currently used in Acropora systematics. We hypothesize that in addition to age, other mechanisms (such as a reticulate ancestry) delimit the contemporary range of some Acropora species, as evidenced by the complex patterns of allele sharing and paraphyly we uncover. Overall, both new and ancient evolutionary information may be lost if geographically restricted and threatened Acropora species are forced to extinction. In order to protect coral biodiversity and resolve the evolutionary history of staghorn coral, further analyses based on comprehensive and heterogeneous morphological and molecular data utilizing reticulate models of evolution are needed.

  10. 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.

  11. Molecular delineation of species in the coral holobiont.

    PubMed

    Stat, Michael; Baker, Andrew C; Bourne, David G; Correa, Adrienne M S; Forsman, Zac; Huggett, Megan J; Pochon, Xavier; Skillings, Derek; Toonen, Robert J; van Oppen, Madeleine J H; Gates, Ruth D

    2012-01-01

    The coral holobiont is a complex assemblage of organisms spanning a diverse taxonomic range including a cnidarian host, as well as various dinoflagellate, prokaryotic and acellular symbionts. With the accumulating information on the molecular diversity of these groups, binomial species classification and a reassessment of species boundaries for the partners in the coral holobiont is a logical extension of this work and will help enhance the capacity for comparative research among studies. To aid in this endeavour, we review the current literature on species diversity for the three best studied partners of the coral holobiont (coral, Symbiodinium, prokaryotes) and provide suggestions for future work on systematics within these taxa. We advocate for an integrative approach to the delineation of species using both molecular genetics in combination with phenetic characters. We also suggest that an a priori set of criteria be developed for each taxonomic group as no one species concept or accompanying set of guidelines is appropriate for delineating all members of the coral holobiont.

  12. 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

  13. 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.

  14. Variable soft sphere molecular model for air species

    NASA Astrophysics Data System (ADS)

    Koura, Katsuhisa; Matsumoto, Hiroaki

    1992-05-01

    A reliable set of cross-section parameters of the variable soft sphere (VSS) molecular model is determined for the Monte Carlo simulation of air species from the transport collision integrals or potential parameters provided by Cubley and Mason (1975) over the high-temperature range 300-15,000 K. The VSS cross-section parameters for the inverse-power-law potential are also determined from the viscosity coefficients recommended by Maitland and Smith (1972) for common species in the low (20-300 K) and high (300-2000 K) temperature ranges.

  15. Variable soft sphere molecular model for air species

    NASA Astrophysics Data System (ADS)

    Koura, Katsuhisa; Matsumoto, Hiroaki

    1992-05-01

    A reliable set of cross-section parameters of the variable soft sphere (VSS) molecular model is determined for the Monte Carlo simulation of air species from the transport collision integrals or potential parameters provided by Cubley and Mason [Phys. Fluids 18, 1109 (1975)] over the high-temperature range 300-15 000 K. The VSS cross-section parameters for the inverse-power-law potential are also determined from the viscosity coefficients recommended by Maitland and Smith [J. Chem. Eng. Data 17, 150 (1972)] for common species in the low (20-300 K) and high (300-2000 K) temperature ranges.

  16. 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

  17. Molecular characterization of Ephedra species found in Pakistan.

    PubMed

    Ghafoor, S; Shah, M M; Ahmad, H; Swati, Z A; Shah, S H; Pervez, A; Farooq, U

    2007-12-11

    Ephedra, also known as "ma huang", is a dioecious, drought- and frost-resistant, perennial, evergreen shrub with compelling medicinal value. The genus is represented by 42 species around the world, 9 of which were provisionally reported from Pakistan. Species of the genus have a controversial taxonomy due to their overlapping morphological features. Conventional tools alone are not sufficient for characterizing the species. The objective of present study was to assess the genetic variability present in different biotypes of Ephedra growing in Pakistan using molecular markers. A total of six genotypes collected from diverse geographic zones of Pakistan were used. The DNA of all genotypes was amplified using nine randomly amplified polymorphic DNA (RAPD) primers to study genetic variability at the molecular level. The dissimilarity coefficient matrix based on the data of 9 RAPD primers was used to construct a dendrogram which was then used to group the genotypes in clusters. Based on the dendrogram and dissimilarity coefficient matrix, the RAPD markers used here revealed a moderate to high level of genetic polymorphism (6 to 49%) among the genotypes. It was found that the collection of genotype accessions from Swat Valley in northwestern Pakistan was most distantly related to the other five collections. More molecular markers including functional genes and ribosomal spacer regions are suggested to find a better estimate of the genetic diversity present in Ephedra growing in Pakistan. The information provided here is useful for identifying valuable Ephedra variants which will be used for medicinal purposes and earning foreign currency.

  18. Molecular species delimitation methods recover most song-delimited cicada species in the European Cicadetta montana complex.

    PubMed

    Wade, E J; Hertach, T; Gogala, M; Trilar, T; Simon, C

    2015-12-01

    Molecular species delimitation is increasingly being used to discover and illuminate species level diversity, and a number of methods have been developed. Here, we compare the ability of two molecular species delimitation methods to recover song-delimited species in the Cicadetta montana cryptic species complex throughout Europe. Recent bioacoustics studies of male calling songs (premating reproductive barriers) have revealed cryptic species diversity in this complex. Maximum likelihood and Bayesian phylogenetic analyses were used to analyse the mitochondrial genes COI and COII and the nuclear genes EF1α and period for thirteen European Cicadetta species as well as the closely related monotypic genus Euboeana. Two molecular species delimitation methods, general mixed Yule-coalescent (GMYC) and Bayesian phylogenetics and phylogeography, identified the majority of song-delimited species and were largely congruent with each other. None of the molecular delimitation methods were able to fully recover a recent radiation of four Greek species.

  19. Biosynthesis of glycerolipid molecular species in photoreceptor membranes of frog retina

    SciTech Connect

    Wiegand, R.D.; Louie, K.; Anderson, R.E. )

    1987-05-01

    Phospholipid (PL) molecular species of vertebrate retinal photoreceptor cells are unique in that they contain two polyunsaturated fatty acids per molecule. Docosahexaenoic acid (22:6 {omega}3) is the major component of these dipolyunsaturate species (DPS), which also contain 20:4{omega}6, 22:4{omega}6, 22:5{omega}6, and 22:5{omega}3. We have studied the de novo synthesis and metabolism of the (DPS) and other PL molecular species in frog rod outer segments (ROS) following intravitreal injection of 2-({sup 3}H)-glycerol. At 1, 2, 4, and 8 days after injection, ROS were prepared, PL extracted, and phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS) isolated. PC, PE, and PS were converted to diglycerides (DG's) with phospholipase C. DG's were derivatized, fractionated into molecular species by HPLC, quantitated, and counted for radioactivity. The following were observed: (1) Specific activities (SA) of the PC DPS were 3-5 times higher than the same species in either PE or PS. (2) SA of the PC monopolyunsaturate species (MPS) (species which contain 22:6{omega}3 and/or 16:0 or 18:0) were 3-5 times lower than the SA of the PC DPS. In contrast, SA of PE MPS were 2-5 times higher than the SA of the PE DPS. (3) The major PS MPS synthesized contained 18:0 and 22:6{omega}3. SA of that species were similar to SA of the PS DPS. The data support the suggestion that PC DPS are synthesized and/or incorporated in ROS at a greater rate than the same species in either PE or PS. Our study thus provides evidence for different rates of synthesis and/or incorporation of the various molecular species of PC, PE, and PS in ROS.

  20. 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

  1. Leaf carbon assimilation and molecular phylogeny in Cattleya species (Orchidaceae).

    PubMed

    Andrade-Souza, V; Almeida, A-A F; Corrêa, R X; Costa, M A; Mielke, M S; Gomes, F P

    2009-08-11

    We examined leaf CO(2) assimilation and how it varied among species within the orchid genus Cattleya. Measurements of CO(2) assimilation and maximum quantum yield of PS II (Fv/Fm) were made for mature leaves of nine species using a portable system for photosynthesis measurement and a portable fluorometer. Leaf area was measured with an area meter, and the specific leaf mass was determined. DNA of nine Cattleya species and two species of Hadrolaelia was extracted using the CTAB protocol. Each sample was amplified and sequenced using primers for the trnL gene. The phylogenetic analyses, using neighbor-joining and maximum parsimony methods, retrieved a group that included Cattleya and Hadrolaelia species, in which the unifoliate species were separated from the bifoliates. The topologies of the two cladograms showed some similarities. However, C. guttata (bifoliate) was placed in the unifoliate clade in the neighbor-joining tree, while C. warneri (unifoliate) was not placed in this clade in the maximum parsimony tree. Most Cattleya species keep the leaf stomata closed from 6 am to 4 pm. We suggest that C. elongata, C. tigrina and C. tenuis have C(3)-crassulacean acid metabolism since they open their stomata around 12 am. The Fv/Fm values remained relatively constant during the measurements of CO(2) assimilation. The same was observed for the specific leaf mass values, although great variations were found in the leaf area values. When the species were grouped using molecular data in the neighbor-joining analysis, no relation was observed with CO(2) assimilation.

  2. Comparison of cytotoxic activities of extracts from Selaginella species

    PubMed Central

    Li, Juan; Lei, Xiang; Chen, Ke-li

    2014-01-01

    Background: Selaginella species are resurrection plants, which are known, possess various molecular bioactivities depending on species, but only a few species have been detailed observe in the advanced research. Objective: The objective of the following study is to compare the chemical profiles of different species of Selaginella and to investigate cytotoxicity and induction of apoptosis activities of some species of Selaginella. Materials and Methods: The high-performance liquid chromatography (HPLC) method was developed for chemical analysis. Ethyl acetate, ethanol and water-soluble extracts from seven Selaginella species were submitted to 3-(4,5-dimenthyl thizol-2-yl)-2,5-diphenyl tetrazolium bromide assay, flow cytometry, deoxyribonucleic acid (DNA) laddering analysis and caspase-3 expression using Bel-7402, HT-29 and HeLa cells. Results: The HPLC analysis revealed two major common peaks, which were identified as amentoflavone and robustaflavone and another three main peaks in their chromatograms. The results showed that S. labordei, Selaginella tamariscina and Selaginella uncinata had relatively stronger activities on Bel-7402 and HeLa cells and Selaginella moellendorfii had moderate antiproliferation activities, but Selaginella remotifolia and Selaginella pulvinata had almost no inhibitory activities. The main active components were in the ethyl acetate extracts which had abundant biflavonoids. The effects of these extracts on cell proliferation and apoptosis in different cells were not the same, they were more apparent on HeLa cells than on HT-29 cells. The assay of DNA laddering analysis and caspase-3 expression further confirmed that inducing cell apoptosis was one of antitumor mechanisms and antitumor activities of Selaginella species were related to apoptosis induced by caspase family. Conclusion: S. labordei, S. tamariscina and S. uncinata would be potential antitumor agents. PMID:25422557

  3. Reliable molecular identification of nine tropical whitefly species

    PubMed Central

    Ovalle, Tatiana M; Parsa, Soroush; Hernández, Maria P; Becerra Lopez-Lavalle, Luis A

    2014-01-01

    The identification of whitefly species in adult stage is problematic. Morphological differentiation of pupae is one of the better methods for determining identity of species, but it may vary depending on the host plant on which they develop which can lead to misidentifications and erroneous naming of new species. Polymerase chain reaction (PCR) fragment amplified from the mitochondrial cytochrome oxidase I (COI) gene is often used for mitochondrial haplotype identification that can be associated with specific species. Our objective was to compare morphometric traits against DNA barcode sequences to develop and implement a diagnostic molecular kit based on a RFLP-PCR method using the COI gene for the rapid identification of whiteflies. This study will allow for the rapid diagnosis of the diverse community of whiteflies attacking plants of economic interest in Colombia. It also provides access to the COI sequence that can be used to develop predator conservation techniques by establishing which predators have a trophic linkage with the focal whitefly pest species. PMID:25614792

  4. Zoonotic potential and molecular epidemiology of Giardia species and giardiasis.

    PubMed

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    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.

  5. Molecular identification of entomopathogenic Fusarium species associated with Tribolium species in stored grains.

    PubMed

    Chehri, Khosrow

    2017-03-01

    Fusarium species are common pathogens of plants, animals and insects worldwide, including Iran. The occurrence of entomopathogenic Fusarium species isolated from Tribolium species as one of the most important insect pests of stored grains were sampled from various provinces in western Iran. In total, 15 Tribolium species belonging to T. castaneum (Herbst) and T. confusum (Du Val) (Col: Tenebrionidae) were detected and 8 isolates from Fusarium spp. were collected from them. Based on morphological features, the Fusarium isolates were classified into F. keratoplasticum and F. proliferatum. The phylogenetic trees based on tef1 dataset clearly separated all morphological taxa. DNA sequences of ITS regions and β-tubulin gene were also confirmed morphological taxa. All of the Fusarium isolates were evaluated for their pathogenicity on T. confusum. Maximum mortality rate was observed for F. keratoplasticum (isolate FSSCker2) and this isolate may be considered as a good candidate for biological control in the ecosystem of stored grains. This is the first report on molecular identification of Fusarium species isolated from insects in Iran and F. keratoplasticum and F. proliferatum were isolated for the first time from Tribolium species as two entomopathogenic fungi.

  6. Molecular detection of Anaplasma species in dogs in Colombia.

    PubMed

    Vargas-Hernandez, Giovanni; André, Marcos Rogério; Cendales, Diana Maria; Sousa, Keyla Carstens Marques de; Gonçalves, Luiz Ricardo; Rondelli, Mariana Cristina Hoeppner; Machado, Rosangela Zacarias; Tinucci-Costa, Mirela

    2016-01-01

    Anaplasma platys and A. phagocytophilum are tick-borne pathogens that parasitize platelets and neutrophils, respectively, of humans and animals. The former is the etiological agent of canine cyclic thrombocytopenia, while the latter is that of canine granulocytic anaplasmosis. This work involved the detection and identification of Anaplasma species in blood samples from dogs in Colombia, using molecular techniques. Between December 2008 and April 2009, blood samples were drawn from the cephalic vein of 91 dogs in the central-western region of Colombia (cities of Bogota, Villavicencio and Bucaramanga) and stored in tubes containing EDTA. These samples were used in 16S rRNA-Anaplasma spp. nPCR and the preparation of blood smears. One (1.1%) of the 91 sampled dogs showed inclusions suggestive of Anaplasmataceae agents in the cytoplasm of platelets. Based on PCR followed by sequencing and phylogenetic analysis, A. platys and Anaplasma sp. closed related to A. phagocytophilum were detected in two and one dog, respectively. Interestingly, all the samples were negative for specific msp-2-A. phagocytophilum real-time qPCR, suggesting the circulation of an Anaplasma species phylogenetically related to A. phagocytophilum in dogs in the aforementioned region. Hence, Anaplasma spp. circulates among dogs in Colombia, albeit with low frequency. To the best of authors' knowledge, this is the first molecular detection of Anaplasma spp. in dogs in Colombia.

  7. Characterization and chillproofing activity of two enzymes from Streptomyces species.

    PubMed

    Etok, C A; Eka, O U

    1996-01-01

    Two enzymes, amylase and protease of Streptomyces species were purified by a combination of ion exchange chromatography and gel filtration and characterized. The amylase had an exoaction on starch yielding maltose as a major end product and was identified as beta-amylase. The purified amylase had a molecular weight of 48,000 and was maximally active at 35 degrees C and at pH 6.0. On the other hand, protease had a molecular weight of 21,000 and was most active at pH 10.0 and at a temperature of 30 degrees C. The Km or MICHAELIS constant of amylase for maize starch was 0.333 mg/ml while that of protease for casein was 2.5 mg/ml. The feasibility of using the purified protease for various industrial application especially in the chillproofing of beer is discussed.

  8. Molecular analysis of phylogenetic relationships among Myrmecophytic macaranga species (Euphorbiaceae).

    PubMed

    Blattner, F R; Weising, K; Bänfer, G; Maschwitz, U; Fiala, B

    2001-06-01

    Many species of the paleotropical pioneer tree genus Macaranga Thou. (Euphorbiaceae) live in association with ants. Various types of mutualistic interactions exist, ranging from the attraction of unspecific ant visitors to obligate myrmecophytism. In the latter, nesting space and food bodies are exchanged for protection by highly specific ant partners (mainly species of the myrmicine genus Crematogaster). As a first step toward elucidating the coevolution of ant-plant interactions in the Macaranga-Crematogaster system, we have initiated a molecular investigation of the plant partners' phylogeny. Nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were analyzed for 73 accessions from 47 Macaranga species, representing 17 sections or informally described species groups. Three accessions from the putative sister taxon Mallotus Lour, were included as outgroups. Cladograms of the ITS data revealed Macaranga to be nested within Mallotus. ITS sequences are highly similar within section Pachystemon s.str., suggesting a relatively recent and rapid radiation of obligate myrmecophytes within this section. Forty-three accessions, mainly of ant-inhabited species, were additionally investigated by random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) techniques. Phenetic analysis of RAPD and MP-PCR banding profiles generally confirmed the ITS results. Best resolutions for individual clades were obtained when ITS and RAPD/MP-PCR data were combined into a single matrix and analyzed phenetically. The combined analysis suggests multiple (four) rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmecophytism to nonmyrmecophytism, and one loss of mutualistic specifity.

  9. Molecular Species Delimitation in the Racomitrium canescens Complex (Grimmiaceae) and Implications for DNA Barcoding of Species Complexes in Mosses

    PubMed Central

    Stech, Michael; Veldman, Sarina; Larraín, Juan; Muñoz, Jesús; Quandt, Dietmar; Hassel, Kristian; Kruijer, Hans

    2013-01-01

    In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses. PMID

  10. Molecular species delimitation in the Racomitrium canescens complex (Grimmiaceae) and implications for DNA barcoding of species complexes in mosses.

    PubMed

    Stech, Michael; Veldman, Sarina; Larraín, Juan; Muñoz, Jesús; Quandt, Dietmar; Hassel, Kristian; Kruijer, Hans

    2013-01-01

    In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses.

  11. 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.

  12. Molecular mechanism of species-dependent sweet taste toward artificial sweeteners.

    PubMed

    Liu, Bo; Ha, Matthew; Meng, Xuan-Yu; Kaur, Tanno; Khaleduzzaman, Mohammed; Zhang, Zhe; Jiang, Peihua; Li, Xia; Cui, Meng

    2011-07-27

    The heterodimer of Tas1R2 and Tas1R3 is a broadly acting sweet taste receptor, which mediates mammalian sweet taste toward natural and artificial sweeteners and sweet-tasting proteins. Perception of sweet taste is a species-selective physiological process. For instance, artificial sweeteners aspartame and neotame taste sweet to humans, apes, and Old World monkeys but not to New World monkeys and rodents. Although specific regions determining the activation of the receptors by these sweeteners have been identified, the molecular mechanism of species-dependent sweet taste remains elusive. Using human/squirrel monkey chimeras, mutagenesis, and molecular modeling, we reveal that the different responses of mammalian species toward the artificial sweeteners aspartame and neotame are determined by the steric effect of a combination of a few residues in the ligand binding pocket. Residues S40 and D142 in the human Tas1R2, which correspond to residues T40 and E142 in the squirrel monkey Tas1R2, were found to be the critical residues for the species-dependent difference in sweet taste. In addition, human Tas1R2 residue I67, which corresponds to S67 in squirrel monkey receptor, modulates the higher affinity of neotame than of aspartame. Our studies not only shed light on the molecular mechanism of species-dependent sweet taste toward artificial sweeteners, but also provide guidance for designing novel effective artificial sweet compounds.

  13. 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.

  14. 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).

  15. Ixodes ventalloi: morphological and molecular support for species integrity.

    PubMed

    Latrofa, Maria Stefania; Giannelli, Alessio; Persichetti, Maria Flaminia; Pennisi, Maria Grazia; Solano-Gallego, Laia; Brianti, Emanuele; Parisi, Antonio; Wall, Richard; Dantas-Torres, Filipe; Otranto, Domenico

    2017-01-01

    Despite their medical and veterinary importance, some tick species are so poorly studied, that their role within pathogen vector transmission cycles is difficult to assess. The tick Ixodes ventalloi is one such species, and its biology and phylogenetic status remain an issue of debate. In the present study, specimens of adult I. ventalloi (n = 65 females; n = 31 males) infesting cats in the Lipari Island (Aeolian archipelago, Sicily, southern Italy) were characterized morphologically and molecularly, the latter based on mitochondrial 16S rRNA and cytochrome c oxidase subunit 1 (cox1) genes. The genetic data and phylogenetic analyses for both mitochondrial genes suggest the existence of two distinct genogroups. The ecological and epidemiological significance of the genetic structure within the I. ventalloi endemic population remains to be determined. The results highlight the need for further analysis of this tick species, including whole mitochondrial genome sequencing and crossbreeding studies, which will be pivotal to complement features of its status as a vector of pathogens.

  16. Molecular changes during egg activation

    PubMed Central

    Krauchunas, Amber R.

    2014-01-01

    Egg activation is the final transition that an oocyte goes through to become a developmentally competent egg. This transition is usually triggered by a calcium-based signal that is often, but not always, initiated by fertilization. Activation encompasses a number of changes within the egg. These include changes to the egg's membranes and outer coverings to prevent polyspermy and support the developing embryo, as well as resumption and completion of the meiotic cell cycle, mRNA poly-adenylation, translation of new proteins, and the degradation of specific maternal mRNAs and proteins. The transition from an arrested, highly differentiated cell, the oocyte, to a developmentally active, totipotent cell, the activated egg or embryo, represents a complete change in cellular state. This is accomplished by altering ion concentrations and widespread changes in both the proteome and the suite of mRNAS present in the cell. Here, we review the role of calcium and zinc in the events of egg activation, and the importance of macromolecular changes during this transition. The latter include the degradation and translation of proteins, protein post-translational regulation through phosphorylation, and the cytoplasmic polyadenylation, or the degradation, of maternal mRNAs. PMID:23287037

  17. Fluidization and Active Thinning by Molecular Kinetics in Active Gels.

    PubMed

    Oriola, David; Alert, Ricard; Casademunt, Jaume

    2017-02-24

    We derive the constitutive equations of an active polar gel from a model for the dynamics of elastic molecules that link polar elements. Molecular binding kinetics induces the fluidization of the material, giving rise to Maxwell viscoelasticity and, provided that detailed balance is broken, to the generation of active stresses. We give explicit expressions for the transport coefficients of active gels in terms of molecular properties, including nonlinear contributions on the departure from equilibrium. In particular, when activity favors linker unbinding, we predict a decrease of viscosity with activity-active thinning-of kinetic origin, which could explain some experimental results on the cell cortex. By bridging the molecular and hydrodynamic scales, our results could help understand the interplay between molecular perturbations and the mechanics of cells and tissues.

  18. Fluidization and Active Thinning by Molecular Kinetics in Active Gels

    NASA Astrophysics Data System (ADS)

    Oriola, David; Alert, Ricard; Casademunt, Jaume

    2017-02-01

    We derive the constitutive equations of an active polar gel from a model for the dynamics of elastic molecules that link polar elements. Molecular binding kinetics induces the fluidization of the material, giving rise to Maxwell viscoelasticity and, provided that detailed balance is broken, to the generation of active stresses. We give explicit expressions for the transport coefficients of active gels in terms of molecular properties, including nonlinear contributions on the departure from equilibrium. In particular, when activity favors linker unbinding, we predict a decrease of viscosity with activity—active thinning—of kinetic origin, which could explain some experimental results on the cell cortex. By bridging the molecular and hydrodynamic scales, our results could help understand the interplay between molecular perturbations and the mechanics of cells and tissues.

  19. Molecular parentage of radical species in the comae of comets

    NASA Astrophysics Data System (ADS)

    Lewis, Benjamin K.

    Understanding the chemical composition of comets is of great interest to the scientific community. In this work, an integral field unit (IFU) spectrograph is used to detect emissions of C2, C3, CH, CN, and NH2. The azimuthal average profile (line integral of the column density as a function of radial distance from the center of the nucleus) is simulated by the Haser model. The Haser model simulates the outgassing and photo-dissociate of molecular species in the coma. In this work, the lifetime of the parent molecule in the photo-dissociation chain is set as a free parameter. The best fit parent lifetimes for observations of comets 4P/Faye, 10P/Tempel 2, and C/2009 P1 Garradd are obtained. The results are compared to parent lifetimes cited in other studies. HCN as a likely dominant parent for CN is eliminated. Constraints on likely parent molecules for C3 and NH 2 are discussed.

  20. 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.

  1. Spectral identification/elimination of molecular species in spacecraft glow

    NASA Astrophysics Data System (ADS)

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

    1985-09-01

    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.

  2. Molecular basis determining inhibition/activation of nociceptive receptor TRPA1 protein: a single amino acid dictates species-specific actions of the most potent mammalian TRPA1 antagonist.

    PubMed

    Banzawa, Nagako; Saito, Shigeru; Imagawa, Toshiaki; Kashio, Makiko; Takahashi, Kenji; Tominaga, Makoto; Ohta, Toshio

    2014-11-14

    The transient receptor potential ankyrin 1 (TRPA1) is a Ca(2+)-permeable, nonselective cation channel mainly expressed in a subset of nociceptive neurons. TRPA1 functions as a cellular sensor detecting mechanical, chemical, and thermal stimuli. Because TRPA1 is considered to be a key player in nociception and inflammatory pain, TRPA1 antagonists have been developed as analgesic agents. Recently, by utilizing species differences, we identified the molecular basis of the antagonistic action of A967079, one of the most potent mammalian TRPA1 antagonists. Here, we show a unique effect of A967079 on TRPA1 from diverse vertebrate species, i.e. it acts as an agonist but not as an antagonist for chicken and frog TRPA1s. By characterizing chimeric channels of human and chicken TRPA1s, as well as point mutants, we found that a single specific amino acid residue located within the putative fifth transmembrane domain was involved in not only the stimulatory but also the inhibitory actions of A967079. AP18, structurally related to A967079, exerted similar pharmacological properties to A967079. Our findings and previous reports on species differences in the sensitivity to TRPA1 antagonists supply useful information in the search for novel analgesic medicines targeting TRPA1.

  3. 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.

  4. 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

  5. Molecular and Cytogenetic Characterization of Wild Musa Species.

    PubMed

    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

  6. 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.

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

    PubMed

    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

  8. 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

  9. Molecular characterisation of species and genotypes of Cryptosporidium and Giardia and assessment of zoonotic transmission

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular characterization of species and genotypes of Cryptosporidium and Giardia is essential for accurately identifying organisms and assessing zoonotic transmission. Results of recent molecular epidemiologic studies strongly suggest that zoonotic transmission plays an important role in crypt...

  10. Molecular identification of iridoviruses infecting various sturgeon species in Europe.

    PubMed

    Bigarré, L; Lesne, M; Lautraite, A; Chesneau, V; Leroux, A; Jamin, M; Boitard, P M; Toffan, A; Prearo, M; Labrut, S; Daniel, P

    2017-01-01

    Iridoviridae are known to cause disease in sturgeons in North America. Here, histological and molecular methods were used to screen for this family of virus in sturgeons from various European farms with low-to-high morbidity. Some histological samples revealed basophilic cells in the gill and labial epithelia, strongly suggesting the accumulation of iridovirus particles. Newly developed generic PCR tests targeting the major capsid protein (MCP) gene of sturgeon iridoviruses identified in North America, namely the white sturgeon iridovirus and the Namao virus (NV), produced positive signals in most samples from four sturgeon species: Russian (Acipenser gueldenstaedtii), Siberian (A. baerii), Adriatic (A. naccarii) and beluga (Huso huso). The sequences of the PCR products were generally highly similar one another, with nucleotide identities greater than 98%. They were also related to (74-88%), although distinct from, American sturgeon iridoviruses. These European viruses were thus considered variants of a single new virus, provisionally named Acipenser iridovirus-European (AcIV-E). Moreover, three samples infected with AcIV-E showed genetic heterogeneity, with the co-existence of two sequences differing by five nucleotides. One of our European samples carried a virus distinct from AcIV-E, but closely related to NV identified in Canada (95%). This study demonstrates the presence of two distinct sturgeon iridoviruses in Europe: a new genotype AcIV-E and an NV-related virus.

  11. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. Rubber molecular weight regulation, in vitro, in plant species that produce high and low molecular weights in vivo.

    PubMed

    Cornish, K; Castillón, J; Scott, D J

    2000-01-01

    In three rubber-producing species, in vitro, the rates of initiation and polymerization and the biopolymer molecular weight produced were affected by the concentration of farnesyl diphosphate (FPP) initiator and isopentenyl diphosphate (IPP) elongation substrate (monomer). Ficus elastica, a low molecular weight-producer in vivo, synthesized rubber polymers approximately twice the molecular weight of those made by Hevea brasiliensis or Parthenium argentatum (which produce high molecular weights in vivo), possibly due to its lower IPP Km. In all species, increasing FPP concentrations increased rubber biosynthetic rate and new molecules initiated but decreased molecular weight by competition with the allylic diphosphate (APP) end of elongating rubber molecules for the APP binding site. Increasing IPP concentrations increased rubber biosynthetic rate and rubber molecular weight, but only when FPP concentrations were below the FPP Km's or where negative cooperativity operated. In conclusion, rubber transferase is not the prime regulator of rubber molecular weight in vivo.

  14. The calmodulin intergenic spacer as molecular target for characterization of Leishmania species

    PubMed Central

    2014-01-01

    Background Human leishmaniasis is a neglected disease caused by parasites of the genus Leishmania. Clinical aspects of this disease can vary significantly, reflecting the wide range of parasites in the genus Leishmania. Knowing accurately the Leishmania species infecting humans is important for clinical case management and evaluation of epidemiological risk. Calmodulin is an essential gene in trypanosomatids that modulates the calcium metabolism in various cellular activities. Despite its strong conservation in trypanosomatids, it has been recently observed that its untranslated regions (UTR) diverge among species. Methods In this study we analyzed the sequences and the absolute dinucleotide frequency of the intergenic spacer of the calmodulin gene (containing both, 3′ and 5′UTR) in nine reference Leishmania species and ten clinical isolates obtained from patients with cutaneous leishmaniasis. Results We show that the short calmodulin intergenic spacers exhibit features that make them interesting for applications in molecular characterization and phylogenetic studies of Leishmania. Dendrograms based on sequence alignments and on the dinucleotide frequency indicate that this particular region of calmodulin gene might be useful for species typing between the Leishmania and Viannia subgenera. Conclusions Mutations and composition of the calmodulin intergenic spacer from Leishmania species might have taxonomic value as parameters to define if an isolate is identical to a certain species or belongs to one of the two current subgenera. PMID:24438764

  15. Chronic ethanol consumption alters the selective usage of phosphatidylethanolamine molecular species by methyltransferases

    SciTech Connect

    Ellingson, J.S.; Pukys, T.; Rubin, E. )

    1992-01-01

    The authors have examined the effects of chronic ethanol consumption on phospholipid methyltransferases, which may play a special role by synthesizing phosphatidylcholine (PC) molecules containing predominantly polyunsaturated fatty acids. Rat liver microsomes from adenosylmethionine to convert endogenous phoshatidylethanolamine (PE) to radiolabeled PC, which was separated into its individual molecular species by reversed-phase HPLC. To assess the selective usage of PE molecular species for methylation, the authors determined the mole % of the PE molecular species in microsomes from control and ethanol-fed rats. Chronic ethanol consumption increased the selective usage of phospholipid molecular species containing palmitic acid combined with arachidonic acid or docosahexaenoic acid, whereas it did not affect the use of the corresponding stearic acid species. These results suggest that the long term interference with cellular physiology by altering the metabolism of a specific metabolic pool of molecular species is a mechanism by which chronic ethanol consumption could exert adverse effects of the liver.

  16. Less-Frequent Fusarium Species of Clinical Interest: Correlation between Morphological and Molecular Identification and Antifungal Susceptibility▿

    PubMed Central

    Azor, Mónica; Gené, Josepa; Cano, Josep; Manikandan, Palanisamy; Venkatapathy, Narendran; Guarro, Josep

    2009-01-01

    Forty-eight Fusarium isolates morphologically identified as belonging to seven species of clinical interest (i.e., Fusarium chlamydosporum, Fusarium dimerum, Fusarium incarnatum, Fusarium napiforme, Fusarium nygamai, Fusarium proliferatum, and Fusarium sacchari) were characterized molecularly by the analysis of the sequences of the TUB region of the β-tubulin gene. F. chlamydosporum and F. dimerum were the most genetically heterogeneous species. A high degree of correlation between the morphological and molecular identification was shown among the isolates studied. A table with the key morphological features for the identification of these Fusarium species is provided. The antifungal susceptibilities of the Fusarium isolates to 11 antifungal drugs were tested; terbinafine was the most active drug against all the species tested with the exception of F. incarnatum, for which amphotericin B was the most active. PMID:19321723

  17. 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

  18. 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

  19. 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)

  20. 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.

  1. Molecular basis for species-specific sensitivity to "hot" chili peppers.

    PubMed

    Jordt, Sven-Eric; Julius, David

    2002-02-08

    Chili peppers produce the pungent vanilloid compound capsaicin, which offers protection from predatory mammals. Birds are indifferent to the pain-producing effects of capsaicin and therefore serve as vectors for seed dispersal. Here, we determine the molecular basis for this species-specific behavioral response by identifying a domain of the rat vanilloid receptor that confers sensitivity to capsaicin to the normally insensitive chicken ortholog. Like its mammalian counterpart, the chicken receptor is activated by heat or protons, consistent with the fact that both mammals and birds detect noxious heat and experience thermal hypersensitivity. Our findings provide a molecular basis for the ecological phenomenon of directed deterence and suggest that the capacity to detect capsaicin-like inflammatory substances is a recent acquisition of mammalian vanilloid receptors.

  2. Molecular Identification and Antifungal Susceptibility Testing of Clinical Isolates of the Candida rugosa Species Complex and Proposal of the New Species Candida neorugosa

    PubMed Central

    Paredes, Katihuska; Sutton, Deanna A.; Cano, Josep; Fothergill, Annette W.; Lawhon, Sara D.; Zhang, Sean; Watkins, Jeffrey P.

    2012-01-01

    Candida rugosa is a poorly known fungal species occasionally involved in human infections. A molecular analysis of the sequences of the D1/D2 domains and the internal transcribed spacer (ITS) region of the ribosomal genes of 24 clinical isolates phenotypically identified as C. rugosa demonstrated that only 10 (41.6%) isolates belonged to that species. The other isolates were identified as Candida pararugosa (41.6%) and Candida pseudorugosa (8.3%). The remaining two isolates, from human and equine infections, respectively, were clearly different from the others and represent a new species proposed here as Candida neorugosa. The closest species by D1/D2 sequences was the type strain of C. rugosa, with only 92.3% similarity. C. neorugosa can also be differentiated from all other species of the C. rugosa complex by phenotypic features. The eight antifungal drugs tested showed high in vitro activity against the 24 isolates included in the study. PMID:22553236

  3. Molecular identification of Pilobolus species from Yellowstone National Park.

    PubMed

    Foos, K Michael; Sheehan, Kathy B

    2011-01-01

    Pilobolus, a widely distributed coprophilous fungus, grows on herbivore dung. Species of Pilobolus traditionally are described with imprecise morphological characteristics potentially leading to misidentification. In this study we used PCR analysis of taxonomically informative sequences to provide more consistent species identification from isolates obtained in Yellowstone National Park. We collected Pilobolus park-wide from six taxa of herbivores over 9 y. Multiple transfers of single sporangium isolates provided pure cultures from which DNA was extracted. Sequence analysis of internal transcribed spacer (ITS) regions of DNA that code for rRNA genes were used to distinguish among similar species. We describe several species of Pilobolus associated with herbivores in various habitats, including two species not previously reported, P. heterosporus and P. sphaerosporus. Our results show that phylogenetic species identification of Pilobolus based on sequence analysis of pure culture isolates provides a more reliable means of identifying species than traditional methods.

  4. 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

  5. Elucidation of molecular dynamics of invasive species of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...

  6. Molecular characterisation of the species of the genus Zygosaccharomyces.

    PubMed

    Esteve-Zarzoso, Braulio; Zorman, Tina; Belloch, Carmela; Querol, Amparo

    2003-09-01

    The restriction fragments polymorphisms of the mitochondrial DNA and the PCR fragment that comprised the internal transcribes spacers and the 5.8S rRNA gene, together with the electrophoretic karyotypes of 40 strains from the 10 species of the genus Zygosaccharomyces, including the new species Z. lentus were examined. The RFLP's of the ITS-5.8S region showed a specific restriction pattern for each species, including the new species Z. lentus. The only exception were the species Z. cidri and Z. fermentati that produced identical restriction profiles. The electrophoretic chromosome patterns confirmed the differences between the species of this genus, including the phylogenetic closest species Z. cidri and Z. fermentati. They present few chromosomes ranging from 3 bands (4 or 5 chromosomes) for Z. florentinus to 7 bands (8 to 10 chromosomes) for Z. cidri and Z. fermentati. The strain level resolution power of RFLP's of mtDNA of this genus enabled the characterisation of strains from the same species, even where they are isolated from the same substrate. However, in the cases of Z. bailii and Z. lentus, electrophoretic karyotyping there was considerable variation.

  7. 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

  8. Docosahexaenoate-containing molecular species of glycerophospholipids from frog retinal rod outer segments show different rates of biosynthesis and turnover

    SciTech Connect

    Louie, K.; Wiegand, R.D.; Anderson, R.E.

    1988-12-13

    The authors have studied the de novo synthesis and subsequent turnover of major docosahexaenoate-containing molecular species in frog rod outer segment (ROS) phospholipids following intravitreal injection of (2-/sup 3/H)glycerol. On selected days after injection, ROS were prepared and phospholipids extracted. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS) were isolated and converted to diradylglycerols with phospholipase C. Diradylglycerols were derivatized with benzoic anhydride and resolve into diacylglycerobenzoates and ether-linked glycerobenzoates. The diacylglycerobenzoates were fractionated into molecular species by HPLC, quantitated, and counted for radioactivity. Label was incorporated into ROS phospholipids by day 1 and was followed up through the eighth day. The dipolyenoic species 22:6-22:6 from PC showed 1 3-5 times higher radiospecific activity than the same species from either PE or PS. The rate of decline was determined by calculating the half-life of each molecular species, which was used as a measure of the turnover of the species. The percent distribution of radioactivity in the molecular species of PC and PE was quite different from the relative mass distribution at day 1. However, percent dpm approached the mole percent by 31 days. In PS, percent dpm and mole percent were the same at all time points. These results indicate that the molecular species composition of PC and PE in frog retinal ROS is determined by a combination of factors, which include rate of synthesis, rate of degradation, and selective interconversions. In contrast, PS composition appears to be determined at the time of synthesis.

  9. Tunable controlled release of molecular species from Halloysite nanotubes

    NASA Astrophysics Data System (ADS)

    Elumalai, Divya Narayan

    Encouraged by potential applications in rust coatings, self-healing composites, selective delivery of drugs, and catalysis, the transport of molecular species through Halloysite nanotubes (HNTs), specifically the storage and controlled release of these molecules, has attracted strong interest in recent years. HNTs are a naturally occurring biocompatible nanomaterial that are abundantly and readily available. They are alumosilicate based tubular clay nanotubes with an inner lumen of 15 nm and a length of 600-900 nm. The size of the inner lumen of HNTs may be adjusted by etching. The lumen can be loaded with functional agents like antioxidants, anticorrosion agents, flame-retardant agents, drugs, or proteins, allowing for a sustained release of these agents for hours. The release times can be further tuned for days and months by the addition of tube end-stoppers. In this work a three-dimensional, time-quantified Monte Carlo model that efficiently describes diffusion through and from nanotubes is implemented. Controlled delivery from Halloysite Nanotubes (HNT) is modeled based on interactions between the HNT's inner wall and the nanoparticles (NP) and among NPs themselves. The model was validated using experimental data published in the literature. The validated model is then used to study the effect of multiple parameters like HNT diameter and length, particle charge, ambient temperature and the creation of smart caps at the tube ends on the release of encapsulated NPs. The results show that release profiles depend on the size distribution of the HNT batch used for the experiment, as delivery is sensitive to HNT lumen and length. The effect of the addition of end-caps to the HNTs, on the rate of release of encapsulated NPs is also studied here. The results show that the release profiles are significantly affected by the addition of end caps to the HNTs and is sensitive to the end-cap pore lumen. A very good agreement with the experiment is observed when a weight

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

    PubMed Central

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

    2015-01-01

    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. PMID:25621335

  11. 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.

  12. Molecular Mechanisms of DNA Replication Checkpoint Activation

    PubMed Central

    Recolin, Bénédicte; van der Laan, Siem; Tsanov, Nikolay; Maiorano, Domenico

    2014-01-01

    The major challenge of the cell cycle is to deliver an intact, and fully duplicated, genetic material to the daughter cells. To this end, progression of DNA synthesis is monitored by a feedback mechanism known as replication checkpoint that is untimely linked to DNA replication. This signaling pathway ensures coordination of DNA synthesis with cell cycle progression. Failure to activate this checkpoint in response to perturbation of DNA synthesis (replication stress) results in forced cell division leading to chromosome fragmentation, aneuploidy, and genomic instability. In this review, we will describe current knowledge of the molecular determinants of the DNA replication checkpoint in eukaryotic cells and discuss a model of activation of this signaling pathway crucial for maintenance of genomic stability. PMID:24705291

  13. Molecular identification of Paragonimus species by DNA pyrosequencing technology.

    PubMed

    Tantrawatpan, Chairat; Intapan, Pewpan M; Janwan, Penchom; Sanpool, Oranuch; Lulitanond, Viraphong; Srichantaratsamee, Chutatip; Anamnart, Witthaya; Maleewong, Wanchai

    2013-06-01

    DNA pyrosequencing for PCR amplicons is an attractive strategy for the identification of microorganisms because of its short time performance for large number of samples. In this study, the primers targeting the fragment of ITS2 region of nuclear ribosomal RNA gene were newly developed for pyrosequencing-based identification of 6 Paragonimus species, Paragonimus bangkokensis, Paragonimus harinasutai, Paragonimus heterotremus, Paragonimus macrorchis, Paragonimus siamensis and Paragonimus westermani. Pyrosequencing determination of 39 nucleotides of partial ITS2 region could discriminate 6 Paragonimus species, and could also detect intra-species genetic variation of P. macrorchis. This DNA pyrosequencing-based identification can be a valuable tool to improve species-level identification of Paragonimus in the endemic areas.

  14. Antifungal activity of heartwood extracts from three Juniperus species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heartwood samples from three species of Juniperus (i.e., J. virginianna, J. occidentalis, and J. ashei) were extracted with hexane, ethanol and methanol and the hexane and ethanol extracts were tested for antifungal activity against four species of wood-rot fungi. These three species represent the ...

  15. Molecular identification of Entamoeba species in savanna woodland chimpanzees (Pan troglodytes schweinfurthii).

    PubMed

    Jirků-Pomajbíková, Kateřina; Čepička, Ivan; Kalousová, Barbora; Jirků, Milan; Stewart, Fiona; Levecke, Bruno; Modrý, David; Piel, Alex K; Petrželková, Klára J

    2016-05-01

    To address the molecular diversity and occurrence of pathogenic species of the genus Entamoeba spp. in wild non-human primates (NHP) we conducted molecular-phylogenetic analyses on Entamoeba from wild chimpanzees living in the Issa Valley, Tanzania. We compared the sensitivity of molecular [using a genus-specific polymerase chain reaction (PCR)] and coproscopic detection (merthiolate-iodine-formaldehyde concentration) of Entamoeba spp. We identified Entamoeba spp. in 72 chimpanzee fecal samples (79%) subjected to species-specific PCRs for six Entamoeba species/groups (Entamoeba histolytica, Entamoeba nuttalli, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba coli and Entamoeba polecki ST2). We recorded three Entamoeba species: E. coli (47%), E. dispar (16%), Entamoeba hartmanni (51%). Coproscopically, we could only distinguish the cysts of complex E. histolytica/dispar/moshkovskii/nuttalli and E. coli. Molecular prevalence of entamoebas was higher than the prevalence based on the coproscopic examination. Our molecular phylogenies showed that sequences of E. dispar and E. coli from Issa chimpanzees are closely related to sequences from humans and other NHP from GenBank. The results showed that wild chimpanzees harbour Entamoeba species similar to those occurring in humans; however, no pathogenic species were detected. Molecular-phylogenetic methods are critical to improve diagnostics of entamoebas in wild NHP and for determining an accurate prevalence of Entamoeba species.

  16. Molecular approaches identify known species, reveal cryptic species and verify host specificity of Chinese Philotrypesis (Hymenoptera: Pteromalidae).

    PubMed

    Zhou, Mei-Jiao; Xiao, Jin-Hua; Bian, Sheng-Nan; Li, Yan-Wei; Niu, Li-Ming; Hu, Hao-Yuan; Wu, Wen-Shan; Murphy, Robert W; Huang, Da-Wei

    2012-07-01

    Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a model taxon for studying male fighting and mating behaviour. Its extreme sexual dimorphism and male polymorphism render species identification uncertain and in-depth research on its ecology, behaviour and other evolutionary topics challenging. The fig wasps' enclosed habitat within the syconia makes their mating behaviour inaccessible, to the extent of matching conspecific females and males. In this study, we combine morphological and molecular analyses to identify species of Philotrypesis sampled from south China and to associate their extraordinarily dimorphic genders and labile male morphologies. Morphological evaluations of females identify 22 species and 28 male morphs. The mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 2 data detect 21 species using females, and 15 species among the males. Most of the males match the species as delimited by females. Both markers reveal cryptic species in P. quadrisetosa on Ficus vasculosa. Most species of wasps live on one species of fig but three species co-occur in two hosts (F. microcarpa and F. benjamina), which indicates host switching.

  17. Molecular characterization of DSC1 orthologs in invertebrate species.

    PubMed

    Cui, Ying-Jun; Yu, Lin-Lin; Xu, Hai-Jun; Dong, Ke; Zhang, Chuan-Xi

    2012-05-01

    DSC1 and BSC1 are two founding members of a novel family of invertebrate voltage-gated cation channels with close structural and evolutionary relationships to voltage-gated sodium and calcium channels. In this study, we searched the published genome sequences for DSC1 orthologs. DSC1 orthologs were found in all 48 insect species, and in other invertebrate species belonging to phyla Mollusca, Cnidaria, Hemichordata and Echinodermata. However, DSC1 orthologs were not found in four arachnid species, Ixodes scapularis, Rhipicephalus microplus, Tetranychus urticae and Varroa destructor, two species in Annelida or any vertebrate species. We then cloned and sequenced NlSC1 and BmSC1 full-length cDNAs from the brown planthopper (Nilaparvata lugens) and the silkworm (Bombyx mori), respectively. NlSC1 and BmSC1 share about 50% identity with DSC1, and the expression of NlSC1 and BmSC1 transcripts was most abundant in the head and antenna in adults. All DSC1 orthologs contain a unique and conserved DEEA motif, instead of the EEEE or EEDD motif in classical calcium channels or the DEKA motif in sodium channels. Phylogenetic analyses revealed that DSC1 and its orthologs form a separate group distinct from the classical voltage-gated sodium and calcium channels and constitute a unique family of cation channels. The DSC1/BSC1-family channels could be potential targets of new and safe insecticides for pest control.

  18. Molecular and biochemical properties of storage mites (except Blomia species).

    PubMed

    Fernández-Caldas, Enrique; Iraola, Victor; Carnés, Jerónimo

    2007-01-01

    In recent years, the allergological importance of different mite species not belonging to the family Pyroglyphidae has been demonstrated. These mites, commonly named storage mites, include Lepidoglyphus destructor, Glycyphagus domesticus, Tyrophagus putrescentiae, Acarus siro, Aleuroglyphus ovatus, Suidasia medanensis and Thyreophagus entomophagus. Several allergens from these species have been purified, sequenced and cloned. Many of these allergens have shown sequence homology and a biological function similar to those previously described in Blomia tropicalis and the Dermatophagoides spp. The main allergens described in storage mites include fatty acid binding proteins, tropomysin and paramyosin homologues, apoliphorine like proteins, alfa-tubulines and other, such as group 2, 5 and 7 allergens, which definitive biological function has not been described yet. Besides the purification and characterization of allergens, the allergenicity of other species such as Acarus farris, Austroglycyphagus malaysiensis, Blomia kulagini and B. tjibodas, Cheyletus eruditus, Chortoglyphus arcuatus, Gohieria fusca, Thyreophagus entomophagus and Tyrophagus longior has been investigated. Research has also been conducted to identify allergens in parasitic mites, such as Psoroptes ovis, Sarcoptes scabiei, Varroa jacobsoni, Diplaegidia columbae and Hemisarcoptes cooremani. The allergenicity of mites present in agricultural environments has been investigated. Crossreactivity studies have also been performed to elucidate to what extent all these mites share common, or species specific epitopes. Herein we present a comprehensive review of the allergenicity of mite species which have been implicated in human respiratory and/or dermatological diseases.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. Molecular analysis of Malassezia species isolated from hospitalized neonates.

    PubMed

    Zomorodain, Kamiar; Mirhendi, Hossein; Tarazooie, Bita; Kordbacheh, Parivash; Zeraati, Hojjat; Nayeri, Fatemeh

    2008-01-01

    Malassezia species are a part of the skin microflora of neonates. Under certain circumstances, they can cause diseases ranging from simple pustulosis to lifethreatening fungemia in newborn infants. Little information is available about the epidemiology of Malassezia species in neonates. In the present study, we successfully isolated Malassezia yeasts from 68.7% of hospitalized neonates. Using the polymerase chain reaction-restriction fragment length polymorphism method (PCR-RFPL), M. furfur (88.06%) was identified as the most isolated species, followed in frequency by M. globosa (10.48%), M. obtusa (0.73%), and M. slooffiae (0.73%). Among the variables studied, only a longer stay in the ward resulted in a higher colonization rate. Using multiple logistic regression, only the type of hospital and ward had some effects on the colonization rate. Our results supported the hypothesis that neonates acquire Malassezia flora through direct contact with their mothers or hospital personnel.

  1. Altered expression of ganglioside GM3 molecular species and a potential regulatory role during myoblast differentiation.

    PubMed

    Go, Shinji; Go, Shiori; Veillon, Lucas; Ciampa, Maria Grazia; Mauri, Laura; Sato, Chihiro; Kitajima, Ken; Prinetti, Alessandro; Sonnino, Sandro; Inokuchi, Jin-Ichi

    2017-03-08

    Gangliosides (sialic acid-containing glycosphingolipids) help regulate many important biological processes, including cell proliferation, signal transduction, and differentiation, via formation of functional microdomains in plasma membranes. The structural diversity of gangliosides arises from both the ceramide moiety and glycan portion. Recently, differing molecular species of a given ganglioside are suggested to have distinct biological properties, and regulate specific and distinct biological events. Elucidation of the function of each molecular species is important and will provide new insights into ganglioside biology. Gangliosides are also suggested to be involved in skeletal muscle differentiation; however, the differential roles of ganglioside molecular species remain unclear. We describe here striking changes in quantity and quality of gangliosides (particularly GM3) during differentiation of mouse C2C12 myoblast cells, and key roles played by distinct GM3 molecular species at each step of the process.

  2. Use of Sloppy Molecular Beacon Probes for Identification of Mycobacterial Species ▿ †

    PubMed Central

    El-Hajj, Hiyam H.; Marras, Salvatore A. E.; Tyagi, Sanjay; Shashkina, Elena; Kamboj, Mini; Kiehn, Timothy E.; Glickman, Michael S.; Kramer, Fred Russell; Alland, David

    2009-01-01

    We report here the use of novel “sloppy” molecular beacon probes in homogeneous PCR screening assays in which thermal denaturation of the resulting probe-amplicon hybrids provides a characteristic set of amplicon melting temperature (Tm) values that identify which species is present in a sample. Sloppy molecular beacons possess relatively long probe sequences, enabling them to form hybrids with amplicons from many different species despite the presence of mismatched base pairs. By using four sloppy molecular beacons, each possessing a different probe sequence and each labeled with a differently colored fluorophore, four different Tm values can be determined simultaneously. We tested this technique with 27 different species of mycobacteria and found that each species generates a unique, highly reproducible signature that is unaffected by the initial bacterial DNA concentration. Utilizing this general paradigm, screening assays can be designed for the identification of a wide range of species. PMID:19171684

  3. Distribution and Molecular Diversity of Arborescent Gossypium Species.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mexico is a center of diversity of Gossypium. As currently circumscribed, arborescent Gossypium species (Section Erioxylum) are widely distributed in dry deciduous forests located from the central state of Sinaloa at the north of its range to the eastern state of Oaxaca in the south. However, extens...

  4. Molecular Structure and Stability of Dissolved Lithium Polysulfide Species

    SciTech Connect

    Vijayakumar, M.; Govind, Niranjan; Walter, Eric D.; Burton, Sarah D.; Shukla, Anil K.; Devaraj, Arun; Xiao, Jie; Liu, Jun; Wang, Chong M.; Karim, Ayman M.; Thevuthasan, Suntharampillai

    2014-01-01

    Ability to predict the solubility and stability of lithium polysulfide is vital in realizing longer lasting lithium-sulfur batteries. Herein we report a combined computational and experimental spectroscopic analysis to understand the dissolution mechanism of lithium polysulfide species in an aprotic solvent medium. Multinuclear NMR and sulfur K-edge X-ray absorption (XAS) analysis reveals that the lithium exchange between polysulfide species and solvent molecule constitutes the first step in the dissolution process. Lithium exchange leads to de-lithiated polysulfide ions which subsequently forms highly reactive free radicals through disproportion reaction. The energy required for the disproportion and possible dimer formation reactions of the polysulfide species are analyzed using density functional theory (DFT) calculations. We validate our calculations with variable temperature electron spin resonance (ESR) measurements. Based on these findings, we discuss approaches to optimize the electrolyte in order to control the polysulfide solubility. The energy required for the disproportion and possible dimer formation reactions of the polysulfide species are analyzed using density functional theory (DFT) calculations. We validate our calculations with variable temperature electron spin resonance (ESR) measurements. Based on these findings, we discuss approaches to optimize the electrolyte in order to control the polysulfide solubility.

  5. Molecular detection of a potentially toxic diatom species.

    PubMed

    Dhar, Bidhan Chandra; Cimarelli, Lucia; Singh, Kumar Saurabh; Brandi, Letizia; Brandi, Anna; Puccinelli, Camilla; Marcheggiani, Stefania; Spurio, Roberto

    2015-05-06

    A few diatom species produce toxins that affect human and animal health. Among these, members of the Pseudo-nitzschia genus were the first diatoms unambiguously identified as producer of domoic acid, a neurotoxin affecting molluscan shell-fish, birds, marine mammals, and humans. Evidence exists indicating the involvement of another diatom genus, Amphora, as a potential producer of domoic acid. We present a strategy for the detection of the diatom species Amphora coffeaeformis based on the development of species-specific oligonucleotide probes and their application in microarray hybridization experiments. This approach is based on the use of two marker genes highly conserved in all diatoms, but endowed with sufficient genetic divergence to discriminate diatoms at the species level. A region of approximately 450 bp of these previously unexplored marker genes, coding for elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), was used to design oligonucleotide probes that were tested for specificity in combination with the corresponding fluorescently labeled DNA targets. The results presented in this work suggest a possible use of this DNA chip technology for the selective detection of A. coffeaeformis in environmental settings where the presence of this potential toxin producer may represent a threat to human and animal health. In addition, the same basic approach can be adapted to a wider range of diatoms for the simultaneous detection of microorganisms used as biomarkers of different water quality levels.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. 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.

  8. Characterization of glycerophospholipid molecular species in six species of edible clams by high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry.

    PubMed

    Liu, Zhong-Yuan; Zhou, Da-Yong; Zhao, Qi; Yin, Fa-Wen; Hu, Xiao-Pei; Song, Liang; Qin, Lei; Zhang, Jian-Run; Zhu, Bei-Wei; Shahidi, Fereidoon

    2017-03-15

    The molecular species of glycerophosphocholine (GPCho), glycerophosphoethanolamine (GPEtn), glycerophosphoserine (GPSer), lysoglycerophosphocholine (LGPCho) and lysoglycerophosphoethanolamine (LGPEtn) from six species of edible clams were characterized by using high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry. At least 435, 453, 468, 443, 427 and 444 glycerophospholipid (GP) molecular species were characterized, respectively, from Cyclina sinensis, Mactra chinensis Philippi, Mactra veneriformis Reeve, Meretrix meretrix, Ruditapes philippinarum and Saxidomus purpurata. Most of the predominant GP molecular species in clam contained polyunsaturated fatty acids (PUFA), mainly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), indicating that clam is a potential resource of GP enriched PUFA. According to the amount of the major molecular species containing EPA and DHA, Cyclina sinensis was the best fit species for GPCho, Mactra veneriformis Reeve was the best fit species for GPEtn, Mactra chinensis Philippi was the best fit species for GPSer and LGPEtn, and Saxidomus purpurata was the best fit species for LGPCho.

  9. Molecular identification and differentiation of Brevibacterium species and strains.

    PubMed

    Hoppe-Seyler, Tobias-Simon; Jaeger, Beate; Bockelmann, Wilhelm; Geis, Arnold; Heller, Knut-Jochem

    2007-01-01

    Amplified ribosomal DNA restriction enzyme analysis (ARDRA), pulsed field gel electrophoresis (PFGE) and ribotyping were used to differentiate among 24 strains of Brevibacterium linens, Brevibacterium casei and Brevibacterium epidermidis obtained from type culture collections or isolated from various smear ripened cheeses. ARDRA was applied to the 16S rDNA. B. linens was shown to be a quite heterogenic group with 2 to at least 4 copies of rrn operons per strain with aberrant nucleotide sequences. AccI gave genus specific restriction patterns and was used to separate Brevibacterium from Corynebacterium species. The expected species specificity of TaqI applied to B. linens type culture strains, but not to all strains isolated from cheese. By AvaI restriction, B. casei and B. linens were differentiated from B. epidermidis and the orange pigmented Arthrobacter casei, a new species of coryneform bacteria; by XmnI restriction, B. linens and B. epidermidis were differentiated from B. casei. One of 4 B. linens genotypes could not be distinguished from B. casei by this method. Here, the typical orange B. linens pigments were used for classification, which was confirmed by partial sequencing of the 16S rDNA.

  10. Quantitative analysis of phosphatidylcholine molecular species using HPLC and light scattering detection.

    PubMed

    Brouwers, J F; Gadella, B M; van Golde, L M; Tielens, A G

    1998-02-01

    A number of HPLC chromatographic procedures can be used to separate intact molecular species of phosphatidylcholine (PC), but on-line quantification has remained problematic due to insensitivity of UV-detection for saturated species. Here, a new method is presented, separating all major PC molecular species from a variety of biological samples in intact form using a single, short and isocratic run. Species were separated on two RP18 reverse-phase columns in series and all species displayed an exponential relation between retention time and the percentage of acetonitrile or triethylamine in the mobile phase, allowing optimization of the mobile phase on a theoretical base, rather than on time-consuming test-runs. The use of triethylamine as a volatile additive instead of choline chloride allowed the use of light scattering detection. On a molar base, the response of the detector was invariant between species and allowed quantification of as little as 50 pmoles. The method was tested using phosphatidylcholines with widely different molecular species patterns, such a PC from rat liver, porcine pulmonary surfactant, bovine heart, boar sperm cells, and the parasite Schistosoma mansoni. As only volatile components are present in the solvents, individual molecular species can easily be recovered in pure form from the column effluent, enabling their further analysis (e.g., scintillation counting).

  11. Molecular method for Bartonella species identification in clinical and environmental samples.

    PubMed

    García-Esteban, Coral; Gil, Horacio; Rodríguez-Vargas, Manuela; Gerrikagoitia, Xeider; Barandika, Jesse; Escudero, Raquel; Jado, Isabel; García-Amil, Cristina; Barral, Marta; García-Pérez, Ana L; Bhide, Mangesh; Anda, Pedro

    2008-02-01

    A new, efficient molecular method for detection of Bartonella, based on the 16S-23S rRNA intergenic spacer and 16S rRNA amplification by multiplex PCR combined with reverse line blotting, was designed. This assay could simultaneously detect 20 different known species and other Bartonella species not described previously.

  12. A Molecular Orbital Study of Atmospherically Important Species.

    DTIC Science & Technology

    1983-06-01

    from the OH to the H2 0 upon formation of the hydrogen bond. The electron density is transferred to the oxygen and terminal hydrogen of the water ...Method," J. Chem. Phys., 52, 3362-3368, 1970. • -o . ..-.. . -34- 48. Chipman, D.M. "Effect of Molecular Geometry on the Electron Affinity of Water ...34 J. Phvs. Chem., 82, 1080-1083, 1978. 49. Benedict, W.S., N. Gailar, and E.K. Plvler, "Rotation-Vibration Spectra of Deuteriated Water Vapor," J. Chem

  13. Molecular characterization of Babesia and Cytauxzoon species in wild South-African meerkats.

    PubMed

    Leclaire, Sarah; Menard, Sandie; Berry, Antoine

    2015-04-01

    Piroplasms, including Babesia, Cytauxzoon and Theileria species, frequently infect domestic and wild mammals. At present, there is no information on the occurrence and molecular identity of these tick-borne blood parasites in the meerkat, one of South Africa's most endearing wildlife celebrities. Meerkats live in territorial groups, which may occur on ranchland in close proximity to humans, pets and livestock. Blood collected from 46 healthy meerkats living in the South-African Kalahari desert was screened by microscopy and molecular methods, using PCR and DNA sequencing of 18S rRNA and ITS1 genes. We found that meerkats were infected by 2 species: one species related to Babesia sp. and one species related to Cytauxzoon sp. Ninety one percent of the meerkats were infected by the Cytauxzoon and/or the Babesia species. Co-infection occurred in 46% of meerkats. The pathogenicity and vectors of these two piroplasm species remains to be determined.

  14. DNA Barcoding and Molecular Phylogeny of Drosophila lini and Its Sibling Species.

    PubMed

    Li, Yi-Feng; Wen, Shuo-Yang; Kawai, Kuniko; Gao, Jian-Jun; Hu, Yao-Guang; Segawa, Ryoko; Toda, Masanori J

    2012-01-01

    Drosophila lini and its two sibling species, D. ohnishii and D. ogumai, are hardly distinguishable from one another in morphology. These species are more or less reproductively isolated. The mitochondrial ND2 and COI-COII and the nuclear ITS1-ITS2 regions were sequenced to seek for the possibility of DNA barcoding and to reconstruct the phylogeny of them. The character-based approach for DNA barcoding detected some diagnostic nucleotides only for monophyletic D. ogumai, but no informative sites for the other two very closely species, D. lini and D. ohnishii, of which strains intermingled in the molecular phylogenetic trees. Thus, this study provides another case of limited applicability of DNA barcoding in species delineation, as in other cases of related Drosophila species. The molecular phylogenetic tree inferred from the concatenated sequences strongly supported the monophyly of the cluster of the three species, that is, the lini clade. We propose some hypotheses of evolutionary events in this clade.

  15. A perfect time to harness advanced molecular technologies to explore the fundamental biology of Toxocara species.

    PubMed

    Gasser, Robin B

    2013-04-15

    Toxocarosis is of major canine health and socioeconomic importance worldwide. Although many studies have given insights into toxocarosis, to date, there has been limited exploration of the molecular biology, biochemistry, genetics, epidemiology and ecology of Toxocara species as well as parasite-host interactions using '-omic' technologies. The present article gives a background on Toxocara species and toxocarosis, describes molecular tools for specific identification and genetic analysis, and provides a prospective view of the benefits that advanced molecular technologies will have towards better understanding the parasites and disease. Tackling key biological questions employing a 'systems biology' approach should lead to new and improved strategies for the treatment, diagnosis and control of toxocarosis.

  16. Cold-active enzymes studied by comparative molecular dynamics simulation.

    PubMed

    Spiwok, Vojtech; Lipovová, Petra; Skálová, Tereza; Dusková, Jarmila; Dohnálek, Jan; Hasek, Jindrich; Russell, Nicholas J; Králová, Blanka

    2007-04-01

    Enzymes from cold-adapted species are significantly more active at low temperatures, even those close to zero Celsius, but the rationale of this adaptation is complex and relatively poorly understood. It is commonly stated that there is a relationship between the flexibility of an enzyme and its catalytic activity at low temperature. This paper gives the results of a study using molecular dynamics simulations performed for five pairs of enzymes, each pair comprising a cold-active enzyme plus its mesophilic or thermophilic counterpart. The enzyme pairs included alpha-amylase, citrate synthase, malate dehydrogenase, alkaline protease and xylanase. Numerous sites with elevated flexibility were observed in all enzymes; however, differences in flexibilities were not striking. Nevertheless, amino acid residues common in both enzymes of a pair (not present in insertions of a structure alignment) are generally more flexible in the cold-active enzymes. The further application of principle component analysis to the protein dynamics revealed that there are differences in the rate and/or extent of opening and closing of the active sites. The results indicate that protein dynamics play an important role in catalytic processes where structural rearrangements, such as those required for active site access by substrate, are involved. They also support the notion that cold adaptation may have evolved by selective changes in regions of enzyme structure rather than in global change to the whole protein.

  17. Molecular characterization of Theileria species associated with mortality in four species of African antelopes.

    PubMed

    Nijhof, A M; Pillay, V; Steyl, J; Prozesky, L; Stoltsz, W H; Lawrence, J A; Penzhorn, B L; Jongejan, F

    2005-12-01

    Pathogen DNA was isolated from roan antelope (Hippotragus equinus), sable antelope (Hippotragus niger), greater kudu (Tragelaphus strepsiceros), and common gray duiker (Sylvicapra grimmia) in South Africa whose deaths were attributed to either theileriosis or cytauxzoonosis. We developed Theileria species-specific probes used in combination with reverse line blot hybridization assays and identified three different species of Theileria in four African antelope species. The close phylogenetic relationship between members of the genera Theileria and Cytauxzoon, similarities in the morphologies of developmental stages, and confusion in the literature regarding theileriosis or cytauxzoonosis are discussed.

  18. Does diet influence salivary enzyme activities in elephant species?

    PubMed

    Boehlke, Carolin; Pötschke, Sandra; Behringer, Verena; Hannig, Christian; Zierau, Oliver

    2017-01-01

    Asian elephants (Elephas maximus) and African elephants (Loxodonta africana) are herbivore generalists; however, Asian elephants might ingest a higher proportion of grasses than Africans. Although some studies have investigated nutrition-specific morphological adaptations of the two species, broader studies on salivary enzymes in both elephant species are lacking. This study focuses on the comparison of salivary enzymes activity profiles in the two elephant species; these enzymes are relevant for protective and digestive functions in humans. We aimed to determine whether salivary amylase (sAA), lysozyme (sLYS), and peroxidase (sPOD) activities have changed in a species-specific pattern during evolutionary separation of the elephant genera. Saliva samples of 14 Asian and eight African elephants were collected in three German zoos. Results show that sAA and sLYS are salivary components of both elephant species in an active conformation. In contrast, little to no sPOD activity was determined in any elephant sample. Furthermore, sAA activity was significantly higher in Asian compared with African elephants. sLYS and sPOD showed no species-specific differences. The time of food provision until sample collection affected only sAA activity. In summary, the results suggest several possible factors modulating the activity of the mammal-typical enzymes, such as sAA, sLYS, and sPOD, e.g., nutrition and sampling procedure, which have to be considered when analyzing differences in saliva composition of animal species.

  19. Molecular characterisation of species and genotypes of Cryptosporidium and Giardia and assessment of zoonotic transmission.

    PubMed

    Xiao, Lihua; Fayer, Ronald

    2008-09-01

    The molecular characterisation of species and genotypes of Cryptosporidium and Giardia is essential for accurately identifying organisms and assessing zoonotic transmission. Results of recent molecular epidemiological studies strongly suggest that zoonotic transmission plays an important role in cryptosporidiosis epidemiology. In such cases the most prevalent zoonotic species is Cryptosporidium parvum. Genotyping and subtyping data suggest that zoonotic transmission is not as prevalent in the epidemiology of giardiasis. Molecular characterisation of Cryptosporidium and Giardia is a relatively recent application that is evolving as new genes are found that increase the accuracy of identification while discovering a greater diversity of species and yet unnamed taxa within these two important genera. As molecular data accumulate, our understanding of the role of zoonotic transmission in epidemiology and clinical manifestations is becoming clearer.

  20. Molecular Ice Nucleation Activity of Birch Pollen

    NASA Astrophysics Data System (ADS)

    Felgitsch, Laura; Bichler, Magdalena; Häusler, Thomas; Weiss, Victor U.; Marchetti-Deschmann, Martina; Allmaier, Günter; Grothe, Hinrich

    2015-04-01

    Heterogeneous ice nucleation plays a major part in ecosystem and climate. Due to the triggering of ice cloud formation it influences the radiation balance of the earth, but also on the ground it can be found to be important in many processes of nature. So far the process of heterogeneous ice nucleation is not fully understood and many questions remain to be answered. Biological ice nucleation is hereby from great interest, because it shows the highest freezing temperatures. Several bacteria and fungi act as ice nuclei. A famous example is Pseudomonas syringae, a bacterium in commercial use (Snomax®), which increases the freezing from homogeneous freezing temperatures of approx. -40° C (for small volumes as in cloud droplets) to temperatures up to -2° C. In 2001 it was found that birch pollen can trigger ice nucleation (Diehl et al. 2001; Diehl et al. 2002). For a long time it was believed that this is due to macroscopic features of the pollen surface. Recent findings of Bernhard Pummer (2012) show a different picture. The ice nuclei are not attached on the pollen surface directly, but on surface material which can be easily washed off. This shows that not only the surface morphology, but also specific molecules or molecular structures are responsible for the ice nucleation activity of birch pollen. With various analytic methods we work on elucidating the structure of these molecules as well as the mechanism with which they trigger ice nucleation. To solve this we use various instrumental analytic techniques like Nuclear Magnetic Resonance spectroscopy (NMR), Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS), and Gas-phase Electrophoretic Mobility Molecular Analysis (GEMMA). Also standard techniques like various chromatographic separation techniques and solvent extraction are in use. We state here that this feature might be due to the aggregation of small molecules, with agglomerates showing a specific surface structure. Our results

  1. How to describe a cryptic species? Practical challenges of molecular taxonomy

    PubMed Central

    2013-01-01

    Background Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment’ in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and –at least for cryptic species – could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. Results The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of

  2. Hybridization and endangered species protection in the molecular era.

    PubMed

    Wayne, Robert K; Shaffer, H Bradley

    2016-06-01

    After decades of discussion, there is little consensus on the extent to which hybrids between endangered and nonendangered species should be protected by US law. As increasingly larger, genome-scale data sets are developed, we can identify individuals and populations with even trace levels of genetic admixture, making the 'hybrid problem' all the more difficult. We developed a decision-tree framework for evaluating hybrid protection, including both the processes that produced hybrids (human-mediated or natural) and the ecological impact of hybrids on natural ecosystems. We then evaluated our decision tree for four case studies drawn from our own work and briefly discuss several other cases from the literature. Throughout, we highlight the management outcomes that our approach provides and the nuances of hybridization as a conservation problem.

  3. Molecular evidence of Sarcocystis species in captive snakes in Japan.

    PubMed

    Abe, Niichiro; Matsubara, Katsuki; Tamukai, Kenichi; Miwa, Yasutsugu; Takami, Kazutoshi

    2015-08-01

    Sarcocystis nesbitti, using snakes as the definitive host, is a causative agent of acute human muscular sarcocystosis in Malaysia. Therefore, it is important to explore the distribution and prevalence of S. nesbitti in snakes. Nevertheless, epizootiological information of S. nesbitti in snakes remains insufficient because few surveys have assessed Sarcocystis infection in snakes in endemic countries. In Japan, snakes are popular exotic pet animals that are imported from overseas, but the degree of Sarcocystis infection in them remains unclear. The possibility exists that muscular sarcocystosis by S. nesbitti occurs in contact with captive snakes in non-endemic countries. For a total of 125 snake faecal samples from 67 snake species collected at animal hospitals, pet shops and a zoo, this study investigated the presence of Sarcocystis using polymerase chain reaction (PCR) for the 18S ribosomal RNA gene (18S rDNA). Four (3.2%) faecal samples were positive by PCR. Phylogenetic analysis of the 18S rDNA sequences obtained from four amplification products revealed one isolate from a beauty snake (Elaphe taeniura), Sarcocystis zuoi, which uses rat snakes as the definitive host. The isolate from a Macklot's python (Liasis mackloti) was closely related with unidentified Sarcocystis sp. from reticulated pythons in Malaysia. The remaining two isolates from tree boas (Corallus spp.) were closely related with Sarcocystis lacertae, Sarcocystis gallotiae and unidentified Sarcocystis sp. from smooth snakes, Tenerife lizards and European shrews, respectively. This report is the first of a study examining the distribution of Sarcocystis species in captive snakes in Japan.

  4. Molecular and morphologic data reveal multiple species in Peromyscus pectoralis

    PubMed Central

    Bradley, Robert D.; Schmidly, David J.; Amman, Brian R.; Platt, Roy N.; Neumann, Kathy M.; Huynh, Howard M.; Muñiz-Martínez, Raúl; López-González, Celia; Ordóñez-Garza, Nicté

    2015-01-01

    DNA sequence and morphometric data were used to re-evaluate the taxonomy and systematics of Peromyscus pectoralis. Phylogenetic analyses (maximum likelihood and Bayesian inference) of DNA sequences from the mitochondrial cytochrome-b gene in 44 samples of P. pectoralis indicated 2 well-supported monophyletic clades. The 1st clade contained specimens from Texas historically assigned to P. p. laceianus; the 2nd was comprised of specimens previously referable to P. p. collinus, P. p. laceianus, and P. p. pectoralis obtained from northern and eastern Mexico. Levels of genetic variation (~7%) between these 2 clades indicated that the genetic divergence typically exceeded that reported for other species of Peromyscus. Samples of P. p. laceianus north and south of the Río Grande were not monophyletic. In addition, samples representing P. p. collinus and P. p. pectoralis formed 2 clades that differed genetically by 7.14%. Multivariate analyses of external and cranial measurements from 63 populations of P. pectoralis revealed 4 morpho-groups consistent with clades in the DNA sequence analysis: 1 from Texas and New Mexico assignable to P. p. laceianus; a 2nd from western and southern Mexico assignable to P. p. pectoralis; a 3rd from northern and central Mexico previously assigned to P. p. pectoralis but herein shown to represent an undescribed taxon; and a 4th from southeastern Mexico assignable to P. p. collinus. Based on the concordance of these results, populations from the United States are referred to as P. laceianus, whereas populations from Mexico are referred to as P. pectoralis (including some samples historically assigned to P. p. collinus, P. p. laceianus, and P. p. pectoralis). A new subspecies is described to represent populations south of the Río Grande in northern and central Mexico. Additional research is needed to discern if P. p. collinus warrants species recognition. PMID:26937045

  5. Thermochemistry of new molecular species: SBr and HSBr

    NASA Astrophysics Data System (ADS)

    Ornellas, Fernando R.

    2007-05-01

    Total energies, optimized geometries, and vibrational frequencies of SBr and HSBr have been evaluated at the coupled cluster level of theory with the correlation consistent basis sets. Extrapolated to the complete basis set limit and with corrections for core-valence, scalar relativistic, and spin-orbit effects, atomization energies were computed and then combined with the experimental heats of formation of the atomic species to generate very accurate heats of formation for the species SBr and HSBr. For SBr, we predict 37.45 and 36.07kcal/mol for ΔHf(0K ) and ΔHf (298.15K ), respectively, in very good agreement with the inferred experimental values of 37.98 and 36.15kcal/mol. For HSBr, the estimate turns out to be 10.38 and 8.29kcal/mol for ΔHf (0K ) and ΔHf (298.15K ), respectively. Using the more recent HBrO experimental heat of formation at 298.15K of Lock et al., [J. Phys. Chem. 100, 7972 (1996)] the inferred experimental value for HSBr is predicted to be 8.15kcal/mol, compared with 8.65kcal/mol derived from the data of Ruscic and Berkowitz [J. Chem. Phys. 101, 7795 (1994)]. Considering the better agreement of the result with that predicted using the experimental value of ΔHf(298.15K ) of Lock et al., the author also supports the suggestion made by Denis [J. Phys. Chem. A. 110, 5887 (2006)] that the result of Lock et al. should be preferred over the one of Ruscic and Berkowitz. For ΔHf(0K ), the author found 10.38 and 10.56kcal/mol, respectively, for the theoretical and inferred experimental estimates.

  6. Molecular and biochemical mechanisms in teratogenesis involving reactive oxygen species.

    PubMed

    Wells, Peter G; Bhuller, Yadvinder; Chen, Connie S; Jeng, Winnie; Kasapinovic, Sonja; Kennedy, Julia C; Kim, Perry M; Laposa, Rebecca R; McCallum, Gordon P; Nicol, Christopher J; Parman, Toufan; Wiley, Michael J; Wong, Andrea W

    2005-09-01

    Developmental pathologies may result from endogenous or xenobiotic-enhanced formation of reactive oxygen species (ROS), which oxidatively damage cellular macromolecules and/or alter signal transduction. This minireview focuses upon several model drugs (phenytoin, thalidomide, methamphetamine), environmental chemicals (benzo[a]pyrene) and gamma irradiation to examine this hypothesis in vivo and in embryo culture using mouse, rat and rabbit models. Embryonic prostaglandin H synthases (PHSs) and lipoxygenases bioactivate xenobiotics to free radical intermediates that initiate ROS formation, resulting in oxidation of proteins, lipids and DNA. Oxidative DNA damage and embryopathies are reduced in PHS knockout mice, and in mice treated with PHS inhibitors, antioxidative enzymes, antioxidants and free radical trapping agents. Thalidomide causes embryonic DNA oxidation in susceptible (rabbit) but not resistant (mouse) species. Embryopathies are increased in mutant mice deficient in the antioxidative enzyme glucose-6-phosphate dehydrogenase (G6PD), or by glutathione (GSH) depletion, or inhibition of GSH peroxidase or GSH reductase. Inducible nitric oxide synthase knockout mice are partially protected. Inhibition of Ras or NF-kB pathways reduces embryopathies, implicating ROS-mediated signal transduction. Atm and p53 knockout mice deficient in DNA damage response/repair are more susceptible to xenobiotic or radiation embryopathies, suggesting a teratological role for DNA damage, consistent with enhanced susceptibility to methamphetamine in ogg1 knockout mice with deficient repair of oxidative DNA damage. Even endogenous embryonic oxidative stress carries a risk, since untreated G6PD- or ATM-deficient mice have increased embryopathies. Thus, embryonic processes regulating the balance of ROS formation, oxidative DNA damage and repair, and ROS-mediated signal transduction may be important determinants of teratological risk.

  7. Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae, Rhodophyta) using molecular and morphological data.

    PubMed

    Lyra, Goia de M; Gurgel, C Frederico D; Costa, Emmanuelle da S; de Jesus, Priscila B; Oliveira, Mariana C; Oliveira, Eurico C; Davis, Charles C; Nunes, José Marcos de Castro

    2016-12-01

    Species in the genus Gracilaria that display conspicuously flattened vegetative morphologies are a taxonomically challenging group of marine benthic red algae. This is a result of their species richness, morphological similarity, and broad phenotypic plasticity. Within this group, the Gracilaria domingensis complex is one of the most common, conspicuous, and morphologically variable species along the tropical western Atlantic Ocean. Previous research has identified that members of this complex belong to two distantly related clades. However, despite this increased phylogentic resolution, species delimitations within each of these clades remain unclear. Our study assessed the species diversity within this difficult complex using morphological and molecular data from three genetic markers (cox1, UPA, and rbcL). We additionally applied six single-marker species delimitation methods (SDM: ABGD, GMYCs, GMYCm, SPN, bPTP, and PTP) to rbcL, which were largely in agreement regarding species delimitation. These results, combined with our analysis of morphology, indicate that the G. domingensis complex includes seven distinct species, each of which are not all most closely related: G. cervicornis; a ressurected G. ferox; G. apiculata subsp. apiculata; a new species, Gracilaria baiana sp. nov.; G. intermedia subsp. intermedia; G. venezuelensis; and G. domingensis sensu stricto, which includes the later heterotypic synonym, G. yoneshigueana. Our study demonstrates the value of multipronged strategies, including the use of both molecular and morphological approaches, to decipher cryptic species of red algae.

  8. Molecular identification of three Indian snake species using simple PCR-RFLP method.

    PubMed

    Dubey, Bhawna; Meganathan, P R; Haque, Ikramul

    2010-07-01

    Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are known to be significantly involved in illegal trade. Effective authentication of species is required to curb this illegal trade. In the absence of morphological features, molecular identification techniques hold promise to address the issue of species identification. We present an effective PCR-restriction fragment length polymorphism method for easy identification of the three endangered snake species, Python molurus, Naja naja, and Xenochrophis piscator. A 431-bp amplicon from cytochrome b gene was amplified using novel snake-specific primers following restriction digestion with enzymes Mbo II and Fok I. The species-specific reference fragment patterns were obtained for the target species, which enabled successful identification of even highly degraded shed skin sample confirming the utility of the technique in case of poor-quality DNA. The assay could be effectively used for forensic authentication of three Indian snake species and would help strengthen conservation efforts.

  9. Morphological and molecular characterization of two novel species of Agaricus section Xanthodermatei.

    PubMed

    Callac, Philippe; Guinberteau, Jacques

    2005-01-01

    Agaricus specimens collected in France belong to two novel entities resembling small forms of A. moelleri and A. xanthodermus, two common species in section Xanthodermatei. Molecular (IT1+ITS2 DNA sequence) and morphological comparisons between eight presumed similar taxa of the section support the elevation of both entities to species rank. The new entities are described as A. parvitigrinus and A. xanthodermulus. They form a group with A. laskibarii, a rare species also recently described from France, and A. californicus, a North-American species. The well known A. moelleri and A. xanthodermus are the most related species among the studied sample. Like other species of the section, both new species have a phenolic odor and are probably toxic.

  10. Quantitation of Interacting Molecular Species and Measurement of Molecular Avidity by Single Radial (Immuno) Diffusion

    DTIC Science & Technology

    1989-09-01

    FIGURE LEGEND 1lL ;Ta ,j - ’V y ilii INTRODUCTION Mancini et al. (1965) developed a single radial immunodiffusion (SRID) method for the quantitation of...quantitation of antigens by single radial immunodiffusion . Immunochem, 2, 5. Mancini , G., Nash, D. R. and Heremans, J. F. (1970) Further studies on...FIELD GROUP SUB-GROUP Single radial immunodiffusion , Single radial diffusion, Molecular interaction, Molecular avidity, endotoxin ’-." 19 A63TRACT

  11. Molecular evidence for cryptic speciation in the Cyclophorus fulguratus (Pfeiffer, 1854) species complex (Caenogastropoda: Cyclophoridae) with description of new species.

    PubMed

    Nantarat, Nattawadee; Wade, Christopher M; Jeratthitikul, Ekgachai; Sutcharit, Chirasak; Panha, Somsak

    2014-01-01

    A high degree of intraspecific variation, both genetic and in shell morphology, of the operculate land snail Cyclophorus fulguratus (Pfeiffer, 1854) suggests that its classification as a single species warrants reconsideration. We sequenced two nuclear (18S and 28S) and two mitochondrial (16S and COI) genes of 46 C. fulguratus specimens and used them to estimate the phylogeny and to determine the validity of species boundaries. Molecular phylogenetic analyses revealed the presence of three lineages corresponding to three geographically disjunctive populations of C. fulguratus in Thailand. Likelihood tests of topologies significantly supported the non-monophyly of the C. fulguratus-complex and Bayesian species delimitation analysis significantly supported the potential representation as distinct species of these three lineages. Discriminant function analysis based on geometric-morphometrics of shell shape allowed for significant distinction of these three candidate species, although they revealed a considerable degree of overlap of shell shape reflecting their crypsis morphologically. The diagnostic characters are provided by color pattern, pattern of protoconch and pattern of jaw. In conclusion, the results support that the C. fulguratus s.l., as currently recognized, consists of three distinct species in Thailand: C. fulguratus s.s., C. rangunensis and C. abditus sp.nov., which are described herein.

  12. 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.

  13. 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.

  14. Molecular cloning and characterization of ligand- and species-specificity of amphibian estrogen receptors.

    PubMed

    Katsu, Yoshinao; Taniguchi, Ena; Urushitani, Hiroshi; Miyagawa, Shinichi; Takase, Minoru; Kubokawa, Kaoru; Tooi, Osamu; Oka, Tomohiro; Santo, Noriaki; Myburgh, Jan; Matsuno, Akira; Iguchi, Taisen

    2010-09-01

    Estrogens are essential for normal reproductive activity in both males and females as well as for ovarian differentiation during a critical developmental stage in most vertebrates. To understand the molecular mechanisms of estrogen action and to evaluate estrogen receptor ligand interactions in amphibians, we isolated cDNAs encoding the estrogen receptors (ERalpha and ERbeta) from the Japanese firebelly newt (Cynops pyrrhogaster), Tokyo salamander (Hynobius tokyoensis), axolotl (Ambystoma mexicanum), and Raucous toad (Bufo rangeri). Full-length amphibian ER cDNAs were obtained using 5' and 3' rapid amplification of cDNA ends. The predicted amino acid sequences of these amphibian ERs showed a high degree of amino acid sequence identity (over 70%) to each other. We analyzed the relationships of these amphibian ER sequences to other vertebrate ER sequences by constructing a phylogenetic tree. We verified that these were bona fide estrogen receptors using receptor dependent reporter gene assays. We analyzed the effects of natural estrogens, ethinylestradiol, and DDT and its metabolites on the transactivation of the four amphibian species listed above, and Xenopus tropicalis ERs and found that there were species-specific differences in the sensitivity of these ERs to hormones and environmental chemicals. These findings will expand our knowledge of endocrine-disrupting events in amphibians.

  15. Identification of molecular species of monoalkyldiacylglycerol from the squid Berryteuthis magister using liquid chromatography-APCI high-resolution mass spectrometry.

    PubMed

    Rybin, Viacheslav G; Imbs, Andrey B; Demidkova, Darja A; Ermolenko, Ekaterina V

    2017-01-01

    Monoalkyldiacylglycerol (MADAG) is an important lipid class in mollusks, corals, starfishes, and some species of zooplankton. Up to 80% of liver oils of squids and sharks are comprised of MADAG. Except for one fish species, there are no data on the composition of MADAG molecular species of marine organisms. The molecular species of MADAG obtained from digestive glands of the deep-sea squid Berryteuthis magister were identified. High-performance liquid chromatography (HPLC) and tandem high-resolution mass spectrometry (HRMS) with atmospheric pressure chemical ionization (APCI) were applied. The mass spectra of each molecular species contained positive quasi-molecular ion [M+H](+) with fragment ions [M-R'CO2](+), [M-R''CO2](+), and [M-OR'''](+), as well as negative cluster ion [M+2H2OH](-) without fragments. The exact masses of the negative ions allowed determination of the molecular formulas and the number of double bonds; the positive fragment ions were used to determine the location of acyl and alkyl groups in MADAG molecules. Ninety molecular species of MADAG were revealed. The regiospecific composition was identified for 72 individual molecular species. Eleven pairs of positional isomers of acyl groups were found. Four molecular ions were produced by a mixture of acyl/alkyl isomers. Most of molecular species contained 16:0e or 18:1e alkyl groups in the sn-1 position, whereas polyunsaturated fatty acids mainly esterified the sn-2 position of MADAG from B. magister. These structural features are supposed to be characteristic for biologically active MADAG.

  16. Volatile species in halide-activated-diffusion coating packs

    NASA Technical Reports Server (NTRS)

    Bianco, Robert; Rapp, Robert A.; Jacobson, Nathan S.

    1992-01-01

    An atmospheric pressure sampling mass spectrometer was used to identify the vapor species generated in a halide-activated cementation pack. Pack powder mixtures containing a Cr-Al binary masteralloy powder, an NH4Cl activator salt, and either ZrO2 or Y2O3 (or neither) were analyzed at 1000 C. Both the equilibrium calculations for the pack and mass spectrometer results indicated that volatile AlCl(x) and CrCl(y) species were generated by the pack powder mixture; in packs containing the reactive element oxide, volatile ZrCl(z) and YCl(w) species were formed by the conversion of their oxide sources.

  17. Molecular species of acylglycerols incorporating radiolabeled fatty acids from castor (Ricinus communis L.) microsomal incubations.

    PubMed

    Lin, Jiann-Tsyh; Chen, Jennifer M; Liao, Lucy P; McKeon, Thomas A

    2002-08-28

    Sixty-one molecular species of triacylglycerols (TAG) and diacylglycerols produced from castor microsomal incubations incorporating six different (14)C-labeled fatty acids have been identified and quantified. The preference for incorporation into TAG was in the order ricinoleate > oleate > linoleate > linolenate > stearate > palmitate. Ricinoleate was the major fatty acid incorporated, whereas stearate, linolenate, and palmitate were incorporated at low levels. Twenty-one molecular species of acylglycerols (HPLC peaks) in castor oil have also been assigned. The levels of TAG in castor oil are RRR (triricinolein) > RR-TAG > R-TAG > no R-TAG. The levels of the molecular species within the groups of RR-TAG, RL-TAG, and LL-TAG individually are ricinoleate > linoleate > oleate > linolenate, stearate, and palmitate. The results of the labeled fatty acid incorporation are consistent with ricinoleate being preferentially driven into TAG and oleate being converted to ricinoleate in castor oil biosynthesis.

  18. European species of Clavaria (Agaricales, Agaricomycetes) with dark basidiomata - a morphological and molecular study.

    PubMed

    Kautmanová, I; Tomšovský, M; Dueñas, M; Martín, M P

    2012-12-01

    Clavaria species with dark basidiomata occurring in Europe were analysed using morphological and molecular methods. Morphological analyses revealed four groups containing seven Clavaria species with dark basidiomata. Phylogenetic analysis of the LSU nrDNA region confirmed the separate positions of all seven Clavaria species within the genus. All sequences were grouped in four well-supported clades, mostly corresponding to defined morphological species. The results of the molecular study are inconsistent with the infrageneric classification of Clavaria based on the presence or absence of clamps on the bases of basidia and two widely accepted subgenera. Clavaria and Holocoryne appear to be polyphyletic. A new approach in species delimitation is presented: 1) C. asperulispora and C. atrofusca are two distinct species recognized by the shape of their spores, and the name C. neo-nigrita is a possible synonym of C. asperulispora; 2) species with clustered fragile basidiomata, C. fumosa and Clavaria cf. fuscoferruginea, which are almost identical in shape and size of spores differing only in the darker basidiomata of the latter, are phylogenetically unrelated; 3) Clavaria atrobadia is a dubious species, the name being most likely a synonym of C. fuscoferruginea; 4) two species with close morphological and phylogenetic affinity, C. atroumbrina and C. pullei, are distinguished based on the more oblong and narrower spores of the former. Comparison of European and North American material suggests the transatlantic nature of the distribution of C. asperulispora, C. atroumbrina and C. fumosa.

  19. 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.

  20. 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

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

    PubMed

    Meyin A Ebong, Solange; Petit, Elsa; 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.

  2. Molecular and morphological description of two new species of Stemphylium from China and France.

    PubMed

    Wang, Yong; Geng, Yun; Pei, Yun-Fei; Zhang, Xiu-Guo

    2010-01-01

    Two new species of Stemphylium (anamorphic Pleospora) are described on the basis of morphological characters and molecular phylogenetic analyses. Stemphylium phaseolina and S. variabilis were isolated respectively from diseased leaves of Phaseolus vulgaris L. in Hebei Province, China, and from diseased leaves of Allium sativum L. in Angres, France. The two species exhibit characteristic Stemphylium morphology but are distinct from similar species based on the morphology and development of conidia. The internal transcribed spacer (ITS) nuclear rDNA region and glyceraldehyde-3-phosphate dehydrogenase (gpd) genes were sequenced. The results of maximum parsimony (MP) and maximum likelihood (ML) phylogenetic analyses of the combined DNA sequences of these two gene regions supported S. phaseolina and S. variabilis as two distinct phylogenetic species. The taxonomic descriptions of the new species and their comparison with related species are presented, together with the phylogenetic analysis based on combined DNA sequences of ITS and gpd gene regions.

  3. 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.

  4. Photodynamic activation as a molecular switch to promote osteoblast cell differentiation via AP-1 activation

    PubMed Central

    Kushibiki, Toshihiro; Tu, Yupeng; Abu-Yousif, Adnan O.; Hasan, Tayyaba

    2015-01-01

    In photodynamic therapy (PDT), cells are impregnated with a photosensitizing agent that is activated by light irradiation, thereby photochemically generating reactive oxygen species (ROS). The amounts of ROS produced depends on the PDT dose and the nature of the photosensitizer. Although high levels of ROS are cytotoxic, at physiological levels they play a key role as second messengers in cellular signaling pathways, pluripotency, and differentiation of stem cells. To investigate further the use of photochemically triggered manipulation of such pathways, we exposed mouse osteoblast precursor cells and rat primary mesenchymal stromal cells to low-dose PDT. Our results demonstrate that low-dose PDT can promote osteoblast differentiation via the activation of activator protein-1 (AP-1). Although PDT has been used primarily as an anti-cancer therapy, the use of light as a photochemical “molecular switch” to promote differentiation should expand the utility of this method in basic research and clinical applications. PMID:26279470

  5. Two new species of Maritrema Nicoll, 1907 (Digenea: Microphallidae) from New Zealand: morphological and molecular characterisation.

    PubMed

    Presswell, Bronwen; Blasco-Costa, Isabel; Kostadinova, Aneta

    2014-05-01

    Two new species of the microphallid genus Maritrema (Maritrema) Nicoll, 1907 are described from freshwaters in the South Island of New Zealand. Maritrema deblocki n. sp. occurs as an adult in the mallard Anas platyrhynchos (L.); Maritrema poulini n. sp. is found as sporocysts/cercariae in Potamopyrgus antipodarum (Gray) and as metacercariae in two species of amphipod and two species of isopod. We use morphological and molecular characterisation to distinguish between the two species, and compare them to their four morphologically closest congeners. M. deblocki n. sp. and M. poulini n. sp. are distinguished from each other by the relative sucker size, the positions of the genital pore and ovary, the convergence of the vitelline ribbons, and overall size. With the aid of molecular data, we matched life cycle stages of M. poulini n. sp. and assessed its use of multiple second intermediate hosts. Phylogenetic analyses included sequences for the two new species and the available microphallid sequences for the large ribosomal subunit and the internal transcribed spacer 1 of the ribosomal RNA gene. Closer to each other than to any other species, the sister species together with Maritrema novaezealandense Martorelli, Fredensborg, Mouritsen & Poulin, 2004, Maritrema heardi (Kinsella & Deblock, 1994), Maritrema eroliae Yamaguti, 1939 and Maritrema oocysta (Lebour, 1907) formed a well-supported clade. In addition, we clarify the taxonomic identity of several unidentified Microphallus spp. in the recent ecological literature from New Zealand and propose corrected spellings for a number of Maritrema species epithets.

  6. 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.

  7. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal.

    PubMed

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-02-04

    Genomic diversity of Portuguese accessions of Avena species--diploid A. strigosa and hexaploids A. sativa and A. sterilis--was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species--rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies--IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)--were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs.

  8. A molecular contribution to the assessment of the Tricholoma equestre species complex.

    PubMed

    Moukha, Serge; Férandon, Cyril; Beroard, Erika; Guinberteau, Jacques; Castandet, Benoît; Callac, Philippe; Creppy, Edmond; Barroso, Gérard

    2013-02-01

    In recent years, interest in the Tricholoma equestre species complex has increased because of several cases of severe and sometimes fatal rhabdomyolysis reported in France and Poland. These occurred after repeated consumption of large portions of T. equestre sporophores during consecutive meals, despite the fact that this species is renowned as a tasty edible wild mushroom. The T. equestre species complex includes three ectomycorrhizal species Tricholoma flavovirens (Pers.) S. Lundell, Tricholoma auratum (Paulet) Gillet, and T. equestre (L.) P. Kummer. All these species produce sporophores with intense yellow gills but are difficult to distinguish by morphological analyses at both the macroscopic and microscopic levels. In T. equestre, two additional varieties are recognized: T. equestre var. populinum (Christensen & Noordeloos) associated with Populus sp. and/or Betula sp. trees and sometimes recognized as Tricholoma frondosae (Kalamees & Shchukin) and T. equestre var. pallidifolia characterized by pale to white gills, frequently recognized as Tricholoma joachimii (Bon & Riva). To explore the taxonomic (species delimitation), ecological, and geographical extent and limits of the T. equestre species complex, we have carried out a molecular comparison of worldwide strains belonging to this complex by using sequences of two molecular markers: the internal transcript spacer (ITS)1/5.8S/ITS2 region of the nuclear ribosomal unit and the 5' part of the mitochondrial cox1 gene. Phylogenetic analyses support the placement of European T. equestre, T. flavovirens, and T. auratum strains as representatives of a single species. This species appears associated with various conifers trees, depending on the geographic origin (Pinus pinaster for T. auratum, Pinus sylvestris or Abies alba for T. equestre and T. flavovirens). However, in the context of a single T. equestre species, the geographical location could lead to the characterization of sub-species or varieties, as suggested

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Morphometric variation and molecular characterization of snow trout species from Kashmir valley, India.

    PubMed

    Bashir, Amir; Bisht, Balwant Singh; Mir, Javaid Iqbal; Patiyal, Rabindar Singh; Kumar, Rohit

    2016-11-01

    There is a significant taxonomic ambiguity among snow trout species due to their morphometric similarities. In view of this, a morphometric and molecular study was conducted on five different species of genus Schizothorax that have been reported from Kashmir valley. Morphometric data analyzed using multivariate statistics (Principal component analysis and cluster analysis) indicated the significant grouping of species to individual clusters. Mitochondrial DNA cytochrome oxidase I (COI) gene analysis revealed 0.2%-4.5% genetic divergence among the five species. This study confirms that utility of cytochrome oxidase I in species delineation along with morphometric data. Phylogenetic tree obtained using Neighbor-Joining method revealed that all the five species represented distinct species group. The Schizothorax genus formed two distinct clades; one containing S. niger, S. curvifrons and S. plagiostomus, while other clade containing S. esocinus and S. labiatus. This phlogeny trend was also supported by cluster analysis of morphometric characters. The phylogenetic analysis with other published COI sequences revealed distinct nature of these five species. The study may aid in the taxonomic identification of snow trout species in India. This may further increase the knowledge of the ichthyologists in planning conservation and management strategies for these important fish species along with their natural habitat.

  14. Unrecognized diversity in New Guinean crayfish species (Decapoda, Parastacidae): The evidence from molecular data.

    PubMed

    Bláha, Martin; Patoka, Jiří; Kozák, Pavel; Kouba, Antonín

    2016-11-01

    The phylogenetic relationships among imported ornamental crayfish belonging to the genus Cherax were inferred from a combined dataset of 3 mitochondrial genes (COI, 16S and 12S) and by comparison with available GenBank sequences of 14 Cherax species. Furthermore, the concordance of previously described species obtained from a wholesaler (Cherax boesemani, C. holthuisi and C. peknyi) with available GenBank sequences was verified based on COI with special respect to comparison with sequences assigned as Cherax species. Recently described species C. gherardiae, C. pulcher and C. subterigneus belong to the northern group of Cherax species. Comparison and analysis with other GenBank COI sequences show previously unreported diversity of New Guinean species, suggesting 5 putative new species. Surprisingly, species assigned to the subgenus Astaconephrops do not form a monophyletic clade; this subgenus should be reappraised relative to the purported typical morphological characteristic of the uncalcified patch on male chelae. Increasing importation of crayfish underscores the importance of accurate species identification. Use of basic molecular methods is a necessary requisite for documenting occurrence, abundance and population trends of target species. Consequently, it helps to support eventual conservation decision-making by stakeholders.

  15. The molecular mechanism of species-specific recognition of lipopolysaccharides by the MD-2/TLR4 receptor complex.

    PubMed

    Oblak, Alja; Jerala, Roman

    2015-02-01

    Lipid A, a component of bacterial lipopolysaccharide, is a conserved microbe-associated molecular pattern that activates the MD-2/TLR4 receptor complex. Nevertheless, bacteria produce lipid A molecules of considerable structural diversity. The human MD-2/TLR4 receptor most efficiently recognizes hexaacylated bisphosphorylated lipid A produced by enterobacteria, but in some animal species the immune response can be elicited also by alternative lipid A varieties, such as tetraacylated lipid IVa or pentaacylated lipid A of Rhodobacter spheroides. Several crystal structures revealed that hexaacylated lipid A and tetraacylated lipid IVa activate the murine MD-2/TLR4 in a similar manner, but failed to explain the antagonistic vs. agonistic activity of lipid IVa in the human vs. equine receptor, respectively. Targeted mutagenesis studies of the receptor complex revealed intricate combination of electrostatic and hydrophobic interactions primarily within the MD-2 co-receptor, but with a contribution of TLR4 as well, that contribute to species-specific recognition of lipid A. We will review current knowledge regarding lipid A diversity and species-specific activation of the MD-2/TLR4 receptor complex in different species (e.g. human, mouse or equine) by lipid A varieties.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  17. Three novel species of Stemphylium from Sinkiang, China: their morphological and molecular characterization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three new species of Stemphylium were isolated from diseased leaves of Luffa cylindrica, Lycium chinense and Cucumis melo growing in the Sinkiang province of Northwest China. Stemphylium luffae, S. lycii and S. cucumis are described by morphological and molecular phylogenetic analyses. The principal...

  18. 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-...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  1. Species identification in the genus Saprolegnia (Oomycetes): defining DNA-based molecular operational taxonomic units.

    PubMed

    Sandoval-Sierra, Jose Vladimir; Martín, María P; Diéguez-Uribeondo, Javier

    2014-07-01

    The lack of a robust taxonomy in the genus Saprolegnia is leading to the presence of incorrectly named isolates in culture collections and of an increasing number of misassigned sequences in DNA databases. Accurate species delimitation is critical for most biological disciplines. A recently proposed approach to solve species delimitation (taxonomic diagnosis system) of difficult organisms is the definition of molecular operational taxonomic units (MOTUs). We have used 961 sequences of nrDNA ITS from culture collections (461 sequences) and GenBank (500 sequences), to perform phylogenetic and clustering optimization analyses. As result, we have identified 29 DNA-based MOTUs in agreement with phylogenetic studies. The resulting molecular clusters support the validity of 18 species of Saprolegnia and identify 11 potential new ones. We have also listed a number of incorrectly named isolates in culture collections, misassigned species names to GenBank sequences, and reference sequences for the species. We conclude that GenBank represents the main source of errors for identifying Saprolegnia species since it possesses sequences with misassigned names and also sequencing errors. The presented taxonomic diagnosis system might help setting the basis for a suitable identification of species in this economically important genus.

  2. Acanthamoeba keratitis: improving the Scottish diagnostic service for the rapid molecular detection of Acanthamoeba species.

    PubMed

    Alexander, Claire Low; Coyne, Michael; Jones, Brian; Anijeet, Deepa

    2015-07-01

    Acanthamoeba species are responsible for causing the potentially sight-threatening condition, Acanthamoeba keratitis, which is commonly associated with contact lens use. In this report, we highlight the challenges faced using conventional laboratory identification methods to identify this often under-reported pathogen, and discuss the reasons for introducing the first national service in Scotland for the rapid and sensitive molecular identification of Acanthamoeba species. By comparing culture and molecular testing data from a total of 63 patients (n = 80 samples) throughout Scotland presenting with ocular eye disease, we describe the improvement in detection rates where an additional four positive cases were identified using a molecular assay versus culture. The testing of a further ten patients by confocal imaging is also presented. This report emphasizes the importance of continuing to improve clinical laboratory services to ensure a prompt, correct diagnosis and better prognosis, in addition to raising awareness of this potentially debilitating opportunistic pathogen.

  3. Comparison of antimicrobial activities of newly obtained low molecular weight scorpion chitosan and medium molecular weight commercial chitosan.

    PubMed

    Kaya, Murat; Asan-Ozusaglam, Meltem; Erdogan, Sevil

    2016-06-01

    In this study the antimicrobial activity of low molecular weight (3.22 kDa) chitosan, obtained for the first time from a species belonging to the Scorpiones, was screened against nine pathogenic microorganisms (seven bacteria and two yeasts) and compared with that of medium molecular weight commercial chitosan (MMWCC). It was observed that the antimicrobial activity of the low molecular weight scorpion chitosan (LMWSC) was specific to bacterial species in general rather than gram-negative or gram-positive bacterial groups. It was also determined that LMWSC had a stronger inhibitory effect than the MMWCC, particularly on the bacterium Listeria monocytogenes and the yeast Candida albicans, which are important pathogens for public health. In addition, it was recorded that the MMWCC had a greater inhibitory effect on Bacillus subtilis than LMWSC. According to the results obtained by the disc diffusion method, the antibacterial activity of both LMWSC and MMWCC against B. subtilis and Salmonella enteritidis was higher than the widely used antibiotic Gentamicin (CN, 10 μg/disc).

  4. 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

    2017-03-18

    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 macro-evolutionary 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 re-visit 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. This article is protected by copyright. All rights reserved.

  5. Quantitative degenerate four-wave mixing spectroscopy: Probes for molecular species

    SciTech Connect

    Farrow, R.; Rakestraw, D.; Paul, P.; Lucht, R.; Danehy, P.; Friedman-Hill, E.; Germann, G.

    1993-12-01

    Resonant degenerate four-wave mixing (DFWM) is currently the subject of intensive investigation as a sensitive diagnostic tool for molecular species. DFWM has the advantage of generating a coherent (beam-like) signal which results in null-background detection and provides excellent immunity to background-light interference. Since multiple one-photon resonances are involved in the signal generation process, the DFWM technique can allow sensitive detection of molecules via electronic, vibrational or rotational transitions. These properties combine to make DFWM a widely applicable diagnostic technique for the probing of molecular species. The authors are conducting fundamental and applied investigations of DFWM for quantitative measurements of trace species in reacting gases. During the past year, efforts have been focussed in two areas: (1) understanding the effects of collisional processes on the DFWM signal generation process, and (2) exploring the applicability of infrared DFWM to detect polyatomic molecules via rovibrational transitions.

  6. Single-strand conformation polymorphism for molecular variability studies of six viroid species.

    PubMed

    Elleuch, Amine; Hamdi, Imen; Bessaies, Nabiha; Fakhfakh, Hatem

    2013-01-01

    Molecular diversity within six viroid species and different molecular variants, in each species infecting fruit trees was first estimated by the single-strand conformation polymorphism (SSCP) technique and then by direct sequencing analysis. The different variants studied are to three Australian grapevine viroids(AGVd), four citrus dwarfing viroids (CDVd), eleven grapevine yellow speckle viroids type-1 (GYSVd-1), four hop stunt viroids (HSVd), seven peach latent mosaic viroids (PLMVd), and eight pear blister canker viroids (PBCVd). Polyacrylamide gel electrophoresis (PAGE) conditions were compared and optimized to improve the sensitivity of the existing SSCP parameters. The relationships among the various SSCP profiles observed and the variation in nucleotide sequences was studied. The results indicate that the variations of some parameters of electrophoresis for each species allowed higher resolution and hence detection of single nucleotide variations among clones initially clustered into the same group.

  7. Molecular strategies for detection and quantification of mycotoxin-producing Fusarium species: a review.

    PubMed

    Gong, Liang; Jiang, Yueming; Chen, Feng

    2015-07-01

    Fusarium contamination is considered a major agricultural problem, which could not only significantly reduce yield and quality of agricultural products, but produce mycotoxins that are virulence factors responsible for many diseases of humans and farm animals. One strategy to identify toxigenic Fusarium species is the use of modern molecular methods, which include the analysis of DNA target regions for differentiation of the Fusarium species, particularly the mycotoxin-producing Fusarium species such as F. verticillioides and F. graminearum. Additionally, polymerase chain reaction assays are used to determine the genes involved in the biosynthesis of the toxins in order to facilitate a qualitative and quantitative detection of Fusarium-producing mycotoxins. Also, it is worth mentioning that some factors that modulate the biosynthesis of mycotoxins are not only determined by their biosynthetic gene clusters, but also by environmental conditions. Therefore, all of the aforementioned factors which may affect the molecular diagnosis of mycotoxins will be reviewed and discussed in this paper.

  8. Molecular Identification of Candida Species Isolated from Onychomycosis in Shanghai, China.

    PubMed

    Feng, Xiaobo; Ling, Bo; Yang, Xianwei; Liao, Wanqing; Pan, Weihua; Yao, Zhirong

    2015-12-01

    Candida is a common cause of onychomycosis, especially for fingernail onychomycosis. In this study, two simple PCR-based assays combined with the internal transcribed spacers sequencing were performed to reveal the prevalence of Candida species including emerging species in onychomycosis, and triazole antifungal susceptibility profiles for Candida species were also evaluated. Among 210 Candida strains isolated from onychomycosis, Candida parapsilosis was the most common species (54.3%), followed by C. albicans (23.3%) and C. metapsilosis (9.5%). However, C. metapsilosis became the second leading species in toenail onychomycosis and accounted for 19.5% of Candida isolates from toenail samples. C. nivariensis, an emerging species, was firstly recovered from a toenail sample. Other emerging species such as C. orthopsilosis, C. pararugosa and C. fabryi were also identified by molecular tools. C. metapsilosis isolates exhibited significantly higher fluconazole minimum inhibitory concentrations than those exhibited by C. parapsilosis and C. albicans (P < 0.001). This study provides insight into the prevalence, distribution and susceptibility profiles of Candida species including emerging Candida species in onychomycosis.

  9. First molecular evidence for underestimated biodiversity of Rhachotropis (Crustacea, Amphipoda), with description of a new species.

    PubMed

    Lörz, Anne-Nina; Linse, Katrin; Smith, Peter J; Steinke, Dirk

    2012-01-01

    The crustacean genus Rhachotropis has a worldwide distribution and amongst the largest bathymetric range known from any amphipod genus. DNA barcoding of new material from around New Zealand and the Ross Sea indicated depth-related biogeographic patterns. New Zealand Rhachotropis do not form a monophyletic clade. Species from bathyal depths on the Chatham Rise, east of New Zealand, show lower sequence divergence to bathyal species from California and the Arctic than to abyssal New Zealand species. Species sampled in the Kermadec Trench, north of New Zealand below 5000 m, seem to be more closely related to Ross Sea abyssal species than to the New Zealand shelf species. The worldwide geographic and bathymetric distribution for all Rhachotropis species is presented here. Depth may have a greater influence on phylogeny than geographic distance.Molecular and morphological investigations of Rhachotropis specimens from the Chatham Rise, New Zealand revealed a species new to science which is described in detail, including scanning electron microscopy. This increases the number of described species of Rhachotropis to 60 worldwide.

  10. Hemolytic Activities of the Candida Species in Liquid Medium

    PubMed Central

    Malcok, Hilal Kuzucu; Aktas, Esin; Ayyildiz, Ahmet; Yigit, Nimet; Yazgi, Halil

    2009-01-01

    Objective The aim of this study was to evaluate the in vitro hemolytic activities of 107 Candida strains isolated from different clinical samples in liquid medium, and to examine the impact of glucose on this activity. Materials and Methods A total of 107 Candida isolates representing seven species (C. albicans, n=28; C. glabrata, n=23; C. tropicalis, n=17; C. parapsilosis, n=16; C. kefyr, n=14; C. krusei, n=5; C. guilliermondii, n=4) were included in the study. The hemolytic activities of the strains were tested on two different Sabouraud dextrose liquid media (SDB) containing 7% defibrinated human blood, one of which is supplemented with 3% glucose and the other without glucose. Cultures were evaluated at the end of a 48-hour incubation. The hemolysis in the media was detected spectrophotometrically by measuring the amount of released hemoglobin and compared with a standard hemolysate which was prepared prior to testing. The degree of hemolysis (percentage value) by an individual strain was calculated according to the following formula below: (Absorbance of supernatant media at 540 nm / Absorbance of standard hemolysate at 540 nm X 100). Results In the liquid medium without glucose, strains generally produced hemolysis at low levels. The degree of hemolysis produced by all species increased noticeably in the liquid medium with glucose. Strains of C. albicans and C.kefyr had demonstrated significant hemolytic activity, whereas others had lower activity. C. parapsilosis exerted very little hemolytic activity in the medium with glucose and showed no activity in the medium without glucose. Conclusion The hemolytic activities of most Candida species was found to be higher in the human blood-enriched SDB medium containing 3% additive glucose than in the one free from additives. This result indicates that increased blood glucose concentration may contribute to increased hemolytic activity in Candida species, and it suggests a parallel with possible pathogenesis of

  11. Morphological and molecular affinities of two East Asian species of Stenhelia (Crustacea, Copepoda, Harpacticoida)

    PubMed Central

    Karanovic, Tomislav; Kim, Kichoon; Lee, Wonchoel

    2014-01-01

    Abstract Definition of monophyletic supraspecific units in the harpacticoid subfamily Stenheliinae Brady, 1880 has been considered problematic and hindered by the lack of molecular or morphology based phylogenies, as well as by incomplete original descriptions of many species. Presence of a modified seta on the fifth leg endopod has been suggested recently as a synapomorphy of eight species comprising the redefined genus Stenhelia Boeck, 1865, although its presence was not known in S. pubescens Chislenko, 1978. We redescribe this species in detail here, based on our freshly collected topotypes from the Russian Far East. The other species redescribed in this paper was collected from the southern coast of South Korea and identified as the Chinese S. taiae Mu & Huys, 2002, which represents its second record ever and the first one in Korea. A fragment of the mtCOI gene was successfully PCR-amplified from two specimens of each species, which represents the first molecular data for this genus, and from additional 19 specimens belonging to six different species of other stenheliins from Korea and Russia. Reconstructed phylogenies confirm previously postulated monophyly of Stenhelia and polyphyly of the closely related genus Delavalia Brady, 1869. Average pairwise maximum likelihood distances between S. pubescens and S. taiae are only slightly above 10%, suggesting a very close relationship despite numerous newly discovered micro-morphological differences and despite macro-morphological similarities being probable plesiomorphies. PMID:24899857

  12. 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.

  13. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal

    PubMed Central

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-01-01

    Genomic diversity of Portuguese accessions of Avena species—diploid A. strigosa and hexaploids A. sativa and A. sterilis—was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species—rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies—IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)—were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs. PMID:26861283

  14. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species.

    PubMed

    Dawson, Michael N; Sen Gupta, Alex; England, Matthew H

    2005-08-23

    The anthropogenic introduction of exotic species is one of the greatest modern threats to marine biodiversity. Yet exotic species introductions remain difficult to predict and are easily misunderstood because knowledge of natural dispersal patterns, species diversity, and biogeography is often insufficient to distinguish between a broadly dispersed natural population and an exotic one. Here we compare a global molecular phylogeny of a representative marine meroplanktonic taxon, the moon-jellyfish Aurelia, with natural dispersion patterns predicted by a global biophysical ocean model. Despite assumed high dispersal ability, the phylogeny reveals many cryptic species and predominantly regional structure with one notable exception: the globally distributed Aurelia sp.1, which, molecular data suggest, may occasionally traverse the Pacific unaided. This possibility is refuted by the ocean model, which shows much more limited dispersion and patterns of distribution broadly consistent with modern biogeographic zones, thus identifying multiple introductions worldwide of this cryptogenic species. This approach also supports existing evidence that (i) the occurrence in Hawaii of Aurelia sp. 4 and other native Indo-West Pacific species with similar life histories is most likely due to anthropogenic translocation, and (ii) there may be a route for rare natural colonization of northeast North America by the European marine snail Littorina littorea, whose status as endemic or exotic is unclear.

  15. Steroid control of steroidogenesis in isolated adrenocortical cells: molecular and species specificity.

    PubMed

    Carsia, R V; Macdonald, G J; Malamed, S

    1983-06-01

    The molecular and species specificity of glucocorticoid suppression of corticosteroidogenesis was investigated in isolated adrenocortical cells. Trypsin-isolated cells from male rat, domestic fowl and bovine adrenal glands were incubated with or without steroidogenic agents and with or without steroids. Glucocorticoids were measured by radioimmunoassay or fluorometric assay after 1-2 h incubation. Glucocorticoids suppressed ACTH-induced steroidogenesis of isolated rat cells with the following relative potencies: corticosterone greater than cortisol = cortisone greater than dexamethasone. The mineralocorticoid, aldosterone did not affect steroidogenesis. Suppression by glucocorticoids was acute (within 1-2 h), and varied directly with the glucocorticoid concentration. Testosterone also suppressed ACTH-induced steroidogenesis. Glucocorticoid-type steroids have equivalent suppressive potencies, thus suggesting that these steroids may induce suppression at least partly by a common mechanism. Although corticosterone caused the greatest suppression, testosterone was more potent. The steroid specificity of suppression of cyclic AMP (cAMP)-induced and ACTH-induced steroidogenesis were similar, suggesting that suppression is not solely the result of interference with ACTH receptor function or the induction of adenylate cyclase activity. Exogenous glucocorticoids also suppressed ACTH-induced steroidogenesis of cells isolated from domestic fowl and beef adrenal glands, thus suggesting that this observed suppression may be a general mechanism of adrenocortical cell autoregulation.

  16. Taxonomic status and molecular phylogeography of two sibling species of Polytremis (Lepidoptera: Hesperiidae).

    PubMed

    Jiang, Weibin; He, Haiyan; Li, Yingdong; Ren, Mengyi; Ma, Yazhong; Zheng, Lingli; Zhu, Jianqing; Yu, Weidong

    2016-02-10

    The skipper Polytremis theca species complex is widely distributed in the south of the Qinling Mountains in China. A recent study of the Polytremis genus suggested that this species might encompass two differentiated lineages. We tested this hypothesis, by carrying out a phylogenetic study of this agricultural pest based on nationwide sampling and the evaluation of mitochondrial and nuclear DNA markers. We show that this species is actually an amalgamation of two sibling taxa (P. t. theca and P. t. fukia), which displayed levels of genetic divergence as great as those generally found between sister species in the Polytremis genus, suggesting that they actually correspond to two distinct species. The Divergence time estimates suggest that an active period of speciation within Polytremis occurred within the Pleistocene eras. Based on its distinct phylogenetic placement and geographical isolation, we suggest that the subspecies should be elevated to full species status under the phylogenetic species concept, which has significant management implications.

  17. [DNA molecular identification of Herba Dendrobii and its adulterant species based on ITS sequence analysis].

    PubMed

    Liu, Jing; He, Tao; Chun, Ze

    2009-11-01

    To identify Herba Dendrobii and its adulterant species on molecular level, the rDNA ITS sequences of 17 species of Herba Dendrobii were studied. Genomic DNA of Dendrobium was extracted using the modified cetyltrimethyl ammonium bromide (CTAB) method. The PCR products of the rDNA ITS sequences of Dendrobium (32 materials) were purified and then sequenced. The characteristic of the sequences and the genetic distance were compared between Bulbophyllum odoratissimum and Dendrobium, Dendrobium interspecies and different populations. Phylogenetic trees were constructed using the UPGMA method by the biology softwares including BioEdit, MEGA4.0 etc. The PCR products were purified and then sequenced. It was built up that the database of rDNA ITS sequences of 17 species of Herba Dendrobii (32 materials). The ITS1 was 228-234 bp, the GC content accounting for 45.7%-53.0%. Its variable sites were 167, accounting for 67.34%. The Parsim-Informative positions were 106, accounting for 42.74%. The ITS2 was 241-247 bp, the GC accounting for 44.8% - 55.7%. The variable sites were 165, accounting for 66.27%. The Parsim-Informative positions were 115, accounting for 46.18%. The genetic distance between B. odoratissimum and Dendrobium was 0.295. The average genetic distance was 0.142 between Dendrobium species, and there were 2-156 variable nucleotides. The average genetic distance between different populations was 0.002, and there were 2-156 variable nucleotides. The genetic distance between B. odoratissimum and Dendrobium was greater than that of Denrobium interspecies. Meanwhile, the genetic distance between Denrobium species was also greater than that of different populations (varieties). The molecular phylogeny tree was constructed on the database of rDNA ITS the sequences of 17 species of Herba Dendrobii using the biology softwares. Then 10 materials on molecular level were authenticated. It is concluded that using of the whole sequences database of 17 species of Herba Dendrobii

  18. Diversity and Activity of Lysobacter Species from Disease Suppressive Soils

    PubMed Central

    Gómez Expósito, Ruth; Postma, Joeke; Raaijmakers, Jos M.; De Bruijn, Irene

    2015-01-01

    The genus Lysobacter includes several species that produce a range of extracellular enzymes and other metabolites with activity against bacteria, fungi, oomycetes, and nematodes. Lysobacter species were found to be more abundant in soil suppressive against the fungal root pathogen Rhizoctonia solani, but their actual role in disease suppression is still unclear. Here, the antifungal and plant growth-promoting activities of 18 Lysobacter strains, including 11 strains from Rhizoctonia-suppressive soils, were studied both in vitro and in vivo. Based on 16S rRNA sequencing, the Lysobacter strains from the Rhizoctonia-suppressive soil belonged to the four species Lysobacter antibioticus, Lysobacter capsici, Lysobacter enzymogenes, and Lysobacter gummosus. Most strains showed strong in vitro activity against R. solani and several other pathogens, including Pythium ultimum, Aspergillus niger, Fusarium oxysporum, and Xanthomonas campestris. When the Lysobacter strains were introduced into soil, however, no significant and consistent suppression of R. solani damping-off disease of sugar beet and cauliflower was observed. Subsequent bioassays further revealed that none of the Lysobacter strains was able to promote growth of sugar beet, cauliflower, onion, and Arabidopsis thaliana, either directly or via volatile compounds. The lack of in vivo activity is most likely attributed to poor colonization of the rhizosphere by the introduced Lysobacter strains. In conclusion, our results demonstrated that Lysobacter species have strong antagonistic activities against a range of pathogens, making them an important source for putative new enzymes and antimicrobial compounds. However, their potential role in R. solani disease suppressive soil could not be confirmed. In-depth omics'–based analyses will be needed to shed more light on the potential contribution of Lysobacter species to the collective activities of microbial consortia in disease suppressive soils. PMID:26635735

  19. Rapid identification of Candida dubliniensis using a species-specific molecular beacon.

    PubMed

    Park, S; Wong, M; Marras, S A; Cross, E W; Kiehn, T E; Chaturvedi, V; Tyagi, S; Perlin, D S

    2000-08-01

    Candida dubliniensis is an opportunistic fungal pathogen that has been linked to oral candidiasis in AIDS patients, although it has recently been isolated from other body sites. DNA sequence analysis of the internal transcribed spacer 2 (ITS2) region of rRNA genes from reference Candida strains was used to develop molecular beacon probes for rapid, high-fidelity identification of C. dubliniensis as well as C. albicans. Molecular beacons are small nucleic acid hairpin probes that brightly fluoresce when they are bound to their targets and have a significant advantage over conventional nucleic acid probes because they exhibit a higher degree of specificity with better signal-to-noise ratios. When applied to an unknown collection of 23 strains that largely contained C. albicans and a smaller amount of C. dubliniensis, the species-specific probes were 100% accurate in identifying both species following PCR amplification of the ITS2 region. The results obtained with the molecular beacons were independently verified by random amplified polymorphic DNA analysis-based genotyping and by restriction enzyme analysis with enzymes BsmAI and NspBII, which cleave recognition sequences within the ITS2 regions of C. dubliniensis and C. albicans, respectively. Molecular beacons are promising new probes for the rapid detection of Candida species.

  20. Antioxidant, antimicrobial and antiproliferative activities of five lichen species.

    PubMed

    Mitrović, Tatjana; Stamenković, Slaviša; Cvetković, Vladimir; Tošić, Svetlana; Stanković, Milan; Radojević, Ivana; Stefanović, Olgica; Comić, Ljiljana; Dačić, Dragana; Curčić, 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.

  1. [L-lysine-alpha-oxidase activity of some Trichoderma species].

    PubMed

    Smirnova, I P; Khaduev, S Kh

    1984-01-01

    Trichoderma cultures were tested for their ability to produce L-lysine-alpha-oxidase. The highest enzyme activity was manifested by T. harzianum (MGU), T. longibrachiatum Rifai VKM F-2025 and T. aureoviride Rifai VKM F-2026. The biosynthesis of the enzyme did not depend on the growth of the cultures and did not vary among the species.

  2. 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

  3. Metabolomic profiling and antioxidant activity of some Acacia species

    PubMed Central

    Abdel-Farid, I.B.; Sheded, M.G.; Mohamed, E.A.

    2014-01-01

    Metabolomic profiling of different parts (leaves, flowers and pods) of Acacia species (Acacia nilotica, Acacia seyal and Acacia laeta) was evaluated. The multivariate data analyses such as principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA) were used to differentiate the distribution of plant metabolites among different species or different organs of the same species. A.nilotica was characterized with a high content of saponins and A.seyal was characterized with high contents of proteins, phenolics, flavonoids and anthocyanins. A.laeta had a higher content of carbohydrates than A. nilotica and A. seyal. On the basis of these results, total antioxidant capacity, DPPH free radical scavenging activity and reducing power of the methanolic extracts of studied parts were evaluated. A.nilotica and A.seyal extracts showed less inhibitory concentration 50 (IC50) compared to A.laeta extracts which means that these two species have the strongest radical scavenging activity whereas A. laeta extracts have the lowest radical scavenging activity. A positive correlation between saponins and flavonoids with total antioxidant capacity and DPPH radical scavenging activity was observed. Based on these results, the potentiality of these plants as antioxidants was discussed. PMID:25313274

  4. Molecular Phylogeny of the Pseudallescheria boydii Species Complex: Proposal of Two New Species†

    PubMed Central

    Gilgado, Felix; Cano, Josep; Gené, Josepa; Guarro, Josep

    2005-01-01

    Pseudallescheria boydii (anamorph Scedosporium apiospermum) is the species responsible for human scedosporiosis, a fungal infection with a high mortality rate and which is difficult to treat. Recently, it has been demonstrated that high genetic variation exists within this species. We have performed a morphological and molecular study involving numerous strains of clinical or environmental origins and from different countries. The analysis of partial sequences of the β-tubulin (two loci) and calmodulin genes and the internal transcribed spacer region of the rRNA gene has demonstrated that P. boydii is a species complex. The combined analysis of the sequences of the four loci of 60 strains has showed the presence of 44 haplotypes in the ingroup. Three species morphologically related to P. boydii sensu stricto, i.e., Pseudallescheria angusta, Pseudallescheria ellipsoidea, and Pseudallescheria fusoidea, which had previously been considered synonyms, could be differentiated genetically from P. boydii in our study. It is relevant that two of the three strains now included in P. ellipsoidea have caused invasive infections. The species Pseudallescheria minutispora and Scedosporium aurantiacum are clearly phylogenetically separated from the other species studied and are here proposed as new. Morphological features support this proposal. All the strains included in S. aurantiacum species have a clinical origin, while those included in P. minutispora are environmental. Further studies are needed to demonstrate whether all the species included in the P. boydii complex have different clinical spectra and antifungal susceptibility. PMID:16207945

  5. Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex

    PubMed Central

    2014-01-01

    Background The moss Physcomitrella patens (Hedw.) Bruch & Schimp. is an important experimental model system for evolutionary-developmental studies. In order to shed light on the evolutionary history of Physcomitrella and related species within the Funariaceae, we analyzed the natural genetic diversity of the Physcomitrium-Physcomitrella species complex. Results Molecular analysis of the nuclear single copy gene BRK1 reveals that three Physcomitrium species feature larger genome sizes than Physcomitrella patens and encode two expressed BRK1 homeologs (polyploidization-derived paralogs), indicating that they may be allopolyploid hybrids. Phylogenetic analyses of BRK1 as well as microsatellite simple sequence repeat (SSR) data confirm a polyphyletic origin for three Physcomitrella lineages. Differences in the conservation of mitochondrial editing sites further support hybridization and cryptic speciation within the Physcomitrium-Physcomitrella species complex. Conclusions We propose a revised classification of the previously described four subspecies of Physcomitrella patens into three distinct species, namely Physcomitrella patens, Physcomitrella readeri and Physcomitrella magdalenae. We argue that secondary reduction of sporophyte complexity in these species is due to the establishment of an ecological niche, namely spores resting in mud and possible spore dispersal by migratory birds. Besides the Physcomitrium-Physcomitrella species complex, the Funariaceae are host to their type species, Funaria hygrometrica, featuring a sporophyte morphology which is more complex. Their considerable developmental variation among closely related lineages and remarkable trait evolution render the Funariaceae an interesting group for evolutionary and genetic research. PMID:25015729

  6. A molecular identification protocol for roots of boreal forest tree species1

    PubMed Central

    Randall, Morgan J.; Karst, Justine; Pec, Gregory J.; Davis, Corey S.; Hall, Jocelyn C.; Cahill, James F.

    2014-01-01

    • Premise of the study: Roots play a key role in many ecological processes, yet our ability to identify species from bulk root samples is limited. Molecular tools may be used to identify species from root samples, but they have not yet been developed for most systems. Here we present a PCR-based method previously used to identify roots of grassland species, modified for use in boreal forests. • Methods: We used repeatable interspecific size differences in fluorescent amplified fragment length polymorphisms of three noncoding chloroplast DNA regions to identify seven woody species common to boreal forests in Alberta, Canada. • Results: Abies balsamea, Alnus crispa, Betula papyrifera, Pinus contorta, and Populus tremuloides were identifiable to species, while Picea glauca and Picea mariana were identifiable to genus. In mixtures of known composition of foliar DNA, species were identified with 98% accuracy using one region. Mixed root samples of unknown composition were identified with 100% accuracy; four species were identified using one region, while three species were identified using two regions. • Discussion: This methodology is accurate, efficient, and inexpensive, and thus a valuable approach for ecological studies of roots. Furthermore, this method has now been validated for both grassland and boreal forest systems, and thus may also have applications in any plant community. PMID:25383267

  7. 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.

  8. Molecular Imaging of the ATM Kinase Activity

    SciTech Connect

    Williams, Terence M.; Nyati, Shyam; Ross, Brian D.; Rehemtulla, Alnawaz

    2013-08-01

    Purpose: Ataxia telangiectasia mutated (ATM) is a serine/threonine kinase critical to the cellular DNA-damage response, including from DNA double-strand breaks. ATM activation results in the initiation of a complex cascade of events including DNA damage repair, cell cycle checkpoint control, and survival. We sought to create a bioluminescent reporter that dynamically and noninvasively measures ATM kinase activity in living cells and subjects. Methods and Materials: Using the split luciferase technology, we constructed a hybrid cDNA, ATM-reporter (ATMR), coding for a protein that quantitatively reports on changes in ATM kinase activity through changes in bioluminescence. Results: Treatment of ATMR-expressing cells with ATM inhibitors resulted in a dose-dependent increase in bioluminescence activity. In contrast, induction of ATM kinase activity upon irradiation resulted in a decrease in reporter activity that correlated with ATM and Chk2 activation by immunoblotting in a time-dependent fashion. Nuclear targeting improved ATMR sensitivity to both ATM inhibitors and radiation, whereas a mutant ATMR (lacking the target phosphorylation site) displayed a muted response. Treatment with ATM inhibitors and small interfering (si)RNA-targeted knockdown of ATM confirm the specificity of the reporter. Using reporter expressing xenografted tumors demonstrated the ability of ATMR to report in ATM activity in mouse models that correlated in a time-dependent fashion with changes in Chk2 activity. Conclusions: We describe the development and validation of a novel, specific, noninvasive bioluminescent reporter that enables monitoring of ATM activity in real time, in vitro and in vivo. Potential applications of this reporter include the identification and development of novel ATM inhibitors or ATM-interacting partners through high-throughput screens and in vivo pharmacokinetic/pharmacodynamic studies of ATM inhibitors in preclinical models.

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

    PubMed

    Farache, Fernando H A; 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. amacayacuensissp. n., I. amazonicussp. n., I. americanaesp. n., I. badiovertexsp. n., I. brevissp. n., I. brunneussp. n., I. comptonisp. n., I. cremersiaesp. n., I. dimorphicussp. n., I. flavicrussp. n., I. flaviventrissp. n., I. gibberosussp. n., I. gordhisp. n., I. maximussp. n., I. nigriventrissp. n., I. pseudoflavussp. n. and I. ramirezisp. 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.

  10. 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

  11. 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

  12. The role of positive selection in determining the molecular cause of species differences in disease

    PubMed Central

    2008-01-01

    Background Related species, such as humans and chimpanzees, often experience the same disease with varying degrees of pathology, as seen in the cases of Alzheimer's disease, or differing symptomatology as in AIDS. Furthermore, certain diseases such as schizophrenia, epithelial cancers and autoimmune disorders are far more frequent in humans than in other species for reasons not associated with lifestyle. Genes that have undergone positive selection during species evolution are indicative of functional adaptations that drive species differences. Thus we investigate whether biomedical disease differences between species can be attributed to positively selected genes. Results We identified genes that putatively underwent positive selection during the evolution of humans and four mammals which are often used to model human diseases (mouse, rat, chimpanzee and dog). We show that genes predicted to have been subject to positive selection pressure during human evolution are implicated in diseases such as epithelial cancers, schizophrenia, autoimmune diseases and Alzheimer's disease, all of which differ in prevalence and symptomatology between humans and their mammalian relatives. In agreement with previous studies, the chimpanzee lineage was found to have more genes under positive selection than any of the other lineages. In addition, we found new evidence to support the hypothesis that genes that have undergone positive selection tend to interact with each other. This is the first such evidence to be detected widely among mammalian genes and may be important in identifying molecular pathways causative of species differences. Conclusion Our dataset of genes predicted to have been subject to positive selection in five species serves as an informative resource that can be consulted prior to selecting appropriate animal models during drug target validation. We conclude that studying the evolution of functional and biomedical disease differences between species is an

  13. Activation mechanism of Gi and Go by reactive oxygen species.

    PubMed

    Nishida, Motohiro; Schey, Kevin L; Takagahara, Shuichi; Kontani, Kenji; Katada, Toshiaki; Urano, Yasuteru; Nagano, Tetsuo; Nagao, Taku; Kurose, Hitoshi

    2002-03-15

    Reactive oxygen species are proposed to work as intracellular mediators. One of their target proteins is the alpha subunit of heterotrimeric GTP-binding proteins (Galpha(i) and Galpha(o)), leading to activation. H(2)O(2) is one of the reactive oxygen species and activates purified Galpha(i2). However, the activation requires the presence of Fe(2+), suggesting that H(2)O(2) is converted to more reactive species such as c*OH. The analysis with mass spectrometry shows that seven cysteine residues (Cys(66), Cys(112), Cys(140), Cys(255), Cys(287), Cys(326), and Cys(352)) of Galpha(i2) are modified by the treatment with *OH. Among these cysteine residues, Cys(66), Cys(112), Cys(140), Cys(255), and Cys(352) are not involved in *OH-induced activation of Galpha(i2). Although the modification of Cys(287) but not Cys(326) is required for subunit dissociation, the modification of both Cys(287) and Cys(326) is necessary for the activation of Galpha(i2) as determined by pertussis toxin-catalyzed ADP-ribosylation, conformation-dependent change of trypsin digestion pattern or guanosine 5'-3-O-(thio)triphosphate binding. Wild type Galpha(i2) but not Cys(287)- or Cys(326)-substituted mutants are activated by UV light, singlet oxygen, superoxide anion, and nitric oxide, indicating that these oxidative stresses activate Galpha(i2) by the mechanism similar to *OH-induced activation. Because Cys(287) exists only in G(i) family, this study explains the selective activation of G(i)/G(o) by oxidative stresses.

  14. Molecular phylogeny of black flies in the Simulium tuberosum (Diptera: Simuliidae) species group in Thailand.

    PubMed

    Sriphirom, Paradee; Sopaladawan, Piyamas Nanork; Wongpakam, Komgrit; Pramual, Pairot

    2014-01-01

    Black flies are medically and ecologically significant insects. They are also interesting from an evolutionary standpoint regarding the role of chromosomal change and ecological adaptation. In this study, molecular genetic markers based on multiple gene sequences were used to assess genetic diversity and to infer phylogenetic relationships for a group of cytologically highly diverse black flies of the Simulium tuberosum species group in Thailand. Ecological affinities of the species were also investigated. High levels of genetic diversity were found in cytological species complexes, S. tani and S. doipuiense, and also in S. rufibasis, which was cytologically nearly monomorphic. The results highlight the necessity of integrating multilevel markers for fully understanding black fly biodiversity. Phylogenetic relationships based on multiple gene sequences were consistent with an existing dendrogram inferred from cytological and morphological data. Simulium tani is the most distinctive taxa among the members of the S. tubersosum species group in Thailand based on its divergent morphological characters. Molecular data supported the monophyletic status of S. tani, S. weji, and S. yuphae, but S. doipuiense and S. rufibasis were polyphyletic, most likely due to incomplete lineage sorting and inadequate phylogenetic signals. Ecological analyses revealed that members of the S. tuberosum species group have clearly different ecological niches. The results thus supported previous views of the importance of ecology in black fly evolution.

  15. 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

  16. In vitro antioxidant and antiproliferative activities of nine Salvia species.

    PubMed

    Loizzo, Monica Rosa; Abouali, Morteza; Salehi, Peyman; Sonboli, Ali; Kanani, Mohammad; Menichini, Francesco; Tundis, Rosa

    2014-01-01

    Supported by a growing increase of scientific research attesting the health properties of salvia species, we have decided to investigate nine Salvia namely Salvia sclarea, Salvia atropatana, Salvia sahendica, Salvia hydrangea, Salvia xanthocheila, Salvia macrosiphon, Salvia glutinosa, Salvia chloroleuca and Salvia ceratophylla species for their antioxidant and antiproliferative activities. In order to correlate the bioactivity with their phytochemical content, the total phenol and total flavonoid contents were also determined. S. ceratophylla exhibited the strongest activity against C32 cells with an IC50 value of 20.8 μg mL(- 1), while S. glutinosa exhibited an IC50 value of 29.5 μg mL(- 1) against ACHN cell line. Interestingly, S. glutinosa displayed also the highest DPPH radical-scavenging activity with an IC50 of 3.2 μg mL(- 1). These species are characterised by the highest total phenol and flavonoid contents. The obtained results suggest that Salvia species are healthy plant foods.

  17. Radical scavenging, antioxidant and antimicrobial activities of halophytic species.

    PubMed

    Meot-Duros, Laetitia; Le Floch, Gaëtan; Magné, Christian

    2008-03-05

    For the first time, both antioxidant and antimicrobial activities are simultaneously reported in halophytic plants, particularly on polar fractions. Chloroformic and methanolic extracts of the halophytes Eryngium maritimum L., Crithmum maritimum L. and Cakile maritima Scop. were tested for their antimicrobial activities against 12 bacterial and yeast strains. In addition, radical scavenging and antioxidant activities were assessed, as well as total phenol contents. Only one bacterial strain (Listeria monocytogenes) was not inhibited by plants extracts, and apolar (chloroformic) fractions were generally more active than polar (methanolic) ones. Eryngium maritimum presented the weakest radical scavenging activity (ABTS IC(50)=0.28 mg ml(-1)), as well as the lowest total phenol content (16.4 mg GAE g(-1) DW). However, the three halophytic species had relatively strong total antioxidant activities (from 32.7 to 48.6 mg ascorbate equivalents g (-1) DW). Consequences on the potential use of these plants in food or cosmetic industry are discussed.

  18. Comparative molecular modelling of biologically active sterols

    NASA Astrophysics Data System (ADS)

    Baran, Mariusz; Mazerski, Jan

    2015-04-01

    Membrane sterols are targets for a clinically important antifungal agent - amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction of amphotericin B with ergosterol as compared with cholesterol. The compounds studied were chosen on the basis of structural features characteristic for cholesterol and ergosterol and on available experimental data on the ability to form complexes with the antibiotic. Statistical analysis of the data obtained has been performed. The results show similarity of the conformational spaces occupied by all the sterols tested. This suggests that the conformational differences of sterol molecules are not the major feature responsible for the differential sterol - drug affinity.

  19. Efficiency of rep-PCR fingerprinting as a useful technique for molecular typing of plant pathogenic fungal species: Botryosphaeriaceae species as a case study.

    PubMed

    Abdollahzadeh, Jafar; Zolfaghari, Sajedeh

    2014-12-01

    Progress in molecular biology and the advent of rapid and accurate molecular techniques have contributed to precise and rapid detection and differentiation of microbial pathogens. Identification of the Botryosphaeriaceae species based on morphology has been problematic over time. In this study, we used rep-PCR technique as a molecular tool for typing and differentiation of the Botryosphaeriaceae species, well-known and cosmopolitan fungal pathogens on woody plants. Three primer sets BOX, ERIC and REP were used to differentiate 27 species belong to eight genera. The majority of them were examined in terms of typing and differentiation using molecular methods for the first time. All the primer sets were able to generate species-specific DNA fingerprints from all the tested strains, with two exceptions in the genera Diplodia and Spencermartinsia. Despite the deficiency of each primer sets to separate a few species, cluster analysis of combined data sets indicated the ability of rep-PCR technique to separate 26 out of 27 examined species in highly supported clusters corresponded to the species recognized based on DNA sequence data. Our findings revealed the efficiency of rep-PCR for detection and differentiation of the Botryosphaeriaceae species, especially cryptic species with the same ITS sequences and similar morphology.

  20. Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species.

    PubMed

    Obst, Matthias; Faurby, Søren; Bussarawit, Somchai; Funch, Peter

    2012-01-01

    Horseshoe crabs are marine invertebrates well known for their exceptionally low rates of diversification during their entire evolutionary history. Despite the low species diversity in the group, the phylogenetic relationships among the extant species, especially among the three Asian species are still unresolved. Here we apply a new set of molecular genetic data in combination with a wide geographic sampling of the intra-specific diversity to reinvestigate the evolutionary history among the four living limulid xiphosurans. Our analysis of the intraspecific diversity reveals low levels of connectivity among Carcinoscorpius rotundicauda lineages, which can be explained by the estuarine-bound ecology of this species. Moreover, a clear genetic break across the Thai-Malay Peninsula suggests the presence of cryptic species in C. rotundicauda. The limulid phylogeny finds strong support for a monophyletic genus Tachypleus and a diversification of the three Asian species during the Paleogene period, with speciation events well separated in time by several million years. The tree topology suggests that the three Asian species originated in central South East Asia from a marine stem group that inhabited the shallow coastal waters between the Andaman Sea, Vietnam, and Borneo. In this region C. rotundicauda probably separated from the Tachypleus stem group by invading estuarine habitats, while Tachypleus tridentatus most likely migrated northeast along the Southern coast of China and towards Japan.

  1. Molecular perspective on the American transisthmian species of Macrobrachium (Caridea, Palaemonidae)

    PubMed Central

    Pileggi, Leonardo G.; Rossi, Natália; Wehrtmann, Ingo S.; Mantelatto, Fernando L.

    2014-01-01

    Abstract The closure of the Isthmus of Panama (about 3.1 million years ago) separated previously continuous populations and created two groups of extant species, which live now in the Pacific and Atlantic drainage systems. This relatively recent event was a trigger to diversification of various species in the Neotropics, nonetheless there are exemplars that do not show sufficient morphologic variability to separate them by traditional morphological tools. About 60 years ago, some freshwater decapod species with high morphological similarity were separate by previous researchers, based on geographical distribution, in Pacific and Atlantic and considered as “sister species”. However, the complete isolation of these prawns by this geographical barrier is questionable, and it has generated doubts about the status of the following transisthmian pairs of sibling species: Macrobrachium occidentale × Macrobrachium heterochirus, Macrobrachium americanum × Macrobrachium carcinus, Macrobrachium digueti × Macrobrachium olfersii, Macrobrachium hancocki × Macrobrachium crenulatum, Macrobrachium tenellum × Macrobrachium acanthurus and Macrobrachium panamense × Macrobrachium amazonicum. Here we evaluated the relation among these pairs of sibling species in a molecular phylogenetic context. We generated 95 new sequences: 26 sequences of 16S rDNA, 25 of COI mtDNA and 44 of 18S nDNA. In total, 181 sequences were analyzed by maximum likelihood phylogenetic method, including 12 Macrobrachium transisthmian species, as well as seven other American Macrobrachium species, and two other palaemonids. Our analysis corroborated the morphological proximity of the sibling species. Despite the high degree of morphological similarities and considerable genetic diversification encountered among the transisthmian sister species, our data support the conclusion that all species included in sibling groups studied herein are valid taxonomic entities, but not all pairs of siblings form natural

  2. 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

  3. Taxonomic identification of algae (morphological and molecular): species concepts, methodologies, and their implications for ecological bioassessment.

    PubMed

    Manoylov, Kalina M

    2014-06-01

    Algal taxonomy is a key discipline in phycology and is critical for algal genetics, physiology, ecology, applied phycology, and particularly bioassessment. Taxonomic identification is the most common analysis and hypothesis-testing endeavor in science. Errors of identification are often related to the inherent problem of small organisms with morphologies that are difficult to distinguish without research-grade microscopes and taxonomic expertise in phycology. Proposed molecular approaches for taxonomic identification from environmental samples promise rapid, potentially inexpensive, and more thorough culture-independent identification of all algal species present in a sample of interest. Molecular identification has been used in biodiversity and conservation, but it also has great potential for applications in bioassessment. Comparisons of morphological and molecular identification of benthic algal communities are improved by the identification of more taxa; however, automated identification technology does not allow for the simultaneous analysis of thousands of samples. Currently, morphological identification is used to verify molecular taxonomic identities, but with the increased number of taxa verified in algal gene libraries, molecular identification will become a universal tool in biological studies. Thus, in this report, successful application of molecular techniques related to algal bioassessment is discussed.

  4. Molecular Basis of ABHD5 Lipolysis Activation

    PubMed Central

    Sanders, Matthew A.; Zhang, Huamei; Mladenovic, Ljiljana; Tseng, Yan Yuan; Granneman, James G.

    2017-01-01

    Alpha-beta hydrolase domain-containing 5 (ABHD5), the defective gene in human Chanarin-Dorfman syndrome, is a highly conserved regulator of adipose triglyceride lipase (ATGL)-mediated lipolysis that plays important roles in metabolism, tumor progression, viral replication, and skin barrier formation. The structural determinants of ABHD5 lipolysis activation, however, are unknown. We performed comparative evolutionary analysis and structural modeling of ABHD5 and ABHD4, a functionally distinct paralog that diverged from ABHD5 ~500 million years ago, to identify determinants of ABHD5 lipolysis activation. Two highly conserved ABHD5 amino acids (R299 and G328) enabled ABHD4 (ABHD4 N303R/S332G) to activate ATGL in Cos7 cells, brown adipocytes, and artificial lipid droplets. The corresponding ABHD5 mutations (ABHD5 R299N and ABHD5 G328S) selectively disrupted lipolysis without affecting ATGL lipid droplet translocation or ABHD5 interactions with perilipin proteins and ABHD5 ligands, demonstrating that ABHD5 lipase activation could be dissociated from its other functions. Structural modeling placed ABHD5 R299/G328 and R303/G332 from gain-of-function ABHD4 in close proximity on the ABHD protein surface, indicating they form part of a novel functional surface required for lipase activation. These data demonstrate distinct ABHD5 functional properties and provide new insights into the functional evolution of ABHD family members and the structural basis of lipase regulation. PMID:28211464

  5. Molecular phylogenetics, seed morphometrics, chromosome number evolution and systematics of European Elatine L. (Elatinaceae) species.

    PubMed

    Sramkó, Gábor; Molnár V, Attila; Tóth, János Pál; Laczkó, Levente; Kalinka, Anna; Horváth, Orsolya; Skuza, Lidia; Lukács, Balázs András; Popiela, Agnieszka

    2016-01-01

    The genus Elatine contains ca 25 species, all of which are small, herbaceous annuals distributed in ephemeral waters on both hemispheres. However, due to a high degree of morphological variability (as a consequence of their amphibious life-style), the taxonomy of this genus remains controversial. Thus, to fill this gap in knowledge, we present a detailed molecular phylogenetic study of this genus based on nuclear (rITS) and plastid (accD-psaI, psbJ-petA, ycf6-psbM-trnD) sequences using 27 samples from 13 species. On the basis of this phylogenetic analysis, we provide a solid phylogenetic background for the modern taxonomy of the European members of the genus. Traditionally accepted sections of this tree (i.e., Crypta and Elatinella) were found to be monophyletic; only E. borchoni-found to be a basal member of the genus-has to be excluded from the latter lineage to achieve monophyly. A number of taxonomic conclusions can also be drawn: E. hexandra, a high-ploid species, is most likely a stabilised hybrid between the main sections; E. campylosperma merits full species status based on both molecular and morphological evidence; E. gussonei is a more widespread and genetically diverse species with two main lineages; and the presence of the Asian E. ambigua in the European flora is questionable. The main lineages recovered in this analysis are also supported by a number of synapomorphic morphological characters as well as uniform chromosome counts. Based on all the evidence presented here, two new subsections within Elatinella are described: subsection Hydropipera consisting of the temperate species of the section, and subsection Macropodae including the Mediterranean species of the section.

  6. The Syllis gracilis species complex: A molecular approach to a difficult taxonomic problem (Annelida, Syllidae).

    PubMed

    Álvarez-Campos, Patricia; Giribet, Gonzalo; Riesgo, Ana

    2017-04-01

    Syllis gracilis is an emblematic member of the subfamily Syllinae (Syllidae, Annelida), which inhabits shallow, temperate coastal waters and can be found on algae, coral rubble, and sponges. Their distinctive ypsiloid chaetae, usually found in specimens from populations all around the world, led to the consideration of the species as cosmopolitan, even though four other species have similar chaetae: Syllis magellanica, S. picta, S. mayeri and S. ypsiloides. The discovery of deeply divergent lineages in the Mediterranean Sea, that were morphologically similar, questioned the cosmopolitanism of S. gracilis and suggested the possibility of it being a species complex. In order to assess the speciation patterns within the putative S. gracilis complex, we undertook species delimitation and phylogenetic analyses on 61 specimens morphologically ascribed to Syllis gracilis and closely related species using a multilocus molecular dataset (two mitochondrial and two nuclear markers). Our results suggest high levels of genetic differentiation between the S. gracilis populations analyzed, some of which have morphologically distinctive features. Five to eight distinct lineages (depending on the analysis) were identified, all with geographically restricted distributions. Although the presence of ypsiloid chaetae has been traditionally considered the main character to identify S. gracilis, we conclude that this feature is homoplastic. Instead, we propose that characters such as the degree of fusion of blades and shafts in chaetae, the morphology of the posterior chaetae or the animal color pattern should be considered to differentiate lineages within the S. gracilis species complex. Our study does not support the cosmopolitanism of S. gracilis, and instead provides morphological and molecular evidence of the existence of a complex of pseudo-cryptic species.

  7. Molecular phylogenetics, seed morphometrics, chromosome number evolution and systematics of European Elatine L. (Elatinaceae) species

    PubMed Central

    Sramkó, Gábor; Tóth, János Pál; Laczkó, Levente; Kalinka, Anna; Horváth, Orsolya; Skuza, Lidia; Lukács, Balázs András; Popiela, Agnieszka

    2016-01-01

    The genus Elatine contains ca 25 species, all of which are small, herbaceous annuals distributed in ephemeral waters on both hemispheres. However, due to a high degree of morphological variability (as a consequence of their amphibious life-style), the taxonomy of this genus remains controversial. Thus, to fill this gap in knowledge, we present a detailed molecular phylogenetic study of this genus based on nuclear (rITS) and plastid (accD-psaI, psbJ-petA, ycf6-psbM-trnD) sequences using 27 samples from 13 species. On the basis of this phylogenetic analysis, we provide a solid phylogenetic background for the modern taxonomy of the European members of the genus. Traditionally accepted sections of this tree (i.e., Crypta and Elatinella) were found to be monophyletic; only E. borchoni—found to be a basal member of the genus—has to be excluded from the latter lineage to achieve monophyly. A number of taxonomic conclusions can also be drawn: E. hexandra, a high-ploid species, is most likely a stabilised hybrid between the main sections; E. campylosperma merits full species status based on both molecular and morphological evidence; E. gussonei is a more widespread and genetically diverse species with two main lineages; and the presence of the Asian E. ambigua in the European flora is questionable. The main lineages recovered in this analysis are also supported by a number of synapomorphic morphological characters as well as uniform chromosome counts. Based on all the evidence presented here, two new subsections within Elatinella are described: subsection Hydropipera consisting of the temperate species of the section, and subsection Macropodae including the Mediterranean species of the section. PMID:28028470

  8. Molecular mechanisms regulating NLRP3 inflammasome activation

    PubMed Central

    Jo, Eun-Kyeong; Kim, Jin Kyung; Shin, Dong-Min; Sasakawa, Chihiro

    2016-01-01

    Inflammasomes are multi-protein signaling complexes that trigger the activation of inflammatory caspases and the maturation of interleukin-1β. Among various inflammasome complexes, the NLRP3 inflammasome is best characterized and has been linked with various human autoinflammatory and autoimmune diseases. Thus, the NLRP3 inflammasome may be a promising target for anti-inflammatory therapies. In this review, we summarize the current understanding of the mechanisms by which the NLRP3 inflammasome is activated in the cytosol. We also describe the binding partners of NLRP3 inflammasome complexes activating or inhibiting the inflammasome assembly. Our knowledge of the mechanisms regulating NLRP3 inflammasome signaling and how these influence inflammatory responses offers further insight into potential therapeutic strategies to treat inflammatory diseases associated with dysregulation of the NLRP3 inflammasome. PMID:26549800

  9. Plant species richness increases phosphatase activities in an experimental grassland

    NASA Astrophysics Data System (ADS)

    Hacker, Nina; Wilcke, Wolfgang; Oelmann, Yvonne

    2014-05-01

    Plant species richness has been shown to increase aboveground nutrient uptake requiring the mobilization of soil nutrient pools. For phosphorus (P) the underlying mechanisms for increased P release in soil under highly diverse grassland mixtures remain obscure because aboveground P storage and concentrations of inorganic and organic P in soil solution and differently reactive soil P pools are unrelated (Oelmann et al. 2011). The need of plants and soil microorganisms for P can increase the exudation of enzymes hydrolyzing organically bound P (phosphatases) which might represent an important release mechanism of inorganic P in a competitive environment such as highly diverse grassland mixtures. Our objectives were to test the effects of i) plant functional groups (legumes, grasses, non-leguminous tall and small herbs), and of (ii) plant species richness on microbial P (Pmic) and phosphatase activities in soil. In autumn 2013, we measured Pmic and alkaline phosphomonoesterase and phosphodiesterase activities in soil of 80 grassland mixtures comprising different community compositions and species richness (1, 2, 4, 8, 16, 60) in the Jena Experiment. In general, Pmic and enzyme activities were correlated (r = 0.59 and 0.46 for phosphomonoesterase and phosphodiesterase activities, respectively; p

  10. 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

  11. Molecular typing of clinical isolates of Cryptococcus neoformans/Cryptococcus gattii species complex from Northeast Mexico.

    PubMed

    González, Gloria M; Casillas-Vega, Néstor; Garza-González, Elvira; Hernández-Bello, Romel; Rivera, Gildardo; Rodríguez, Jesús Ancer; Bocanegra-Garcia, Virgilio

    2016-01-01

    Cryptococcosis is caused by members of the Cryptococcus neoformans/Cryptococcus gattii species complex. Based on molecular identification, these two species have been further differentiated into molecular types. The aim of this work was to characterize clinical cryptococcal isolates recovered from six hospitals in Northeast Mexico from 1995 to 2011. One hundred and sixty-six isolates, which were characterized by biochemical tests and in vitro susceptibility to amphotericin B, fluconazole, and voriconazole, and M13 PCR fingerprinting, were included in this study. Utilizing phenotypic tests, 153 isolates (92.16 %) were identified as C. neoformans and 13 (7.83 %) as C. gattii. All isolates were susceptible to all antifungals tested. Employing M13 PCR fingerprinting, eight molecular types were detected. VNI was the most common genotype (124 cases; 74.6 %), followed by VNII (15 cases; 9 %), VNIII (8 cases; 4.8 %), VNIV (6 cases; 3.6 %), VGI (6 cases; 3.6 %), VGII (3 cases; 1.8 %), and VGIII and VGIV (2 cases, 1.2 % each). We confirm the presence of C. gattii in clinical isolates in Northeast Mexico, and a high clonal diversity in the studied strains of C. neoformans/C. gattii species complex.

  12. 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

  13. 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

  14. Species limits in Diaporthe: molecular re-assessment of D. citri, D. foeniculina and D. rudis with a new species on Citrus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species of Diaporthe are important plant pathogens associated with a wide range of hosts throughout the world. In the present study, the species causing melanose and stem end rot diseases on Citrus spp. were revised. Morphology and molecular phylogenetic analyses of the complete nuclear ribosomal in...

  15. Demonstration of neuraminidase activity in Mycoplasma neurolyticum and of neuraminidase proteins in three canine Mycoplasma species.

    PubMed

    Berčič, Rebeka Lucijana; Cizelj, Ivanka; Benčina, Mateja; Narat, Mojca; Bradbury, Janet M; Dovč, Peter; Benčina, Dušan

    2012-03-23

    Neuraminidases are virulence factors in many pathogenic microorganisms. They are present also in some Mycoplasma species that cause disease in birds, dogs and alligators. Thirty-seven Mycoplasma species have been examined previously for neuraminidase (sialidase) activity, whereas many of the species causing disease in man, ruminants, pigs, rodents and other animals have not. In this study neuraminidase enzymatic activity (NEAC) was examined in 45 previously untested Mycoplasma species, including those causing diseases in man, farm animals and laboratory animals. The only species in which NEAC was found was Mycoplasma neurolyticum, specifically, its type strain (Type A(T)) which is capable of inducing neurologic signs in inoculated young mice and rats. The NEAC of washed cells was relatively weak, but it differed even more than 10-fold among cells of cultures derived from individual colonies of M. neurolyticum. A weak NEAC was also detected in the supernatant of the M. neurolyticum broth culture. Canine Mycoplasma spp. with high sialidase activity reported previously, Mycoplasma canis, Mycoplasma cynos and Mycoplasma molare had 100-fold more NEAC than M. neurolyticum, but apparent differences in NEAC levels existed among strains of M. canis and of M. cynos. Zymograms using neuraminidase-specific chromogenic substrate were used to show proteins having NEAC. In M. canis (a field isolate Larissa and the type strain PG14(T)), M. cynos (isolate 896) and M. molare (type strain H542(T)) proteins with NEAC had molecular masses of ∼130kDa, 105kDa and 110kDa, respectively. Identification of these neuraminidases could provide the basis for their molecular characterization.

  16. Characterization of phospholipid molecular species and peptide molecules in wheat sprout hydroalcoholic extract.

    PubMed

    Lucci, Paolo; Pacetti, Deborah; Calzuola, Isabella; Marsili, Valeria; Perni, Stefano; Giavarini, Flavio; Frega, Natale Giuseppe; Gianfranceschi, Gian Luigi

    2013-11-27

    The phospholipid molecular species and the main peptide molecules of wheat sprout hydroalcoholic extract have been fully characterized by normal-phase high performance liquid chromatography coupled online with positive electrospray ionization tandem mass spectrometry. The extract that resulted was rich in phospholipid molecular species formed by the combination of the two essential fatty acids (α-linoleic and α-linolenic). These species accounted for 51.7% of total phosphatidic acid, 47.3% of total phosphatidylethanolamine, 37.7% of total phosphatidylcholine, and 14.1% of total phosphatidylinositol. The last one showed the highest amounts of species containing palmitic acid, thus representing the most saturated phospholipid class. The extract was also shown to contain several peptide sequences with both potential antioxidant domains and interaction sites for phospholipids (i.e., H-Ala-Gly-Ser-Met-Met-Cys-NH2, H-Tyr-Met-Thr-Val-Val-Ala-Cys-NH2, etc.); this latter finding can have a highly positive impact on the poor peptides bioavailability. Because of the presence of essential fatty acids-rich phospholipids and bioactive peptides, wheat sprout hydroalcoholic extract can be considered a potential functional food ingredient.

  17. 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.

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

    PubMed

    Soldánová, Miroslava; Georgieva, Simona; Roháčová, 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

    2017-03-14

    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.

  19. The taxonomic foundation, species circumscription and continental endemisms of Singerocybe: evidence from morphological and molecular data.

    PubMed

    Qin, Jiao; Feng, Bang; Yang, Zhu L; Li, Yan-Chun; Ratkowsky, David; Gates, Genevieve; Takahashi, Haruki; Rexer, Karl-Heinz; Kost, Gerhard W; Karunarathna, Samantha C

    2014-01-01

    The genus Singerocybe (Tricholomataceae, Agaricales, Basidiomycota) has been the subject of controversy since its proposal in 1988. Its taxonomic foundation, species circumscription and geographical distribution have not yet been examined with molecular sequence data. In this study phylogenetic analyses on this group of fungi were conducted based on collections from Europe, eastern Asia, southern Asia, North America and Australia, with four nuclear markers, ITS, nrLSU, tef1-α and rpb2. Molecular phylogenetic analyses, together with morphological observations, strongly support Singerocybe as a monophyletic group and identify the vesicles in the pileal and stipe cuticle as a synapomorphy of this genus. Seven species are recognized in the genus, including one new species and four new combinations. Clitocybe trogioides and Clitocybe trogioides var. odorifera are synonyms of Singerocybe humilis and Singerocybe alboinfundibuliformis respectively. Most of these species are geographically restricted in their distributions. Furthermore our study expands the distribution range of Singerocybe from the North Temperate Zone to Australia (Tasmania) and tropical southern Asia.

  20. Assessment of two new molecular methods for identification of Candida parapsilosis sensu lato species.

    PubMed

    Garcia-Effron, Guillermo; Canton, Emilia; Pemán, Javier; Dilger, Amanda; Romá, Eva; Perlin, David S

    2011-09-01

    Candida parapsilosis sensu stricto, C. orthopsilosis, and C. metapsilosis replaced C. parapsilosis groups I, II, and III in 2005. Since then, an increased interest in studying their epidemiology has arisen based on the observed differences in antifungal susceptibilities and virulence the three species. A strict differentiation of these species cannot be achieved by phenotypic methods. We evaluate two new molecular methodologies to differentiate among these species by the use of a collection of 293 bloodstream infection isolates of C. parapsilosis sensu lato. For the first method, the isolates were studied using PCR amplification of a fragment of the C. parapsilosis sensu lato FKS1 gene and a universal primer pair followed by EcoRI enzyme digestion. The other method used the allele discrimination ability of molecular beacons in a multiplex real-time PCR format. Both methods of identification showed 100% concordance with internal transcribed spacer 1 (ITS1)/ITS2 sequencing and proved to be effective for clinical applications, even with mixed-species DNAs.

  1. Measurement of Metabolic Activity in Dormant Spores of Bacillus Species

    DTIC Science & Technology

    2015-01-14

    SECURITY CLASSIFICATION OF: Spores of Bacillus megaterium and Bacillus subtilis were harvested shortly after release from sporangia, incubated under...Dec-2014 Approved for Public Release; Distribution Unlimited Final Report: Measurement of Metabolic Activity in Dormant Spores of Bacillus Species...Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 spores, Bacillus , spore dormancy, 3-phosphoglycerate REPORT DOCUMENTATION PAGE 11

  2. 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.

  3. 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

  4. 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.

  5. Molecular characterization of Morchella species from the Western Himalayan region of India.

    PubMed

    Kanwal, Harpreet Kaur; Acharya, Karan; Ramesh, G; Reddy, M Sudhakara

    2011-04-01

    The molecular diversity of thirty-two different Morchella cultures/fruiting bodies, collected from the Western Himalayan region was studied in this investigation. Considerable taxonomic confusion exists regarding many species of Morchella. Although classical taxonomy is helpful in identification for many ascomycetes, morels exhibit considerable morphological diversity and there is disagreement in the identification of morel species. Phylogenetic analyses based on DNA sequences could help in sorting out morel taxonomy which is essential to better define the morel diversity. In this study, sequence analysis revealed that in the Western Himalayan region of India, both yellow (M. crassipes, M. spongiola) and black morels (M. elata, M. angusticeps, and M. gigas) were prominent along with two Verpa species. Phylogenetic analysis by maximum parsimony, maximum likelihood and Bayesian inference revealed two different clades and a clear distinction between yellow and black morels.

  6. Morphological and Molecular Phylogenetic Data Reveal a New Species of Primula (Primulaceae) from Hunan, China

    PubMed Central

    Yu, Xun-Lin; Hu, Chi-Ming; Hao, Gang

    2016-01-01

    A new species of Primulaceae, Primula undulifolia, is described from the hilly area of Hunan province in south-central China. Its morphology and distributional range suggest that it is allied to P. kwangtungensis, both adapted to subtropical climate, having contiguous distribution and similar habitat, growing on shady and moist cliffs. Petioles, scapes and pedicels of them are densely covered with rusty multicellular hairs, but the new species can be easily distinguished by its smaller flowers and narrowly oblong leaves with undulate margins. Molecular phylogenetic analysis based on four DNA markers (ITS, matK, trnL-F and rps16) confirmed the new species as an independent lineage and constitutes a main clade together with P. kwangtungensis, P. kweichouensis, P. wangii and P. hunanensis of Primula sect. Carolinella. PMID:27579832

  7. 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

  8. 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

  9. Biodegradable Plastic-degrading Activity of Various Species of Paraphoma.

    PubMed

    Koitabashi, Motoo; Sameshima-Yamashita, Yuka; Koike, Hideaki; Sato, Toyozo; Moriwaki, Jouji; Morita, Tomotake; Watanabe, Takashi; Yoshida, Shigenobu; Kitamoto, Hiroko

    2016-07-01

    The fungal strain B47-9, isolated from barley, was previously selected as an effective degrader of various biodegradable plastic (BP) films such as poly(butylene succinate-co-adipate) (PBSA) and poly(butylene succinate) (PBS). The strain has not been identified based on mycological methods because it does not form fruiting bodies, which are the key to morphological identification. Here, we performed molecular phylogenetic analyses of the nuclear ribosomal RNA gene regions and their internal transcribed spacer region of B47-9 and related fungi. The results suggest that B47-9 is closely related to the genus Paraphoma. Investigation of the abilities of six strains belonging to the genus Paraphoma to degrade BPs indicated that all strains could degrade PBSA and PBS films to varying degrees. Based on our approach, we conclude that strain B47-9 is a species belonging to the genus Paraphoma.

  10. Molecular characterisation of Anaplasma species from African buffalo (Syncerus caffer) in Kruger National Park, South Africa.

    PubMed

    Sisson, Danielle; Hufschmid, Jasmin; Jolles, Anna; Beechler, Brianna; Jabbar, Abdul

    2017-03-01

    Bovine anaplasmosis is a tick-borne disease, mainly caused by Anaplasma marginale and A. centrale and is distributed in tropical and sub-tropical areas. This study aimed to characterise A. marginale and A. centrale from African buffaloes in Kruger National Park (KNP), South Africa, using the DNA sequences of the genes coding for major surface protein (msp1β) and heat shock protein (groEL), respectively. A total of 747 blood samples were collected from February 2014 to August 2016 from African buffaloes kept in KNP, and DNAs were tested using a molecular-phylogenetic approach. Out of 747 samples tested, 129 (17.3%) and 98 (13.1%) were positive for single infection with A. marginale and A. centrale, respectively; whereas 113 (15.1%) were positive for both Anaplasma spp. Pairwise difference of 1.6-8.5% was observed in msp1β sequences of A. marginale whereas that was only 0.3-2.4% for groEL sequences of A. centrale. Separate phylogenetic analyses of msp1β and groEL sequences of A. marginale and A. centrale, respectively, revealed that sequences of Anaplasma spp. from African buffaloes were unique and they grouped separately when compared with previously published sequences of both species. This is the first study to characterise A. marginale and A. centrale from African buffalo using species specific molecular markers. This study will pave the way for future studies to assess genetic variation among Anaplasma spp. from wild ruminants using molecular markers that are better at differentiating between species and strains than the more commonly used 16S rRNA gene, and help to undertake health and fitness studies and host-parasite dynamics using quantitative molecular tools.

  11. 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

  12. 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.

  13. Magnetically active biosorbent for chromium species removal from aqueous media.

    PubMed

    Abdel-Fattah, Tarek M; Mahmoud, Mohamed E; Osmam, Maher M; Ahmed, Somia B

    2014-01-01

    A magnetically active composite as adsorbent was synthesized via a facile in situ one-pot impregnation of magnetic nano-iron oxide (Fe₃O₄) on the surface of activated carbon (AC) for the formation of AC-Fe₃O₄. Baker(')s yeast was physically loaded on the resultant adsorbent AC-Fe₃O₄ to form a novel yeast coated magnetic composite AC-Fe₃O₄-Yst as biosorbent. The two synthesized adsorbents were characterized by using a scanning electron microscope (SEM) and assessed using Langmuir, the Brunauer-Emmet-Teller (BET) and Dubinin-Radushkevich (D-R) isotherm models. The validity and applicability of these two sorbents in adsorptive removal of chromium species, Cr(VI) and Cr(III), from aqueous solutions under the effect of a magnetic field were studied and evaluated in the presence of various controlling parameters in order to identify the optimal pH, contact time, mass dose and chromium concentrations for such adsorption process. Also, single and multi-stage micro-column techniques were used to study the potential applications of AC-Fe₃O₄ as magnetically active adsorbents and AC-Fe₃O₄-Yst as magnetically active biosorbents, for the removal of chromium species from various real water samples.

  14. 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.

  15. Chemical constituents and biological activities of two Iranian Cystoseira species.

    PubMed

    Yegdaneh, Afsaneh; Ghannadi, Alireza; Dayani, Ladan

    2016-07-01

    The marine environment represents approximately half of the global biodiversity and could provide unlimited biological resources for the production of therapeutic drugs. Marine seaweeds comprise few thousands of species representing a considerable part of the littoral biomass. Extracts of the Cystoseira indica and Cystoseira merica were subjected to phytochemical and cytotoxicity evaluation. The amount of total phenol was determined with Folin-Ciocalteu reagent. Cytotoxicity was characterized by IC50 of human cancer cell lines including MCF-7 (human breast adenocarcinoma), HeLa (cervical carcinoma), and HT-29 (human colon adenocarcinoma) using Sulforhodamin assay. Antioxidant activities were evaluated using 2,2-diphenylpicrylhydrazyl (DPPH) method. The analysis revealed that tannins, saponins, sterols and triterpenes were the most abundant constituents in these Cystoseira species while cyanogenic and cardiac glycosides were the least ones. C. indica had the higher content of total phenolics and also showed higher antioxidant activity. Cytotoxic results showed that both species inhibited cell growth effectively, especially against MCF-7 cell line. The present findings suggest potential pharmacological applications of selected seaweeds but require further investigation and identification of their bioactive principles.

  16. Chemical constituents and biological activities of two Iranian Cystoseira species

    PubMed Central

    Yegdaneh, Afsaneh; Ghannadi, Alireza; Dayani, Ladan

    2016-01-01

    The marine environment represents approximately half of the global biodiversity and could provide unlimited biological resources for the production of therapeutic drugs. Marine seaweeds comprise few thousands of species representing a considerable part of the littoral biomass. Extracts of the Cystoseira indica and Cystoseira merica were subjected to phytochemical and cytotoxicity evaluation. The amount of total phenol was determined with Folin-Ciocalteu reagent. Cytotoxicity was characterized by IC50 of human cancer cell lines including MCF-7 (human breast adenocarcinoma), HeLa (cervical carcinoma), and HT-29 (human colon adenocarcinoma) using Sulforhodamin assay. Antioxidant activities were evaluated using 2,2-diphenylpicrylhydrazyl (DPPH) method. The analysis revealed that tannins, saponins, sterols and triterpenes were the most abundant constituents in these Cystoseira species while cyanogenic and cardiac glycosides were the least ones. C. indica had the higher content of total phenolics and also showed higher antioxidant activity. Cytotoxic results showed that both species inhibited cell growth effectively, especially against MCF-7 cell line. The present findings suggest potential pharmacological applications of selected seaweeds but require further investigation and identification of their bioactive principles. PMID:27651811

  17. Phytochemical profiles, antioxidant and antimicrobial activities of three Potentilla species

    PubMed Central

    2013-01-01

    Background Extracts from Potentilla species have been applied in traditional medicine and exhibit antioxidant, hypoglycemic, anti-inflammatory, antitumor and anti-ulcerogenic properties, but little has been known about the diversity of phytochemistry and pharmacology on this genus. This study investigated and compared the phytochemical profiles, antioxidant and antimicrobial activities of leaf extracts from three Potentilla species (Potentilla fruticosa, Potentilla glabra and Potentilla parvifolia) in order to discover new resources for lead structures and pharmaceutical products. Methods Chemical composition and content of six phenolic compounds were evaluated and determined by RP-HPLC; Total phenolic and total flavonoid content were determined using Folin-Ciocalteau colourimetric method and sodium borohydride/chloranil-based method (SBC); Antioxidant activities were determined using DPPH, ABTS and FRAP assays; Antimicrobial properties were investigated by agar dilution and mycelial growth rate method. Results The results showed hyperoside was the predominant phenolic compound in three Potentilla species by RP-HPLC assay, with the content of 8.86 (P. fruticosa), 2.56 (P. glabra) and 2.68 mg/g (P. parvifolia), respectively. The highest content of total identified phenolic compounds (hyperoside, (+)-catechin, caffeic acid, ferulic acid, rutin and ellagic acid) was observed in P. parvifolia (14.17 mg/g), follow by P. fruticosa (10.01 mg/g) and P. glabra (7.01 mg/g). P. fruticosa possessed the highest content of total phenolic (84.93 ± 0.50 mmol gallic acid equivalent/100 g) and total flavonoid (84.14 ± 0.03 mmol quercetin equivalent/100 g), which were in good correlation with its significant DPPHIC50 (16.87 μg/mL), ABTS (2763.48 μmol Trolox equivalent/g) and FRAP (1398.70 μmol Trolox equivalent/g) capacities. Furthermore, the effective methodology to distinguish the different species of Potentilla was also established by chromatographic fingerprint analysis for

  18. Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus.

    PubMed

    Fouquet, Antoine; Recoder, Renato; Teixeira, Mauro; Cassimiro, José; Amaro, Renata Cecília; Camacho, Agustín; Damasceno, Roberta; Carnaval, Ana Carolina; Moritz, Craig; Rodrigues, Miguel Trefaut

    2012-03-01

    Dendrophryniscus is an early diverging clade of bufonids represented by few small-bodied species distributed in Amazonia and the Atlantic Forest. We used mitochondrial (414 bp of 12S, 575 bp of 16S genes) and nuclear DNA (785 bp of RAG-1) to investigate phylogenetic relationships and the timing of diversification within the genus. These molecular data were gathered from 23 specimens from 19 populations, including eight out of the 10 nominal species of the genus as well as Rhinella boulengeri. Analyses also included sequences of representatives of 18 other bufonid genera that were publically available. We also examined morphological characters to analyze differences within Dendrophryniscus. We found deep genetic divergence between an Amazonian and an Atlantic Forest clade, dating back to Eocene. Morphological data corroborate this distinction. We thus propose to assign the Amazonian species to a new genus, Amazonella. The species currently named R. boulengeri, which has been previously assigned to the genus Rhamphophryne, is shown to be closely related to Dendrophryniscus species. Our findings illustrate cryptic trends in bufonid morphological evolution, and point to a deep history of persistence and diversification within the Amazonian and Atlantic rainforests. We discuss our results in light of available paleoecological data and the biogeographic patterns observed in other similarly distributed groups.

  19. 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.

  20. Molecular Variation in Chloroplast DNA Regions in Ancestral Species of Wheat

    PubMed Central

    Miyashita, N. T.; Mori, N.; Tsunewaki, K.

    1994-01-01

    Restriction map variation in two 5-6-kb chloroplast DNA regions of five diploid Aegilops species in the section Sitopsis and two wild tetraploid wheats, Triticum dicoccoides and Triticum araraticum, was investigated with a battery of four-cutter restriction enzymes. A single accession each of Triticum durum, Triticum timopheevi and Triticum aestivum was included as a reference. More than 250 restriction sites were scored, of which only seven sites were found polymorphic in Aegilops speltoides. No restriction site polymorphisms were detected in all of the other diploid and tetraploid species. In addition, six insertion/deletion polymorphisms were detected, but they were mostly unique or species-specific. Estimated nucleotide diversity was 0.0006 for A. speltoides, and 0.0000 for all the other investigated species. In A. speltoides, none of Tajima's D values was significant, indicating no clear deviation from the neutrality of molecular polymorphisms. Significant non-random association was detected for three combinations out of 10 possible pairs between polymorphic restriction sites in A. speltoides. Phylogenetic relationship among all the plastotypes (plastid genotype) suggested the diphyletic origin of T. dicoccoides and T. araraticum. A plastotype of one A. speltoides accession was identical to the major type of T. araraticum (T. timopheevi inclusively). Three of the plastotypes found in the Sitopsis species are very similar, but not identical, to that of T. dicoccoides, T. durum and T. aestivum. PMID:7916310

  1. Phylogenetic relationships among Neoechinorhynchus species (Acanthocephala: Neoechinorhynchidae) from North-East Asia based on molecular data.

    PubMed

    Malyarchuk, Boris; Derenko, Miroslava; Mikhailova, Ekaterina; Denisova, Galina

    2014-02-01

    Phylogenetic and statistical analyses of DNA sequences of two genes, cytochrome oxidase subunit 1 (cox 1) of the mitochondrial DNA and 18S subunit of the nuclear ribosomal RNA (18S rRNA), was used to characterize Neoechinorhynchus species from fishes collected in different localities of North-East Asia. It has been found that four species can be clearly recognized using molecular markers-Neoechinorhynchus tumidus, Neoechinorhynchus beringianus, Neoechinorhynchus simansularis and Neoechinorhynchus salmonis. 18S sequences ascribed to Neoechinorhynchus crassus specimens from North-East Asia were identical to those of N. tumidus, but differed substantially from North American N. crassus. We renamed North-East Asian N. crassus specimens to N. sp., although the possibility that they represent a subspecies of N. tumidus cannot be excluded, taking into account a relatively small distance between cox 1 sequences of North-East Asian specimens of N. crassus and N. tumidus. Maximum likelihood, maximum parsimony and Bayesian inference analyses were performed for phylogeny reconstruction. All the phylogenetic trees showed that North-East Asian species of Neoechinorhynchus analyzed in this study represent independent clades, with the only exception of N. tumidus and N. sp. for 18S data. Phylogenetic analysis has shown that the majority of species sampled (N. tumidus+N. sp., N. simansularis and N. beringianus) are probably very closely related, while N. salmonis occupies separate position in the trees, possibly indicating a North American origin of this species.

  2. Taxonomic and Molecular Identification of Hemicaloosia, Hemicycliophora, Gracilacus and Paratylenchus Species (Nematoda: Criconematidae)

    PubMed Central

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

    2013-01-01

    Populations of Hemicycliophora epicharoides, H. gigas, H. labiata, H. pruni, H. shepherdi, H. vidua, H. zuckermani, Gracilacus straeleni, and Paratylenchus labiosus were obtained from different geographical areas in the continental United States and characterized morphological and molecularly. Two new species of Hemicycliophorinae: Hemicaloosia uarki n. sp from Pinetree, St. Francis County, Arkansas, and Hemicycliophora wyei n. sp from Wayne County, North Carolina, are also described. Hemicaloosia uarki n. sp. is characterized by having two lip annuli separated from the rest of body and directed anteriorly, a long stylet (106-124 μm), long body length (1,081-1,326 μm) and a single lateral fields demarcated by interruptions of the body annuli. Hemicycliophora wyei n. sp. showed a lateral fields demarked by two faint lines with transverse anastomoses and/or breaks of the striae; an elongated not offset conical tail with distinct annulations and a rounded tip and long vulval lips with a vulval sleeve. The molecular characterizations of the new (H. uarki n. sp. and H. wyei n. sp.) and known species of Criconematidae using the ITS1 rDNA gene sequence and the molecular phylogenetic relationships are provided. PMID:24115782

  3. Taxonomic and Molecular Identification of Bakernema, Criconema, Hemicriconemoides, Ogma and Xenocriconemella Species (Nematoda: Criconematidae)

    PubMed Central

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

    2012-01-01

    Populations of Bakernema inaequale, C. petasum, C. sphagni, C. mutabile, Ogma octangulare, Xenocriconemella macrodora and Hemicriconemoides chitwoodi were identified and re-described from different geographical areas in the continental United States and molecularly characterized. Two new species of spine nematodes Criconema arkaense n. sp. from Washington County and Lee County, Arkansas and Criconema warrenense n. sp from Warren, Bradley County, Arkansas are also described and named. Criconema arkaense is characterize by having a conspicuous lip region offset from the body with two annuli, short rounded tail with a thin cuticular sheath and subterminal anus. Criconema warrenense n. sp. has two lip region annuli about the same width, first annulus directed posteriorly, separated by a narrow neck annulus and a short conoid tail, unilobed non-folded annulus. The molecular characterization of Criconema arkaense and Criconema warrenense using ITS1 rDNA gene sequence and the molecular phylogenetic relationships of these new species along with the known spines nematodes are provided. PMID:23482683

  4. 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

  5. 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.

  6. Using Combined Morphological, Allometric and Molecular Approaches to Identify Species of the Genus Raillietiella (Pentastomida)

    PubMed Central

    Kelehear, Crystal; Spratt, David M.; Dubey, Sylvain; Brown, Gregory P.; Shine, Richard

    2011-01-01

    Taxonomic studies of parasites can be severely compromised if the host species affects parasite morphology; an uncritical analysis might recognize multiple taxa simply because of phenotypically plastic responses of parasite morphology to host physiology. Pentastomids of the genus Raillietiella are endoparasitic crustaceans primarily infecting the respiratory system of carnivorous reptiles, but also recorded from bufonid anurans. The delineation of pentastomids at the generic level is clear, but the taxonomic status of many species is not. We collected raillietiellids from lungs of the invasive cane toad (Rhinella marina), the invasive Asian house gecko (Hemidactylus frenatus), and a native tree frog (Litoria caerulea) in tropical Australia, and employed a combination of genetic analyses, and traditional and novel morphological methods to clarify their identity. Conventional analyses of parasite morphology (which focus on raw values of morphological traits) revealed two discrete clusters in terms of pentastome hook size, implying two different species of pentastomes: one from toads and a tree frog (Raillietiella indica) and another from lizards (Raillietiella frenatus). However, these clusters disappeared in allometric analyses that took pentastome body size into account, suggesting that only a single pentastome taxon may be involved. Our molecular data revealed no genetic differences between parasites in toads versus lizards, confirming that there was only one species: R. frenatus. This pentastome (previously known only from lizards) clearly is also capable of maturing in anurans. Our analyses show that the morphological features used in pentastomid taxonomy change as the parasite transitions through developmental stages in the definitive host. To facilitate valid descriptions of new species of pentastomes, future taxonomic work should include both morphological measurements (incorporating quantitative measures of body size and hook bluntness) and molecular data

  7. 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

  8. Length regulation of active biopolymers by molecular motors.

    PubMed

    Johann, Denis; Erlenkämper, Christoph; Kruse, Karsten

    2012-06-22

    For biopolymers like cytoskeletal actin filaments and microtubules, assembly and disassembly are inherently dissipative processes. Molecular motors can affect the rates of subunit removal at filament ends. We introduce a driven lattice-gas model to study the effects of motor-induced depolymerization on the length of active biopolymers and find that increasing motor activity sharpens unimodal steady-state length distributions. Furthermore, for sufficiently fast moving motors, the relative width of the length distribution is determined only by the attachment rate of motors. Our results show how established molecular processes can be used to robustly regulate the size of cytoskeletal structures like mitotic spindles.

  9. Antimicrobial activity of some Clerodendrum species from Egypt.

    PubMed

    Abouzid, Sameh F; Wahba, Haytham M; Elshamy, Ali; Cos, Paul; Maes, Louis; Apers, Sandra; Pieters, Luc; Shahat, Abdelaaty A

    2013-01-01

    Chloroformic and methanolic extracts of four Clerodendrum species cultivated in Egypt were screened for antimicrobial activities. Chloroformic extracts of the flowers of Clerodendrum chinense and Clerodendrum splendens were active against Plasmodium falciparum (IC50 < 10 µg mL(-1)). Chloroformic extracts of the stem and flowers of C. chinense were active against Trypanosoma cruzi (IC50 = 1.21 and 1.12 µg mL(-1), respectively) with marginal cytotoxicity. Chloroformic extracts of the leaves of C. chinense and C. splendens showed promising activities against T. cruzi (IC50 = 3.39 and 1.98 µg mL(-1), respectively) without cytotoxic effect on a human cell line. None of the selected plants showed significant activity against Gram-negative or Gram-positive bacteria or Candida albicans. Verbascoside, a phenyl propanoid glycoside isolated from the leaves of C. chinense, showed marginal activity against T. cruzi. Rengyolone, a cyclohexyl ethanoid isolated from the leaves of C. chinense, showed a broad but not specific activity against the tested organisms.

  10. 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.

  11. Simultaneous analysis of glycolipids and phospholids molecular species in avocado (Persea americana Mill) fruit.

    PubMed

    Pacetti, Deborah; Boselli, Emanuele; Lucci, Paolo; Frega, Natale G

    2007-05-25

    The molecular species of phospholipids (PLs) and glycolipids (GLs) were simultaneously characterized in the pulp and almond of the avocado fruit (Persea americana Mill) of four varieties by means of high performance liquid chromatography-electrospray ionisation ion-trap tandem mass spectrometry. In the pulp, the predominant species of monoglycosyldiglycerides (MGD) were m/z 796.6 (oleic/linolenic and linoleic/linoleic acids) and m/z 800.4 (stearic/linoleic and oleic/oleic acids). One of the main diglycosyldiglycerides (DGD) both in the pulp and almond was m/z 958.5 (oleic/linolenic); however, the pulp was also rich of m/z 962.4 (oleic/oleic), whereas in the almond, m/z 934.5 (palmitic/linoleic and palmitoleic/oleic) and m/z 960.5 (oleic/linoleic and stearic/linolenic) were more abundant. In the almond, the main PL classes (phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI)) contained always palmitic/linoleic acids. Alpha-linolenic acid was contained as MGD (linolenic/linolenic) and DGD (linolenic/linolenic), more present in the pulp than in the almond. The major molecular species of glycocerebrosides (GCer) in the pulp and almond carried hydroxy-palmitic acid (C(16h:0))/4,8-sphyngadienine (d(18:2)).

  12. 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.

  13. Molecular tools for species and sex identification in the mixed-species flocks of bean geese and white-fronted geese.

    PubMed

    Kim, Min-kyung; Lee, Sang-im; Lee, Hang; Lee, Sangdon

    2012-11-01

    Genetic studies on protected species can be difficult, particularly when they form a mixed-species flock with other species. The bean goose (Anser fabalis), which is internationally recognized as a threatened species, was observed to form overwintering foraging flocks with white-fronted goose (Anser albifrons) at agricultural lands to feed on the grains in Korea. Non-invasive samples such as feces and feather that are readily available in their foraging ground can be useful for understanding the structure and composition of populations, but they often require specific experimental conditions due to small amount or low quality of DNA. In this study, we designed sets of primers that would allow efficient molecular identification of species and sex of individuals of bean geese and white-fronted geese. Species-specific primers (WFG-F/BG-F and G-R), developed from ND2 region of mitochondrial DNA, produced PCR products with different sizes which allow easy species identification without further sequencing. Based on published CHD 1 sequences, we designed internal primers (Gsex-F and Gsex-R) for sex determination that can be used in nested PCR after applying P2/P8 primers, and our methods clearly showed high success rate of molecular sexing from non-invasive samples. These molecular tools open the possibilities for genetic studies using non-invasive samples collected from a mixed-species aggregation containing bean geese and white-fronted geese.

  14. Artificial hydrogenase: biomimetic approaches controlling active molecular catalysts.

    PubMed

    Onoda, Akira; Hayashi, Takashi

    2015-04-01

    Hydrogenase catalyses reversible transformation of H2 to H(+) using an active site which includes an iron or nickel atom. Synthetic model complexes and molecular catalysts inspired by nature have unveiled the structural and functional basis of the active site with remarkable accuracy and this has led to the discovery of active synthetic catalysts. To further improve the activity of such molecular catalysts, both the first and outer coordination spheres should be well-organized and harmonized for an efficient shuttling of H(+), electrons, and H2. This article reviews recent advances in the design and catalytic properties of artificial enzymes that mimic the hydrogenase active site and the outer coordination sphere in combination with a peptide or protein scaffold.

  15. The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats

    PubMed Central

    Gager, Yann; Tarland, Emilia; Lieckfeldt, Dietmar; Ménage, Matthieu; Botero-Castro, Fidel; Rossiter, Stephen J.; Kraus, Robert H. S.; Ludwig, Arne; Dechmann, Dina K. N.

    2016-01-01

    A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative. PMID:26943355

  16. Systematics and molecular phylogeny of the family oscarellidae (homoscleromorpha) with description of two new oscarella species.

    PubMed

    Gazave, Eve; Lavrov, Dennis V; Cabrol, Jory; Renard, Emmanuelle; Rocher, Caroline; Vacelet, Jean; Adamska, Maja; Borchiellini, Carole; Ereskovsky, Alexander V

    2013-01-01

    The family Oscarellidae is one of the two families in the class Homoscleromorpha (phylum Porifera) and is characterized by the absence of a skeleton and the presence of a specific mitochondrial gene, tatC. This family currently encompasses sponges in two genera: Oscarella with 17 described species and Pseudocorticium with one described species. Although sponges in this group are relatively well-studied, phylogenetic relationships among members of Oscarellidae and the validity of genus Pseudocorticium remain open questions. Here we present a phylogenetic analysis of Oscarellidae using four markers (18S rDNA, 28S rDNA, atp6, tatC), and argue that it should become a mono-generic family, with Pseudocorticium being synonymized with Oscarella, and with the transfer of Pseudocorticium jarrei to Oscarella jarrei. We show that the genus Oscarella can be subdivided into four clades, each of which is supported by either a small number of morphological characters or by molecular synapomorphies. In addition, we describe two new species of Oscarella from Norwegian fjords: O. bergenensis sp. nov. and O. nicolae sp. nov., and we compare their morphology, anatomy, and cytology with other species in this genus. Internal anatomical characters are similar in both species, but details of external morphology and particularly of cytological characters provide diagnostic features. Our study also confirms that O. lobularis and O. tuberculata are two distinct polychromic sibling species. This study highlights the difficulties of species identification in skeleton-less sponges and, more generally, in groups where morphological characters are scarce. Adopting a multi-marker approach is thus highly suitable for these groups.

  17. Systematics and Molecular Phylogeny of the Family Oscarellidae (Homoscleromorpha) with Description of Two New Oscarella Species

    PubMed Central

    Gazave, Eve; Lavrov, Dennis V.; Cabrol, Jory; Renard, Emmanuelle; Rocher, Caroline; Vacelet, Jean; Adamska, Maja; Borchiellini, Carole; Ereskovsky, Alexander V.

    2013-01-01

    The family Oscarellidae is one of the two families in the class Homoscleromorpha (phylum Porifera) and is characterized by the absence of a skeleton and the presence of a specific mitochondrial gene, tatC. This family currently encompasses sponges in two genera: Oscarella with 17 described species and Pseudocorticium with one described species. Although sponges in this group are relatively well-studied, phylogenetic relationships among members of Oscarellidae and the validity of genus Pseudocorticium remain open questions. Here we present a phylogenetic analysis of Oscarellidae using four markers (18S rDNA, 28S rDNA, atp6, tatC), and argue that it should become a mono-generic family, with Pseudocorticium being synonymized with Oscarella, and with the transfer of Pseudocorticium jarrei to Oscarella jarrei. We show that the genus Oscarella can be subdivided into four clades, each of which is supported by either a small number of morphological characters or by molecular synapomorphies. In addition, we describe two new species of Oscarella from Norwegian fjords: O. bergenensis sp. nov. and O. nicolae sp. nov., and we compare their morphology, anatomy, and cytology with other species in this genus. Internal anatomical characters are similar in both species, but details of external morphology and particularly of cytological characters provide diagnostic features. Our study also confirms that O. lobularis and O. tuberculata are two distinct polychromic sibling species. This study highlights the difficulties of species identification in skeleton-less sponges and, more generally, in groups where morphological characters are scarce. Adopting a multi-marker approach is thus highly suitable for these groups. PMID:23737959

  18. Molecular and Morphological Evidence Demonstrating Two Species of Helicometrina Linton 1910 (Digenea: Opecoelidae) in Northern Chile.

    PubMed

    Oliva, Marcelo E; Valdivia, Isabel M; Chavez, Rosa A; Molina, Horacio; Cárdenas, Leyla

    2015-12-01

    The opecoelid Helicometrina nimia Linton, 1910 has been reported from numerous marine fishes along the Pacific and Atlantic coasts of the Americas. Along the Chilean coast, H. nimia is found in fishes belonging to at least 9 families. This surprisingly low host specificity of H. nimia raises question about the correct identification of specimens assigned to this species. Here we evaluate whether H. nimia specimens isolated from sympatric fish species in northern Chile but with different diets and found in different habitats (water column and demersal) are the same species. Our results demonstrate that specimens from the shallow benthic fish Labrisomus philippii (Steindachner) do not correspond to H. nimia but instead belong to a new species of Helicometrina. This species is described and distinguished from H. nimia using morphological descriptions and 2 molecular markers (the cytochrome c oxidase subunit 1 gene and the V4 region of the SSU rRNA gene). The new species Helicometrina labrisomi (Digenea: Opecoelidae), is found in the intestine of L. philippii (Steindachner, 1866) (Pisces: Labrisomidae), a shallow benthic fish that inhabits the northern coast of Chile. We also studied the related Helicometrina nimia Linton, 1910 from the benthopelagic fishes Paralabrax humeralis (Valenciennes, 1828) and Acanthistius pictus (Tschudi, 1846) (Serranidae). The new species differs from H. nimia by a combination of characters that include ovary shape, number of uterine loops, and position of the genital pore. Our results indicate that morphological characteristics, such as body size, extent of the vitellarium, shape of the testes, and cirrus sac size and extent, traditionally used in the taxonomy of Helicometrina are highly variable. In contrast, meristic and morphological characteristics, such as a lobed ovary, the number of uterine loops, dimensions of the pharynx, and the opening of the genital pore, are highly constant.

  19. Molecular species-sensitive optical coherence tomography using coherent anti-stokes Raman scattering spectroscopy

    NASA Astrophysics Data System (ADS)

    Marks, Daniel L.; Bredfeldt, Jeremy; Hambir, Selezion; Dlott, Dana D.; Kitchell, Barbara; Gruebele, Martin; Boppart, Stephen A.

    2003-07-01

    We present our progress in developing a novel technique and instrument that images specific molecular species in biological tissues using Optical Coherence Tomography (OCT). Standard OCT instruments measure only the scattering from structural features, such as refractive index changes. We utilize Coherent Anti-Stokes Raman Scattering (CARS) Spectroscopy, a nonlinear optics technique that can selectively stimulate molecular groups, to gather compositional information from the sample. Being a coherent process, our instrument will produce interference between the nonlinear anti-Stokes signal produced in the sample and a reference molecular sample to both exclude background and nonresonant signals and range features in the tissue. Because of this, we will also gain the benefits of sensitivity that interferometry can provide. By utilizing the tunability of an optical parametric oscillator, we can address a range of molecular resonances from 1500 cm-1 to 3500 cm-1. This frequency range offers the possibility of measuring the distributions and densities of proteins, lipids, and nuclear material that we believe will be useful for determining the early presence of epithelial carcinomas. We demonstrate the principle of this imaging method by producing interference between two separately produced CARS signals from the same probe and Stokes beams.

  20. 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.

  1. Antiinflammatory activities of Hungarian Stachys species and their iridoids.

    PubMed

    Háznagy-Radnai, Erzsébet; Balogh, Ágnes; Czigle, Szilvia; Máthé, Imre; Hohmann, Judit; Blazsó, Gábor

    2012-04-01

    The antiinflammatory activities of aqueous extracts prepared from the aerial parts of ten Hungarian Stachys species were investigated in vivo in the carrageenan-induced paw oedema test after intraperitoneal and oral administration to rats. Some of the extracts were found to display significant antiphlogistic effects when administered intraperitoneally and orally; in particular, the extracts of S. alpina, S. germanica, S. officinalis and S. recta demonstrated high activity following intraperitoneal administration. At the same dose of 5.0 mg/kg, these extracts exhibited similar or greater potency than that of the positive control diclofenac-Na. The main iridoids present in the investigated extracts, ajugoside, aucubin, acetylharpagide, harpagide and harpagoside, were also assayed in the same test, and high dose-dependent antiphlogistic effects were recorded for aucubin and harpagoside. These results led to the conclusion that most probably iridoids are responsible for the antiinflammatory effect of Stachys species, but other active constituents or their synergism must also be implicated in the antiinflammatory effect.

  2. Cryptic species of hairworm parasites revealed by molecular data and crowdsourcing of specimen collections.

    PubMed

    Hanelt, Ben; Schmidt-Rhaesa, Andreas; Bolek, Matthew G

    2015-01-01

    Recognizing cryptic species promotes a better understanding of biodiversity, systematics, evolutionary biology, and biogeography. When cryptic species are disease-causing organisms, such as parasites, their correct recognition has important implications for the study of epidemiology, disease ecology, and host-parasite relationships. Freshwater nematomorphs (Nematomorpha: Gordiida) or hairworms, are an enigmatic yet fascinating group of parasites that are known to manipulate host behavior to aid transition from the parasitic phase, within terrestrial insects, to the free-living aquatic stage. Hairworm taxonomy has been hampered by a paucity of informative diagnostic characters and it has long been suspected that this group contains numerous cryptic species. Study of single hairworm species over large geographical areas has been difficult due to extremely rare encounters and unreliable methods of collecting adult worms. Here we report that by using crowdsourcing, citizen scientists have collected and submitted samples of Gordius cf. robustus from throughout its range in North America making its genetic study possible. Combined with our own collections, we examined samples from 28 localities within the USA; despite the collection of numerous hairworms from Canada and Mexico, G. cf. robustus were not collected outside of the contiguous United States. Mitochondrial CO1 genetic distances revealed that specimens grouped into 8 clades separated by 8-24.3%. In addition, molecular evidence from mitochondrial (CO1 and cytB) and nuclear (partial 28S, ITS1, 5.8S and ITS2) DNA suggests that these 8 clades are distinct species and that this group of species is paraphyletic, since the North American species G. attoni and the European species G. aquaticus and G. balticus group among the G. robustus lineages. Furthermore, there was a significant correlation between genetic (CO1) and geographic distance between the 8 Gordius species. This study demonstrates the value of involving the

  3. Large Roads Reduce Bat Activity across Multiple Species

    PubMed Central

    Kitzes, Justin; Merenlender, Adina

    2014-01-01

    Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis), big brown bat (Eptesicus fuscus), hoary bat (Lasiurus cinereus), and silver-haired bat (Lasionycteris noctivagans). The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations. PMID:24823689

  4. Large roads reduce bat activity across multiple species.

    PubMed

    Kitzes, Justin; Merenlender, Adina

    2014-01-01

    Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis), big brown bat (Eptesicus fuscus), hoary bat (Lasiurus cinereus), and silver-haired bat (Lasionycteris noctivagans). The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations.

  5. Active hydrogen species on TiO2 for photocatalytic H2 production.

    PubMed

    Wu, Zongfang; Zhang, Wenhua; Xiong, Feng; Yuan, Qing; Jin, Yuekang; Yang, Jinlong; Huang, Weixin

    2014-04-21

    Photocatalytic H2 production over TiO2 has attracted tremendous attention and achieved great progress, but the active hydrogen species is still unknown. Employing a rutile TiO2(110) surface as a model catalyst we report here for the first time the direct observation of photocatalytic H2 production under ultrahigh vacuum conditions during UV-light irradiation at 115 K and the identification of negatively-charged hydride-type H-Ti species as the corresponding photoactive surface species by means of thermal desorption spectroscopy, photon-stimulated desorption spectroscopy, X-ray photoelectron spectroscopy and DFT calculations. The formation and stability of H-Ti species are closely related to available surplus electrons on the rutile TiO2(110) surface that can be created by the formation of surface BBO vacancies or by the formation of surface hydroxyls via the adsorption of atomic H or molecular H2 on O sites. The photocatalytic H2 production from H-Ti species is hole-mediated and co-existing water exerts a negative effect on this process.

  6. Lectin activity in mycelial extracts of Fusarium species.

    PubMed

    Bhari, Ranjeeta; Kaur, Bhawanpreet; Singh, Ram S

    2016-01-01

    Lectins are non-immunogenic carbohydrate-recognizing proteins that bind to glycoproteins, glycolipids, or polysaccharides with high affinity and exhibit remarkable ability to agglutinate erythrocytes and other cells. In the present study, ten Fusarium species previously not explored for lectins were screened for the presence of lectin activity. Mycelial extracts of F. fujikuroi, F. beomiformii, F. begoniae, F. nisikadoi, F. anthophilum, F. incarnatum, and F. tabacinum manifested agglutination of rabbit erythrocytes. Neuraminidase treatment of rabbit erythrocytes increased lectin titers of F. nisikadoi and F. tabacinum extracts, whereas the protease treatment resulted in a significant decline in agglutination by most of the lectins. Results of hapten inhibition studies demonstrated unique carbohydrate specificity of Fusarium lectins toward O-acetyl sialic acids. Activity of the majority of Fusarium lectins exhibited binding affinity to d-ribose, l-fucose, d-glucose, l-arabinose, d-mannitol, d-galactosamine hydrochloride, d-galacturonic acid, N-acetyl-d-galactosamine, N-acetyl-neuraminic acid, 2-deoxy-d-ribose, fetuin, asialofetuin, and bovine submaxillary mucin. Melibiose and N-glycolyl neuraminic acid did not inhibit the activity of any of the Fusarium lectins. Mycelial extracts of F. begoniae, F. nisikadoi, F. anthophilum, and F. incarnatum interacted with most of the carbohydrates tested. F. fujikuroi and F. anthophilum extracts displayed strong interaction with starch. The expression of lectin activity as a function of culture age was investigated. Most species displayed lectin activity on the 7th day of cultivation, and it varied with progressing of culture age.

  7. Molecular phylogeny of Ascotricha, including two new marine algae-associated species.

    PubMed

    Cheng, Xiaoli; Li, Wei; Cai, Lei

    2015-01-01

    Phylogenetic analyses based on a broad taxonomic sampling of Ascotricha were conducted using the sequences of nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS), partial nuc 18S rDNA (18S) and partial β-tubulin gene (TUB2). Hypoxyloid Xylariaceae and xylarioid Xylariaceae were inferred as two distinct lineages in the Xylariaceae in the combined ITS-TUB2 phylogeny. Within xylarioid Xylariaceae species of Ascotricha form a monophyletic group. Two new marine algae-associated fungi, Ascotricha longipila and A. parvispora, are described on the basis of morphological and molecular characters and the combination, A. sinuosa, is proposed. A synopsis of the morphological characters and a dichotomous key to Ascotricha species are provided.

  8. Morphological and molecular evidence for two new species of Laetiporus (Basidiomycota, Polyporales) from southwestern China.

    PubMed

    Song, Jie; Chen, Yuanyuan; Cui, Baokai; Liu, Honggao; Wang, Yuanzhong

    2014-01-01

    Two Laetiporus species, L. ailaoshanensis and L. zonatus spp. nov., are described from southwestern China based on morphological and molecular characters. Laetiporus ailaoshanensis is characterized by orange-yellow to reddish orange pileal surface and cream to buff pores when fresh, azonate to faintly zonate pileus, ovoid to ellipsoid basidiospores (5.0-6.2 × 4.0-5.0 μm), and it has been observed only on Lithocarpus. Laetiporus zonatus is characterized by white to cream pileal surface with buff to clay-buff base when fresh, concentrically zonate basidiocarps, ellipsoid to pyriform or drop-shaped basidiospores (5.8-7.2 × 4.3-5.5 μm), and it has been found only on Quercus. The phylogenetic relationships of all recognized Laetiporus species were inferred from a combined dataset of ITS and nLSU-rDNA sequences, and L. ailaoshanensis and L. zonatus represent two new lineages in this group.

  9. Development of a novel, simple and rapid molecular identification system for clinical Candida species.

    PubMed

    Deák, R; Bodai, L; Aarts, H J M; Maráz, A

    2004-08-01

    Identification of clinical yeast isolates causing candidiasis is routinely performed by commercial yeast identification systems based on biochemical, morphological and physiological tests. These systems require 3-5 days and the proportion of identifications that are incorrect is high. Our novel and rapid molecular identification system for clinical Candida species is based on the analysis of restriction patterns obtained from PCR-generated ribosomal DNA sequences using five restriction enzymes. A software package (CandID) was designed to include a database of restriction fragment length polymorphism (RFLP) patterns for 29 Candida species. For 'in-house' validation, 122 clinical isolates that had previously identified in clinical laboratories were typed by this system. These clinical isolates were also independently re-identified by the API 20C AUX system. The ribosomal DNA RFLP database in the context of supporting analytical software allowed simple and rapid (1 work day) identification.

  10. Molecular data for Crenavolva species (Gastropoda, Ovulidae) reveals the synonymy of C. chiapponii

    PubMed Central

    Reijnen, Bastian T.

    2015-01-01

    Abstract During fieldwork in Indonesia and Malaysia, eight lots containing 33 specimens belonging to the genus Crenavolva (Ovulidae) were collected. Species were initially identified as Crenavolva aureola, Crenavolva chiapponii, Crenavolva striatula and Crenavolva trailli, respectively. For Crenavolva chiapponii this is the second record. In contrast to the ecological data available from the original description of this species, it was found in shallow water on a gorgonian host coral, i.e. Acanthogorgia sp. A molecular analysis based on COI and 16S mtDNA markers, including sequence data obtained from GenBank, showed that Crenavolva chiapponii should be considered a junior synonym of Crenavolva aureola and that previously identified ovulid specimens are probably misidentified. PMID:25987877

  11. Improved ex vivo method for microbiocidal activity across vertebrate species

    PubMed Central

    French, Susannah S.; Neuman-Lee, Lorin A.

    2012-01-01

    Summary The field of ecoimmunology is currently undergoing rapid expansion, whereby biologists from a wide range of ecological disciplines are increasingly interested in assessing immunocompetence in their study organisms. One of the key challenges to researchers is determining what eco-immune measures to use in a given experiment. Moreover, there are limitations depending on study species, requirements for specific antibodies, and relevance of the methodology to the study organism. Here we introduce an improved ex vivo method for microbiocidal activity across vertebrate species. The utility of this assay is that it determines the ability of an organism to remove a pathogen that could be encountered in the wild, lending ecological relevancy to the technique. The applications of this microbiocidal assay are broad, as it is readily adaptable to different types of microbes as well as a wide variety of study species. We describe a method of microbiocidal analysis that will enable researchers across disciplines to effectively employ this method to accurately quantify microbial killing ability, using readily available microplate absorbance readers. PMID:23213440

  12. Anticancer activities of selected species of North American lichen extracts.

    PubMed

    Shrestha, Gajendra; El-Naggar, Atif M; St Clair, Larry L; O'Neill, Kim L

    2015-01-01

    Cancer is the second leading cause of human deaths in the USA. Despite continuous efforts to treat cancer over the past 50 years, human mortality rates have not decreased significantly. Natural products, such as lichens, have been good sources of anticancer drugs. This study reports the cytotoxic activity of crude extracts of 17 lichen species against Burkitt's lymphoma (Raji) cells. Out of the 17 lichen species, extracts from 14 species showed cytotoxicity against Raji cells. On the basis of IC50 values, we selected Xanthoparmelia chlorochroa and Tuckermannopsis ciliaris to study the mechanism of cell death. Viability of normal lymphocytes was not affected by the extracts of X. chlorochroa and T. ciliaris. We found that extracts from both lichens decreased proliferation, accumulated cells at the G0 /G1 stage, and caused apoptosis in a dose-dependent manner. Both lichen extracts also caused upregulation of p53. The T. ciliaris extract upregulated the expression of TK1 but X. chlorochroa did not. We also found that usnic, salazinic, constictic, and norstictic acids were present in the extract of X. chlorochroa, whereas protolichesterinic acid in T. ciliaris extracts. Our data demonstrate that lichen extracts merit further research as a potential source of anticancer drugs.

  13. Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales.

    PubMed

    Naushad, Hafiz Sohail; Gupta, Radhey S

    2013-01-01

    The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs) in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD) are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1-3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential targets

  14. Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

    PubMed Central

    Naushad, Hafiz Sohail; Gupta, Radhey S.

    2013-01-01

    The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs) in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD) are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1–3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential

  15. Putative hybrids between two Anisakis cryptic species: molecular genotyping using High Resolution Melting.

    PubMed

    Cavallero, S; Costa, A; Caracappa, S; Gambetta, B; D'Amelio, S

    2014-11-01

    The genus Anisakis includes nine recognized species and the complex of cryptic species Anisakis simplex s. l. is often associated with the human disease known as anisakiasis. During the last decades the use of nuclear ribosomal ITS allowed the identification and description of numerous anisakid nematodes and the discovery of recombinant genotypes or putative hybrids even in other parasitic helminths, such as those between A. simplex sensu stricto and A. pegreffii. The existence of pure hybrids of the two sibling species has been long debated due to the large recovery of larval forms from sympatric areas and the rare observation of adult hybrids. The aims of the present report were to identify anisakid nematodes collected from Stenella coeruleoalba using PCR-RFLP of ITS and to focus the interest on hybrid forms using a High Resolution Melting (HRM) and direct sequencing analyses, since the new record of putative hybrid at adult stage. The PCR-RFLP analysis enabled to identify A. simplex s.s., A. pegreffii, the heterozygous genotype of the two species and A. physeteris. The use of the genotyping approach based on HRM confirmed the profiles of the two species A. simplex s.s. and A. pegreffii, and of the hybrid individuals. The new record of adult hybrids in definitive hosts rekindles the long debate about their existence and their evolutionary meaning. Since the reproductive isolation between A. simplex s.s. and A. pegreffii is the assumption for their existence as separated species, the use of alternative molecular markers and population genetic studies on adult anisakids are recommended.

  16. Molecular Identification of Closely Related Candida Species Using Two Ribosomal Intergenic Spacer Fingerprinting Methods

    PubMed Central

    Cornet, Muriel; Sendid, Boualem; Fradin, Chantal; Gaillardin, Claude; Poulain, Daniel; Nguyen, Huu-Vang

    2011-01-01

    Recent changes in the epidemiology of candidiasis highlighted an increase in non- Candida albicans species emphasizing the need for reliable identification methods. Molecular diagnostics in fungal infections may improve species characterization, particularly in cases of the closely related species in the Candida complexes. We developed two PCR/restriction fragment length polymorphism assays, targeting either a part of the intergenic spacer 2 or the entire intergenic spacer (IGS) of ribosomal DNA using a panel of 270 isolates. A part of the intergenic spacer was used for discrimination between C. albicans and C. dubliniensis and between species of the C. glabrata complex (C. glabrata/C. bracarensis/C. nivariensis). The whole IGS was applied to C. parapsilosis, C. metapsilosis, and C. orthopsilosis, and to separate C. famata (Debaryomyces hansenii) from C. guilliermondii (Pichia guilliermondii) and from the other species within this complex (ie, C. carpophila, C. fermentati and C. xestobii). Sharing similar biochemical patterns, Pichia norvegensis and C. inconspicua exhibited specific IGS profiles. Our study confirmed that isolates of C. guilliermondii were frequently mis-identified as C. famata. As much as 67% of the clinical isolates phenotypically determined as C. famata were recognized mostly as true P. guilliermondii. Conversely, 44% of the isolates initially identified as C. guilliermondii were corrected by the IGS fingerprints as C. parapsilosis, C. fermentati, or C. zeylanoides. These two PCR/restriction fragment length polymorphism methods may be used as reference tools [either alternatively or adjunctively to the existing ribosomal DNA (26S or ITS) sequence comparisons] for unambiguous determination of the Candida species for which phenotypic characterization remains problematic. PMID:21227390

  17. 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

  18. Decolorization / deodorization of zein via activated carbons and molecular sieves

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective is to evaluate a series of granular media consisting of activated carbons and molecular sieves in a batch process for the purpose of clarifying and removal of color and odor components from yellow zein dispersed in an aqueous alcohol medium. The major contributors of yellow zein is du...

  19. Species-specific size expansion and molecular evolution of the oleosins in angiosperms.

    PubMed

    Liu, Qi; Sun, Yepeng; Su, Wujie; Yang, Jing; Liu, Xiuming; Wang, Yanfang; Wang, Fawei; Li, Haiyan; Li, Xiaokun

    2012-11-10

    Oleosins are hydrophobic plant proteins thought to be important for the formation of oil bodies, which supply energy for seed germination and subsequent seedling growth. To better understand the evolutionary history and diversity of the oleosin gene family in plants, especially angiosperms, we systematically investigated the molecular evolution of this family using eight representative angiosperm species. A total of 73 oleosin members were identified, with six members in each of four monocot species and a greater but variable number in the four eudicots. A phylogenetic analysis revealed that the angiosperm oleosin genes belonged to three monophyletic lineages. Species-specific gene duplications, caused mainly by segmental duplication, led to the great expansion of oleosin genes and occurred frequently in eudicots after the monocot-eudicot divergence. Functional divergence analyses indicate that significant amino acid site-specific selective constraints acted on the different clades of oleosins. Adaptive evolution analyses demonstrate that oleosin genes were subject to strong purifying selection after their species-specific duplications and that rapid evolution occurred with a high degree of evolutionary dynamics in the pollen-specific oleosin genes. In conclusion, this study serves as a foundation for genome-wide analyses of the oleosins. These findings provide insight into the function and evolution of this gene family in angiosperms and pave the way for studies in other plants.

  20. Diversity of Clonostachys species assessed by molecular phylogenetics and MALDI-TOF mass spectrometry.

    PubMed

    Abreu, Lucas M; Moreira, Gláucia M; Ferreira, Douglas; Rodrigues-Filho, Edson; Pfenning, Ludwig H

    2014-12-01

    We assessed the species diversity among 45 strains of Clonostachys from different substrates and localities in Brazil using molecular phylogenetics, and compared the results with the phenotypic classification of strains obtained from matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Phylogenetic analyses were based on beta tubulin (Tub), ITS-LSU rDNA, and a combined Tub-ITS DNA dataset. MALDI-TOF MS analyses were performed using intact conidia and conidiophores of strains cultivated on oatmeal agar and 4% malt extract agar. Six known species were identified: Clonostachys byssicola, Clonostachys candelabrum, Clonostachys pseudochroleuca, Clonostachys rhizophaga, Clonostachys rogersoniana, and Clonostachys rosea. Two clades and two singleton lineages did not correspond to known species represented in the reference DNA dataset and were identified as Clonostachys sp. 1-4. Multivariate cluster analyses of MALDI-TOF MS data classified the strains into eight clusters and three singletons, corresponding to the ten identified species plus one additional cluster containing two strains of C. rogersoniana that split from the other co-specific strains. The consistent results of MALDI-TOF MS supported the identification of strains assigned to C. byssicola and C. pseudochroleuca, which did not form well supported clades in all phylogenetic analyses, but formed distinct clusters in the MALDI-TOF dendrograms.

  1. Molecular Characterization of Cyclamen Species Collected from Different Parts of Turkey by RAPD and SRAP Markers.

    PubMed

    Simsek, Ozhan; Curuk, Pembe; Aslan, Fatma; Bayramoglu, Melda; Izgu, Tolga; da Silva, Jaime A Teixeira; Kacar, Yildiz Aka; Mendi, Yesim Yalcin

    2017-02-01

    The genus Cyclamen (family Myrsinaceae) contains about 20 species, most of which occur in the Mediterranean region. Turkey has critically important Cyclamen genetic resources. Molecular characterization of plant materials collected from different regions of Turkey in which Cyclamen species grow naturally, namely Adana, Antalya, Aydın, Muğla, İzmir, Denizli, Kahramanmaraş, Osmaniye, Eskişehir, Trabzon, and Rize provinces, was performed using RAPD and SRAP markers. DNA was successfully amplified by 30 RAPD primers and 14 SRAP primer pairs. Among the 470 bands generated by the RAPD primers, 467 were polymorphic. The number of bands detected by a single primer set ranged from 11 to 22 (average of 15.6). The percentage polymorphism was 99.3 % based on the RAPD data. In the SRAP analysis, a total of 216 bands were generated, showing 100 % polymorphism. The number of bands detected by a single primer set ranged from 9 to 22 (average of 15.4). All data were scored and UPGMA dendrograms were constructed with similar results in both marker systems, i.e., different species from nine provinces of Turkey were separated from each other in the dendrograms with the same species being clustered together.

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

    PubMed

    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.

  3. Molecular and morphological divergence in a pair of bird species and their ectoparasites.

    PubMed

    Whiteman, Noah K; Dosanjh, Vishal S; Palma, Ricardo L; Hull, Joshua M; Kimball, Rebecca T; Sánchez, Pablo; Sarasola, José Hernán; Parker, Patricia G

    2009-12-01

    In an evolutionary context, parasites tend to be morphologically conservative relative to their hosts. However, the rate of neutral molecular evolution across many parasite lineages is faster than in their hosts. Although this relationship is apparent at the macroevolutionary scale, insight into the processes underpinning it may be gained through investigations at the microevolutionary scale. Birds and their ectoparasitic lice have served as important natural experiments in co-evolution. Here, we compared mitochondrial and morphological divergence in 2 recently diverged avian host lineages and their parasites. Gálapagos hawks (Buteo galapagoensis) are phenotypically divergent from their closest mainland relatives, the Swainson's hawk (Buteo swainsoni). Both species are host to a feather louse species of Craspedorrhynchus (Insecta: Phthiraptera: Ischnocera, Philopteridae). We sequenced the 5′ end of the mitochondrial gene cytochrome oxidase c subunit I (COI) from a set of hawks and lice. Although this fragment allowed unambiguous identification of host and parasite lineages on the islands and the mainland, only a single variable site was present in the 2 hosts, but 2 major Craspedorrhynchus clades divergent by ~10% were recovered that sorted perfectly with host species. We found significant population genetic structure within the Galápagos Craspedorrhynchus lineage. While the host species are highly differentiated phenotypically, the 2 Craspedorrhynchus louse lineages are phenotypically overlapping, although subtle but significant morphological differences exist.

  4. Molecular Diagnosis and Identification of Leishmania Species in Jordan from Saved Dry Samples

    PubMed Central

    Hijjawi, Nawal; Kanani, Kalil A.; Rasheed, Malak; Atoum, Manar; Abdel-Dayem, Mona; Irhimeh, Mohammad R.

    2016-01-01

    Diagnosis of the endemic cutaneous leishmaniasis (CL) in Jordan relies on patient clinical presentation and microscopic identification. Studies toward improved identification of the causative Leishmania species, especially in regions where multiple species exist, and the introduction of these techniques into medical diagnosis is paramount. This study looked at the current epidemiology of CL in Jordan. Clinically diagnosed 41 patients with CL were tested for the presence of Leishmania parasite using both Giemsa staining from skin scraps on glass slides and ITS1-PCR from samples blotted onto storage cards (NucleoCards®). Microscopically, 28 out of the 41 (68.3%) collected samples were positive for amastigotes, whereas the molecular ITS1-PCR amplification successfully identified 30 of the 41 samples (73.2%). Furthermore, PCR-RFLP analysis allowed species identification which is impossible microscopically. Of the 30 PCR positive samples, 28 were Leishmania major positive and the other two samples were Leishmania tropica. This indicates that L. major is the most prevalent species in Jordan and the two L. tropica cases originated from Syria indicating possible future L. tropica outbreaks. Diagnosis of CL based on clinical presentation only may falsely increase its prevalence. Although PCR is more sensitive, it is still not available in our medical laboratories in Jordan. PMID:27403435

  5. Morphological and molecular variation in Tylototriton (Caudata: Salamandridae) in Laos, with description of a new species.

    PubMed

    Phimmachak, Somphouthone; Aowphol, Anchalee; Stuart, Bryan L

    2015-08-24

    The salamandrid genus Tylototriton is poorly known in Laos, with one described species and unverified reports of two others. We undertook new fieldwork and obtained samples of Tylototriton at six localities across northern Laos during 2009-2013. Bayesian phylogenetic analysis of mitochondrial DNA, principal component analyses of 13 mensural characters, and qualitative morphological comparisons with samples from across the geographic range of Tylototriton were performed. Samples from Laos fell into four molecular and morphological groups, consisting of T. notialis, T. panhai, T. anguliceps, and a fourth lineage that is hypothesized here to be an undescribed species. Tylototriton podichthys sp. nov. is distinguished from its congeners by having distinct mitochondrial DNA haplotypes and in characteristics of the glandular skin on the head and body, shape of the rib nodules, and coloration of the body and limbs. This study expands the number of confirmed Tylototriton species in Laos from one to four, with the description of one species and extension of the ranges of T. panhai and T. anguliceps to Laos. An improved understanding of the geographic ranges of T. podichthys sp. nov. and T. anguliceps within Laos is needed.

  6. ALV-J GP37 molecular analysis reveals novel virus-adapted sites and three tyrosine-based Env species.

    PubMed

    Ye, Jianqiang; Fan, Zhonglei; Shang, Jianjun; Tian, Xiaoyan; Yang, Jialiang; Chen, Hongjun; Shao, Hongxia; Qin, Aijian

    2015-01-01

    Compared to other avian leukosis viruses (ALV), ALV-J primarily induces myeloid leukemia and hemangioma and causes significant economic loss for the poultry industry. The ALV-J Env protein is hypothesized to be related to its unique pathogenesis. However, the molecular determinants of Env for ALV-J pathogenesis are unclear. In this study, we compared and analyzed GP37 of ALV-J Env and the EAV-HP sequence, which has high homology to that of ALV-J Env. Phylogenetic analysis revealed five groups of ALV-J GP37 and two novel ALV-J Envs with endemic GP85 and EAV-HP-like GP37. Furthermore, at least 15 virus-adapted mutations were detected in GP37 compared to the EAV-HP sequence. Further analysis demonstrated that three tyrosine-based motifs (YxxM, ITIM (immune tyrosine-based inhibitory motif) and ITAM-like (immune tyrosine-based active motif like)) associated with immune disease and oncogenesis were found in the cytoplasmic tail of GP37. Based on the potential function and distribution of these motifs in GP37, ALV-J Env was grouped into three species, inhibitory Env, bifunctional Env and active Env. Accordingly, 36.91%, 61.74% and 1.34% of ALV-J Env sequences from GenBank are classified as inhibitory, bifunctional and active Env, respectively. Additionally, the Env of the ALV-J prototype strain, HPRS-103, and 17 of 18 EAV-HP sequences belong to the inhibitory Env. And models for signal transduction of the three ALV-J Env species were predicted. Our findings and models provide novel insights for identifying the roles and molecular mechanism of ALV-J Env in the unique pathogenesis of ALV-J.

  7. Molecular detection and species identification of Alexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline

    PubMed Central

    Jedlicki, Ana; Fernández, Gonzalo; Astorga, Marcela; Oyarzún, Pablo; Toro, Jorge E.; Navarro, Jorge M.; Martínez, Víctor

    2012-01-01

    Background and aims On the basis of morphological evidence, the species involved in South American Pacific coast harmful algal blooms (HABs) has been traditionally recognized as Alexandrium catenella (Dinophyceae). However, these observations have not been confirmed using evidence based on genomic sequence variability. Our principal objective was to accurately determine the species of Alexandrium involved in local HABs in order to implement a real-time polymerase chain reaction (PCR) assay for its rapid and easy detection on filter-feeding shellfish, such as mussels. Methodology For species-specific determination, the intergenic spacer 1 (ITS1), 5.8S subunit, ITS2 and the hypervariable genomic regions D1–D5 of the large ribosomal subunit of local strains were sequenced and compared with two data sets of other Alexandrium sequences. Species-specific primers were used to amplify signature sequences within the genomic DNA of the studied species by conventional and real-time PCR. Principal results Phylogenetic analysis determined that the Chilean strain falls into Group I of the tamarensis complex. Our results support the allocation of the Chilean Alexandrium species as a toxic Alexandrium tamarense rather than A. catenella, as currently defined. Once local species were determined to belong to Group I of the tamarensis complex, a highly sensitive and accurate real-time PCR procedure was developed to detect dinoflagellate presence in Mytilus spp. (Bivalvia) samples after being fed (challenged) in vitro with the Chilean Alexandrium strain. The results show that real-time PCR is useful to detect Alexandrium intake in filter-feeding molluscs. Conclusions It has been shown that the classification of local Alexandrium using morphological evidence is not very accurate. Molecular methods enabled the HAB dinoflagellate species of the Chilean coast to be assigned as A. tamarense rather than A. catenella. Real-time PCR analysis based on A. tamarense primers allowed the

  8. Reactive oxygen species-activated nanomaterials as theranostic agents

    PubMed Central

    Kim, Kye S; Lee, Dongwon; Song, Chul Gyu; Kang, Peter M

    2015-01-01

    Reactive oxygen species (ROS) are generated from the endogenous oxidative metabolism or from exogenous pro-oxidant exposure. Oxidative stress occurs when there is excessive production of ROS, outweighing the antioxidant defense mechanisms which may lead to disease states. Hydrogen peroxide (H2O2) is one of the most abundant and stable forms of ROS, implicated in inflammation, cellular dysfunction and apoptosis, which ultimately lead to tissue and organ damage. This review is an overview of the role of ROS in different diseases. We will also examine ROS-activated nanomaterials with emphasis on hydrogen peroxide, and their potential medical implications. Further development of the biocompatible, stimuli-activated agent responding to disease causing oxidative stress, may lead to a promising clinical use. PMID:26328770

  9. ALDH2 Mediates 5-Nitrofuran Activity in Multiple Species

    PubMed Central

    Zhou, Linna; Ishizaki, Hironori; Spitzer, Michaela; Taylor, Kerrie L.; Temperley, Nicholas D.; Johnson, Stephen L.; Brear, Paul; Gautier, Philippe; Zeng, Zhiqiang; Mitchell, Amy; Narayan, Vikram; McNeil, Ewan M.; Melton, David W.; Smith, Terry K.; Tyers, Mike; Westwood, Nicholas J.; Patton, E. Elizabeth

    2012-01-01

    Summary Understanding how drugs work in vivo is critical for drug design and for maximizing the potential of currently available drugs. 5-nitrofurans are a class of prodrugs widely used to treat bacterial and trypanosome infections, but despite relative specificity, 5-nitrofurans often cause serious toxic side effects in people. Here, we use yeast and zebrafish, as well as human in vitro systems, to assess the biological activity of 5-nitrofurans, and we identify a conserved interaction between aldehyde dehydrogenase (ALDH) 2 and 5-nitrofurans across these species. In addition, we show that the activity of nifurtimox, a 5-nitrofuran anti-trypanosome prodrug, is dependent on zebrafish Aldh2 and is a substrate for human ALDH2. This study reveals a conserved and biologically relevant ALDH2-5-nitrofuran interaction that may have important implications for managing the toxicity of 5-nitrofuran treatment. PMID:22840776

  10. Morphological redescription and molecular characterization of three species of Travassosinematidae (Nematoda: Oxyurida: Thelastomatoidea) from Gryllotalpa africana Beauv (Orthoptera: Gryllotalpidae).

    PubMed

    Singh, Neetu; Chaudhary, Anshu; Singh, Hridaya Shanker

    2013-01-01

    Binema mirzaia (Basir, 1942a) Basir, 1956, Cameronia nisari (Parveen and Jairajpuri, 1985) Adamson and Van Waerebeke, 1992a and Mirzaiella meerutensis Singh and Malti, 2003 are redescribed morphologically along with molecular identification from the intestine of mole cricket Gryllotalpa africana. Molecular characterization was carried out using the D2-D3 expansion domains of the 18S ribosomal DNA region. This study first time presents molecular data for the above three nematode species.

  11. 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).

  12. Molecular phylogeny and biogeography of the widely distributed Amanita species, A. muscaria and A. pantherina.

    PubMed

    Oda, Takashi; Tanaka, Chihiro; Tsuda, Mitsuya

    2004-08-01

    The molecular phylogeny and biogeography of two widely distributed Amanita species, A. muscaria and A. pantherina, were studied based on specimens from diverse localities. Analyses of both a partial sequence of the ITS region of nuclear DNA and a partial sequence of the beta-tubulin gene were able to resolve specimens of each species. Analyses revealed a greater divergence of the beta-tubulin region than the ITS region. Based on molecular phylogeny of the combination of the ITS and beta-tubulin regions, A. muscaria could be separated into at least three groups (Eurasian, Eurasian subalpine, and North American), and A. pantherina could be separated into at least two groups (North American and Eurasian). We hypothesize that the speciation of A. muscaria occurred in Eurasia with subsequent migration to North America via land bridges. However, it is impossible to determine whether A. pantherina moved from Eurasia to North America or vice versa. For both A. muscaria and A. pantherina, the intracontinental relationships of both Eurasia and North America were closer than the relationships between eastern Asia and eastern North America.

  13. 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.

  14. Molecular Identification of Mucor and Lichtheimia Species in Pure Cultures of Zygomycetes

    PubMed Central

    Ziaee, Ardeshir; Zia, Mohammadali; Bayat, Mansour; Hashemi, Jamal

    2016-01-01

    Background The Mucorales are an important opportunistic fungi that can cause mucormycosis in immunocompromised patients. The fast and precise diagnosis of mucormycosis is very important because, if the diagnosis is not made early enough, dissemination often occurs. It is now well established that molecular methods such as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) are feasible and reliable tools for the early and accurate diagnosis of mucormycosis agents. Objectives The present study was conducted to evaluate the validity of PCR-RFLP for the identification of Mucorales and some important Mucor and Lichtheimia species in pure cultures of Zygomycetes. Materials and Methods Specific sense and anti-sense primers were used to amplify the Mucorales, Mucor, and Lichtheimia DNA. The PCR products were digested by AfIII, XmnI, and AcII restriction enzymes, and the resultant restriction pattern was analyzed. Results On the basis of the molecular and morphological data, we identified Mucor plumbeus (10.83%), M. circinelloides (9.17%), Lichtheimia corymbifera (9.17%), M. racemosus (5.83%), M. ramosissimus (3.33%), and L. blakesleeana (0.83%). Conclusions It seems that PCR-RFLP is a suitable technique for the identification of Mucorales at the species level. PMID:27284399

  15. 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

  16. Two known and one new species of Proctoeces from Australian teleosts: Variable host-specificity for closely related species identified through multi-locus molecular data.

    PubMed

    Wee, Nicholas Q-X; Cribb, Thomas H; Bray, Rodney A; Cutmore, Scott C

    2017-04-01

    Species of Proctoeces Odhner, 1911 (Trematoda: Fellodistomidae) have been reported from a wide range of marine animals globally. Members of the genus tend to lack strongly distinguishing morphological features for diagnosis, making identification difficult and the true number of species in the genus contentious. Combined morphological and molecular analyses were used to characterise three species of Proctoeces from Moreton Bay and the southern Great Barrier Reef. Data for two ribosomal regions and one mitochondrial region were generated for specimens collected from Australia. Three unique 18S-genotypes were identified which corresponded to subtle, but reliable, morphological differences. Two species of Proctoeces were identified from fishes of Moreton Bay, Proctoeces insolitus (Nicoll, 1915) Yamaguti, 1953 and P. major Yamaguti, 1934, and a third, P. choerodoni n. sp. from off Heron Island on the southern Great Barrier Reef. Phylogenetic analyses of partial 18S and partial 28S rDNA indicated that these three species differ from the four species reported outside of Australia for which sequence data are available. Phylogenetically, Proctoeces proved to be a reliable concept, with all species of Proctoeces that have been characterised genetically forming a well-supported clade in all analyses. Dramatically different patterns of host-specificity were identified for each of the three Australian species; P. insolitus apparently infects a single species of fish, P. choerodoni n. sp. infects multiple species of a single genus of fish, and P. major infects multiple species of two teleost orders.

  17. Hydrazide derivatives produce active oxygen species as hydrazine.

    PubMed

    Timperio, Anna Maria; Rinalducci, Sara; Zolla, Lello

    2005-12-01

    It is well documented that some hydrazines are quite sensitive to oxidation and may serve as the electron donor for the reduction of oxygen, whereas hydrazides are not believed to react directly with oxygen. Data presented in this paper show that both hydrazides and hydrazines share an N-N moiety, which is assumed to react with atmospheric oxygen and produce oxygen radicals, at various degrees of efficiency. Since spectrometric measurements of hydrazide just after solubilization showed that the molecular mass remains constant in the absence of oxygen, we can conclude that hydrazides do not react with the oxygen through a slow spontaneous hydrolytic release of hydrazine. However, hydrazine is more reactive than hydrazide, which requires hours rather than minutes to produce measurable quantities of radical species. Differences were also apparent for various substituted derivatives. The reaction was significantly enhanced by the presence of metal ions. Data reported here demonstrate that hydrazides cause irreversible damage to the prosthetic group of proteins as well as causing degradation of the polypeptide chain into small fragments.

  18. Anticholinesterase and Antityrosinase Activities of Ten Piper Species from Malaysia

    PubMed Central

    Salleh, Wan Mohd Nuzul Hakimi Wan; Hashim, Nur Athirah; Ahmad, Farediah; Heng Yen, Khong

    2014-01-01

    Purpose: The aim of this study was to investigate acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and antityrosinase activities of extracts from ten Piper species namely; P. caninum, P. lanatum, P. abbreviatum, P. aborescens, P. porphyrophyllum, P. erecticaule, P. ribesioides, P. miniatum, P. stylosum, and P. majusculum. Methods: Anticholinesterase and antityrosinase activities were evaluated against in vitro Ellman spectroscopy method and mushroom tyrosinase, respectively. Results: The EtOAc extract of P. erecticaule showed the highest AChE and BChE inhibitory with 22.9% and 70.9% inhibition, respectively. In antityrosinase activity, all extracts of P. porphyrophyllum showed the highest inhibitory effects against mushroom tyrosinase, compared to standard, kojic acid. Conclusion: This study showed that P. erecticaule and P. porphyrophyllum have potential AChE/BChE and tyrosinase inhibition activities. The respective extracts can be explored further for the development of novel lead as AChE/BChE and tyrosinase inhibitors in therapeutic management of Alzheimer’s disease. PMID:25671185

  19. Sarcocystis in moose (Alces alces): molecular identification and phylogeny of six Sarcocystis species in moose, and a morphological description of three new species.

    PubMed

    Dahlgren, Stina S; Gjerde, Bjørn

    2008-06-01

    Muscle tissues from 34 moose from Southeastern Norway and two moose from Canada were examined. Sarcocysts were excised and morphologically classified by light microscopy, and some cysts were further examined by scanning electron microscopy or DNA amplification and sequencing at the small subunit (ssu) rRNA gene. In Norwegian moose, three sarcocyst types were recognized, yet five Sarcocystis species were found by sequence analysis. New names were proposed for three species which could be characterised by both morphological and molecular methods, i.e., Sarcocystis alces, Sarcocystis ovalis, and Sarcocystis scandinavica. S. alces was the most prevalent species, whereas S. scandinavica and the two unnamed species were rare and might either use another principal intermediate host or a rare definitive host. The five species in Norwegian moose were different from Sarcocystis alceslatrans isolated from a Canadian moose. Phylogenetic analyses based on complete ssu rRNA gene sequences revealed a close relationship between the six Sarcocystis species from moose and species from reindeer and Sika deer. We conclude that molecular methods are necessary for unequivocal species identification, as different cervid hosts harbour morphologically indistinguishable sarcocysts.

  20. 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

  1. Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies.

    PubMed

    Steiner, Cynthia C; Mitelberg, Anna; Tursi, Rosanna; Ryder, Oliver A

    2012-11-01

    Short divergence times and processes such as incomplete lineage sorting and species hybridization are known to hinder the inference of species-level phylogenies due to the lack of sufficient informative genetic variation or the presence of shared but incongruent polymorphism among taxa. Extant equids (horses, zebras, and asses) are an example of a recently evolved group of mammals with an unresolved phylogeny, despite a large number of molecular studies. Previous surveys have proposed trees with rather poorly supported nodes, and the bias caused by genetic introgression or ancestral polymorphism has not been assessed. Here we studied the phylogenetic relationships of all extant species of Equidae by analyzing 22 partial mitochondrial and nuclear genes using maximum likelihood and Bayesian inferences that account for heterogeneous gene histories. We also examined genetic signatures of lineage sorting and/or genetic introgression in zebras by evaluating patterns of intraspecific genetic variation. Our study improved the resolution and support of the Equus phylogeny and in particular the controversial positions of the African wild ass (E. asinus) and mountain zebra (E. zebra): the African wild ass is placed as a sister species of the Asiatic asses and the mountain zebra as the sister taxon of Grevy's and Burchell's zebras. A shared polymorphism (indel) detected among zebra species in the Estrogen receptor 1 gene was likely due to incomplete lineage sorting and not genetic introgression as also indicated by other mitochondrial (Cytochrome b) and nuclear (Y chromosome and microsatellites) markers. Ancestral polymorphism in equids might have contributed to the long-standing lack of clarity in the phylogeny of this highly threatened group of mammals.

  2. 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.

  3. 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.

  4. A simplified molecular method for distinguishing among species and ploidy levels in European water frogs (Pelophylax).

    PubMed

    Hauswaldt, J Susanne; Höer, Manuela; Ogielska, Maria; Christiansen, Ditte G; Dziewulska-Szwajkowska, Daria; Czernicka, Elżbieta; Vences, Miguel

    2012-09-01

    Western Palearctic water frogs in the genus Pelophylax are a set of morphologically similar anuran species that form hybridogenetic complexes. Fully reliable identification of species and especially of hybrid ploidy depends on karyological and molecular methods. In central Europe, native water frog populations consist of the Pelophylax esculentus complex, that is, P. lessonae (LL), P. ridibundus (RR) and the hybrid form P. esculentus that can have different karyotypes (RL, LLR and RRL). We developed existing molecular methods further and propose a simple PCR method based on size-differences in the length of the serum albumin intron-1 and the RanaCR1, a non-LTR retrotransposon of the chicken repeat (CR) family. This PCR yields taxon-specific banding patterns that can easily be screened by standard agarose gel electrophoresis and correctly identify species in all of the 160 samples that had been identified to karyotype with other methods. To distinguish ploidy levels in LR, LLR and RRL specimens, we used the ratio of the peak heights of the larger (ridibundus specific) to the smaller (lessonae specific) bands of fluorescently labelled PCR products resolved on a capillary DNA sequencer and obtained a correct assignment of the karyotype in 93% of cases. Our new method will cut down time and expenses drastically for a reliable identification of water frogs of the P. esculentus complex and potentially for identification of other hybridogenetic complexes and/or taxa, and it even serves as a good indicator of the ploidy status of hybrid individuals.

  5. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers

    PubMed Central

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  6. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    PubMed

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil.

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

    PubMed

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

    2012-01-01

    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.

  8. 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

  9. Electrospray Ionization Tandem Mass Spectrometry (Esi-Ms/Ms) Analysis of the Lipid Molecular Species Composition of Yeast Subcellular Membranes Reveals Acyl Chain-Based Sorting/Remodeling of Distinct Molecular Species En Route to the Plasma Membrane

    PubMed Central

    Schneiter, Roger; Brügger, Britta; Sandhoff, Roger; Zellnig, Günther; Leber, Andrea; Lampl, Manfred; Athenstaedt, Karin; Hrastnik, Claudia; Eder, Sandra; Daum, Günther; Paltauf, Fritz; Wieland, Felix T.; Kohlwein, Sepp D.

    1999-01-01

    Nano-electrospray ionization tandem mass spectrometry (nano-ESI-MS/MS) was employed to determine qualitative differences in the lipid molecular species composition of a comprehensive set of organellar membranes, isolated from a single culture of Saccharomyces cerevisiae cells. Remarkable differences in the acyl chain composition of biosynthetically related phospholipid classes were observed. Acyl chain saturation was lowest in phosphatidylcholine (15.4%) and phosphatidylethanolamine (PE; 16.2%), followed by phosphatidylserine (PS; 29.4%), and highest in phosphatidylinositol (53.1%). The lipid molecular species profiles of the various membranes were generally similar, with a deviation from a calculated average profile of ∼± 20%. Nevertheless, clear distinctions between the molecular species profiles of different membranes were observed, suggesting that lipid sorting mechanisms are operating at the level of individual molecular species to maintain the specific lipid composition of a given membrane. Most notably, the plasma membrane is enriched in saturated species of PS and PE. The nature of the sorting mechanism that determines the lipid composition of the plasma membrane was investigated further. The accumulation of monounsaturated species of PS at the expense of diunsaturated species in the plasma membrane of wild-type cells was reversed in elo3Δ mutant cells, which synthesize C24 fatty acid-substituted sphingolipids instead of the normal C26 fatty acid-substituted species. This observation suggests that acyl chain-based sorting and/or remodeling mechanisms are operating to maintain the specific lipid molecular species composition of the yeast plasma membrane. PMID:10459010

  10. Molecular characterization of patulin producing and non-producing Penicillium species in apples from Morocco.

    PubMed

    Rharmitt, Sanae; Hafidi, Majida; Hajjaj, Hassan; Scordino, Fabio; Giosa, Domenico; Giuffrè, Letterio; Barreca, Davide; Criseo, Giuseppe; Romeo, Orazio

    2016-01-18

    The isolation of patulin-producing Penicillia in apples collected in different markets in four localities in Morocco is reported. Fungi were identified by β-tubulin sequencing and further characterized using a specific PCR-based method targeting the isoepoxydon dehydrogenase (IDH) gene to discriminate between patulin-producing and non-producing strains. Production of patulin was also evaluated using standard cultural and biochemical methods. Results showed that 79.5% of contaminant fungi belonged to the genus Penicillium and that Penicillium expansum was the most isolated species (83.9%) followed by Penicillium chrysogenum (~9.7%) and Penicillium crustosum (~6.4%). Molecular analysis revealed that 64.5% of the Penicillium species produced the expected IDH-amplicon denoting patulin production in these strains. However, patulin production was not chemically confirmed in all P. expansum strains. The isolation of IDH(-)/patulin(+) strains poses the hypothesis that gentisylaldehyde is not a direct patulin precursor, supporting previous observations that highlighted the importance of the gentisyl alcohol in the production of this mycotoxin. Total agreement between IDH-gene detection and cultural/chemical methods employed was observed in 58% of P. expansum strains and for 100% of the other species isolated. Overall the data reported here showed a substantial genetic variability within P. expansum population from Morocco.

  11. 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.

  12. Morphological and Molecular Discrimination of Fasciola Species Isolated From Domestic Ruminants of Urmia City, Iran

    PubMed Central

    YAKHCHALI, Mohammad; MALEKZADEH-VIAYEH, Reza; IMANI-BARAN, Abbas; MARDANI, Karim

    2015-01-01

    Background: The trematodes of the genus Fasciola (the liver flukes) are among the well-known instances of food-borne parasites worldwide. Differentiation of Fasciola species is important because of their different transmission and epidemiological characteristics. The current study was undertaken to discriminate Fasciola species in the domestic ruminants of Urmia city, Iran. Methods: Adult flukes were isolated from the naturally infected livers of the slaughtered water buffaloes and sheep. The flukes were initially identified based on morphological and morphometric parameters. A 618-bp-long fragment of the 28SrRNA gene of Fasciola was amplified by polymerase chain reaction (PCR). The amplified fragment was digested by DraII or AvaII enzymes for a restriction fragment length polymorphism (RFLP) analysis and sequenced for the phylogenetic tree construction. Results: Based on the morphometric examination, the flukes belonged to F. hepatica, F. gigantica and an intermediate Fasciola form. The PCR-RFLP analysis was able to differentiate F. hepatica from F. gigantica. While the phylogenetic reconstruction justified, to some extent, the morphological diagnosis, it failed to segregate F. hepatica from F. gigantica identified in this and the previous studies. Conclusion: To resolve fully the problem of taxonomy and evolution in Fasciola species, employing a broad range of molecular and morphological approaches is necessary. This is crucial for epidemiological surveys and successful clinical management of their infection. PMID:25904945

  13. Molecular detection of Rickettsia species in Amblyomma ticks collected from snakes in Thailand.

    PubMed

    Sumrandee, Chalao; Hirunkanokpun, Supanee; Doornbos, Kathryn; Kitthawee, Sangvorn; Baimai, Visut; Grubhoffer, Libor; Trinachartvanit, Wachareeporn; Ahantarig, Arunee

    2014-10-01

    Some reptile ticks are potential vectors of pathogens such as spotted fever group (SFG) rickettsiae. Here, we report for the first time in detail the molecular evidence, DNA sequences and phylogenetic studies, for the presence of Rickettsia spp. in Amblyomma ticks (Amblyomma helvolum and Amblyomma varanense) from snakes in Thailand. A total of 24 tick samples was collected from 4 snake species and identified. A phylogenetic analysis inferred from the partial sequences of the gltA gene indicated that the Rickettsia spp. from 2 Amblyomma helvolum and 1 Amblyomma varanense belong to the same group as the SFG rickettsiae, which are closely related to Rickettsia raoultii strains. In contrast, there was 1 Rickettsia sp. from Amblyomma helvolum grouped into the same clade with other SFG rickettsiae (Rickettsia tamurae, Rickettsia monacensis, and a Rickettsia endosymbiont of Amblyomma dubitatum from Brazil). However, another Rickettsia sp. from Amblyomma varanense was closely related to Rickettsia bellii and Rickettsia sp. strain RDa420 from Thailand. In addition, from phylogenetic results based on the 16S rRNA gene and a concatenated tree of the 3 genes (gltA, ompA, and ompB), we found what may be a novel SFG rickettsia species closely related to Rickettsia raoultii (from both Amblyomma varanense and Amblyomma helvolum). In conclusion, our findings are the first report on the presence of novel SFG rickettsiae in 2 snake tick species, Amblyomma varanense and Amblyomma helvolum in Thailand and in south-eastern Asia.

  14. Morphological and molecular characterization of Endophyllum species on perennial asteraceous plants in South Africa.

    PubMed

    Wood, Alan R; Crous, Pedro W

    2005-04-01

    Endophyllum osteospermi is an autoecious, endocyclic rust fungus, which has only been recorded on Chrysanthemoides monilifera ssp. monilifera (Asteraceae, Calendulae), a perennial woody shrub. Both organisms are indigenous to South Africa. Because E. osteospermi is being considered for release in Australia as a biocontrol agent against C. monilifera ssp. monilifera, it was necessary to determine its host range and natural distribution in South Africa. To address this, natural stands of Chrysanthemoides species, as well as other South African asteraceous plants, were monitored for E. osteospermi between 1992 and 2003. A morphological and molecular comparison of specimens referable to Endophyllum was undertaken. Based on these results, E. osteospermi was recorded on C. monilifera sspp. monilifera, pisifera, rotundata, canescens, and subcanescens, C. incana, and an undescribed taxon. E. osteospermi was also recorded on Osteospermum ciliatum, O. pollgaloides, and O. potbergense. Furthermore, a closely related but previously undescribed species, E. dimorphothecae sp. nov. is described on Dimorphotheca cuneata. Aecidium elytropappi is transferred to Endophyllum as E. elytropappi comb. nov., being recorded on Elytropappus rhinocerostis and Stoebe plumosa. This study shows that in South Africa E. osteospermi is restricted to a small group of related plant species in the Calenduleae. This rust is therefore considered suitable as a candidate agent for the biocontrol of C. monilifera ssp. monilifera, and pending the results of host specificity testing, would most likely be safe to introduce into Australia.

  15. In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations

    PubMed Central

    Bhardwaj, Archana; Dhar, Yogeshwar Vikram; Asif, Mehar Hasan; Bag, Sumit K

    2016-01-01

    Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases. Out of these, 1838 SNPs were non-synonymous and distributed in 988 protein coding genes. Among these, 23 genes containing 96 SNPs were involved in traits markedly different between the two species. Furthermore, there were 28 deleterious SNPs distributed in 27 genes and a few of these genes were involved in plant pathogen interaction and plant hormone pathways. Molecular docking and simulations of several selected proteins showed the effect of SNPs in terms of compactness, conformation and interaction ability. Observed SNPs exhibited various types of motif binding effects due to nucleotide changes. SNPs that provide the evidence of differential motif binding and interaction behaviour could be effectively used for the crop improvement program. PMID:27929054

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

    PubMed

    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.

  17. Species identification of Mycobacterium avium complex isolates by a variety of molecular techniques.

    PubMed

    Beggs, M L; Stevanova, R; Eisenach, K D

    2000-02-01

    Organisms in the Mycobacterium avium complex (MAC; M. avium, M. intracellulare, and "nonspecific or X" MAC) are emerging pathogens among individual organisms of which significant genetic variability is displayed. The objective of the present study was to evaluate various molecular methods for the rapid and definitive identification of MAC species. Isolates were obtained from both human immunodeficiency virus (HIV)-positive patients and HIV-negative patients with and without known predisposing conditions. The isolates were initially hybridized with nucleic acid probes complementary to the rRNA of the respective mycobacterial species (AccuProbe Culture Confirmation kits for M. avium, M. intracellulare, and MAC species; Gen-Probe). Isolates were also examined by PCR and in some cases by Southern blot hybridization for the insertion element IS1245. Two other techniques included a PCR assay that amplifies the mig gene, a putative virulence factor for MAC, and hsp65 gene amplification and sequencing. This study led to the following observations. Eighty-five percent of the isolates from HIV-positive patients were M. avium and 86% of the isolates from HIV-negative patients were M. intracellulare. Fifteen of the M. avium isolates did not contain IS1245 and 7% of the M. intracellulare isolates were found to carry IS1245. All of the M. avium strains were mig positive, and all of the M. intracellulare strains were mig negative.

  18. Morphological and molecular characterisation of Diaporthe species associated with grapevine trunk disease in China.

    PubMed

    Dissanayake, Asha J; Liu, Mei; Zhang, Wei; Chen, Zhen; Udayanga, Dhanushka; Chukeatirote, Ekachai; Li, XingHong; Yan, JiYe; Hyde, Kevin D

    2015-05-01

    Trunk diseases in grapevine (Vitis spp.) are major problems in the wine and table-grape industries reducing the productivity, quality and longevity of vineyards. Species of Diaporthe are important fungal pathogens of grapevine trunk disease worldwide. A survey of 14 grape vineyards located in different provinces of China was yielded Diaporthe isolates associated with symptomatic grapevine wood. These isolates were identified based on morphology and a combined data matrix of rDNA ITS, partial sequences of translation elongation factor 1-α (EF 1-α), β-tubulin (TUB) and calmodulin (CAL) gene regions. Four species of Diaporthe were identified, which included Diaporthe eres, Diaporthe hongkongensis, Diaporthe phaseolorum and Diaporthe sojae. All isolates of Diaporthe caused disease on detached grape shoots in pathogenicity experiments but differed in virulence. The incidence in local vineyards and the pathogenicity results indicate that D. eres is an important pathogen of grapevine in Chinese vineyards, where it may significantly limit grape production. This is the first detailed report of Diaporthe species associated with grapevine trunk diseases in China with morphology, pathogenicity and molecular data.

  19. 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

  20. 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.

  1. Investigation of the local structure of mixtures of an ionic liquid with polar molecular species through molecular dynamics: cluster formation and angular distributions.

    PubMed

    Carrete, Jesús; Méndez-Morales, Trinidad; Cabeza, Óscar; Lynden-Bell, Ruth M; Gallego, Luis J; Varela, Luis M

    2012-05-24

    In this work, we used molecular dynamics simulations to analyze in detail the spatial distributions of the different constituents in mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate with three polar molecular species: water and two alcohols of different chain lengths (methanol and ethanol). In particular, we report results regarding the influence of the chosen species and its concentration on the formation of ionic and molecular clusters over the whole miscibility range, as well as on the angular distribution of polar molecules around the anion and the cation in these systems. Both analyses showed that addition of a molecular species breaks down the polar network of the pure ionic liquid in clusters whose mean size decreases progressively as more molecules are added. At very high concentrations of the molecular species, the ions are found to be isolated in mixtures with water and methanol, but they tend to form pairs in ethanol. In mixtures with water we identified large clusters that form a water network at very high water concentrations, while at low water concentrations polar molecules tend to form smaller aggregates. In contrast, in mixtures with alkanols there is no evidence of the formation of large alcohol clusters at any concentration. Spatial order in alcohol was also studied by means of the Kirkwood G factor, reaching the conclusion that the angular correlations which appear in pure alcohols due to dipole interactions are destroyed by the ionic liquid, even when present only in tiny amounts.

  2. Biological spectra analysis: Linking biological activity profiles to molecular structure

    PubMed Central

    Fliri, Anton F.; Loging, William T.; Thadeio, Peter F.; Volkmann, Robert A.

    2005-01-01

    Establishing quantitative relationships between molecular structure and broad biological effects has been a longstanding challenge in science. Currently, no method exists for forecasting broad biological activity profiles of medicinal agents even within narrow boundaries of structurally similar molecules. Starting from the premise that biological activity results from the capacity of small organic molecules to modulate the activity of the proteome, we set out to investigate whether descriptor sets could be developed for measuring and quantifying this molecular property. Using a 1,567-compound database, we show that percent inhibition values, determined at single high drug concentration in a battery of in vitro assays representing a cross section of the proteome, provide precise molecular property descriptors that identify the structure of molecules. When broad biological activity of molecules is represented in spectra form, organic molecules can be sorted by quantifying differences between biological spectra. Unlike traditional structure–activity relationship methods, sorting of molecules by using biospectra comparisons does not require knowledge of a molecule's putative drug targets. To illustrate this finding, we selected as starting point the biological activity spectra of clotrimazole and tioconazole because their putative target, lanosterol demethylase (CYP51), was not included in the bioassay array. Spectra similarity obtained through profile similarity measurements and hierarchical clustering provided an unbiased means for establishing quantitative relationships between chemical structures and biological activity spectra. This methodology, which we have termed biological spectra analysis, provides the capability not only of sorting molecules on the basis of biospectra similarity but also of predicting simultaneous interactions of new molecules with multiple proteins. PMID:15625110

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

    PubMed Central

    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.

    2016-01-01

    Background 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. Methodology/Principal Findings 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). Conclusions/Significance 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

  4. Molecular Simulation of the Diffusion of Uranyl Carbonate Species in Aqueous Solution

    SciTech Connect

    Kerisit, Sebastien N.; Liu, Chongxuan

    2010-09-01

    Molecular dynamics simulations of aqueous uranyl carbonate species were carried out with two different potential models to gain molecular-level insight into the hydration properties of these species and evaluate the ability of the two models to reproduce published ab initio and experimental data. The simulation results were used to estimate the self-diffusion coefficients of uranyl carbonate species that often dominate uranyl speciation in groundwater systems. The first potential model was based on a series of shell models developed by Parker and co-workers (including (DE LEEUW and PARKER, 1998; KERISIT and PARKER, 2004; PAVESE et al., 1996). The second potential model was a rigid-ion model based on the flexible SPC water model (TELEMAN et al., 1987), the uranyl model of Guilbaud and Wipff (GUILBAUD and WIPFF, 1996), and the parameters for the carbonate ion given by Greathouse and co-workers (GREATHOUSE and CYGAN, 2005; GREATHOUSE et al., 2002). Analysis of structural (mean interatomic distances and coordination numbers) and dynamical (water residence times in hydration shell and self-diffusion coefficients) properties showed that, overall, the first potential model performed best when compared to published data, although the only major discrepancy with the second model was a misrepresentation of the configuration adopted by the alkaline-earth uranyl carbonate ions. The diffusion coefficients obtained for the alkaline-earth cations and the uranyl ion were compared with three variants of the Stokes-Einstein (SE) equation and it was found that none of the three SE models were able to reproduce both the absolute values and the overall trend determined from the molecular dynamics simulations. However, as would be expected based on the SE equation, a plot of the diffusion coefficients of the uranyl carbonate complexes as a function of the inverse of the equivalent spherical radius showed a general linear dependence with the two models yielding almost identical gradients

  5. Characterization of molecular and atomic species adsorbed on ferroelectric and semiconductor surfaces

    NASA Astrophysics Data System (ADS)

    Bharath, Satyaveda Chavi

    In order to clarify the mechanisms behind the adsorption of atomic and molecular species adsorbed on ferroelectric surfaces, single crystalline lithium niobate (LiNbO3, LN), 'Z-cut' along the (0001) plane, has been prepared, characterized and subsequently exposed to molecular and atomic species. 4-n-octyl-4'-cyanobiphenyl (8CB) liquid crystal was chosen as a polar molecule for our model system for this study. Low-energy electron diffraction (LEED), atomic force microscopy (AFM), surface contact angles (CA), and X-ray photoelectron spectroscopy (XPS) were used to characterize the surface of LN as well as the nature of the liquid crystal films grown on the surface. Atomically flat LN surfaces were prepared as a support for monolayer thick, 8CB molecular domains. Also, for the purpose of gaining a fundamental understanding of low coverage interactions of metal atoms on ferroelectric surfaces, we choose to deposit gold onto the LN surface. These gold atomic layers were grown under UHV conditions and characterized. Understanding anchoring mechanisms and thin film organization for LC molecules and metal atoms on uniformly poled surfaces allows for a fuller appreciation of how molecular deposition of other polarizable molecules on patterned poled LN surfaces would occur as well as yielding greater insight on the atomic characteristics of metal on ferroelectric interfaces. Also, to reveal the mechanisms involved in the adsorption of organic aromatic molecules on high-index Si surfaces, thiophene (C4H 4S) and pyrrole (C4H5N) molecules were dosed on prepared Si(5 5 12)-2x1 surfaces as our experimental system. The Si(5 5 12) surface was prepared to produce a 2x1 reconstruction after which molecules were dosed at low exposure to observe the preferred adsorption sites on the surface. All surface preparation and experiments were performed in UHV and measurements of the surface before and after deposition were performed using scanning tunneling microscopy (STM). Fundamental

  6. 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

  7. Molecular characterisation of Mycoplasma species isolated from the genital tract of Dorper sheep in South Africa.

    PubMed

    Kalshingi, Habu A; Bosman, Anna-Mari; Gouws, Johan; van Vuuren, Moritz

    2015-06-08

    Biochemical and molecular analysis were conducted on 34 strains of Mycoplasma species isolated between 2003 and 2009 from the genital tract of clinically healthy Dorper sheep and sheep with ulcerative vulvitis and balanitis. Earlier publications identified the causative agent as Mycoplasma mycoides mycoides large colony (MmmLC) and Arcanobacterium pyogenes. The aims of the study were to characterise Mycoplasma species isolated from the genital tract of Dorper sheep with polymerase chain reaction assay, cloning and gene sequencing. Basic Local Alignment Search Tool (BLAST) results revealed six predominant Mycoplasma species: Mycoplasma arginini, Mycoplasma bovigenitalium, Arcanobacterium laidlawii, MmmLC, Mycoplasma sp. ovine/caprine serogroup II and M. canadense. Sequencing of the 34 isolates were analysed using phylogenetic methods, and 18 (50%) were identified as M. arginini with 99% - 100% similarity to M. arginini from England and Sweden. Six isolates showed 99% similarity to M. bovigenitalium strains from Turkey and Germany. Two isolates had 99% similarity to an M. sp. ovine/caprine sero group II from the United Kingdom. BLAST for two isolates revealed 99% similarity to Acholeplasma laidlawii from India, another two were 99% similar to MmmLC strain from Sweden, two showed 98% similarity to Mycoplasma sp. Usp 120 from Brazil, and two isolates have a 97% - 99% similarity to M. mm. Jcv1 strain from the United States of America. Finally, one isolate showed similarity of 99% to Mycoplasma canadense strain from Italy. The findings support the hypothesis that ulcerative vulvitis and balanitis of Dorper sheep in South Africa (SA) is a multifactorial disease with involvement of different Mycoplasma species.

  8. Morphological and molecular analyses of larval taeniid species in small mammals from contrasting habitats in Denmark.

    PubMed

    Al-Sabi, M N S; Jensen, P M; Christensen, M U; Kapel, C M O

    2015-01-01

    Taeniid infections in intermediate hosts manifest themselves as extraintestinal larval stages which, in early development, lack species-specific characteristics. The inability to distinguish infections of zoonotic importance such as Echinococcus multilocularis from other taeniid infections that have mainly veterinary significance stimulated the development of species-specific molecular diagnostics. In this study, the prevalence of taeniid infections in potential intermediate hosts was evaluated using both morphological diagnosis and a newly described multiplex polymerase chain reaction (PCR) for species determination. Small mammals (N= 719) were trapped in three different types of habitats in north-east Zealand, Denmark. The sensitivity of the multiplex PCR (90.5%) exceeded that of morphological examination (57.9%) for identifying 95 taeniid infections. The use of the multiplex PCR resulted in higher prevalence rates due to improved detection of immature liver infections with Hydatigera taeniaeformis and Versteria mustelae, but did not affect the observed prevalence rates of peritoneal metacestodes of Taenia polyacantha. The prevalence of taeniid infections showed a significant difference according to habitat type, potentially identifying a 'sylvatic' transmission and an 'urban' transmission, with marked variation among different taeniid species. Versteria mustelae and T. polyacantha were more prevalent in rural forests, while infections with H. taeniaeformis were dominant in urban parks/forests and in residential and farm gardens. The multiplex PCR facilitated a better utilization of wildlife samples by yielding a higher number of definitive diagnoses of ambiguous taeniid infections in liver lesions, allowing for more accurate epidemiological data and, hence, a more accurate risk assessment.

  9. Molecular Epidemiology of Mycobacterium avium subsp. paratuberculosis Isolates Recovered from Wild Animal Species

    PubMed Central

    Motiwala, Alifiya S.; Amonsin, Alongkorn; Strother, Megan; Manning, Elizabeth J. B.; Kapur, Vivek; Sreevatsan, Srinand

    2004-01-01

    Mycobacterial isolates were obtained by radiometric culture from 33 different species of captive or free-ranging animals (n = 106) and environmental sources (n = 3) from six geographic zones within the United States. The identities of all 109 isolates were confirmed by using mycobactin J dependence and characterization of five well-defined molecular markers, including two integration loci of IS900 (loci L1 and L9), one Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis)-specific sequence (locus 251), and one M. avium subsp. avium-specific marker (IS1245), as well as hsp65 and IS1311 restriction endonuclease analyses. Seventy-six acid-fast isolates were identified as M. paratuberculosis, 15 were identified as belonging to the M. avium-M. intracellulare complex (but not M. paratuberculosis), and the remaining 18 were identified as mycobacteria outside the M. avium-M. intracellulare complex. Fingerprinting by multiplex PCR for IS900 integration loci clustered 67 of the 76 M. paratuberculosis strains into a single clade (designated clade A18) and had a Simpson's diversity index (D) of 0.53. In contrast, sequence-based characterization of a recently identified M. paratuberculosis short sequence repeat (SSR) region enabled the differentiation of the M. paratuberculosis isolates in clade A18 into seven distinct alleles (D = 0.75). The analysis revealed eight subtypes among the 33 species of animals, suggesting the interspecies transmission of specific strains. Taken together, the results of our analyses demonstrate that SSR analysis enables the genetic characterization of M. paratuberculosis isolates from different host species and provide evidence for the host specificity of some M. paratuberculosis strains as well as sharing of strains between wild and domesticated animal species. PMID:15071028

  10. Molecular analysis of the in situ growth rates of subsurface Geobacter species.

    PubMed

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

    2013-03-01

    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 (r(2) = 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.

  11. Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

    PubMed Central

    Cimarelli, Lucia; Singh, Kumar Saurabh; Mai, Nguyen Thi Nhu; Dhar, Bidhan Chandra; Brandi, Anna; Brandi, Letizia; Spurio, Roberto

    2015-01-01

    Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed. PMID:26006124

  12. De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species

    PubMed Central

    Huang, Xiu; Yan, Hai-Dong; Zhang, Xin-Quan; Zhang, Jian; Frazier, Taylor P.; Huang, De-Jun; Lu, Lu; Huang, Lin-Kai; Liu, Wei; Peng, Yan; Ma, Xiao; Yan, Yan-Hong

    2016-01-01

    Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa “Yaan” and H. altissima “1110.” Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for “Yaan” and “1110,” respectively. In addition, a total of 86,731 “Yaan” and 48,645 “1110” unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11–87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus. PMID:27148320

  13. Molecular tools for the selective detection of nine diatom species biomarkers of various water quality levels.

    PubMed

    Cimarelli, Lucia; Singh, Kumar Saurabh; Mai, Nguyen Thi Nhu; Dhar, Bidhan Chandra; Brandi, Anna; Brandi, Letizia; Spurio, Roberto

    2015-05-22

    Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

  14. Cellular and Molecular Mechanisms Underpinning Macrophage Activation during Remyelination

    PubMed Central

    Lloyd, Amy F.; Miron, Veronique E.

    2016-01-01

    Remyelination is an example of central nervous system (CNS) regeneration, whereby myelin is restored around demyelinated axons, re-establishing saltatory conduction and trophic/metabolic support. In progressive multiple sclerosis, remyelination is limited or fails altogether which is considered to contribute to axonal damage/loss and consequent disability. Macrophages have critical roles in both CNS damage and regeneration, such as remyelination. This diverse range in functions reflects the ability of macrophages to acquire tissue microenvironment-specific activation states. This activation is dynamically regulated during efficient regeneration, with a switch from pro-inflammatory to inflammation-resolution/pro-regenerative phenotypes. Although, some molecules and pathways have been implicated in the dynamic activation of macrophages, such as NFκB, the cellular and molecular mechanisms underpinning plasticity of macrophage activation are unclear. Identifying mechanisms regulating macrophage activation to pro-regenerative phenotypes may lead to novel therapeutic strategies to promote remyelination in multiple sclerosis. PMID:27446913

  15. Molecular Signaling Pathways Behind the Biological Effects of Salvia Species Diterpenes in Neuropharmacology and Cardiology.

    PubMed

    Akaberi, M; Iranshahi, M; Mehri, S

    2016-06-01

    The genus Salvia, from the Lamiaceae family, has diverse biological properties that are primarily attributable to their diterpene contents. There is no comprehensive review on the molecular signaling pathways of these active components. In this review, we investigated the molecular targets of bioactive Salvia diterpenes responsible for the treatment of nervous and cardiovascular diseases. The effects on different pathways, including apoptosis signaling, oxidative stress phenomena, the accumulation of amyloid beta plaques, and tau phosphorylation, have all been considered to be mechanisms of the anti-Alzheimer properties of Salvia diterpenes. Additionally, effects on the benzodiazepine and kappa opioid receptors and neuroprotective effects are noted as neuropharmacological properties of Salvia diterpenes, including tanshinone IIA, salvinorin A, cryptotanshinone, and miltirone. Tanshinone IIA, as the primary diterpene of Salvia miltiorrhiza, has beneficial activities in heart diseases because of its ability to scavenge free radicals and its effects on transcription factors, such as nuclear transcription factor-kappa B (NF-κB) and the mitogen-activated protein kinases (MAPKs). Additionally, tanshinone IIA has also been proposed to have cardioprotective properties including antiarrhythmic activities and effects on myocardial infarction. With respect to the potential therapeutic effects of Salvia diterpenes, comprehensive clinical trials are warranted to evaluate these valuable molecules as lead compounds. Copyright © 2016 John Wiley & Sons, Ltd.

  16. A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests

    PubMed Central

    Zeng, Weixian; Zhou, Bo; Lei, Pifeng; Zeng, Yeling; Liu, Yan; Liu, Cong; Xiang, Wenhua

    2015-01-01

    Understanding of belowground interactions among tree species and the fine root (≤2 mm in diameter) contribution of a species to forest ecosystem production are mostly restricted by experimental difficulties in the quantification of the species composition. The available approaches have various defects. By contrast, DNA-based methods can avoid these drawbacks. Quantitative real-time polymerase chain reaction (PCR) is an advanced molecular technology, but it is difficult to develop specific primer sets. The method of next-generation sequencing has several limitations, such as inaccurate sequencing of homopolymer regions, as well as being time-consuming, and requiring special knowledge for data analysis. This study evaluated the potential of the DNA-sequence-based method to identify tree species and to quantify the relative proportion of each species in mixed fine root samples. We discriminated the species by isolating DNA from individual fine roots and amplifying the plastid trnL(UAA; i.e., tRNA-Leu-UAA) intron using the PCR. To estimate relative proportions, we extracted DNA from fine root mixtures. After the plastid trnL(UAA) intron amplification and TA-cloning, we sequenced the positive clones from each mixture. Our results indicated that the plastid trnL(UAA) intron spacer successfully distinguished tree species of fine roots in subtropical forests. In addition, the DNA-sequence-based approach could reliably estimate the relative proportion of each species in mixed fine root samples. To our knowledge, this is the first time that the DNA-sequence-based method has been used to quantify tree species proportions in mixed fine root samples in Chinese subtropical forests. As the cost of DNA-sequencing declines and DNA-sequence-based methods improve, the molecular method will be more widely used to determine fine root species and abundance. PMID:25999977

  17. Molecular Species of Phosphatidylinositol-Cycle Intermediates in the Endoplasmic Reticulum and Plasma Membrane†

    PubMed Central

    Shulga, Yulia V.; Myers, David S.; Ivanova, Pavlina T.; Milne, Stephen B.; Brown, H. Alex; Topham, Matthew K.; Epand, Richard M.

    2009-01-01

    Phosphatidylinositol (PI) turnover is a process requiring both the plasma and ER membranes. We have determined the distribution of phosphatidic acid (PA) and PI and their acyl chain compositions in these two subcellular membranes using mass spectrometry. We assessed the role of PI cycling in determining the molecular species and quantity of these lipids by comparing the compositions of the two membranes isolated from embryonic fibroblasts obtained from diacylglycerol kinase epsilon (DGKε) knock out (KO) and wild type (WT) mice. In the KO cells the conversion of arachidonoyl-rich DAG to PA is blocked by the absence of DGKε, resulting in reducing the rate of PI-cycling. The acyl chain composition is very similar for PI or PA in the endoplasmic reticulum (ER) vs. plasma membrane (PM) and for WT vs. KO. However, the acyl chain profile for PI is very different from that for PA. This indicates that DGKε is not facilitating the direct transfer of a specific species of PA between the PM and the ER. About 20% of the PA in the ER membrane has one short acyl chain of 14 carbons or less. These species of PA are not converted into PI but may play a role in stabilizing regions of high positive curvature in the ER. There are also PI species in both the ER and PM for which there is no detectable PA precursor, indicating that these species of PI are unlikely to arise via the PI-cycle. We find that in the PM of KO cells the levels of PI and of PA are decreased about three-fold in comparison with either the PM of WT cells or in comparison with the ER of KO cells. The PI-cycle is slowed in the KO cells, hence the lipid intermediates of the PI-cycle can no longer be interconverted and are depleted from the PI-cycle by conversion to other species. There is less of an effect of the depletion in the ER where de novo synthesis of PA occurs in comparison with the PM. PMID:20000336

  18. A new tool for the molecular identification of Culicoides species of the Obsoletus group: the glass slide microarray approach.

    PubMed

    Deblauwe, I; de Witte, J C; de Deken, G; de Deken, R; Madder, M; van Erk, S; Hoza, F A; Lathouwers, D; Geysen, D

    2012-03-01

    Culicoides species of the Obsoletus group (Diptera: Ceratopogonidae) are potential vectors of bluetongue virus serotype 8 (BTV 8), which was introduced into central Western Europe in 2006. Correct morphological species identification of Obsoletus group females is especially difficult and molecular identification is the method of choice. In this study we present a new molecular tool based on probe hybridization using a DNA microarray format to identify Culicoides species of the Obsoletus group. The internal transcribed spacer 1 (ITS1) gene sequences of 55 Culicoides belonging to 13 different species were determined and used, together with 19 Culicoides ITS1 sequences sourced from GenBank, to design species-specific probes for the microarray test. This test was evaluated using the amplified ITS1 sequences of another 85 Culicoides specimens, belonging to 11 species. The microarray test successfully identified all samples (100%) of the Obsoletus group, identifying each specimen to species level within the group. This test has several advantages over existing polymerase chain reaction (PCR)-based molecular tools, including possible capability for parallel analysis of many species, high sensitivity and specificity, and low background signal noise. Hand-spotting of the microarray slide and the use of detection chemistry make this alternative technique affordable and feasible for any diagnostic laboratory with PCR facilities.

  19. Molecular phylogenetics, systematics and host-plant associations of the Bruchidius albosparsus (Fåhraeus) species group (Coleoptera, Chrysomelidae, Bruchinae) with the description of four new species.

    PubMed

    Delobel, Alex; Le Ru, Bruno; Genson, Gwenaëlle; Musyoka, Boaz K; Kergoat, Gael J

    2015-03-16

    Bruchidius Schilsky is a large paraphyletic genus of seed beetles (Coleoptera: Chrysomelidae: Bruchinae) which consists of multiple lineages that are usually associated with narrow sets of host-plants. In this study we focus on a group that mostly develops on wattle trees (acacias) belonging to the genus Vachellia Wight & Arn. This group originally included nine species and was designated as the Bruchidius centromaculatus (Allard) species group, but recent phylogenetic analyses revealed that these species belong to a much wider group of species with similar morphologies. For reasons of anteriority we call this enlarged group Bruchidius albosparsus (Fåhraeus). Here we review the morphology of species in this group and provide new diagnoses and ecological data for 10 species. The following combinations and synonymies are proposed: Bruchidius tanaensis (Pic, 1921) (= Bruchus tanaensis Pic, 1921) comb. nov. and Bruchidius albosparsus (Fåhraeus, 1839) (= Bruchus spadiceus Fåhraeus, 1839) syn. nov. Four new species are also described: B. eminingensis sp. nov., B. gerrardiicola sp. nov., B. glomeratus sp. nov. and B. haladai sp. nov. Finally we carried out molecular phylogenetic analyses on a multi-marker dataset of 59 specimens and 35 species, including 14 species from the group. The resulting trees allow us to confirm the monophyly of the group of interest and provide a more detailed picture of their evolutionary relationships.

  20. Fiber optic apparatus for detecting molecular species by surface enhanced Raman spectroscopy

    DOEpatents

    Angel, S.M.; Sharma, S.K.

    1987-11-30

    Optrode apparatus for detecting constituents of a fluid medium includes an optical fiber having a metal coating on at least a portion of a light transmissive core. The metal is one, such as silver, gold or copper, which enhances emission of Raman signal frequencies by molecules adsorbed on the surface of the coating when monochromatic probe light of a different frequency is scattered by such molecules and the metal coating is sufficiently thin to transmit light between the adsorbed molecules and the core of the fiber. Probe light is directed into one end of the fiber and a detector analyzes light emitted from the fiber for Raman frequencies that identify one or more particular molecular species. In one form, the optrode may function as a working electrode of an electrochemical cell while also serving to detect the products of oxidation or reduction reactions which occur at the electrode surface. 6 figs.

  1. Fiber optic apparatus for detecting molecular species by surface enhanced Raman spectroscopy

    DOEpatents

    Angel, S.M.; Sharma, S.K.

    1988-11-01

    Optrode apparatus for detecting constituents of a fluid medium includes an optical fiber having a metal coating on at least a portion of a light transmissive core. The metal is one, such as silver, gold or copper, which enhances emission of Raman signal frequencies by molecules adsorbed on the surface of the coating when monochromatic probe light of a different frequency is scattered by such molecules and the metal coating is sufficiently thin to transmit light between the absorbed molecules and the core of the fiber. Probe light is directed into one end of the fiber and a detector analyzes light emitted from the fiber for Raman frequencies that identify one or more particular molecular species. In one form, the optrode may function as a working electrode of an electrochemical cell while also serving to detect the products of oxidation or reduction reactions which occur at the electrode surface. 6 figs.

  2. Vibrational Frequencies of Fractionally Charged Molecular Species: Benchmarking DFT Results against ab Initio Calculations.

    PubMed

    Bâldea, Ioan

    2017-03-23

    Recent advances in nano/molecular electronics and electrochemistry made it possible to continuously tune the fractional charge q of single molecules and to use vibrational spectroscopic methods to monitor such changes. Approaches to compute vibrational frequencies ω(q) of fractionally charged species based on the density functional theory (DFT) are faced with an important issue: the basic quantity used in these calculations, the total energy, should exhibit piecewise linearity with respect to the fractional charge, but approximate, commonly utilized exchange correlation functionals do not obey this condition. In this paper, with the aid of a simple and representative example, we benchmark results for ω(q) obtained within the DFT against ab initio methods, namely, coupled cluster singles and doubles and also second- and third-order Møller-Plesset perturbation) expansions. These results indicate that, in spite of missing the aforementioned piecewise linearity, DFT-based values ω(q) can reasonably be trusted.

  3. Molecular identification of novel intermediate host species of Angiostrongylus vasorum in Greater London.

    PubMed

    Patel, Zainab; Gill, A Christina; Fox, Mark T; Hermosilla, Carlos; Backeljau, Thierry; Breugelmans, Karin; Keevash, Esther; McEwan, Claudia; Aghazadeh, Mahdis; Elson-Riggins, Jocelyn G

    2014-12-01

    Angiostrongylus vasorum is a parasitic nematode that can cause serious and potentially fatal disease in dogs and other canids. The aim of this study was to determine the intermediate slug species infected in nature by sampling sites in Greater London and Hertfordshire located within a known hyperendemic region. Overall, A. vasorum larvae were recovered from 6/381 slugs (1.6%) by tissue digestion, and their identity was confirmed by PCR. Infected slugs originated from three different sites in the Greater London area: one in Waltham Forest and two in Bromley. Slugs parasitised by A. vasorum were identified by a combination of external morphological characteristics and molecular techniques and belonged to three different families: the Arionidae, the Milacidae and the Limacidae. This includes two new host records for the parasite: Arion distinctus and Tandonia sowerbyi. This is the first record of A. vasorum in the family Milacidae, indicating that the parasite has a broader intermediate host range than previously recognised.

  4. Phylogenetic relationships among some Ateles species: the use of chromosomic and molecular characters.

    PubMed

    Nieves, Mariela; Ascunce, Marina Sofía; Rahn, Mónica Inés; Mudry, Marta Dolores

    2005-07-01

    As with most platyrrhines, the systematics of Ateles is under discussion. In order to help clarify its systematic, we employed chromosomic and molecular characters to analyze the phylogenetic relationship among some species of the genus Ateles. Chromosomic studies were conducted on 14 atelid specimens: eight Ateles from A. paniscus, A. chamek, A. belzebuth and A. geoffroyi, and six Alouatta caraya. Ateles paniscus showed 2N=32, whereas A. chamek, A. belzebuth and A. geoffroyi presented 2N=34, XX/XY (with a submetacentric X and a variable Y) corroborated by male meiosis. Nucleotide sequence variation at the mitochondrial cytochrome c oxidase subunit II gene (COII) was analyzed in ten New World monkey specimens. Parsimony trees showed consistent phylogenetic relationships using both chromosomic forms and mitochondrial COII gene sequences as characters. Particularly, chromosomic phylogenies showed A. hybridus as a divergent taxon from the remaining group, whereas A. chamek, A. belzebuth and A. marginatus form an unresolved clade with A. geoffroyi as sister group.

  5. A SEARCH FOR CO-EVOLVING ION AND NEUTRAL GAS SPECIES IN PRESTELLAR MOLECULAR CLOUD CORES

    SciTech Connect

    Tassis, Konstantinos; Hezareh, Talayeh; Willacy, Karen

    2012-11-20

    A comparison between the widths of ion and neutral molecule spectral lines has been recently used to estimate the strength of the magnetic field in turbulent star-forming regions. However, the ion (HCO{sup +}) and neutral (HCN) species used in such studies may not be necessarily co-evolving at every scale and density, and thus, may not trace the same regions. Here, we use coupled chemical/dynamical models of evolving prestellar molecular cloud cores including non-equilibrium chemistry, with and without magnetic fields, to study the spatial distribution of HCO{sup +} and HCN, which have been used in observations of spectral line width differences to date. In addition, we seek new ion-neutral pairs that are good candidates for such observations, because they have similar evolution and are approximately co-spatial in our models. We identify three such good candidate pairs: HCO{sup +}/NO, HCO{sup +}/CO, and NO{sup +}/NO.

  6. Cryptic Caribbean species of Scorpaena (Actinopterygii: Scorpaeniformes) suggested by cytogenetic and molecular data.

    PubMed

    Nirchio, M; Oliveira, C; Siccha-Ramirez, Z R; Sene, V F; Sánchez-Romero, O R; Ehemann, N R; Milana, V; Rossi, A R; Sola, L

    2016-10-01

    Cytogenetic and molecular analyses enabled identification of two cytotypes among individuals of the spotted scorpion fish Scorpaena plumieri from Margarita Island, Venezuela. Cytotype 1 was characterized by 48 subtelo-acrocentric chromosomes and fundamental number (number of chromosome arms; FN) equalled 48, while cytotype 2 was characterized by two metacentric and 46 subtelo-acrocentric chromosomes and FN was 50. These cytotypes also differed in the location of the ribosomal gene clusters and in the distribution of the constitutive heterochromatin. Moreover, fish from the cytotypes 1 and 2 were found to belong to distinct mitochondrial lineages. The presence of two S. plumieri cytotypes from two lineages separated by high genetic distance suggests that they correspond to sympatric cryptic species.

  7. Substrate Specificity of Equine and Human Influenza A Virus Sialidase to Molecular Species of Sialic Acid.

    PubMed

    Takahashi, Tadanobu; Unuma, Saori; Kawagishi, Sawako; Kurebayashi, Yuuki; Takano, Maiko; Yoshino, Hiroki; Minami, Akira; Yamanaka, Takashi; Otsubo, Tadamune; Ikeda, Kiyoshi; Suzuki, Takashi

    2016-01-01

    Most equine influenza A viruses (IAVs) show strong binding to glycoconjugates containing N-glycolylneuraminic acid (Neu5Gc) as well as N-acetylneuraminic acid (Neu5Ac). Therefore, the progeny of equine IAV is thought to be released from the infected cell surface through removal of sialic acids by the viral sialidase. In the present study, equine IAV sialidases showed significantly lower substrate affinity than that of human IAV sialidases to artificial and natural Neu5Gc-conjugated substrates. The substrate specificity of equine IAV sialidases is in disagreement with their binding specificity to molecular species of sialic acid. The results suggest that substrate specificity of equine IAV sialidase for Neu5Ac, rather than for Neu5Gc, is important for an advantage at the early infection stage and the process of progeny virus release from the surface of infected cells.

  8. Molecular differentiation of Central European blowfly species (Diptera, Calliphoridae) using mitochondrial and nuclear genetic markers.

    PubMed

    GilArriortua, Maite; Saloña Bordas, Marta I; Köhnemann, Stephan; Pfeiffer, Heidi; de Pancorbo, Marian M

    2014-09-01

    A challenging step in medical, veterinary and forensic entomology casework is the rapid and accurate identification of insects to estimate the period of insect activity (PIA), which usually approximates the post-mortem interval (PMI). The morphological identification of insect evidence is hampered by species similarities, especially at the early larval stages. However, DNA-based species identification is more accurate and reliable. In this study, we improved the suitability and efficacy of the standard mitochondrial cytochrome c oxidase subunit I (COI) barcode region of 658 bp combined with an additional region of 616 bp of the same gene. We also tested the usefulness of other mitochondrial and nuclear loci, such as the non-coding region included in mitochondrial Cyt-b-tRNA(ser)-ND1 (495-496 bp) and the second internal transcribed spacer (ITS2) region of nuclear ribosomal DNA (rDNA) (310-337 bp). We classified a total of 54 specimens from five blowfly species belonging to three Calliphoridae genera commonly found in Central Europe: Phormia (P. regina), Calliphora (C. vicina) and Lucilia (L. sericata, L. ampullacea and L. caesar). Additionally included were the Cyt-b (307 bp) sequences for P. regina species and GenBank recorded information about the studied loci for select species. The results revealed the robustness of COI (616 bp) and ITS2 (310-337 bp) as diagnostic tools to be added to the widely established COI barcode (658 bp). Their higher discriminatory power allows for more precise and reliable identifications, even within more complex genera (Lucilia). This work also contributes new nucleotide sequences that are useful for accurate species diagnosis and new sequence data of Calliphoridae interspecific variability in the European Westphalia region (Germany).

  9. Anthelmintic activity of the latex of Ficus species.

    PubMed

    de Amorin, A; Borba, H R; Carauta, J P; Lopes, D; Kaplan, M A

    1999-03-01

    The latex of some species of Ficus (Moraceae) has been traditionally used as vermifuge in Central and South America. It has been accepted that anthelmintic activity is due to a proteolytic fraction called ficin. In the present study, the anthelmintic activity of the latex of Ficus insipida Willd. and Ficus carica L. has been investigated in NIH mice naturally infected with Syphacia obvelata, Aspiculuris tetraptera and Vampirolepis nana. The latex of F. insipida, administered by intragastric route in doses of 4 ml/kg/day during three consecutive days, were effective in the removal of 38.6% of the total number of S. obvelata, being inexpressive in the removal of A. tetraptera (8.4%) and segments of V. nana (6.3%). The latex of F. carica, administered in doses of 3 ml/kg/day, during three consecutive days, was effective in the removal of S. obvelata (41.7%) and it did not produce significant elimination of A. tetraptera (2.6%) and V. nana (8.3%). The observed high acute toxicity with hemorrhagic enteritis, in addition to a weak anthelmintic efficacy, do not recommend the use of these lattices in traditional medicine.

  10. Generation and remote delivery of plasma activated species

    NASA Astrophysics Data System (ADS)

    Maguire, Paul; Mahony, Charles; Kelsey, Colin; Rutherford, David; Mariotti, Davide; Macias-Montero, Manuel; Perez-Martin, Fatima; Diver, Declan

    2016-09-01

    Plasma interactions with microdroplets offer new opportunities to deliver active chemical agents and nanoparticles to remote substrates downstream with many potential applications from cancer theranostics and wound healing in biomedicine, gentle food decontamination and seed germination in plasma agriculture to catalyst production and photonic structures fabrication, among others. We demonstrate plasma-liquid based pristine nanomaterials synthesis in flight and subsequent delivery up to 120mm from the atmospheric pressure plasma source. Monosized and non-aggregating metal nanoparticles are formed in the rf plasma in less than 100us, representing an increase in precursor reduction rate that is many (>4) orders of magnitude faster than that observed with standard colloidal chemistry or via high energy radiolytic techniques. Also the collection and purification limitations of the latter are avoided. Plasma activated liquid including OH radicals and H2O2 are transported over 120mm and have demonstrated high efficacy bacterial decontamination. These results will be compared with charge species and radical transport from the rf plasma without microdroplets. Reaction models based on high solvated surface electron concentrations will be presented. Funding from EPSRC acknowledged (Grants EP/K006088/1 and EP/K006142/1).

  11. Relationship between antimold activity and molecular structure of cinnamaldehyde analogues.

    PubMed

    Zhang, Yuanyuan; Li, Shujun; Kong, Xianchao

    2013-03-01

    A quantitative structure-activity relationship (QSAR) modeling of the antimold activity of cinnamaldehyde analogues against of Aspergillus niger and Paecilomyces variotii was presented. The molecular descriptors of cinnamaldehyde analogues were calculated by the CODESSA program, and these descriptors were selected by best multi-linear regression method (BMLR). Satisfactory multilinear regression models of Aspergillus niger and Paecilomyces variotii were obtained with R(2)=0.9099 and 0.9444, respectively. The models were also satisfactorily validated using internal validation and leave one out validation. The QSAR models provide the guidance for further synthetic work.

  12. Molecular Properties of the Anti-Aromatic Species Cyclopentadienone, C5H5=0

    NASA Astrophysics Data System (ADS)

    Ormond, Thomas; Ellison, Barney; Daily, John W.; Stanton, John F.; Ahmed, Musahid; Zwier, Timothy S.; Hemberger, Patrick

    2015-06-01

    A common intermediate in the high temperature combustion of benzene is cyclopentadienone, C5H4=O. Cyclopentadienone is considered to be an "anti-aromatic" molecule. It is certainly a metastable species; samples persist at LN2 temperatures but dimerize upon warming to -80°C. It is of great interest to physically characterize this "anti-aromatic" species. The microwave spectrum, the infrared spectrum, the ionization energy, and the electron affinity of cyclopentadienone have been measured. Flash pyrolysis of o-phenylene sulfite (C6H4O2SO) provides molecular beams of C5H4=O entrained in a rare gas carrier. The beams are interrogated with time-of-flight photoionization mass spectrometry, confirming the clean, intense production of C5H4=O. a) Chirped-pulse Fourier transform microwave spectroscopy and CCSD(T) electronic structure calculations have combined to determine the re molecular structure of C5H4=O. b) Guided by CCSD(T) electronic structure calculations, the matrix infrared absorbance spectrum of C5H4=O isolated in a 4 K neon matrix has been used to assign 20 of the 24 fundamental vibrational frequencies. c) Imaging photoelectron photoion coincidence (iPEPICO) spectra of cyclopentadienone establishes the ionization energy, IE(C5H4=O), to be 9.41 ± 0.01 eV. d) Prof. A. Sanov's group has reported the electron affinity, EA(C5H4=O), to be 1.06 ± 0.01 eV. Kidwell et al. J. Phys. Chem. Letts. 2201 (2014) Ormond et al. J. Phys. Chem. A 118, 708 (2014) Ormond et al. Mol. Phys. in press (2015) Khuseynov et al. J. Phys. Chem. A 118, 6965 (2014)

  13. Development and understanding of cobaloxime activity through electrochemical molecular catalyst screening.

    PubMed

    Wakerley, David W; Reisner, Erwin

    2014-03-28

    Electrochemical molecular catalyst screening (EMoCS) has been developed. This technique allows fast analysis and identification of homogeneous catalytic species through tandem catalyst assembly and electrochemistry. EMoCS has been used to study molecular proton reduction catalysts made from earth abundant materials to improve their viability for water splitting systems. The efficacy of EMoCS is proven through investigation of cobaloxime proton reduction activity with respect to the axial ligand in aqueous solution. Over 20 axial ligands were analysed, allowing rapid identification of the most active catalysts. Structure-activity relationships showed that more electron donating pyridine ligands result in enhanced catalytic currents due to the formation of a more basic Co-H species. The EMoCS results were validated by isolating and assaying the most electroactive cobaloximes identified during screening. The most active catalyst, [Co(III)Cl(dimethyl glyoximato)2(4-methoxypyridine)], showed high electro- and photoactivity in both anaerobic and aerobic conditions in pH neutral aqueous solution.

  14. Toward Understanding the Molecular Bases of Stretch Activation

    PubMed Central

    Sanfelice, Domenico; Sanz-Hernández, Máximo; de Simone, Alfonso; Bullard, Belinda; Pastore, Annalisa

    2016-01-01

    Muscles are usually activated by calcium binding to the calcium sensory protein troponin-C, which is one of the three components of the troponin complex. However, in cardiac and insect flight muscle activation is also produced by mechanical stress. Little is known about the molecular bases of this calcium-independent activation. In Lethocerus, a giant water bug often used as a model system because of its large muscle fibers, there are two troponin-C isoforms, called F1 and F2, that have distinct roles in activating the muscle. It has been suggested that this can be explained either by differences in structural features or by differences in the interactions with other proteins. Here we have compared the structural and dynamic properties of the two proteins and shown how they differ. We have also mapped the interactions of the F2 isoform with peptides spanning the sequence of its natural partner, troponin-I. Our data have allowed us to build a model of the troponin complex and may eventually help in understanding the specialized function of the F1 and F2 isoforms and the molecular mechanism of stretch activation. PMID:27226601

  15. Molecular analysis of phylogeographic subspecies in three Ponto-Caspian sturgeon species

    PubMed Central

    Dudu, Andreea; Georgescu, Sergiu Emil; Costache, Marieta

    2014-01-01

    Sturgeons (Order Acipenseriformes) represent an extremely valuable natural resource that is now facing depletion. In the current study we evaluate if the traditional classification in subspecies of Acipenser gueldenstaedtii, Acipenser stellatus and Huso huso, endemic to Ponto-Caspian region is sustained by molecular analysis and if these represent Evolutionary Significant Units (ESUs) that should be managed separately in conservation programs. To examine the classification of taxonomic entities we sequenced a fragment of the mitochondrial control region in case of three sturgeon species that inhabit the North-western of Black Sea and migrate for reproduction in the Lower Danube. Beside these sequences, we used previously published sequences from sturgeon individuals sampled in the Black Sea, Azov Sea and Caspian Sea. We determined the genetic diversity and genetic differentiation, conducted a Population Aggregation Analysis (PAA) and inferred an intraspecific molecular phylogeny and haplotype network. The results indicated a low level of genetic differentiation between the geographically designated subspecies and did not support a significant divergence or reciprocal monophyly between them. Our results confirm previous genetic studies with smaller samples sizes, but additional analyses including nuclear markers should be conducted for proper recommendations aiming at the development of conservation programs. PMID:25249783

  16. 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.

  17. 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.

  18. Capturing the transient species at the electrode–electrolyte interface by in situ dynamic molecular imaging

    SciTech Connect

    Yu, Jiachao; Zhou, Yufan; Hua, Xin; Liu, Songqin; Zhu, Zihua; Yu, Xiao-Ying

    2016-01-01

    The electrochemical interface between the solid electrode and liquid electrolyte has long been studied because of its importance in electrical energy storage, material synthesis, catalysis, and energy conversions.1 However, such interfaces are complex and extremely difficult to observe directly and are poorly under-stood due to lack of true in situ tools.2 Although electrochemical techniques have been widely used to investigate such interfaces, they are based on macroscopic models or current changes that could not provide direct ionic and molecular information of the interfacial structure. Many in situ and ex situ spectroscopy and microscopy techniques have been used to study the solid–liquid (s–l) interface.3,4 In situ TEM in sealed liquid cells has notably become a popular choice to provide structural information of s–l at the atomic level.5,6 However, real-time spatial mapping of the ionic and molecular intermediate species at the dynamic inter-face still remains a key challenge.

  19. Discovering Engangered Species. A Learning and Activity Book.

    ERIC Educational Resources Information Center

    Field, Nancy; Machlis, Sally

    Up to 33 million species share the earth; no one knows the exact number for sure. All over the world, many species are becoming extinct. This workbook is designed to help children become more aware of the concept of extinction, and to develop personal strategies for helping with the problem of endangered species. Included are 31 activities…

  20. Non-Invasive Molecular Imaging of Disease Activity in Atherosclerosis

    PubMed Central

    Dweck, Marc R; Aikawa, Elena; Newby, David E; Tarkin, Jason; Rudd, James; Narula, Jagat; Fayad, Zahi A.

    2016-01-01

    Major focus has been placed on the identification of vulnerable plaques as a means of improving the prediction of myocardial infarction. However, this strategy has recently been questioned on the basis that the majority of these individual coronary lesions do not in fact go on to cause clinical events. Attention is therefore shifting to alternative imaging modalities that might provide a more complete pan-coronary assessment of the atherosclerotic disease process. These include markers of disease activity with the potential to discriminate between patients with stable burnt-out disease that is no longer metabolically active and those with active atheroma, faster disease progression and increased risk of infarction. This review will examine how novel molecular imaging approaches can provide such assessments, focusing on inflammation and microcalcification activity, the importance of these processes to coronary atherosclerosis and the advantages and challenges posed by these techniques. PMID:27390335

  1. 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.

  2. Trace species detection: Spectroscopy and molecular energy transfer at high temperature

    SciTech Connect

    Gray, J.A.

    1993-12-01

    Monitoring the concentration of trace species such as atomic and molecular free radicals is essential in forming predictive models of combustion processes. LIF-based techniques have the necessary sensitivity for concentration and temperature measurements but have limited accuracy due to collisional quenching in combustion applications. The goal of this program is to use spectroscopic and kinetic measurements to quantify nonradiative and collisional effects on LIF signals and to develop new background-free alternatives to LIF. The authors have measured the natural linewidth of several OH A-X (3,0) rotational transitions to determine predissociation lifetimes in the upper state, which were presumed to be short compared to quenching lifetimes, and as a result, quantitative predictions about the applicability of predissociation fluorescence methods at high pressures are made. The authors are investigating collisional energy transfer in the A-state of NO. Quenching rates which enable direct corrections to NO LIF quantum yields at high temperature were calculations. These quenching rates are now being used in studies of turbulence/chemistry interactions. The authors have measured the electric dipole moment {mu} of excited-state NO using Stark quantum-beat spectroscopy. {mu} is an essential input to a harpoon model which predicts quenching efficiencies for NO (A) by a variety of combustion-related species. The authors are developing new coherent multiphoton techniques for measurements of atomic hydrogen concentration in laboratory flames to avoid the quenching problems associated with previous multiphoton LIF schemes.

  3. 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.

  4. Molecular phylogeny of the genus Lepidophthalmus (Decapoda, Callianassidae), with re-examination of its species composition.

    PubMed

    Robles, Rafael; Felder, Darryl L

    2015-09-23

    Ghost shrimps (Decapoda: Callianassidae) are common estuarine and marine burrowing organisms of tropical to temperate waters, typically found in intertidal to shallow subtidal habitats. Except for an abbreviated planktonic larval phase, most callianassids live as obligate burrowers and appear to depend on the burrow for shelter, reproduction, and feeding. Recent studies have shown the genus Lepidophthalmus, a group largely restricted to estuaries and river mouths, to be surprisingly speciose, but relationships among these taxa and driving forces for their separation remain poorly understood. We include fifteen described species of Lepidophthalmus in a molecular phylogenetic analysis based upon sequence analyses of the 16S and 12S mitochondrial genes. Our findings clarify the monophyletic membership of the genus and confirm postulated species separations. We reconfirm validity of Lepidophthalmus eiseni, reject two recently proposed new genera for selected members of Lepidophthalmus, and define ecologically and morphologically informative clades among congeners. Limited capability for larval dispersal and regional biogeographic history could well account for high diversity and regional endemism observed within the genus. Biogeographic scenarios, including continental drift, closure of the Panamanian Isthmus, and post-glacial dispersals, are invoked to account for proposed reconstructions of historical relationships.

  5. Molecular Characterization of Leishmania Species Isolated from Cutaneous Leishmaniasis in Yemen

    PubMed Central

    Mahdy, Mohammed A. K.; Al-Mekhlafi, Hesham M.; Al-Mekhlafi, Abdulsalam M.; Lim, Yvonne A. L.; Bin Shuaib, Naemah O. M.; Azazy, Ahmed A.; Mahmud, Rohela

    2010-01-01

    Background Cutaneous leishmaniasis (CL) is a neglected tropical disease endemic in the tropics and subtropics with a global yearly incidence of 1.5 million. Although CL is the most common form of leishmaniasis, which is responsible for 60% of DALYs lost due to tropical-cluster diseases prevalent in Yemen, available information is very limited. Methodology/Principal Findings This study was conducted to determine the molecular characterization of Leishmania species isolated from human cutaneous lesions in Yemen. Dermal scrapes were collected and examined for Leishmania amastigotes using the Giemsa staining technique. Amplification of the ribosomal internal transcribed spacer 1(ITS-1) gene was carried out using nested PCR and subsequent sequencing. The sequences from Leishmania isolates were subjected to phylogenetic analysis using the neighbor-joining and maximum parsimony methods. The trees identified Leishmania tropica from 16 isolates which were represented by two sequence types. Conclusions/Significance The predominance of the anthroponotic species (i.e. L. tropica) indicates the probability of anthroponotic transmission of cutaneous leishmaniasis in Yemen. These findings will help public health authorities to build an effective control strategy taking into consideration person–to-person transmission as the main dynamic of transmission of CL. PMID:20862227

  6. Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods.

    PubMed

    Guevara, Elaine E; Steiper, Michael E

    2014-01-01

    The Papionina is a geographically widespread subtribe of African cercopithecid monkeys whose evolutionary history is of particular interest to anthropologists. The phylogenetic relationships among arboreal mangabeys (Lophocebus), baboons (Papio), and geladas (Theropithecus) remain unresolved. Molecular phylogenetic analyses have revealed marked gene tree incongruence for these taxa, and several recent concatenated phylogenetic analyses of multilocus datasets have supported different phylogenetic hypotheses. To address this issue, we investigated the phylogeny of the Lophocebus + Papio + Theropithecus group using concatenation methods, as well as alternative methods that incorporate gene tree heterogeneity to estimate a 'species tree.' Our compiled DNA sequence dataset was ∼56 kb pairs long and included 57 independent partitions. All analyses of concatenated alignments strongly supported a Lophocebus + Papio clade and a basal position for Theropithecus. The Bayesian concordance analysis supported the same phylogeny. A coalescent-based Bayesian method resulted in a very poorly resolved species tree. The topological agreement between concatenation and the Bayesian concordance analysis offers considerable support for a Lophocebus + Papio clade as the dominant relationship across the genome. However, the results of the Bayesian concordance analysis indicate that almost half the genome has an alternative history. As such, our results offer a well-supported phylogenetic hypothesis for the Papio/Lophocebus/Theropithecus trichotomy, while at the same time providing evidence for a complex evolutionary history that likely includes hybridization among lineages.

  7. First flowering hybrid between autotrophic and mycoheterotrophic plant species: breakthrough in molecular biology of mycoheterotrophy.

    PubMed

    Ogura-Tsujita, Yuki; Miyoshi, Kazumitsu; Tsutsumi, Chie; Yukawa, Tomohisa

    2014-03-01

    Among land plants, which generally exhibit autotrophy through photosynthesis, about 880 species are mycoheterotrophs, dependent on mycorrhizal fungi for their carbon supply. Shifts in nutritional mode from autotrophy to mycoheterotrophy are usually accompanied by evolution of various combinations of characters related to structure and physiology, e.g., loss of foliage leaves and roots, reduction in seed size, degradation of plastid genome, and changes in mycorrhizal association and pollination strategy. However, the patterns and processes involved in such alterations are generally unknown. Hybrids between autotrophic and mycoheterotrophic plants may provide a breakthrough in molecular studies on the evolution of mycoheterotrophy. We have produced the first hybrid between autotrophic and mycoheterotrophic plant species using the orchid group Cymbidium. The autotrophic Cymbidium ensifolium subsp. haematodes and mycoheterotrophic C. macrorhizon were artificially pollinated, and aseptic germination of the hybrid seeds obtained was promoted by sonication. In vitro flowering was observed five years after seed sowing. Development of foliage leaves, an important character for photosynthesis, segregated in the first generation; that is, some individuals only developed scale leaves on the rhizome and flowering stems. However, all of the flowering plants formed roots, which is identical to the maternal parent.

  8. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa).

    PubMed

    Postaire, Bautisse; Magalon, Hélène; Bourmaud, Chloé A-F; Bruggemann, J Henrich

    2016-12-01

    A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and temperate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho-species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylogenies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo-Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South-Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence-based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms.

  9. Molecular detection and species identification of Enterocytozoon bieneusi isolated from immunocompetent Orang Asli in Malaysia.

    PubMed

    Ashikin, Azah; Al-Mekhlafi, Hesham M; Moktar, Norhayati; Anuar, Tengku Shahrul

    2017-04-01

    Most studies of opportunistic infections focus on immunocompromised patients. However, there is a lack of information on microsporidiosis in healthy people (immunocompetent) worldwide. This study aimed to detect and identify microsporidia species in immunocompetent Orang Asli living in Pahang, Malaysia. Orang Asli is a collective term for a group of indigenous people that usually reside in the interior regions of Peninsular Malaysia. They comprise about 0.7% of the total population in Malaysia and 76% of them lived below the poverty line i.e., poor housing conditions with the lack of access to safe drinking water and adequate sanitation, contaminated environment, high illiteracy rate and unhygienic practices by these people. Stool samples were collected from 209 Orang Asli and analyzed for detecting the presence of Enterocytozoon bieneusi and Encephalitozoon intestinalis by polymerase chain reaction assay targeting small subunit ribosomal RNA gene. E. bieneusi was detected in 8 individuals (3.83%). This infection was commonly found in males than females (5.2% vs. 2.7%). All infected Orang Asli were adults, with a mean age of 44years. Diarrhea and other gastrointestinal symptoms were reported in one case (12.5%) among individuals infected with this species. These findings clearly show that exposure to E. bieneusi may actually be common than reported. The accurate detection and identification of microsporidian species by molecular technique will improve therapy, clinical manifestations and prognosis of this infection, as no antiparasitic therapy has been approved for E. bieneusi. It is hoped that these findings will allow the formulation of better health management and disease prevention advisories, and improvement in the standards of health in similar communities.

  10. 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

  11. Molecular diagnostic for boll weevil (Coleoptera: Curculionidae) based on amplification of three species-specific microsatellites.

    PubMed

    Kim, Kyung Seok; Szendrei, Zsofia; Rodriguez-Saona, Cesar; Mulder, Phillip G; Sappington, Thomas W

    2009-04-01

    The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a serious pest of cultivated cotton, Gossypium hirsutum L., in the Americas, and reinfestation of zones from which they have been eradicated is of perpetual concern. Extensive arrays of pheromone traps monitor for reintroductions, but occasionally the traps collect nontarget weevils that can be misidentified by scouts. For example, the congeneric pepper weevil, Anthonomus eugenii Cano, and other superficially similar weevils are attracted to components of the boll weevil lure or trap color. Although morphologically distinguishable by trained personnel, the potential for misidentification is compounded when captured weevils are dismembered or partially consumed by ants or ground beetles that sometimes feed on them in the traps. Because misidentification can have expensive consequences, a molecular diagnostic tool would be of great value to eradication managers. We demonstrate that a cocktail of three primer pairs in a single polymerase chain reaction (PCR) amplify species-specific microsatellites that unambiguously distinguish the boll weevil from three other weevil species tested, including pepper weevil; cranberry weevil, Anthonomus eugenii musculus Say; and pecan weevil, Curculio caryae Horn. However, it does not distinguish the boll weevil from the subspecific "thurberia" weevil. A universal internal transcribed spacer primer pair included in the cocktail cross-amplifies DNA from all species, serving as a positive control. Furthermore, the diagnostic primers amplified the target microsatellites from various boll weevil adult body parts, indicating that the PCR technology using the primer cocktail is sensitive enough to positively identify a boll weevil even when the body is partly degraded.

  12. Genetic diversity and molecular characterization of several Heliconia species in Colombia.

    PubMed

    Isaza, L; Marulanda, M L; López, A M

    2012-12-19

    Researchers have classified the Heliconia genus as a group of highly variable and diverse plants. Species and cultivars are visually differentiated primarily on the basis of the color and size of inflorescence bracts. At taxonomic level, flower type (parabolic, sigmoid, or erect) and size are taken into account. The vast morphological diversity of heliconias at intra-specific, intra-population, and varietal levels in central-west Colombia prompted the present study. We characterized the genetic variability of 67 genotypes of cultivated heliconias belonging to Heliconia caribaea Lamarck, H. bihai (L.) L., H. orthotricha L. Andersson, H. stricta Huber, H. wagneriana Petersen, and H. psittacorum L. f., as well as that of several interspecific hybrids such as H. psittacorum L. f. x H. spathocircinata Aristeguieta and H. caribaea Lamarck x H. bihai (L.) L. We also created an approximation to their phylogenetic analysis. Molecular analysis using amplified fragment length polymorphism (AFLP) markers revealed a total of 170 bands. Two large, well-defined groups resulted: the first grouped cultivars of the very closely related H. caribaea and H. bihai species with those of H. orthotricha and H. psittacorum, and the second grouped H. stricta and H. wagneriana cultivars. The lowest percentage of polymorphism was found in H. psittacorum (17.65%) and the highest was in H. stricta (55.88%). Using AFLP, phylogenetic analysis of the species studied revealed the monophyletic origin of the Heliconiaceae family, and identified the Heliconia subgenus as monophyletic while providing evidence of the polyphyletic origin of several representatives of the Stenochlamys subgenus.

  13. Molecular determinants of the species selectivity of neurokinin type 1 receptor antagonists.

    PubMed

    Pradier, L; Habert-Ortoli, E; Emile, L; Le Guern, J; Loquet, I; Bock, M D; Clot, J; Mercken, L; Fardin, V; Garret, C

    1995-02-01

    Most nonpeptide neurokinin (NK)1 antagonists display a marked difference in affinity for rat versus human NK1 receptors. The molecular basis for the species selectivity of RP67580 and CP96,345 has been previously addressed [J. Biol. Chem. 267:25668-25671 (1992); J. Biol. Chem. 268:2319-2323 (1993)]. We are extending these previous results to additional NK1 antagonists, which are members of different chemical families. Included is a new perhydroisoindolol, RPR100893, which unlike its parent compound (RP67580) is human receptor selective. Chimeric rat/human NK1 receptors, as well as rat and human mutant NK1 receptors, were constructed and expressed in COS-1 cells, and affinities for substance P and the various antagonists were determined in binding studies. With human receptor-selective antagonists, the rat R290(S-->I) mutation was the most effective in increasing antagonist affinity (from 7- to 23-fold). Combination with the R116(L-->V) mutation led to an additional increase in affinity for trans-4-hydroxy-1-(1H-indol-3-ylcarbonyl)-L-prolyl-N- methyl-N-(phenylmethyl)-L-tyrosineamide (a derivative of FK888) and to nearly full human receptor affinity for RPR100893 and (+/-)-CP99,994. Based on the gains in affinities, these results confirm and extend the role of residues 116 and 290 of the NK1 receptor in the species selectivity of these three new human receptor-selective NK1 antagonists. In comparison, the affinity of RP67580, the least selective molecule, was most affected by changes at position 116, and combination with mutations at either position 97 (V-->E) or position 290 led to the human receptor phenotype. For the heterosteroid KAN610857, modifications of the rat receptor at positions 97 and 290, and to a lesser degree position 116, were the most effective in reducing affinity. Two double-mutants [R(97,290) and R(116,290)], although different from those identified for RP67580, also displayed human receptor-like affinity. Therefore, the molecular determinants of

  14. Molecular systematics of Serrasalmidae: Deciphering the identities of piranha species and unraveling their evolutionary histories

    USGS Publications Warehouse

    Freeman, B.; Nico, L.G.; Osentoski, M.; Jelks, H.L.; Collins, T.M.

    2007-01-01

    Piranhas and their relatives have proven to be a challenging group from a systematic perspective, with difficulties in identification of species, linking of juveniles to adults, diagnosis of genera, and recognition of higher-level clades. In this study we add new molecular data consisting of three mitochondrial regions for museum vouchered and photo-documented representatives of the Serrasalmidae. These are combined with existing serrasalmid sequences in GenBank to address species and higher-level questions within the piranhas using parsimony and Bayesian methods. We found robust support for the monophyly of Serrasalmus manueli, but not for Serrasalmus gouldingi when GenBank specimens identified as S. gouldingi were included in the analysis. "Serrasalmus gouldingi" sequences in GenBank may, however, be misidentified. Linking of juveniles to adults of the same species was greatly facilitated by the addition of sequence data. Based on our sampling and identifications, our data robustly reject the monophyly of the genera Serrasalmus and Pristobrycon. We found evidence for a well-supported clade comprised of Serrasalmus, Pygocentrus, and Pristobrycon (in part). This clade was robustly supported in separate and combined analyses of gene regions, and was also supported by a unique molecular character, the loss of a tandem repeat in the control region. Analysis of specimens and a literature review suggest this clade is also characterized by the presence of a pre-anal spine and ectopterygoid teeth. A persistent polytomy at the base of this clade was dated using an independent calibration as 1.8 million years old, corresponding to the beginning of the Pleistocene Epoch, and suggesting an origin for this clade more recent than dates cited in the recent literature. The sister group to this clade is also robustly supported, and consists of Catoprion, Pygopristis, and Pristobrycon striolatus. If the term piranha is to refer to a monophyletic clade, it should be restricted to

  15. Quantification of triacylglycerol molecular species in cocoa butter using high-performance liquid chromatography equipped with nano quantity analyte detector.

    PubMed

    Beppu, Fumiaki; Nagai, Toshiharu; Yoshinaga, Kazuaki; Mizobe, Hoyo; Kojima, Koichi; Gotoh, Naohiro

    2013-01-01

    Triacylglycerol (TAG) molecular species were quantified through high-performance liquid chromatography (HPLC) equipped with a nano quantity analyte detector (NQAD). TAG standard compounds, i.e., 1,3-dipalmitoyl-2-oleoylglycerol (β-POP), 1-palmitoyl-2-oleoyl-3-stearoyl-rac-glycerol (β-POS), and 1,3-distearoyl-2-oleoylglycerol (β-SOS), and natural cocoa butter were used for analyses. NQAD gave the first order equation passing through the origin for all TAG standard compounds. TAG molecular species in cocoa butter were quantified using the calibration curves and the obtained values were almost the same as the reported ones of conventional cocoa butter. Furthermore, a recovery test was also carried out and the values were almost 100. Therefore, HPLC-NQAD can be successfully used for the quantification of TAG molecular species in natural fats and oils.

  16. Molecular evolution and phylogenetic analysis of genes related to cotton fibers development from wild and domesticated cotton species in Gossypium.

    PubMed

    Zhu, Huayu; Lv, Junhong; Zhao, Liang; Tong, Xiangchao; Zhou, Baoliang; Zhang, Tianzhen; Guo, Wangzhen

    2012-06-01

    The domestication of both diploid and tetraploid cotton species was carried out for fiber utilization. To understand the origin and domestication of fibers, 18 genes related to fiber development were individually cloned and sequenced from 22 different cotton species. Their structures, phylogenetic relationship and molecular evolution were further studied. In the orthologous and homeologous loci of the 18 genes, the sequence and structure of 72.22% were conserved and 27.78% were diverse. Tree topologies constructed based on the combined sequences showed that all 13 D-genome species were congruent with Fryxell's subsection taxonomy, the A- and D-subgenomes independently evolved in the allopolyploid after polyploid formation, and Gossypium raimondii had the closest relationship with all allotetraploids of D-subgenomes. The molecular evolutionary rates revealed approximately equivalent rates among different D-genome species, and purifying selection acted on all genes in the wild D-genome species. Among orthologs and homeologs, the D-subgenomes had higher evolutionary rates than the A-subgenomes in tetraploid cotton species, and the cultivars had higher evolutionary rates than either the semi-domesticated or wild species. Our study revealed that human domestication altered the molecular evolutionary pattern of genes related to fiber development, and Gossypium hirsutum endured greater selective pressures than Gossypium barbadense during the domestication process.

  17. Species Boundaries and Host Range of Tortoise Mites (Uropodoidea) Phoretic on Bark Beetles (Scolytinae), Using Morphometric and Molecular Markers

    PubMed Central

    Knee, Wayne; Beaulieu, Frédéric; Skevington, Jeffrey H.; Kelso, Scott; Cognato, Anthony I.; Forbes, Mark R.

    2012-01-01

    Understanding the ecology and evolutionary history of symbionts and their hosts requires accurate taxonomic knowledge, including clear species boundaries and phylogenies. Tortoise mites (Mesostigmata: Uropodoidea) are among the most diverse arthropod associates of bark beetles (Curculionidae: Scolytinae), but their taxonomy and host associations are largely unstudied. We tested the hypotheses that (1) morphologically defined species are supported by molecular data, and that (2) bark beetle uropodoids with a broad host range comprise cryptic species. To do so, we assessed the species boundaries of uropodoid mites collected from 51 host species, across 11 countries and 103 sites, using morphometric data as well as partial cytochrome oxidase I (COI) and nuclear large subunit ribosomal DNA (28S). Overall, morphologically defined species were confirmed by molecular datasets, with a few exceptions. Twenty-nine of the 36 uropodoid species (Trichouropoda, Nenteria and Uroobovella) collected in this study had narrow host ranges, while seven species had putative broad host ranges. In all but one species, U. orri, our data supported the existence of these host generalists, which contrasts with the typical finding that widespread generalists are actually complexes of cryptic specialists. PMID:23071768

  18. The genome as a life-history character: why rate of molecular evolution varies between mammal species

    PubMed Central

    Bromham, Lindell

    2011-01-01

    DNA sequences evolve at different rates in different species. This rate variation has been most closely examined in mammals, revealing a large number of characteristics that can shape the rate of molecular evolution. Many of these traits are part of the mammalian life-history continuum: species with small body size, rapid generation turnover, high fecundity and short lifespans tend to have faster rates of molecular evolution. In addition, rate of molecular evolution in mammals might be influenced by behaviour (such as mating system), ecological factors (such as range restriction) and evolutionary history (such as diversification rate). I discuss the evidence for these patterns of rate variation, and the possible explanations of these correlations. I also consider the impact of these systematic patterns of rate variation on the reliability of the molecular date estimates that have been used to suggest a Cretaceous radiation of modern mammals, before the final extinction of the dinosaurs. PMID:21807731

  19. Molecular Requirements for the Biological Activity of Ethylene 1

    PubMed Central

    Burg, Stanley P.; Burg, Ellen A.

    1967-01-01

    The molecular requirements for ethylene action were investigated using the pea straight growth test. Biological activity requires an unsaturated bond adjacent to a terminal carbon atom, is inversely related to molecular size, and is decreased by substitutions which lower the electron density in the unsaturated position. Evidence is presented that ethylene binds to a metal containing receptor site. CO2 is a competitive inhibitor of ethylene action, and prevents high concentrations of auxin (which stimulate ethylene formation) from retarding the elongation of etiolated pea stem sections. It is suggested that CO2 delays fruit ripening by displacing the ripening hormone, ethylene, from its receptor site. Binding of ethylene to the receptor site is also impeded when the O2 concentration is lowered, and this may explain why fruit ripening is delayed at low O2 tensions. PMID:16656478

  20. Molecular models of the Mojave rattlesnake (Crotalus scutulatus scutulatus) venom metalloproteinases reveal a structural basis for differences in hemorrhagic activities.

    PubMed

    Dagda, Ruben K; Gasanov, Sardar E; Zhang, Boris; Welch, William; Rael, Eppie D

    2014-03-01

    Rattlesnake venom can differ in composition and in metalloproteinase-associated activities. The molecular basis for this intra-species variation in Crotalus scutulatus scutulatus (Mojave rattlesnake) remains an enigma. To understand the molecular basis for intra-species variation of metalloproteinase-associated activities, we modeled the three-dimensional structures of four metalloproteinases based on the amino acid sequence of four variations of the proteinase domain of the C. s. scutulatus metalloproteinase gene (GP1, GP2, GP3, and GP4). For comparative purposes, we modeled the atrolysin metalloproteinases of C. atrox as well. All molecular models shared the same topology. While the atrolysin metalloproteinase molecular models contained highly conserved substrate binding sites, the Mojave rattlesnake metalloproteinases showed higher structural divergence when superimposed onto each other. The highest structural divergence among the four C. s. scutulatus molecular models was located at the northern cleft wall and the S'1-pocket of the substrate binding site, molecular regions that modulate substrate selectivity. Molecular dynamics and field potential maps for each C. s. scutulatus metalloproteinase model demonstrated that the non-hemorrhagic metalloproteinases (GP2 and GP3) contain highly basic molecular and field potential surfaces while the hemorrhagic metalloproteinases GP1 and atrolysin C showed extensive acidic field potential maps and shallow but less dynamic active site pockets. Hence, differences in the spatial arrangement of the northern cleft wall, the S'1-pocket, and the physico-chemical environment surrounding the catalytic site contribute to differences in metalloproteinase activities in the Mojave rattlesnake. Our results provide a structural basis for variation of metalloproteinase-associated activities in the rattlesnake venom of the Mojave rattlesnake.

  1. "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…

  2. Antifungal activities of azole agents against the Malassezia species.

    PubMed

    Miranda, Karla Carvalho; de Araujo, Crystiane Rodrigues; Costa, Carolina Rodrigues; Passos, Xisto Sena; de Fátima Lisboa Fernandes, Orionalda; do Rosário Rodrigues Silva, Maria

    2007-03-01

    In this paper, we identified 95 Malassezia isolates by morphological and biochemical criteria and assessed the in vitro activity of fluconazole, itraconazole, ketoconazole and voriconazole by broth microdilution against these species using slightly modified Leeming-Notman medium. The Malassezia isolates were identified as M. furfur (74), M. sympodialis (11), M. obtusa (8) and M. globosa (2). The modified Leeming-Notman medium used for susceptibility testing allowed good growth of Malassezia spp. Visual reading of the minimal inhibitory concentration (MIC) was readily achieved until Day 5 of incubation at 32 degrees C. Although high MIC values of 16 microg/mL for fluconazole were observed in 9.5% of Malassezia isolates, in general these microorganisms were susceptible to all drugs studied. Interestingly, one M. globosa isolate showed high MIC values for voriconazole, itraconazole and fluconazole. For the 95 strains, the MIC ranges were <0.03-4 microg/mL for ketoconazole, <0.03 to >16 microg/mL for voriconazole, <0.125 to >64 microg/mL for fluconazole and <0.03-16 microg/mL for itraconazole. In summary, the good reproducibility and visual readings obtained using modified Leeming-Notman medium suggest that this medium should be proposed for antifungal testing of drugs against Malassezia spp.

  3. Linking neural activity and molecular oscillations in the SCN

    PubMed Central

    Colwell, Christopher S.

    2015-01-01

    Neurons in the suprachiasmatic nucleus (SCN) function as part of a central timing circuit that drives daily changes in our behaviour and underlying physiology. A hallmark feature of SCN neuronal populations is that they are mostly electrically silent during the night, start to fire action potentials near dawn and then continue to generate action potentials with a slow and steady pace all day long. Sets of currents are responsible for this daily rhythm, with the strongest evidence for persistent Na+ currents, L-type Ca2+ currents, hyperpolarization-activated currents (IH), large-conductance Ca2+ activated K+ (BK) currents and fast delayed rectifier (FDR) K+ currents. These rhythms in electrical activity are crucial for the function of the circadian timing system, including the expression of clock genes, and decline with ageing and disease. This article reviews our current understanding of the ionic and molecular mechanisms that drive the rhythmic firing patterns in the SCN. PMID:21886186

  4. Studies on two closely related species of octocorallians: biochemical and molecular characteristics of the organic matrices of endoskeletal sclerites.

    PubMed

    Rahman, M Azizur; Isa, Y; Uehara, T

    2006-01-01

    Two species of alcyonarian corals, Lobophytum crassum and Sinularia polydactyla, are closely related to each other. It is reported that the calcified organic substances in the skeletons of both contain a protein-polysaccharide complex playing a key role in the regulation of biocalcification. However, information on the matrix proteins of endoskeletal sclerite has been lacking. Hence we studied the proteinaceous organic matrices of sclerites for both species, to analyze the sequences and the functional properties of the proteins present. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the preparations showed four bands of proteins with apparent molecular masses of 102, 67, 48, and 37 kDa for L. crassum and seven bands of 109, 83, 70, 63, 41, 30, and 22 kDa for S. polydactyla. A major protein band of about 67 kDa in L. crassum and two bands of proteins of about 70 and 63 kDa in S. polydactyla yielded N-terminal amino acid sequences. Periodic acid-Schiff staining indicated that the 67-kDa protein in L. crassum, and 83- and 63-kDa proteins in S. polydactyla were glycosylated. For detection of calcium binding proteins, a Ca(2+) overlay analysis was conducted in the extract via (45)Ca autoradiography. The 102- and 67-kDa calcium binding proteins in L. crassum, and the 109- and 63-kDa Ca(2+) binding proteins in S. polydactyla were found to be radioactive. An assay for carbonic anhydrase (CA), which is thought to play an important role in the process of calcification, revealed specific activities. Newly derived protein sequences were subjected to standard sequence analysis involving identification of similarities to other proteins in databases. The significantly different protein expressions and compositional analysis of sequences between two species were demonstrated.

  5. THE TRANSITION OF THE 37-kDa LAMININ RECEPTOR (RPSA) TO HIGHER MOLECULAR WEIGHT SPECIES: SUMOylation OR ARTIFACT?

    PubMed Central

    DIGIACOMO, VINCENT; GANDO, IVAN A.; VENTICINQUE, LISA; HURTADO, ALICIA; MERUELO, DANIEL

    2017-01-01

    The 37-kDa laminin receptor (37LRP or RPSA) is a remarkable, multifaceted protein that functions in processes ranging from matrix adhesion to ribosome biogenesis. Its ability to engage extracellular laminin is further thought to contribute to cellular migration and invasion. Most commonly associated with metastatic cancer, RPSA is also increasingly found to be important in other pathologies, including microbial infection, neurodegenerative disease and developmental malformations. Importantly, it is thought to have higher molecular weight forms, including a 67-kDa species (67LR), the expression of which is linked to strong laminin binding and metastatic behavior. The composition of these larger forms has remained elusive and controversial. Homo- and heterodimerization have been proposed as events capable of building the larger species from the monomeric 37-kDa precursor, but solid evidence is lacking. Here, we present data suggesting that higher molecular weight species require SUMOylation to form. We also comment on the difficulty of isolating larger RPSA species for unambiguous identification and demonstrate that cell lines stably expressing tagged RPSA for long periods of time fail to produce tagged higher molecular weight RPSA. It is possible that higher molecular weight species like 67LR are not derived from RPSA. PMID:26146125

  6. Distribution of plasma phosphatidylcholine molecular species in rabbits fed fish oil is modulated by dietary n-6 fatty acids.

    PubMed

    Koba, K; Horrobin, D F; DeMarco, A C; Ni, I H; Huang, Y S

    1995-12-01

    The present study examined the distribution of plasma phosphatidylcholine (PC) molecular species in rabbits fed a chow diet supplemented with fish oil (FO) in combination with either hydrogenated coconut oil or the n-6 fatty acid-rich evening primrose oil (EPO) for 4 weeks. Significant proportions of plasma PC molecular species contained long-chain n-3 fatty acids. Addition of EPO to the FO supplemented diet increased the incorporation of n-6 fatty acids into plasma PC molecules; it also raised the proportions of 16:0-18:2, n-6, 18:1-18:2, n-6, 18:2, n-6-18:2, n-6, and 16:0-20:4, n-6. The increase of n-6 fatty acid-containing PC was at the expense of n-3 fatty acid containing PC species. However, feeding n-6 fatty acids did not affect the distribution of PC molecular species based on total carbon chain length. The most interesting observation was that dietary suplementation with EPO, raised the ratio of 22:6, n-3-containing to 20:5, n-3-containing molecular species, suggesting an enhanced conversion of 20:5, n-3 to 22:6, n-3.

  7. Molecular phylogeny and taxonomy of the Epictia goudotii Species complex (Serpentes: Leptotyphlopidae: Epictinae) in Middle America and northern South America

    PubMed Central

    McCranie, James R.

    2016-01-01

    Here we review the systematics of the threadsnakes of the Epictia goudotii Species complex in Middle and northern South America using external morphology and molecular data. Two species, Epictia goudotii and E. magnamaculata, are currently recognized from that region, but we provide evidence for recognizing, as species, three other nominal forms usually treated as subspecies of E. goudotii: E. ater, E. bakewelli, and E. phenops. Thus, together with E. columbi (Bahamas), we recognize six species in the Epictia goudotii Species complex. Because E. albifrons from northern South America has been confused with E. goudotii in the past, we also briefly discuss the taxonomic status of that species and its apparent close relative E. tenella, which are not members of the E. goudotii complex. PMID:26788430

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

    PubMed

    Torres-Carvajal, Omar; Lobos, Simón E

    2014-01-01

    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.

  9. Molecular hydrogen suppresses activated Wnt/β-catenin signaling

    PubMed Central

    Lin, Yingni; Ohkawara, Bisei; Ito, Mikako; Misawa, Nobuaki; Miyamoto, Kentaro; Takegami, Yasuhiko; Masuda, Akio; Toyokuni, Shinya; Ohno, Kinji

    2016-01-01

    Molecular hydrogen (H2) is effective for many diseases. However, molecular bases of H2 have not been fully elucidated. Cumulative evidence indicates that H2 acts as a gaseous signal modulator. We found that H2 suppresses activated Wnt/β-catenin signaling by promoting phosphorylation and degradation οf β-catenin. Either complete inhibition of GSK3 or mutations at CK1- and GSK3-phosphorylation sites of β-catenin abolished the suppressive effect of H2. H2 did not increase GSK3-mediated phosphorylation of glycogen synthase, indicating that H2 has no direct effect on GSK3 itself. Knock-down of adenomatous polyposis coli (APC) or Axin1, which form the β-catenin degradation complex, minimized the suppressive effect of H2 on β-catenin accumulation. Accordingly, the effect of H2 requires CK1/GSK3-phosphorylation sites of β-catenin, as well as the β-catenin degradation complex comprised of CK1, GSK3, APC, and Axin1. We additionally found that H2 reduces the activation of Wnt/β-catenin signaling in human osteoarthritis chondrocytes. Oral intake of H2 water tended to ameliorate cartilage degradation in a surgery-induced rat osteoarthritis model through attenuating β-catenin accumulation. We first demonstrate that H2 suppresses abnormally activated Wnt/β-catenin signaling, which accounts for the protective roles of H2 in a fraction of diseases. PMID:27558955

  10. New molecular phylogeny of Lucinidae: increased taxon base with focus on tropical Western Atlantic species (Mollusca: Bivalvia).

    PubMed

    Taylor, John D; Glover, Emily A; Smith, Lisa; Ikebe, Chiho; Williams, Suzanne T

    2016-11-23

    A new molecular phylogeny of the Lucinidae using 18S and 28S rRNA and cytochrome b genes includes many species from the tropical Western Atlantic as well as additional taxa from the Indo-West Pacific. This study provides a phylogenetic framework for a new taxonomy of tropical Western Atlantic lucinids. The analysis confirmed five major clades-Pegophyseminae, Leucosphaerinae, Myrteinae, Codakiinae and Lucininae, with Monitilorinae and Fimbriinae represented by single species. The Leucosphaerinae are expanded and include Callucina winckworthi and the W. Atlantic Myrtina pristiphora that groups with several Indo-West Pacific Myrtina species. Within the Codakiinae two abundant species of Ctena from the Western Atlantic with similar shells are discriminated as C. orbiculata and C. imbricatula, while in the Indo-West Pacific Ctena bella is a probable species complex. The Lucininae is the most species rich and disparate subfamily with several subclades apparent. Three species of Lucina are recognized in the W. Atlantic L. aurantia, L. pensylvanica and L. roquesana. Pleurolucina groups near to Cavilinga and Lucina, while Lucinisca muricata is more closely related to the E. Pacific L. fenestrata than to the Atlantic L. nassula. A new species of Parvilucina is identified from molecular analyses having been confounded with Parvilucina pectinata but differs in ligament structure. Also, the former Parvilucina clenchi is more distant and assigned to Guyanella.

  11. Species and sex identification of the Korean goral (Nemorhaedus caudatus) by molecular analysis of non-invasive samples.

    PubMed

    Kim, Baek Jun; Lee, Yun-Sun; An, Jung-hwa; Park, Han-Chan; Okumura, Hideo; Lee, Hang; Min, Mi-Sook

    2008-09-30

    Korean long-tailed goral (Nemorhaedus caudatus) is one of the most endangered species in South Korea. However, detailed species distribution and sex ratio data on the elusive goral are still lacking due to difficulty of identification of the species and sex in the field. The primary aim of this study was to develop an economical PCR-RFLP method to identify species using invasive or non-invasive samples from five Korean ungulates: goral (N. caudatus), roe deer (Capreolus pygargus), feral goat (Capra hircus), water deer (Hydropotes inermis) and musk deer (Moschus moschiferus). The secondary aim was to find more efficient molecular sexing techniques that may be applied to invasive or non-invasive samples of ungulate species. We successfully utilized PCR-RFLP of partial mitochondrial cytochrome b gene (376 bp) for species identification, and sex-specific amplification of ZFX/Y and AMELX/Y genes for sexing. Three species (goral, goat and water deer) showed distinctive band patterns by using three restriction enzymes (XbaI, StuI or SspI). Three different sexing primer sets (LGL331/335 for ZFX/Y gene; SE47/48 or SE47/53 for AMELX/Y gene) produced sex-specific band patterns in goral, goat and roe deer. Our results suggest that the molecular analyses of non-invasive samples might provide us with potential tools for the further genetic and ecological study of Korean goral and related species.

  12. 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.

  13. Chronology of the extant African elephant species and case study of the species identification of the small African elephant with the molecular phylogenetic method.

    PubMed

    Murata, Yumie; Yonezawa, Takahiro; Kihara, Ichiro; Kashiwamura, Toshihide; Sugihara, Yuji; Nikaido, Masato; Okada, Norihiro; Endo, Hideki; Hasegawa, Masami

    2009-07-15

    Despite vigorous genetic studies of African elephants (Loxodonta africana and L. cyclotis) during the last decade, their evolutionary history is still obscure. Phylogenetic studies and coalescence time estimation using longer nucleotide sequence data from denser samplings are necessary to better understand the natural history of African elephants. Further, species identification among African elephants is sometimes very difficult using only the external morphological characteristics. This is a serious problem for making an adequate breeding plan in zoological gardens. In this paper, we investigated the continent-wide phylogeographical pattern of the African elephants and estimated the coalescence times among them. From these molecular data and geological evidence, we proposed an evolutionary scenario for the African elephants. We further demonstrated the effectiveness of molecular phylogenetic methods in species identification.

  14. Nanoplasmonic molecular ruler for nuclease activity and DNA footprinting

    DOEpatents

    Chen, Fanqing Frank; Liu, Gang L; Lee, Luke P

    2013-10-29

    This invention provides a nanoplasmonic molecular ruler, which can perform label-free and real-time monitoring of nucleic acid (e.g., DNA) length changes and perform nucleic acid footprinting. In various embodiments the ruler comprises a nucleic acid attached to a nanoparticle, such that changes in the nucleic acid length are detectable using surface plasmon resonance. The nanoplasmonic ruler provides a fast and convenient platform for mapping nucleic acid-protein interactions, for nuclease activity monitoring, and for other footprinting related methods.

  15. Antituberculosis activity of the molecular libraries screening center network library.

    PubMed

    Maddry, Joseph A; Ananthan, Subramaniam; Goldman, Robert C; Hobrath, Judith V; Kwong, Cecil D; Maddox, Clinton; Rasmussen, Lynn; Reynolds, Robert C; Secrist, John A; Sosa, Melinda I; White, E Lucile; Zhang, Wei

    2009-09-01

    There is an urgent need for the discovery and development of new antitubercular agents that target novel biochemical pathways and treat drug-resistant forms of the disease. One approach to addressing this need is through high-throughput screening of drug-like small molecule libraries against the whole bacterium in order to identify a variety of new, active scaffolds that will stimulate additional biological research and drug discovery. Through the Molecular Libraries Screening Center Network, the NIAID Tuberculosis Antimicrobial Acquisition and Coordinating Facility tested a 215,110-compound library against Mycobacterium tuberculosis strain H37Rv. A medicinal chemistry survey of the results from the screening campaign is reported herein.

  16. 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

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

    PubMed

    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.

  18. Molecular Identification and Susceptibility of Trichosporon Species Isolated from Clinical Specimens in Qatar: Isolation of Trichosporon dohaense Taj-Aldeen, Meis & Boekhout sp. nov.▿

    PubMed Central

    Taj-Aldeen, Saad J.; Al-Ansari, Nasser; El Shafei, Sittana; Meis, Jacques F.; Curfs-Breuker, Ilse; Theelen, Bart; Boekhout, Teun

    2009-01-01

    Trichosporon species have been reported as emerging pathogens and usually occur in severely immunocompromised patients. In the present work, 27 clinical isolates of Trichosporon species were recovered from 27 patients. The patients were not immunocompromised, except for one with acute myeloid leukemia. Sequence analysis revealed the isolation of Trichosporon dohaense Taj-Aldeen, Meis & Boekhout sp. nov., with CBS 10761T as the holotype strain, belonging to the Ovoides clade. In the D1-D2 large-subunit rRNA gene analysis, T. dohaense is a sister species to T. coremiiforme, and in the internal transcribed spacer analysis, the species is basal to the other species of this clade. Molecular identification of the strains yielded 17 T. asahii, 3 T. inkin, 2 T. japonicum, 2 T. faecale, and 3 T. dohaense isolates. The former four species exhibited low MICs for five antifungal azoles but showed high MICs for amphotericin B. T. dohaense demonstrated the lowest amphotericin B MIC (1 mg/liter). For the majority of T. asahii isolates, amphotericin B MICs were high (MIC at which 90% of isolates were inhibited [MIC90], ≥16 mg/liter), and except for fluconazole (MIC90, 8 mg/liter), the azole MICs were low: MIC90s were 0.5 mg/liter for itraconazole, 0.25 mg/liter for voriconazole, 0.25 mg/liter for posaconazole, and 0.125 mg/liter for isavuconazole. The echinocandins, caspofungin and anidulafungin, demonstrated no activity against Trichosporon species. PMID:19321719

  19. Giant Electron-Hole Interactions in Confined Layered Structures for Molecular Oxygen Activation.

    PubMed

    Wang, Hui; Chen, Shichuan; Yong, Dingyu; Zhang, Xiaodong; Li, Shuang; Shao, Wei; Sun, Xianshun; Pan, Bicai; Xie, Yi

    2017-04-05

    Numerous efforts have been devoted to understanding the excitation processes of photocatalysts, whereas the potential Coulomb interactions between photogenerated electrons and holes have been long ignored. Once these interactions are considered, excitonic effects will arise that undoubtedly influence the sunlight-driven catalytic processes. Herein, by taking bismuth oxyhalide as examples, we proposed that giant electron-hole interactions would be expected in confined layered structures, and excitons would be the dominating photoexcited species. Photocatalytic molecular oxygen activation tests were performed as a proof of concept, where singlet oxygen generation via energy transfer process was brightened. Further experiments verify that structural confinement is curial to the giant excitonic effects, where the involved catalytic process could be readily regulated via facet-engineering, thus enabling diverse reactive oxygen species generation. This study not only provides an excitonic prospective on photocatalytic processes, but also paves a new approach for pursuing systems with giant electron-hole interactions.

  20. Molecular Mechanisms of Sulbactam Antibacterial Activity and Resistance Determinants in Acinetobacter baumannii

    PubMed Central

    Penwell, William F.; Shapiro, Adam B.; Giacobbe, Robert A.; Gu, Rong-Fang; Gao, Ning; Thresher, Jason; McLaughlin, Robert E.; Huband, Michael D.; DeJonge, Boudewijn L. M.; Ehmann, David E.

    2015-01-01

    Sulbactam is a class A β-lactamase inhibitor with intrinsic whole-cell activity against certain bacterial species, including Acinetobacter baumannii. The clinical use of sulbactam for A. baumannii infections is of interest due to increasing multidrug resistance in this pathogen. However, the molecular drivers of its antibacterial activity and resistance determinants have yet to be precisely defined. Here we show that the antibacterial activities of sulbactam vary widely across contemporary A. baumannii clinical isolates and are mediated through inhibition of the penicillin-binding proteins (PBPs) PBP1 and PBP3, with very low frequency of resistance; the rare pbp3 mutants with high levels of resistance to sulbactam are attenuated in fitness. These results support further investigation of the potential clinical utility of sulbactam. PMID:25561334

  1. Molecular mechanisms of sulbactam antibacterial activity and resistance determinants in Acinetobacter baumannii.

    PubMed

    Penwell, William F; Shapiro, Adam B; Giacobbe, Robert A; Gu, Rong-Fang; Gao, Ning; Thresher, Jason; McLaughlin, Robert E; Huband, Michael D; DeJonge, Boudewijn L M; Ehmann, David E; Miller, Alita A

    2015-03-01

    Sulbactam is a class A β-lactamase inhibitor with intrinsic whole-cell activity against certain bacterial species, including Acinetobacter baumannii. The clinical use of sulbactam for A. baumannii infections is of interest due to increasing multidrug resistance in this pathogen. However, the molecular drivers of its antibacterial activity and resistance determinants have yet to be precisely defined. Here we show that the antibacterial activities of sulbactam vary widely across contemporary A. baumannii clinical isolates and are mediated through inhibition of the penicillin-binding proteins (PBPs) PBP1 and PBP3, with very low frequency of resistance; the rare pbp3 mutants with high levels of resistance to sulbactam are attenuated in fitness. These results support further investigation of the potential clinical utility of sulbactam.

  2. Analysis of Molecular Species Profiles of Ceramide-1-phosphate and Sphingomyelin Using MALDI-TOF Mass Spectrometry.

    PubMed

    Yamashita, Ryouhei; Tabata, Yumika; Iga, Erina; Nakao, Michiyasu; Sano, Shigeki; Kogure, Kentaro; Tokumura, Akira; Tanaka, Tamotsu

    2016-02-01

    Ceramide-1-phosphate (C1P) is a potential signaling molecule that modulates various cellular functions in animals. It has been known that C1P with different N-acyl lengths induce biological responses differently. However, molecular species profiles of the C1P in animal tissues have not been extensively examined yet. Here, we developed a method for determination of the molecular species of a C1P using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with Phos-tag, a phosphate capture molecule. The amounts of total C1P in skin, brain, liver, kidney and small intestine of mice were determined to be 344, 151, 198, 96 and 90 pmol/g wet weight, respectively. We found a C1P species having an α-hydroxypalmitoyl residue (h-C1P, 44 pmol/g wet weight) in mouse skin. The h-C1P was detected only in the skin, and not other tissues of mice. The same analysis was applied to sphingomyelin after conversion of sphingomyelin to C1P by Streptomyces chromofuscus phospholipase D. We found that molecular species profiles of sphingomyelin in skin, kidney and small intestine of mice were similar to those of C1P in corresponding tissues. In contrast, molecular species profiles of sphingomyelin in liver and brain were quite different from those of C1P in these tissues, indicating selective synthesis or degradation of C1P in these tissues. The method described here will be useful for detection of changes in molecular species profiles of C1P and sphingomyelin.

  3. Molecular systematics of marine gregarine apicomplexans from Pacific tunicates, with descriptions of five novel species of Lankesteria.

    PubMed

    Rueckert, Sonja; Wakeman, Kevin C; Jenke-Kodama, Holger; Leander, Brian S

    2015-08-01

    The eugregarines are a group of apicomplexan parasites that mostly infect the intestines of invertebrates. The high level of morphological variation found within and among species of eugregarines makes it difficult to find consistent and reliable traits that unite even closely related lineages. Based mostly on traits observed with light microscopy, the majority of described eugregarines from marine invertebrates has been classified into a single group, the Lecudinidae. Our understanding of the overall diversity and phylogenetic relationships of lecudinids is very poor, mainly because only a modest amount of exploratory research has been done on the group and very few species of lecudinids have been characterized at the molecular phylogenetic level. In an attempt to understand the diversity of marine gregarines better, we surveyed lecudinids that infect the intestines of Pacific ascidians (i.e. sea squirts) using ultrastructural and molecular phylogenetic approaches; currently, these species fall within one genus, Lankesteria. We collected lecudinid gregarines from six ascidian host species, and our data demonstrated that each host was infected by a different species of Lankesteria: (i) Lankesteria hesperidiiformis sp. nov., isolated from Distaplia occidentalis, (ii) Lankesteria metandrocarpae sp. nov., isolated from Metandrocarpa taylori, (iii) Lankesteria halocynthiae sp. nov., isolated from Halocynthia aurantium, (iv) Lankesteria herdmaniae sp. nov., isolated from Herdmania momus, (v) Lankesteria cf. ritterellae, isolated from Ritterella rubra, and (vi) Lankesteria didemni sp. nov., isolated from Didemnum vexillum. Visualization of the trophozoites with scanning electron microscopy showed that four of these species were covered with epicytic folds, whereas two of the species were covered with a dense pattern of epicytic knobs. The molecular phylogenetic data suggested that species of Lankesteria with surface knobs form a clade that is nested within a paraphyletic

  4. A new species of Haemoproteus from a tortoise (Testudo graeca) in Turkey, with remarks on molecular phylogenetic and morphological analysis.

    PubMed

    Orkun, Ömer; Güven, Esin

    2013-02-01

    Haemoproteus anatolicum n. sp. was identified in the tortoise Testudo graeca. The new species is described based on the morphology of its blood stages and a segment of the mitochondrial cytochrome b gene, which can be used for molecular identification and diagnosis. Chelonian haemoproteids recorded in the past were defined solely on the basis of their morphological characteristics. The chelonian haemoproteid we describe as a new species has a close genetic relationship to lizard haemoproteids, i.e., Haemoproteus ptyodactylii and Haemoproteus kopki. The new species description provides significant new information for little-known chelonian haemoproteids.

  5. 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

  6. RNA polymerase active center: the molecular engine of transcription.

    PubMed

    Nudler, Evgeny

    2009-01-01

    RNA polymerase (RNAP) is a complex molecular machine that governs gene expression and its regulation in all cellular organisms. To accomplish its function of accurately producing a full-length RNA copy of a gene, RNAP performs a plethora of chemical reactions and undergoes multiple conformational changes in response to cellular conditions. At the heart of this machine is the active center, the engine, which is composed of distinct fixed and moving parts that serve as the ultimate acceptor of regulatory signals and as the target of inhibitory drugs. Recent advances in the structural and biochemical characterization of RNAP explain the active center at the atomic level and enable new approaches to understanding the entire transcription mechanism, its exceptional fidelity and control.

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

    DTIC Science & Technology

    2015-11-18

    SECURITY CLASSIFICATION OF: The Laboratory for Ecological , Evolutionary and Conservation Genetics in the College of Natural Resources at the...Monitoring of Species of Conservation Concern on Department of Defense Lands Report Title The Laboratory for Ecological , Evolutionary and Conservation...sympatric carnivores, Molecular Ecology Resources, (07 2015): 1. doi: 10.1111/1755-0998.12356 Susannah P. Woodruff, Jennifer R. Adams, Timothy R

  8. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp.) in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry

    PubMed Central

    Cunha, Haydée A.; de Castro, Rocio Loizaga; Secchi, Eduardo R.; Crespo, Enrique A.; Lailson-Brito, José; Azevedo, Alexandre F.; Lazoski, Cristiano; Solé-Cava, Antonio M.

    2015-01-01

    The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution. PMID:26559411

  9. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp.) in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry.

    PubMed

    Cunha, Haydée A; de Castro, Rocio Loizaga; Secchi, Eduardo R; Crespo, Enrique A; Lailson-Brito, José; Azevedo, Alexandre F; Lazoski, Cristiano; Solé-Cava, Antonio M

    2015-01-01

    The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution.

  10. Molecular, morphological, and ecological niche differentiation of sympatric sister oak species, Quercus virginiana and Q. geminata (Fagaceae).

    PubMed

    Cavender-Bares, Jeannine; Pahlich, Annette

    2009-09-01

    The genus Quercus (the oaks) is notorious for interspecific hybrization, generating questions about the mechanisms that permit coexistence of closely related species. Two sister oak species, Quercus virginiana and Q. geminata, occur in sympatry in Florida and throughout the southeastern United States. In 11 sites from northern and southeastern regions of Florida, we used a leaf-based morphological index to identify individuals to species. Eleven nuclear microsatellite markers significantly differentiated between the species with a high correspondence between molecular and morphological typing of specimens. Nevertheless, Bayesian clustering analysis indicates interspecific gene flow, and six of 109 individuals had mixed ancestry. The identity of several individuals also was mismatched using molecular markers and morphological characters. In a common environment, the two species performed differently in terms of photosynthetic performance and growth, corresponding to their divergent ecological niches with respect to soil moisture and other edaphic properties. Our data support earlier hypotheses that divergence in flowering time causes assortative mating, allowing these ecologically distinct sister species to occur in sympatry. Limited gene flow that permits ecological differentiation helps to explain the overdispersion of oak species in local communities.

  11. Revision of the Sundaland species of the genus Dysphaea Selys, 1853 using molecular and morphological methods, with notes on allied species (Odonata: Euphaeidae).

    PubMed

    Hämäläinen, Matti; Dow, Rory A; Stokvis, Frank R

    2015-04-29

    The Sundaland species of the genus Dysphaea were studied using molecular and morphological methods. Four species are recognized: D. dimidiata Selys, D. lugens Selys, D. ulu spec. nov. (holotype ♂, from Borneo, Sarawak, Miri division, Upper Baram, Sungai Pejelai, Ulu Moh, 24 viii 2014; deposited in RMNH) and D. vanida spec. nov. (holotype ♂, from Thailand, Ranong province, Khlong Nakha, Khlong Bang Man, 12-13 v 1999; deposited in RMNH). The four species are described and illustrated for both sexes, with keys provided. The type specimens of the four Dysphaea taxa named by E. de Selys Longchamps, i.e. dimidiata, limbata, semilimbata and lugens, were studied and their taxonomic status is discussed. Lectotypes are designated for D. dimidiata and D. limbata. D. dimidiata is recorded from Palawan (the Philippines) for the first time. A molecular analysis using three markers (COI, 16S and 28S) is presented. This includes specimens of three Sundaland species of the genus (D. lugens missing) and two congeners from other regions (D. basi-tincta and D. gloriosa). Notes and photographs of the male holotype of D. walli Fraser (from Maymyo, Burma) are provided.

  12. Hydrogen species in diamond: Molecular dynamics simulation in bulk diamond for fusion applications

    NASA Astrophysics Data System (ADS)

    Delgado, D.; Vila, R.

    2014-09-01

    For an electron cyclotron resonance heating system, a diamond window seems to be the only material able to withstand the high microwave power and radiation effects and at the same time act as a tritium barrier. Therefore it is important to understand the evolution of hydrogen isotopes in diamond. Both, hydrogen content and radiation can quite rapidly degrade its excellent properties. Hydrogen isotopes can be introduced in the material by two processes: (1) during the growth process of synthetic samples and (2) as a neutron radiation effect when devices are exposed to a fusion irradiation environment. In the last case, both device performance (thermal, optical and dielectric properties degradation) and hands-on maintenance of the window (tritium inventory), demand a good knowledge of hydrogen species concentrations and their evolution with lattice damage. In this paper, a classical molecular dynamics study analyses the hydrogen equilibrium sites in diamond, and also their bulk and interstitial vibrational characteristics, including isotopic shifts. Some interesting results are presented and discussed. We confirm that the bond-centred site is the more stable configuration for H. Vibrational studies show lines in the C-H stretching region. Isotopic studies reveal ratios close to the theoretical ones for BC and ET sites. On the contrary, the AB site vibrations obtained suggest the existence of a local carbon oscillation.

  13. Susceptibility and molecular characterization of Candida species from patients with vulvovaginitis.

    PubMed

    Fornari, Gheniffer; Vicente, Vania Aparecida; Gomes, Renata Rodrigues; Muro, Marisol Dominguez; Pinheiro, Rosangela Lameira; Ferrari, Carolina; Herkert, Patricia Fernanda; Takimura, Marcos; Carvalho, Newton Sérgio de; Queiroz-Telles, Flavio

    2016-01-01

    Vulvovaginal candidiasis affects women of reproductive age, which represents approximately 15-25% of vaginitis cases. The present study aimed to isolate and characterize yeast from the patients irrespective of the presentation of clinical symptoms. The isolates were subjected to in vitro susceptibility profile and characterization by molecular markers, which intended to assess the distribution of species. A total of 40 isolates were obtained and identified through the CHROMagar, API20aux and by ITS and D1/D2 regions sequencing of DNAr gene. Candida albicans strains were genotyped by the ABC system and the isolates were divided into two genotypic groups. The identity of the C. albicans, C. glabrata, C. guilliermondii, C. kefyr and Saccharomyces cerevisiae isolates was confirmed by the multilocus analysis. The strains of Candida, isolated from patients with complications, were found to be resistant to nystatin but sensitive to fluconazole, amphotericin B and ketoconazole, as observed by in vitro sensitivity profile. The isolates from asymptomatic patients, i.e., the colonized group, showed a dose-dependent sensitivity to the anti-fungal agents, fluconazole and amphotericin B. However, the isolates of C. albicans that belong to distinct genotypic groups showed the same in vitro susceptibility profile.

  14. Molecular evidence for a spotted fever group Rickettsia species in the tick Amblyomma longirostre in Brazil.

    PubMed

    Labruna, Marcelo B; McBride, Jere W; Bouyer, Donal H; Camargo, Luis Marcelo A; Camargo, Erney P; Walker, David H

    2004-05-01

    Two Amblyomma longirostre adult male ticks were collected from a Brazilian porcupine Coendou prehensilis L. in the state of Rondonia, Western Amazon, Brazil. The two ticks were pooled for DNA extraction and tested for the presence of rickettsial DNA by amplifying portions of the gltA, 17-kDa, ompA, and ompB rickettsial genes by polymerase chain reaction (PCR). Portions of the four genes were amplified from the sample and subsequently sequenced. These results indicated the presence of a Rickettsia strain infecting A. longirostre, which was designated as strain Aranha. Compared with homologous ompA rickettsial sequences, "Rickettsia amblyommii" ompA seemed to be the closest relative to Aranha (similarity values: 99.0-99.3%). Phylogenetic analyses of more conserved genes including 17-kDa and gtlA partial sequences indicated that this Rickettsia sp. is a spotted fever group rickettsia. The partial ompB sequence of strain Aranha was distinct from all homologous sequences available in GenBank. Although our ompA analysis suggested a very close molecular phylogenetic relationship of Aranha with "R. amblyommii," we cannot at this time determine if Aranha is a new strain of "R. amblyommii" or a new Rickettsia species in South America.

  15. Studies for the Loss of Atomic and Molecular Species from Io

    NASA Technical Reports Server (NTRS)

    Combi, Michael R.

    1997-01-01

    The general objective of this project has been to advance our 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 scientific objectives of the larger collaborative program between AER, Inc., and the University of Michigan have been to undertake theoretical modeling studies to simulate the distributions of the exospheric gases in Io's corona and extended clouds, to investigate the importance of the various physical processes that shape their relative abundances, and with these tools to analyze observations of O, S and Na obtained by four observers: M.A. McGrath of the Space Telescope Science Institute and G.E. Ballester of the University of Michigan who each have obtained Hubble Space Telescope observations of O and S near Io, F. Scherb who continues an effort to obtain 6300 A OI observations as part of the University of Wisconsin Fabry-Perot program, and N.M. Schneider of the University of Colorado who obtained an extensive set of spectral and spatial observations of the Na emission near Io in the D-lines.

  16. Molecular characterization of five betacryptoviruses infecting four clover species and dill.

    PubMed

    Lesker, Till; Rabenstein, Frank; Maiss, Edgar

    2013-09-01

    The family Partitiviridae includes plant (Alphacryptovirus and Betacryptovirus), fungal (Partitivirus) and protozoan (Cryspovirus) viruses with bisegmented dsRNA genomes and isometric virions. Cryptic viruses commonly occur in different plant species without causing any symptoms. So far, numerous sequences have been determined for viruses of the genus Alphacryptovirus, but no sequence is available for any assigned member of the genus Betacryptovirus. Following extraction, cloning and sequence analysis of double-stranded RNA in this study, we report the molecular properties of three assigned members of the genus Betacryptovirus, white clover cryptic virus 2, red clover cryptic virus 2 and hop trefoil cryptic virus 2, and two new putative betacryptoviruses found in crimson clover and dill. Betacryptoviruses share sequence motifs with members of the genus Partitivirus. In phylogenetic analyses, members of the genus Betacryptovirus formed a new sub-cluster within the clusters containing members of the genus Partitivirus. Our results provide evidence for a distinct evolutionary lineage of dsRNA viruses of plants and fungi.

  17. What causes canine sino-nasal aspergillosis? A molecular approach to species identification.

    PubMed

    Talbot, Jessica J; Johnson, Lynelle R; Martin, Patricia; Beatty, Julia A; Sutton, Deanna A; Billen, Frédéric; Halliday, Catriona L; Gibson, Justine S; Kidd, Sarah; Steiner, Jörg M; Ujvari, Beata; Barrs, Vanessa R

    2014-04-01

    On the basis of phenotypic identification methods, Aspergillus fumigatus is reported as the most commonly identified aetiological agent of canine sino-nasal aspergillosis (SNA). However, definitive identification of Aspergillus spp. using phenotypic features alone is unreliable. The aim of this study was to determine the molecular identities of fungal species causing SNA in dogs. Genomic DNA was extracted from 91 fungal isolates from 90 dogs diagnosed with SNA in Australia, the USA and Belgium, and the ITS1-5.8S-ITS2 ribosomal DNA and partial β-tubulin regions were sequenced. Eighty-eight of 91 (96.7%) isolates were identified as A. fumigatus and 3/91 (3.3%) belonged to Aspergillus section Nigri spp. (Aspergillus tubingensis: 2/91; Aspergillus uvarum: 1/91). These findings confirm that A. fumigatus is the most common aetiological agent of canine SNA. This is the first report to document a pathogenic role for A. tubingensis and A. uvarum in dogs.

  18. Fiber optic apparatus for detecting molecular species by surface enhanced Raman spectroscopy

    DOEpatents

    Angel, Stanley M.; Sharma, Shiv K.

    1988-01-01

    Optrode apparatus for detecting constituents of a fluid medium includes an optical fiber (13, 13a to 13e) having a metal coating (22, 22a to 22e) on at least a portion of a light transmissive core (17, 17a to 17d). The metal is one, such as silver, gold or copper, which enhances emission of Raman signal frequencies by molecules adsorbed on the surface of the coating when monochromatic probe light of a different frequency is scattered by such molecules and the metal coating is sufficiently thin to transmit light between the absorbed molecules and the core of the fiber. Probe light is directed into one end of the fiber and a detector (16, 16d, 16e) analyzes light emitted from the fiber for Raman frequencies that identify one or more particular molecular species. In one form, the optrode (13e) may function as a working electrode of an electrochemical cell (53) while also serving to detect the products of oxidation or reduction reactions which occur at the electrode surface.

  19. Studies for the Loss of Atomic and Molecular Species from Io

    NASA Technical Reports Server (NTRS)

    Smyth, William H.

    1999-01-01

    A summary discussion of research undertaken in this project is presented and is related to six published papers attached in the appendix. The discussion is divided into six sections describing a variety of studies for the loss of atomic and molecular species from Io. They include studies for: (1) atomic sodium, (2) SO2, (3) O and S, (4) spectacular high-spatial resolution ultraviolet image observations of O, S, and possibly H in Io's atmosphere and/or corona acquired by the Space Telescope Imaging Spectrometer (STIS) of the Hubble Space Telescope (HST), (5) spectacular high-spatial resolution visible Io eclipse image observations acquired by the Solid State Imager (SSI) of Galileo spacecraft, (6) ground-based observations acquired by the Solid State Imager (SSI) of Galileo spacecraft, and (7) ground-based observations of Io's neutral cloud in [OI] 6300 angstrom emission. New source rates at Io's exobase for SO2, O, and H are given and a variety of interesting implications for Io's atmosphere and for the Io plasma torus are discussed. Appendices that are comprised of articles published during the contract are also presented.

  20. Heterogeneous rates of molecular evolution among cryptic species of the ciliate morphospecies Chilodonella uncinata

    PubMed Central

    Katz, Laura A.; DeBerardinis, Jennifer; Hall, Meaghan S.; Kovner, Alexandra M.; Dunthorn, Micah; Muse, Spencer V.

    2012-01-01

    While molecular analyses have provided insight into the phylogeny of ciliates, the few studies assessing intraspecific variation have largely relied on just a single locus (e.g. nuclear small subunit rDNA (nSSU-rDNA) or mitochondrial cytochrome oxidase I). In this study, we characterize the diversity of several nuclear protein-coding genes plus both nSSU-rDNA and mitochondrial small subunit rDNA (mtSSU-rDNA) of five isolates of the ciliate morphospecies Chilodonella uncinata. Although these isolates have nearly identical nSSU-rDNA sequences, they differ by up to 8.0% in mtSSU-rDNA. Comparative analyses of all loci, including β-tubulin paralogs, indicate a lack of recombination between strains, demonstrating that the morphospecies C. uncinata consists of multiple cryptic species. Further, there is considerable variation in substitution rates among loci as some protein-coding domains are nearly identical between isolates while others differ by up to 13.2% at the amino acid level. Combining insights on macronuclear variation among isolates, the focus of this study, with published data from the micronucleus of two of these isolates indicates that C. uncinata lineages are able to maintain both highly divergent and highly conserved genes within a rapidly evolving germline genome. PMID:22258433

  1. New Molecular Species In Comet C/1995 (Hale-Bopp) Observed with the Caltech Submillimeter Observatory

    NASA Technical Reports Server (NTRS)

    Lis, D. C.; Mehringer, D. M.; Benford, D.; Gardner, M.; Phillips, T. G.; Bockelee-Morvan, D.; Biver, N.; Colom, P.; Crovisier, J.; Despois, D.; Rauer, H.

    1998-01-01

    We present millimeter-wave observations of HNCO, HC3N, SO, NH2CHO, H(13)CN, and H3O(+) in comet C/1995 O1 (Hale-Bopp) obtained in February-April, 1997 with the Caltech Submillimeter Observatory (CSO). HNCO, first detected at the CSO in comet C/1996 B2 (Hyakutake), is securely confirmed in comet Hale-Bopp via observations of three rotational transitions. The derived abundance with respect to H2O is (4-13) x 10(exp -4). HC3N, SO, and NH2CHO are detected for the first time in a comet. The fractional abundance of HC3N based on observations of three rotational lines is (1.9 +/- 0.2) x 10(exp -4). Four transitions of SO are detected and the derived fractional abundance, (2-8) x 10(exp -3), is higher than the upper limits derived from UV observations of previous comets. Observations of NH2CHO imply a fractional abundance of (1-8) x 10(exp -4). H3O(+) is detected for the first time from the ground. The H(13)CN (3-2) transition is also detected and the derived HCN/H(13)CN abundance ratio is 90 +/- 15, consistent with the terrestrial C-13/C-12 ratio. in addition, a number of other molecular species are detected, including HNC, OCS, HCO(+), CO(+), and CN (the last two are first detections in a comet at radio wavelengths).

  2. Direct spectroscopy of exoplanets revealing the presence of various molecular species

    NASA Astrophysics Data System (ADS)

    Konopacky, Quinn M.

    2017-01-01

    In the past decade, several new jovian exoplanets at wide separations have been revealed using ground based telescopes equipped with adaptive optics systems. These planets, with masses between ~2-14 MJup, remain a puzzle for both major planet formation models - core accretion and gravitational instability. At the same time, they offer a powerful tool in the hunt for observational constraints of formation, as they can be characterized with both imaging and spectroscopy. I will describe our recent efforts to push beyond the discovery phase into the realm of detailed characterization of these planetary systems. Using Keck, we have been targeting the HR 8799 multiplanet system. OSIRIS observations of HR 8799b and c have yielded the best-ever spectra for any exoplanet. These observations have allowed us to resolve molecular lines for species such as water, carbon monoxide and methane. Using these observations, we have measured the C/O ratio in these planets, which can be used as a diagnostic for planet formation. Our observations demonstrate the power of the Keck adaptive optics instrument suite to offer a new window into planet formation and evolution.

  3. Poly(ADP-ribose) polymerase activity in mononuclear leukocytes of 13 mammalian species correlates with species-specific life span.

    PubMed Central

    Grube, K; Bürkle, A

    1992-01-01

    Poly(ADP-ribosyl)ation is a eukaryotic posttranslational modification of proteins that is strongly induced by the presence of DNA strand breaks and plays a role in DNA repair and the recovery of cells from DNA damage. We compared poly(ADP-ribose) polymerase (PARP; EC 2.4.2.30) activities in Percoll gradient-purified, permeabilized mononuclear leukocytes from mammalian species of different maximal life span. Saturating concentrations of a double-stranded octameric oligonucleotide were applied to provide a direct and maximal stimulation of PARP. Our results on 132 individuals from 13 different species yield a strong positive correlation between PARP activity and life span (r = 0.84; P << 0.001), with human cells displaying approximately 5 times the activity of rat cells. Intraspecies comparisons with both rat and human cells from donors of all age groups revealed some decline of PARP activity with advancing age, but it was only weakly correlated. No significant polymer degradation was detectable under our assay conditions, ruling out any interference by poly(ADP-ribose) glycohydrolase activity. By Western blot analysis of mononuclear leukocytes from 11 species, using a crossreactive antiserum directed against the extremely well-conserved NAD-binding domain, no correlation between the amount of PARP protein and the species' life spans was found, suggesting a greater specific enzyme activity in longer-lived species. We propose that a higher poly(ADP-ribosyl)ation capacity in cells from long-lived species might contribute to the efficient maintenance of genome integrity and stability over their longer life span. Images PMID:1465394

  4. Molecular abundances and low-mass star formation. 1: Si- and S-bearing species toward IRAS 16293-2422

    NASA Technical Reports Server (NTRS)

    Blake, Geoffrey A.; Dishoek, Ewine F. Van; Jansen, David J.; Groesbeck, T. D.; Mundy, Lee G.

    1994-01-01

    Results from millimeter and submillimeter spectral line surveys of the protobinary source Infrared Astronomical Satellite (IRAS) 16293-2422 are presented. Here we outline the abundances of silicon- and sulfur-containing species. A combination of rotation diagram and full statistical equilibrium/radiative transfer calculations is used to constrain the physical conditions toward IRAS 16293 and to construct its beam-averaged chemical composition over a 10 to 20 sec (1600 to 3200 AU) scale. The chemical complexity as judged by species such as SiO, OCS, and H2S, is intermediate between that of dark molecular clouds such as L134N and hot molecular cloud cores such as Orion KL. From the richness of the spectra compared to other young stellar objects of similar luminosity, it is clear that molecular abundances do not scale simply with mass; rather, the chemistry is a strong function of evolutionary state, i.e., age.

  5. 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

  6. Molecular characterization of high plant species using PCR with primers designed from consensus branch point signal sequences.

    PubMed

    Xiong, Faqian; Jiang, Jing; Han, Zhuqiang; Zhong, Ruichun; He, Liangqiong; Zhuang, Weijian; Tang, Ronghua

    2011-06-01

    A novel method is introduced for producing molecular markers in plants using single 15- to 18-mer PCR primers designed from the short conserved consensus branch point signal sequences and standard agarose gel electrophoresis. This method was tested on cultivated peanut and verified to give good fingerprinting results in other plant species (mango, banana, and longan). These single primers, designed from relatively conserved branch point signal sequences within gene introns, should be universal across other plant species. The method is rapid, simple, and efficient, and it requires no sequence information of the plant genome of interest. It could be used in conjunction with, or as a substitute for, conventional RAPD or ISSR techniques for applications including genetic diversity analysis, phylogenetic tree construction, and quantitative trait locus mapping. This technique provides a new way to develop molecular markers for assessing genetic diversity of germplasm in diverse species based on conserved branch point signal sequences.

  7. Molecular phylogeny of the genus Asparagus (Asparagaceae) explains interspecific crossability between the garden asparagus (A. officinalis) and other Asparagus species.

    PubMed

    Kubota, Shosei; Konno, Itaru; Kanno, Akira

    2012-02-01

    The genus Asparagus comprises approximately 200 species, some of which are commercially cultivated, such as the garden asparagus (A. officinalis). Many Asparagus species, including A. officinalis, are dioecious and have been grouped into a subgenus distinct from that of hermaphroditic species. Although many interspecific crossings have been attempted to introduce useful traits into A. officinalis, only some of the dioecious species were found to be cross-compatible with A. officinalis. Here, molecular phylogenetic analyses were conducted to determine whether interspecific crossability is proportional to the genetic distance between the crossing pairs and to further clarify the evolutionary history of the Asparagus genus. A clade with all cross-compatible species and no cross-incompatible species was recovered in the phylogenetic tree based on analyses of non-coding cpDNA regions. In addition, a sex-linked marker developed for A. officinalis amplified a male-specific region in all cross-compatible species. The phylogenetic analyses also provided some insights about the evolutionary history of Asparagus; for example, by indicating that the genus had its origin in southern Africa, subsequently spreading throughout the old world through intensive speciation and dispersal. The results also suggest that dioecious species were derived from a single evolutionary transition from hermaphroditism in Asparagus. These findings not only contribute towards the understanding of the evolutionary history of the genus but may also facilitate future interspecific hybridization programs involving Asparagus species.

  8. The evolution of endothermy: role for membranes and molecular activity.

    PubMed

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

    2004-01-01

    On the basis of the comparative approach and three models of metabolism (endothermic and ectothermic vertebrates, body mass, and mammalian development), we suggest that a few common cellular processes, linked either directly or indirectly to membranes, consume the majority of energy used by most organisms; that membranes act as pacemakers of metabolism through changes in lipid composition, altering membrane characteristics and the working environment of membrane proteins--specifically, that changes in the membrane environment similarly affect the molecular activities (specific rates of activity) of membrane-bound proteins; and that polyunsaturation of membranes increases whereas monounsaturation decreases the activity of membrane proteins. Experiments designed to test this theory using the sodium pump support this supposition. Potential mechanisms considered include fluidity, electrical fields, and related surface area requirements of lipids. In considering the evolution of endothermy in mammals, for example, if the first mammals were small, possibly nocturnal and active organisms, all these factors would favour increased polyunsaturation of membranes. Such changes (from monounsaturated to polyunsaturated membranes) would allow membranes to set the pace of metabolism in the evolution of endothermy.

  9. Interfacial activation-based molecular bioimprinting of lipolytic enzymes.

    PubMed Central

    Mingarro, I; Abad, C; Braco, L

    1995-01-01

    Interfacial activation-based molecular (bio)-imprinting (IAMI) has been developed to rationally improve the performance of lipolytic enzymes in nonaqueous environments. The strategy combinedly exploits (i) the known dramatic enhancement of the protein conformational rigidity in a water-restricted milieu and (ii) the reported conformational changes associated with the activation of these enzymes at lipid-water interfaces, which basically involves an increased substrate accessibility to the active site and/or an induction of a more competent catalytic machinery. Six model enzymes have been assayed in several model reactions in nonaqueous media. The results, rationalized in light of the present biochemical and structural knowledge, show that the IAMI approach represents a straightforward, versatile method to generate manageable, activated (kinetically trapped) forms of lipolytic enzymes, providing under optimal conditions nonaqueous rate enhancements of up to two orders of magnitude. It is also shown that imprintability of lipolytic enzymes depends not only on the nature of the enzyme but also on the "quality" of the interface used as the template. PMID:7724558

  10. Interfacial activation-based molecular bioimprinting of lipolytic enzymes.

    PubMed

    Mingarro, I; Abad, C; Braco, L

    1995-04-11

    Interfacial activation-based molecular (bio)-imprinting (IAMI) has been developed to rationally improve the performance of lipolytic enzymes in nonaqueous environments. The strategy combinedly exploits (i) the known dramatic enhancement of the protein conformational rigidity in a water-restricted milieu and (ii) the reported conformational changes associated with the activation of these enzymes at lipid-water interfaces, which basically involves an increased substrate accessibility to the active site and/or an induction of a more competent catalytic machinery. Six model enzymes have been assayed in several model reactions in nonaqueous media. The results, rationalized in light of the present biochemical and structural knowledge, show that the IAMI approach represents a straightforward, versatile method to generate manageable, activated (kinetically trapped) forms of lipolytic enzymes, providing under optimal conditions nonaqueous rate enhancements of up to two orders of magnitude. It is also shown that imprintability of lipolytic enzymes depends not only on the nature of the enzyme but also on the "quality" of the interface used as the template.

  11. 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

  12. An optimized molecular inclusion complex of diferuloylmethane: enhanced physical properties and biological activity

    PubMed Central

    Tan, Qunyou; Li, Yi; Wu, Jianyong; Mei, Hu; Zhao, Chunjing; Zhang, Jingqing

    2012-01-01

    Objective The purpose of this study was to explore and evaluate the enhanced physical properties and biological activity of a molecular inclusion complex (MICDH) comprising diferuloylmethane (DFM) and hydroxypropyl-β-cyclodextrin. Methods The preparation conditions of MICDH were optimized using an orthogonal experimental design. The solubility, in vitro release and model fitting, microscopic morphology, molecular structure simulation, anti-lung cancer activity, and action mechanism of MICDH were evaluated. Results The solubility of DFM was improved 4400-fold upon complexation with hydroxypropyl-β-cyclodextrin. The release rate of DFM was significantly higher from MICDH than from free DFM. MICDH exhibited higher antitumor activity against human lung adenocarcinoma A549 cells than free DFM. More cells were arrested in the S/G2 phase of the cell cycle or were induced to undergo apoptosis when treated with MICDH than when treated with free DFM. Furthermore, increased reactive oxygen species and intracellular calcium ion levels and decreased mitochondrial membrane potential were observed in cells treated with MICDH. Conclusion MICDH markedly improved the physical properties and antitumor activity of DFM. MICDH may prove to be a preferred alternative to free DFM as a formulation for DFM delivery in lung cancer treatment. PMID:23091376

  13. Regional endemism and cryptic species revealed by molecular and morphological analysis of a widespread species of Neotropical catfish.

    PubMed

    Martin, A P; Bermingham, E

    2000-06-07

    The lower Central American landscape was fully emergent approximately three million years ago, an event which marked the beginning of the Great American biotic interchange. Freshwater fishes participated in the biotic interchange. Because primary freshwater fishes are restricted to freshwater, they provide an excellent system for investigating the interplay of historical and recent processes on the assembly, structure and diversity of the regions' aquatic ecosystems. We focused on examining the history of diversification for a species of catfish (Pimelodella chagresi) whose distribution spans multiple, isolated drainage basins across the Isthmian landscape and into north-western South America. Analysis of mitochondrial DNA haplotypes and morphological traits indicated that P. chagresi, as currently recognized, comprises a species complex. In addition, along the Pacific slope of Panama, repeated dispersion, diversification, extinction and possibly hybridization are thought to underlie a complex distribution of haplotypes. Overall, the results underscore the tremendous importance of historical processes on regional biodiversity.

  14. Molecular evolution and species-specific expansion of the NAP members in plants.

    PubMed

    Fan, Kai; Shen, Hao; Bibi, Noreen; Li, Feng; Yuan, Shuna; Wang, Ming; Wang, Xuede

    2015-08-01

    The NAP (NAC-Like, Activated by AP3 /PI) subfamily is one of the important plant-specific transcription factors, and controls many vital biological processes in plants. In the current study, 197 NAP proteins were identified from 31 vascular plants, but no NAP members were found in eight non-vascular plants. All NAP proteins were phylogenetically classified into two groups (NAP I and NAP II), and the origin time of the NAP I group might be relatively later than that of the NAP II group. Furthermore, species-specific gene duplications, caused by segmental duplication events, resulted in the expansion of the NAP subfamily after species-divergence. Different groups have different expansion rates, and the NAP group preference was found during the expansion in plants. Moreover, the expansion of NAP proteins may be related to the gain and loss of introns. Besides, functional divergence was limited after the gene duplication. Abscisic acid (ABA) might play an important role in leaf senescence, which is regulated by NAP subfamily. These results could lay an important foundation for expansion and evolutionary analysis of NAP subfamily in plants.

  15. Mosquito larvicidal activity of active constituent derived from Chamaecyparis obtusa leaves against 3 mosquito species.

    PubMed

    Jang, Young-Su; Jeon, Ju-Hyun; Lee, Hoi-Seon

    2005-12-01

    Mosqutio larvicidal activity of Chamaecyparis obtusa leaf-derived materials against the 4th-stage larvae of Aedes aegypti (L.), Ochlerotatus togoi (Theobald), and Culex pipiens pallens (Coquillett) was examined in the laboratory. A crude methanol extract of C. obtusa leaves was found to be active (percent mortality rough) against the 3 species larvae; the hexane fraction of the methanol extract showed a strong larvicidal activity (100% mortality) at 100 ppm. The bioactive component in the C. obtusa leaf extract was characterized as beta-thujaplicin by spectroscopic analyses. The LC50 value of beta-thujaplicin was 2.91, 2.60, and 1.33 ppm against Ae. aegypti, Oc. togoi, and Cx. pipiens pallens larvae. This naturally occurring C. obtusa leaves-derived compound merits further study as a potential mosquito larval control agent or lead compound.

  16. Long-Term Retention of Small, Volatile Molecular Species within Metallic Microcapsules.

    PubMed

    Hitchcock, James P; Tasker, Alison L; Baxter, Elaine A; Biggs, Simon; Cayre, Olivier J

    2015-07-15

    Encapsulation and full retention of small molecular weight active ingredients is a challenging task that remains unsolved by current technologies used in industry and academia. In particular, certain everyday product formulations provide difficult environments in which preventing active leakage through capsule walls is not feasible. For example, a continuous phase that can fully dissolve an encapsulated active will typically force full release over a fraction of the intended lifetime of a product. This is due to the inherent porosity of polymeric membranes typically used as capsule wall material in current technologies. In this study, we demonstrate a method for preventing undesired loss of encapsulated actives under these extreme conditions using a simple threestep process. Our developed methodology, which forms an impermeable metal film around polymer microcapsules, prevents loss of small, volatile oils within an ethanol continuous phase for at least 21 days while polymeric capsules lose their entire content in less than 30 min under the same conditions. Polymer shell-oil core microcapsules are produced using a well-known cosolvent extraction method to precipitate a polymeric shell around the oil core. Subsequently, metallic catalytic nanoparticles are physically adsorbed onto the microcapsule polymeric shells. Finally, this nanoparticle coating is used to catalyze the growth of a secondary metallic film. Specifically, this work shows that it is possible to coat polymeric microcapsules containing a model oil system or a typical fragrance oil with a continuous metal shell. It also shows that the coverage of nanoparticles on the capsule surface can be controlled, which is paramount for obtaining a continuous impermeable metal film. In addition, control over the metal shell thickness is demonstrated without altering the capability of the metal film to retain the encapsulated oils.

  17. Killer activity of yeasts isolated from natural environments against some medically important Candida species.

    PubMed

    Vadkertiová, Renata; Sláviková, Elena

    2007-01-01

    Twenty-five yeast cultures, mainly of human origin, belonging to four pathogenic yeast species--Candida albicans, Candida krusei, Candida parapsilosis, and Candida tropicalis were tested for their sensitivity to ten basidiomycetous and eleven ascomycetous yeast species isolated from the water and soil environments and from tree leaves. The best killer activity among basidiomycetous species was exhibited by Rhodotorula glutinis, and R. mucilaginosa. The other carotenoid producing species Cystofilobasidium capitatum, Sporobolomyces salmonicolor, and S. roseus were active only against about 40% of the tested strains and exhibited weak activity. The broadest killer activity among ascomycetous yeasts was shown by the strains Pichia anomala and Metschnikowia pulcherrima. The species Debaryomyces castellii, Debaryomyces hansenii, Hanseniaspora guilliermondii, Pichia membranifaciens, and Williopsis californica did not show any killer activity. The best killer activity exhibited the strains isolated from leafy material. The lowest activity pattern was found among strains originating from soil environment.

  18. Infrared Optical Properties of Solid Mixtures of Molecular Species at 20 K

    DTIC Science & Technology

    1981-01-01

    including transmittance and reflectance measurements, internal reflection spectroscopy (IRS), and polarimetry methods such as ellipsometry. Kramers-Kronig...S., Barnes, A. J., Cowieson, D., Mielke, Z., and Purnell, C. J. "Studies of Molecular Complexes by Matrix Isolation Spectroscopy ." Molecular... Spectroscopy of Dense Phases - - Proceedings of the 12th European Congress on Molecular Spectroscopy , Strasbourg, France, July l - - 4, 1975. Elsevier

  19. Molecular Evolution of the Porcine Type I Interferon Family: Subtype-Specific Expression and Antiviral Activity

    PubMed Central

    Sang, Yongming; Bergkamp, Joseph; Blecha, Frank

    2014-01-01

    Type I interferons (IFNs), key antiviral cytokines, evolve to adapt with ever-changing viral threats during vertebrate speciation. Due to novel pathogenic pressure associated with Suidae speciation and domestication, porcine IFNs evolutionarily engender both molecular and functional diversification, which have not been well addressed in pigs, an important livestock species and animal model for biomedical sciences. Annotation of current swine genome assembly Sscrofa10.2 reveals 57 functional genes and 16 pseudogenes of type I IFNs. Subfamilies of multiple IFNA, IFNW and porcine-specific IFND genes are separated into four clusters with ∼60 kb intervals within the IFNB/IFNE bordered region in SSC1, and each cluster contains mingled subtypes of IFNA, IFNW and IFND. Further curation of the 57 functional IFN genes indicates that they include 18 potential artifactual duplicates. We performed phylogenetic construction as well as analyses of gene duplication/conversion and natural selection and showed that porcine type I IFN genes have been undergoing active diversification through both gene duplication and conversion. Extensive analyses of the non-coding sequences proximal to all IFN coding regions identified several genomic repetitive elements significantly associated with different IFN subtypes. Family-wide studies further revealed their molecular diversity with respect to differential expression and restrictive activity on the resurgence of a porcine endogenous retrovirus. Based on predicted 3-D structures of representative animal IFNs and inferred activity, we categorized the general functional propensity underlying the structure-activity relationship. Evidence indicates gene expansion of porcine type I IFNs. Genomic repetitive elements that associated with IFN subtypes may serve as molecular signatures of respective IFN subtypes and genomic mechanisms to mediate IFN gene evolution and expression. In summary, the porcine type I IFN profile has been phylogenetically

  20. Development of Two Molecular Approaches for Differentiation of Clinically Relevant Yeast Species Closely Related to Candida guilliermondii and Candida famata

    PubMed Central

    Feng, Xiaobo; Wu, Jingsong; Ling, Bo; Yang, Xianwei; Liao, Wanqing

    2014-01-01

    The emerging pathogens Candida palmioleophila, Candida fermentati, and Debaryomyces nepalensis are often misidentified as Candida guilliermondii or Candida famata in the clinical laboratory. Due to the significant differences in antifungal susceptibilities and epidemiologies among these closely related species, a lot of studies have focused on the identification of these emerging yeast species in clinical specimens. Nevertheless, limited tools are currently available for their discrimination. Here, two new molecular approaches were established to distinguish these closely related species. The first approach differentiates these species by use of restriction fragment length polymorphism analysis of partial internal transcribed spacer 2 (ITS2) and large subunit ribosomal DNA with the enzymes BsaHI and XbaI in a double digestion. The second method involves a multiplex PCR based on the intron size differences of RPL18, a gene coding for a protein component of the large (60S) ribosomal subunit, and species-specific amplification. These two methods worked well in differentiation of these closely related yeast species and have the potential to serve as effective molecular tools suitable for laboratory diagnoses and epidemiological studies. PMID:24951804

  1. Development of two molecular approaches for differentiation of clinically relevant yeast species closely related to Candida guilliermondii and Candida famata.

    PubMed

    Feng, Xiaobo; Wu, Jingsong; Ling, Bo; Yang, Xianwei; Liao, Wanqing; Pan, Weihua; Yao, Zhirong

    2014-09-01

    The emerging pathogens Candida palmioleophila, Candida fermentati, and Debaryomyces nepalensis are often misidentified as Candida guilliermondii or Candida famata in the clinical laboratory. Due to the significant differences in antifungal susceptibilities and epidemiologies among these closely related species, a lot of studies have focused on the identification of these emerging yeast species in clinical specimens. Nevertheless, limited tools are currently available for their discrimination. Here, two new molecular approaches were established to distinguish these closely related species. The first approach differentiates these species by use of restriction fragment length polymorphism analysis of partial internal transcribed spacer 2 (ITS2) and large subunit ribosomal DNA with the enzymes BsaHI and XbaI in a double digestion. The second method involves a multiplex PCR based on the intron size differences of RPL18, a gene coding for a protein component of the large (60S) ribosomal subunit, and species-specific amplification. These two methods worked well in differentiation of these closely related yeast species and have the potential to serve as effective molecular tools suitable for laboratory diagnoses and epidemiological studies.

  2. 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.

  3. Unravelling molecular mechanisms from floral initiation to lipid biosynthesis in a promising biofuel tree species, Pongamia pinnata using transcriptome analysis

    PubMed Central

    Sreeharsha, Rachapudi V.; Mudalkar, Shalini; Singha, Kambam T.; Reddy, Attipalli R.

    2016-01-01

    Pongamia pinnata (L.) (Fabaceae) is a promising biofuel tree species which is underexploited in the areas of both fundamental and applied research, due to the lack of information either on transcriptome or genomic data. To investigate the possible metabolic pathways, we performed whole transcriptome analysis of Pongamia through Illumina NextSeq platform and generated 2.8 GB of paired end sequence reads. The de novo assembly of raw reads generated 40,000 contigs and 35,000 transcripts, representing leaf, flower and seed unigenes. Spatial and temporal expression profiles of photoperiod and floral homeotic genes in Pongamia, identified GIGANTEA (GI) - CONSTANS (CO) - FLOWERING LOCUS T (FT) as active signal cascade for floral initiation. Four prominent stages of seed development were selected in a high yielding Pongamia accession (TOIL 1) to follow the temporal expression patterns of key fatty acid biosynthetic genes involved in lipid biosynthesis and accumulation. Our results provide insights into an array of molecular events from flowering to seed maturity in Pongamia which will provide substantial basis for modulation of fatty acid composition and enhancing oil yields which should serve as a potential feedstock for biofuel production. PMID:27677333

  4. Active fluidization of polymer networks through molecular motors.

    PubMed

    Humphrey, D; Duggan, C; Saha, D; Smith, D; Käs, J

    2002-03-28

    Entangled polymer solutions and melts exhibit elastic, solid-like resistance to quick deformations and a viscous, fluid-like response to slow deformations. This viscoelastic behaviour reflects the dynamics of individual polymer chains driven by brownian motion: since individual chains can only move in a snake-like fashion through the mesh of surrounding polymer molecules, their diffusive transport, described by reptation, is so slow that the relaxation of suddenly imposed stress is delayed. Entangled polymer solutions and melts therefore elastically resist deforming motions that occur faster than the stress relaxation time. Here we show that the protein myosin II permits active control over the viscoelastic behaviour of actin filament solutions. We find that when each actin filament in a polymerized actin solution interacts with at least one myosin minifilament, the stress relaxation time of the polymer solution is significantly shortened. We attribute this effect to myosin's action as a 'molecular motor', which allows it to interact with randomly oriented actin filaments and push them through the solution, thus enhancing longitudinal filament motion. By superseding reptation with sliding motion, the molecular motors thus overcome a fundamental principle of complex fluids: that only depolymerization makes an entangled, isotropic polymer solution fluid for quick deformations.

  5. 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

  6. Molecular Epidemiology of Cross-Species Giardia duodenalis Transmission in Western Uganda

    PubMed Central

    Johnston, Amanda R.; Gillespie, Thomas R.; Rwego, Innocent B.; Tranby McLachlan, Traci L.; Kent, Angela D.; Goldberg, Tony L.

    2010-01-01

    Background Giardia duodenalis is prevalent in tropical settings where diverse opportunities exist for transmission between people and animals. We conducted a cross-sectional study of G. duodenalis in people, livestock, and wild primates near Kibale National Park, Uganda, where human-livestock-wildlife interaction is high due to habitat disturbance. Our goal was to infer the cross-species transmission potential of G. duodenalis using molecular methods and to investigate clinical consequences of infection. Methodology/Principal Findings Real-time PCR on DNA extracted from fecal samples revealed a combined prevalence of G. duodenalis in people from three villages of 44/108 (40.7%), with prevalence reaching 67.5% in one village. Prevalence rates in livestock and primates were 12.4% and 11.1%, respectively. Age was associated with G. duodenalis infection in people (higher prevalence in individuals ≤15 years) and livestock (higher prevalence in subadult versus adult animals), but other potential risk factors in people (gender, contact with domestic animals, working in fields, working in forests, source of drinking water, and medication use) were not. G. duodenalis infection was not associated with gastrointestinal symptoms in people, nor was clinical disease noted in livestock or primates. Sequence analysis of four G. duodenalis genes identified assemblage AII in humans, assemblage BIV in humans and endangered red colobus monkeys, and assemblage E in livestock and red colobus, representing the first documentation of assemblage E in a non-human primate. In addition, genetic relationships within the BIV assemblage revealed sub-clades of identical G. duodenalis sequences from humans and red colobus. Conclusions/Significance Our finding of G. duodenalis in people and primates (assemblage BIV) and livestock and primates (assemblage E) underscores that cross-species transmission of multiple G. duodenalis assemblages may occur in locations such as western Uganda where people

  7. Characterizing the Immune-Eliciting Activity of Putative Microbe-Associated Molecular Patterns in Tomato.

    PubMed

    Clarke, Christopher R; Vinatzer, Boris A

    2017-01-01

    Detection of conserved microbe-associated molecular patterns (MAMPs), such as bacterial flagellin, is the first line of active defense in plants against pathogenic invaders. Successful pathogens must subvert this immune response to grow to high population density and cause disease. Flagellin from the bacterial pathogen Pseudomonas was the first identified bacterial MAMP and many species across the plant kingdom have sensitive perception systems for detecting the 22-amino acid epitope known as flg22. Tomato and several other solanaceous plants are also able to independently detect a second epitope of flagellin known as flgII-28. This chapter details four experimental protocols to identify and confirm the immune response-eliciting activity of flagellin and putative MAMPs with focus on the Pseudomonas-tomato pathosystem.

  8. Antituberculosis Activity of the Molecular Libraries Screening Center Network Library

    PubMed Central

    MADDRY, JOSEPH A.; ANANTHAN, SUBRAMANIAM; GOLDMAN, ROBERT C.; HOBRATH, JUDITH V.; KWONG, CECIL D.; MADDOX, CLINTON; RASMUSSEN, LYNN; REYNOLDS, ROBERT C.; SECRIST, JOHN A.; SOSA, MELINDA I.; WHITE, E. LUCILE; ZHANG, WEI

    2009-01-01

    SUMMARY There is an urgent need for the discovery and development of new antitubercular agents that target novel biochemical pathways and treat drug-resistant forms of the disease. One approach to addressing this need is through high-throughput screening of drug-like small molecule libraries against the whole bacterium in order to identify a variety of new, active scaffolds that will stimulate additional biological research and drug discovery. Through the Molecular Libraries Screening Center Network, the NIAID Tuberculosis Antimicrobial Acquisition and Coordinating Facility tested a 215,110-compound library against M. tuberculosis strain H37Rv. A medicinal chemistry survey of the results from the screening campaign is reported herein. PMID:19783214

  9. Deconstructing a Species-Complex: Geometric Morphometric and Molecular Analyses Define Species in the Western Rattlesnake (Crotalus viridis).

    PubMed

    Davis, Mark A; Douglas, Marlis R; Collyer, Michael L; Douglas, Michael E

    2016-01-01

    Morphological data are a conduit for the recognition and description of species, and their acquisition has recently been broadened by geometric morphometric (GM) approaches that co-join the collection of digital data with exploratory 'big data' analytics. We employed this approach to dissect the Western Rattlesnake (Crotalus viridis) species-complex in North America, currently partitioned by mitochondrial (mt)DNA analyses into eastern and western lineages (two and seven subspecies, respectively). The GM data (i.e., 33 dorsal and 50 lateral head landmarks) were gleaned from 2,824 individuals located in 10 museum collections. We also downloaded and concatenated sequences for six mtDNA genes from the NCBI GenBank database. GM analyses revealed significant head shape differences attributable to size and subspecies-designation (but not their interactions). Pairwise shape distances among subspecies were significantly greater than those derived from ancestral character states via squared-change parsimony, with the greatest differences separating those most closely related. This, in turn, suggests the potential for historic character displacement as a diversifying force in the complex. All subspecies, save one, were significantly differentiated in a Bayesian discriminant function analysis (DFA), regardless of whether our priors were uniform or informative (i.e., mtDNA data). Finally, shape differences among sister-clades were significantly greater than expected by chance alone under a Brownian model of evolution, promoting the hypothesis that selection rather than drift was the driving force in the evolution of the complex. Lastly, we combine head shape and mtDNA data so as to derived an integrative taxonomy that produced robust boundaries for six OTUs (operational taxonomic units) of the C. viridis complex. We suggest these boundaries are concomitant with species-status and subsequently provide a relevant nomenclature for its recognition and representation.

  10. Deconstructing a Species-Complex: Geometric Morphometric and Molecular Analyses Define Species in the Western Rattlesnake (Crotalus viridis)

    PubMed Central

    Davis, Mark A.; Douglas, Marlis R.; Collyer, Michael L.; Douglas, Michael E.

    2016-01-01

    Morphological data are a conduit for the recognition and description of species, and their acquisition has recently been broadened by geometric morphometric (GM) approaches that co-join the collection of digital data with exploratory ‘big data’ analytics. We employed this approach to dissect the Western Rattlesnake (Crotalus viridis) species-complex in North America, currently partitioned by mitochondrial (mt)DNA analyses into eastern and western lineages (two and seven subspecies, respectively). The GM data (i.e., 33 dorsal and 50 lateral head landmarks) were gleaned from 2,824 individuals located in 10 museum collections. We also downloaded and concatenated sequences for six mtDNA genes from the NCBI GenBank database. GM analyses revealed significant head shape differences attributable to size and subspecies-designation (but not their interactions). Pairwise shape distances among subspecies were significantly greater than those derived from ancestral character states via squared-change parsimony, with the greatest differences separating those most closely related. This, in turn, suggests the potential for historic character displacement as a diversifying force in the complex. All subspecies, save one, were significantly differentiated in a Bayesian discriminant function analysis (DFA), regardless of whether our priors were uniform or informative (i.e., mtDNA data). Finally, shape differences among sister-clades were significantly greater than expected by chance alone under a Brownian model of evolution, pro