Mating-type locus characterization and variation in Pyrenophora semeniperda

Treesearch

Julie Leanna Henry

2015-01-01

Pyrenophora semeniperda is a generalist fungal pathogen that occurs primarily on monocot seed hosts. It is in the phylum Ascomycota, which includes both self-compatible (homothallic) and self-incompatible (heterothallic) species. Homothallic fungal species contain complementary mating-type (MAT) idiomorphs in a single unikaryotic strain, while heterothallic strains...

Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis in Podospora anserina

PubMed Central

Grognet, Pierre; Bidard, Frédérique; Kuchly, Claire; Tong, Laetitia Chan Ho; Coppin, Evelyne; Benkhali, Jinane Ait; Couloux, Arnaud; Wincker, Patrick; Debuchy, Robert; Silar, Philippe

2014-01-01

Pseudo-homothallism is a reproductive strategy elected by some fungi producing heterokaryotic sexual spores containing genetically different but sexually compatible nuclei. This lifestyle appears as a compromise between true homothallism (self-fertility with predominant inbreeding) and complete heterothallism (with exclusive outcrossing). However, pseudohomothallic species face the problem of maintaining heterokaryotic mycelia to fully benefit from this lifestyle, as homokaryons are self-sterile. Here, we report on the structure of chromosome 1 in mat+ and mat− isolates of strain S of the pseudohomothallic fungus Podospora anserina. Chromosome 1 contains either one of the mat+ and mat− mating types of P. anserina, which is mostly found in nature as a mat+/mat− heterokaryotic mycelium harboring sexually compatible nuclei. We identified a “mat” region ∼0.8 Mb long, devoid of meiotic recombination and containing the mating-type idiomorphs, which is a candidate to be involved in the maintenance of the heterokaryotic state, since the S mat+ and S mat− strains have different physiology that may enable hybrid-vigor-like phenomena in the heterokaryons. The mat region contains 229 coding sequences. A total of 687 polymorphisms were detected between the S mat+ and S mat− chromosomes. Importantly, the mat region is colinear between both chromosomes, which calls for an original mechanism of recombination inhibition. Microarray analyses revealed that 10% of the P. anserina genes have different transcriptional profiles in S mat+ and S mat−, in line with their different phenotypes. Finally, we show that the heterokaryotic state is faithfully maintained during mycelium growth of P. anserina, yet mat+/mat+ and mat−/mat− heterokaryons are as stable as mat+/mat− ones, evidencing a maintenance of heterokaryosis that does not rely on fitness-enhancing complementation between the S mat+ and S mat− strains. PMID:24558260

Functional Analysis of Mating Type Genes and Transcriptome Analysis during Fruiting Body Development of Botrytis cinerea

PubMed Central

2018-01-01

ABSTRACT Botrytis cinerea is a plant-pathogenic fungus producing apothecia as sexual fruiting bodies. To study the function of mating type (MAT) genes, single-gene deletion mutants were generated in both genes of the MAT1-1 locus and both genes of the MAT1-2 locus. Deletion mutants in two MAT genes were entirely sterile, while mutants in the other two MAT genes were able to develop stipes but never formed an apothecial disk. Little was known about the reprogramming of gene expression during apothecium development. We analyzed transcriptomes of sclerotia, three stages of apothecium development (primordia, stipes, and apothecial disks), and ascospores by RNA sequencing. Ten secondary metabolite gene clusters were upregulated at the onset of sexual development and downregulated in ascospores released from apothecia. Notably, more than 3,900 genes were differentially expressed in ascospores compared to mature apothecial disks. Among the genes that were upregulated in ascospores were numerous genes encoding virulence factors, which reveals that ascospores are transcriptionally primed for infection prior to their arrival on a host plant. Strikingly, the massive transcriptional changes at the initiation and completion of the sexual cycle often affected clusters of genes, rather than randomly dispersed genes. Thirty-five clusters of genes were jointly upregulated during the onset of sexual reproduction, while 99 clusters of genes (comprising >900 genes) were jointly downregulated in ascospores. These transcriptional changes coincided with changes in expression of genes encoding enzymes participating in chromatin organization, hinting at the occurrence of massive epigenetic regulation of gene expression during sexual reproduction. PMID:29440571

Functional characterization of MAT1-1-specific mating-type genes in the homothallic ascomycete Sordaria macrospora provides new insights into essential and nonessential sexual regulators.

PubMed

Klix, V; Nowrousian, M; Ringelberg, C; Loros, J J; Dunlap, J C; Pöggeler, S

2010-06-01

Mating-type genes in fungi encode regulators of mating and sexual development. Heterothallic ascomycete species require different sets of mating-type genes to control nonself-recognition and mating of compatible partners of different mating types. Homothallic (self-fertile) species also carry mating-type genes in their genome that are essential for sexual development. To analyze the molecular basis of homothallism and the role of mating-type genes during fruiting-body development, we deleted each of the three genes, SmtA-1 (MAT1-1-1), SmtA-2 (MAT1-1-2), and SmtA-3 (MAT1-1-3), contained in the MAT1-1 part of the mating-type locus of the homothallic ascomycete species Sordaria macrospora. Phenotypic analysis of deletion mutants revealed that the PPF domain protein-encoding gene SmtA-2 is essential for sexual reproduction, whereas the alpha domain protein-encoding genes SmtA-1 and SmtA-3 play no role in fruiting-body development. By means of cross-species microarray analysis using Neurospora crassa oligonucleotide microarrays hybridized with S. macrospora targets and quantitative real-time PCR, we identified genes expressed under the control of SmtA-1 and SmtA-2. Both genes are involved in the regulation of gene expression, including that of pheromone genes.

Functional Characterization of MAT1-1-Specific Mating-Type Genes in the Homothallic Ascomycete Sordaria macrospora Provides New Insights into Essential and Nonessential Sexual Regulators▿†

PubMed Central

Klix, V.; Nowrousian, M.; Ringelberg, C.; Loros, J. J.; Dunlap, J. C.; Pöggeler, S.

2010-01-01

Mating-type genes in fungi encode regulators of mating and sexual development. Heterothallic ascomycete species require different sets of mating-type genes to control nonself-recognition and mating of compatible partners of different mating types. Homothallic (self-fertile) species also carry mating-type genes in their genome that are essential for sexual development. To analyze the molecular basis of homothallism and the role of mating-type genes during fruiting-body development, we deleted each of the three genes, SmtA-1 (MAT1-1-1), SmtA-2 (MAT1-1-2), and SmtA-3 (MAT1-1-3), contained in the MAT1-1 part of the mating-type locus of the homothallic ascomycete species Sordaria macrospora. Phenotypic analysis of deletion mutants revealed that the PPF domain protein-encoding gene SmtA-2 is essential for sexual reproduction, whereas the α domain protein-encoding genes SmtA-1 and SmtA-3 play no role in fruiting-body development. By means of cross-species microarray analysis using Neurospora crassa oligonucleotide microarrays hybridized with S. macrospora targets and quantitative real-time PCR, we identified genes expressed under the control of SmtA-1 and SmtA-2. Both genes are involved in the regulation of gene expression, including that of pheromone genes. PMID:20435701

Comparative Genomics of the Mating-Type Loci of the Mushroom Flammulina velutipes Reveals Widespread Synteny and Recent Inversions

PubMed Central

van Peer, Arend F.; Park, Soon-Young; Shin, Pyung-Gyun; Jang, Kab-Yeul; Yoo, Young-Bok; Park, Young-Jin; Lee, Byoung-Moo; Sung, Gi-Ho; James, Timothy Y.; Kong, Won-Sik

2011-01-01

Background Mating-type loci of mushroom fungi contain master regulatory genes that control recognition between compatible nuclei, maintenance of compatible nuclei as heterokaryons, and fruiting body development. Regions near mating-type loci in fungi often show adapted recombination, facilitating the generation of novel mating types and reducing the production of self-compatible mating types. Compared to other fungi, mushroom fungi have complex mating-type systems, showing both loci with redundant function (subloci) and subloci with many alleles. The genomic organization of mating-type loci has been solved in very few mushroom species, which complicates proper interpretation of mating-type evolution and use of those genes in breeding programs. Methodology/Principal Findings We report a complete genetic structure of the mating-type loci from the tetrapolar, edible mushroom Flammulina velutipes mating type A3B3. Two matB3 subloci, matB3a that contains a unique pheromone and matB3b, were mapped 177 Kb apart on scaffold 1. The matA locus of F. velutipes contains three homeodomain genes distributed over 73 Kb distant matA3a and matA3b subloci. The conserved matA region in Agaricales approaches 350 Kb and contains conserved recombination hotspots showing major rearrangements in F. velutipes and Schizophyllum commune. Important evolutionary differences were indicated; separation of the matA subloci in F. velutipes was diverged from the Coprinopsis cinerea arrangement via two large inversions whereas separation in S. commune emerged through transposition of gene clusters. Conclusions/Significance In our study we determined that the Agaricales have very large scale synteny at matA (∼350 Kb) and that this synteny is maintained even when parts of this region are separated through chromosomal rearrangements. Four conserved recombination hotspots allow reshuffling of large fragments of this region. Next to this, it was revealed that large distance subloci can exist in matB as well. Finally, the genes that were linked to specific mating types will serve as molecular markers in breeding. PMID:21799803

a/alpha-specific effect on the mms3 mutation on ultraviolet mutagenesis in Saccharomyces cerevisiae.

PubMed

Martin, P; Prakash, L; Prakash, S

1981-05-01

A new gene involved in error-prone repair of ultraviolet (UV) damage has been identified in Saccharomyces cerevisiae by the mms3-1 mutation. UV-induced reversion is reduced in diploids that are homozygous for mms3-1, only if they are also heterozygous (MATa/MAT alpha) at the mating type locus. The mms3-1 mutation has no effect on UV-induced reversion either in haploids or MATa/MATa or MAT alpha/MAT alpha diploids. The mutation confers sensitivity to UV and methyl methane sulfonate in both haploids and diploids. Even though mutation induction by UV is restored to wild-type levels in MATa/MATa mms3-1/mms3-1 or MAT alpha/MAT alpha mms3-1/mms3-1 diploids, such strains still retain sensitivity to the lethal effects of UV. Survival after UV irradiation in mms3-1 rad double mutant combinations indicates that mms3-1 is epistatic to rad6-1 whereas non-epistatic interactions are observed with rad3 and rad52 mutants. When present in the homozygous state in MATa/MAT alpha his1-1/his1-315 heteroallelic diploids, mms3-1 was found to lower UV-induced mitotic recombination.

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

Chan, R.K.; Otte, C.A.

Eight independently isolated mutants which are supersensitive (Sst/sup -/) to the G1 arrest induced by the tridecapeptide pheromone ..cap alpha.. factor were identified by screening mutagenized Saccharomyces cerevisiae MATa cells on solid medium for increased growth inhibition by ..cap alpha.. factor. These mutants carries lesions in two complementation groups, sst1 and sst2. Mutations at the sst1 locus were mating type specific: MATa sst1 cells were supersensitive to ..cap alpha.. factor, but MAT..cap alpha.. sst1 cells were not supersensitive to a factor. In contrast, mutations at the sst2 locus conferred supersensitivity to the pheromones of the opposite mating type on bothmore » MATa and MAT..cap alpha.. cells. Even in the absence of added ..cap alpha.. pheromone, about 10% of the cells in exponentially growing cultures of MATa strains carrying any of three different alleles of sst2 (including the ochre mutation sst2-4) had the aberrant morphology (''shmoo'' shape) that normally develops only after MATa cells are exposed to ..cap alpha.. factor. This ''self-shmooing'' phenotype was genetically linked to the sst2 mutations, although the leakiest allele isolated (sst2-3) did not display this characteristic. Normal MATa/MAT..cap alpha.. diploids do not respond to pheromones; diploids homozygous for an sst2 mutation (MATa/MAT..cap alpha.. sst2-1/sst2-1) were still insensitive to ..cap alpha.. factor. The sst1 gene was mapped to within 6.9 centimorgans of his6 on chromosome IX. The sst2 gene was unlinked to sst1, was not centromere linked, and was shown to be neither linked nor centromere distal to MAT on the right arm of chromosome III.« less

Asexual propagation of a virulent clone complex in a human and feline outbreak of sporotrichosis.

PubMed

Teixeira, Marcus de Melo; Rodrigues, Anderson Messias; Tsui, Clement K M; de Almeida, Luiz Gonzaga Paulo; Van Diepeningen, Anne D; van den Ende, Bert Gerrits; Fernandes, Geisa Ferreira; Kano, Rui; Hamelin, Richard C; Lopes-Bezerra, Leila Maria; Vasconcelos, Ana Tereza Ribeiro; de Hoog, Sybren; de Camargo, Zoilo Pires; Felipe, Maria Sueli Soares

2015-02-01

Sporotrichosis is one of the most frequent subcutaneous fungal infections in humans and animals caused by members of the plant-associated, dimorphic genus Sporothrix. Three of the four medically important Sporothrix species found in Brazil have been considered asexual as no sexual stage has ever been reported in Sporothrix schenckii, Sporothrix brasiliensis, or Sporothrix globosa. We have identified the mating type (MAT) loci in the S. schenckii (strain 1099-18/ATCC MYA-4821) and S. brasiliensis (strain 5110/ATCC MYA-4823) genomes by using comparative genomic approaches to determine the mating type ratio in these pathogen populations. Our analysis revealed the presence of a MAT1-1 locus in S. schenckii while a MAT1-2 locus was found in S. brasiliensis representing genomic synteny to other Sordariomycetes. Furthermore, the components of the mitogen-activated protein kinase (MAPK)-pheromone pathway, pheromone processing enzymes, and meiotic regulators have also been identified in the two pathogens, suggesting the potential for sexual reproduction. The ratio of MAT1-1 to MAT1-2 was not significantly different from 1:1 for all three Sporothrix species, but the population of S. brasiliensis in the outbreaks originated from a single mating type. We also explored the population genetic structure of these pathogens using sequence data of two loci to improve our knowledge of the pattern of geographic distribution, genetic variation, and virulence phenotypes. Population genetics data showed significant population differentiation and clonality with a low level of haplotype diversity in S. brasiliensis isolates from different regions of sporotrichosis outbreaks in Brazil. In contrast, S. schenckii isolates demonstrated a high degree of genetic variability without significant geographic differentiation, indicating the presence of recombination. This study demonstrated that two species causing the same disease have contrasting reproductive strategies and genetic variability patterns. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Asexual Propagation of a Virulent Clone Complex in a Human and Feline Outbreak of Sporotrichosis

PubMed Central

Teixeira, Marcus de Melo; Tsui, Clement K. M.; de Almeida, Luiz Gonzaga Paulo; Van Diepeningen, Anne D.; van den Ende, Bert Gerrits; Fernandes, Geisa Ferreira; Kano, Rui; Hamelin, Richard C.; Lopes-Bezerra, Leila Maria; Vasconcelos, Ana Tereza Ribeiro; de Hoog, Sybren; de Camargo, Zoilo Pires

2014-01-01

Sporotrichosis is one of the most frequent subcutaneous fungal infections in humans and animals caused by members of the plant-associated, dimorphic genus Sporothrix. Three of the four medically important Sporothrix species found in Brazil have been considered asexual as no sexual stage has ever been reported in Sporothrix schenckii, Sporothrix brasiliensis, or Sporothrix globosa. We have identified the mating type (MAT) loci in the S. schenckii (strain 1099-18/ATCC MYA-4821) and S. brasiliensis (strain 5110/ATCC MYA-4823) genomes by using comparative genomic approaches to determine the mating type ratio in these pathogen populations. Our analysis revealed the presence of a MAT1-1 locus in S. schenckii while a MAT1-2 locus was found in S. brasiliensis representing genomic synteny to other Sordariomycetes. Furthermore, the components of the mitogen-activated protein kinase (MAPK)-pheromone pathway, pheromone processing enzymes, and meiotic regulators have also been identified in the two pathogens, suggesting the potential for sexual reproduction. The ratio of MAT1-1 to MAT1-2 was not significantly different from 1:1 for all three Sporothrix species, but the population of S. brasiliensis in the outbreaks originated from a single mating type. We also explored the population genetic structure of these pathogens using sequence data of two loci to improve our knowledge of the pattern of geographic distribution, genetic variation, and virulence phenotypes. Population genetics data showed significant population differentiation and clonality with a low level of haplotype diversity in S. brasiliensis isolates from different regions of sporotrichosis outbreaks in Brazil. In contrast, S. schenckii isolates demonstrated a high degree of genetic variability without significant geographic differentiation, indicating the presence of recombination. This study demonstrated that two species causing the same disease have contrasting reproductive strategies and genetic variability patterns. PMID:25480940

Sex-linked phenotypic divergence in the hermaphrodite fungus Neurospora tetrasperma

USDA-ARS?s Scientific Manuscript database

Here we present a study of the molecular phenotype linked to a large region of suppressed recombination (extending over ~ 7 Mbp and >1,500 genes) surrounding the mating-type (mat) locus of the filamentous ascomycete Neurospora tetrasperma. While the remainder of the genome is largely homoallelic, th...

Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination

PubMed Central

Yadav, Vikas; Billmyre, R. Blake; Cuomo, Christina A.; Nowrousian, Minou; Wang, Liuyang; Souciet, Jean-Luc; Boekhout, Teun; Porcel, Betina; Wincker, Patrick; Granek, Joshua A.; Sanyal, Kaustuv; Heitman, Joseph

2017-01-01

Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing approximately 1 million annual infections globally. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large mating type (MAT) locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with 2 MAT loci (P/R and HD) located on different chromosomes. Thus, studying C. amylolentus will shed light on the transition from tetrapolar to bipolar mating systems in the pathogenic Cryptococcus species, as well as its possible link with the origin and evolution of pathogenesis. In this study, we sequenced, assembled, and annotated the genomes of 2 C. amylolentus isolates, CBS6039 and CBS6273, which are sexual and interfertile. Genome comparison between the 2 C. amylolentus isolates identified the boundaries and the complete gene contents of the P/R and HD MAT loci. Bioinformatic and chromatin immunoprecipitation sequencing (ChIP-seq) analyses revealed that, similar to those of the pathogenic Cryptococcus species, C. amylolentus has regional centromeres (CENs) that are enriched with species-specific transposable and repetitive DNA elements. Additionally, we found that while neither the P/R nor the HD locus is physically closely linked to its centromere in C. amylolentus, and the regions between the MAT loci and their respective centromeres show overall synteny between the 2 genomes, both MAT loci exhibit genetic linkage to their respective centromere during meiosis, suggesting the presence of recombinational suppressors and/or epistatic gene interactions in the MAT-CEN intervening regions. Furthermore, genomic comparisons between C. amylolentus and related pathogenic Cryptococcus species provide evidence that multiple chromosomal rearrangements mediated by intercentromeric recombination have occurred during descent of the 2 lineages from their common ancestor. Taken together, our findings support a model in which the evolution of the bipolar mating system was initiated by an ectopic recombination event mediated by similar repetitive centromeric DNA elements shared between chromosomes. This translocation brought the P/R and HD loci onto the same chromosome, and further chromosomal rearrangements then resulted in the 2 MAT loci becoming physically linked and eventually fusing to form the single contiguous MAT locus that is now extant in the pathogenic Cryptococcus species. PMID:28800596

An Evolutionary Perspective on Yeast Mating-Type Switching

PubMed Central

Hanson, Sara J.; Wolfe, Kenneth H.

2017-01-01

Cell differentiation in yeast species is controlled by a reversible, programmed DNA-rearrangement process called mating-type switching. Switching is achieved by two functionally similar but structurally distinct processes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In both species, haploid cells possess one active and two silent copies of the mating-type locus (a three-cassette structure), the active locus is cleaved, and synthesis-dependent strand annealing is used to replace it with a copy of a silent locus encoding the opposite mating-type information. Each species has its own set of components responsible for regulating these processes. In this review, we summarize knowledge about the function and evolution of mating-type switching components in these species, including mechanisms of heterochromatin formation, MAT locus cleavage, donor bias, lineage tracking, and environmental regulation of switching. We compare switching in these well-studied species to others such as Kluyveromyces lactis and the methylotrophic yeasts Ogataea polymorpha and Komagataella phaffii. We focus on some key questions: Which cells switch mating type? What molecular apparatus is required for switching? Where did it come from? And what is the evolutionary purpose of switching? PMID:28476860

Transitions in Sexuality: Recapitulation of an Ancestral Tri- and Tetrapolar Mating System in Cryptococcus neoformans▿ †

PubMed Central

Hsueh, Yen-Ping; Fraser, James A.; Heitman, Joseph

2008-01-01

Sex is orchestrated by the mating-type locus (MAT) in fungi and by sex chromosomes in plants and animals. In fungi, two patterns of sexuality occur: bipolar with a single, typically biallelic sex determinant that promotes inbreeding, and tetrapolar with two unlinked, often multiallelic sex determinants that restrict inbreeding. Multiallelism in either bipolar or tetrapolar mating systems promotes outcrossing. Cryptococcus neoformans is a pathogenic bipolar yeast with two unusually large MAT alleles (a/α) spanning >100 kb, ∼100-fold larger than many other fungal MAT loci. Based on comparative genomic analysis, this unusual MAT locus is hypothesized to have evolved from an ancestral tetrapolar system. In this model, the unlinked homeodomain (HD) transcription factor and pheromone/receptor tetrapolar loci acquired additional sex-related genes and then fused via chromosomal translocation, forming an intermediate transitional mating system (which we term tripolar), which then underwent recombination and gene conversion to fashion the extant bipolar MAT alleles. To experimentally validate this model, C. neoformans was engineered to have a tetrapolar mating system by relocating the MAT SXI1α and SXI2a HD genes to an unlinked genomic locale. Genetic and molecular analyses revealed that this modified organism could complete a tetrapolar sexual cycle. Analysis of progeny generated from bipolar, tripolar, and tetrapolar crosses provides direct experimental evidence that the tripolar state confers decreased fertility and therefore may represent an unstable evolutionary intermediate. These findings illustrate how transitions between outcrossing and inbreeding preference occur by involving sex determinant linkage and collapse from multiallelic to biallelic sex determination, providing insights into both fungal sex evolution and early steps in sex chromosome evolution. PMID:18723606

Maternal inheritance of mitochondria: multipolarity, multiallelism and hierarchical transmission of mitochondrial DNA in the true slime mold Physarum polycephalum.

PubMed

Moriyama, Yohsuke; Kawano, Shigeyuki

2010-03-01

Direct evidence of digestion of paternal mitochondrial DNA (mtDNA) has been found in the true slime mold Physarum polycephalum. This is the first report on the selective digestion of mtDNA inside the zygote, and is striking evidence for the mechanism of maternal inheritance of mitochondria. Moreover, two mitochondrial nuclease activities were detected in this organism as-candidates for the nucleases responsible for selective digestion of mtDNA. In the true slime mold, there is an additional-feature of the uniparental inheritance of mitochondria.Although mitochondria are believed to be inherited from the maternal lineage in nearly all eukaryotes, the mating types of the true slime mold P. polycephalum is not restricted to two: there are three mating loci--matA, matB,and matC--and these loci have 16, 15, and 3 alleles,-respectively. Interestingly, the transmission patterns of mtDNA are determined by the matA locus, in a hierarchical-fashion (matA hierarchy) as follows: matA7[matA2[matA11[matA12[matA15/matA16[matA1[matA6.The strain possessing the higher status of matA would be the mtDNA donor in crosses. Furthermore, we have found that some crosses showed biparental inheritance of mitochondria.This review describes the phenomenon of hierarchical transmission of mtDNA in true slime molds, and discusses the presumed molecular mechanism of maternal and biparental inheritance.

rbcL and matK earn two thumbs up as the core DNA barcode for ferns.

PubMed

Li, Fay-Wei; Kuo, Li-Yaung; Rothfels, Carl J; Ebihara, Atsushi; Chiou, Wen-Liang; Windham, Michael D; Pryer, Kathleen M

2011-01-01

DNA barcoding will revolutionize our understanding of fern ecology, most especially because the accurate identification of the independent but cryptic gametophyte phase of the fern's life history--an endeavor previously impossible--will finally be feasible. In this study, we assess the discriminatory power of the core plant DNA barcode (rbcL and matK), as well as alternatively proposed fern barcodes (trnH-psbA and trnL-F), across all major fern lineages. We also present plastid barcode data for two genera in the hyperdiverse polypod clade--Deparia (Woodsiaceae) and the Cheilanthes marginata group (currently being segregated as a new genus of Pteridaceae)--to further evaluate the resolving power of these loci. Our results clearly demonstrate the value of matK data, previously unavailable in ferns because of difficulties in amplification due to a major rearrangement of the plastid genome. With its high sequence variation, matK complements rbcL to provide a two-locus barcode with strong resolving power. With sequence variation comparable to matK, trnL-F appears to be a suitable alternative barcode region in ferns, and perhaps should be added to the core barcode region if universal primer development for matK fails. In contrast, trnH-psbA shows dramatically reduced sequence variation for the majority of ferns. This is likely due to the translocation of this segment of the plastid genome into the inverted repeat regions, which are known to have a highly constrained substitution rate. Our study provides the first endorsement of the two-locus barcode (rbcL+matK) in ferns, and favors trnL-F over trnH-psbA as a potential back-up locus. Future work should focus on gathering more fern matK sequence data to facilitate universal primer development.

Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants.

PubMed

Maloukh, Lina; Kumarappan, Alagappan; Jarrar, Mohammad; Salehi, Jawad; El-Wakil, Houssam; Rajya Lakshmi, T V

2017-06-01

DNA barcoding of United Arab Emirates (UAE) native plants is of high practical and scientific value as the plants adapt to very harsh environmental conditions that challenge their identification. Fifty-one plant species belonged to 22 families, 2 monocots, and 20 eudicots; a maximum number of species being legumes and grasses were collected. To authenticate the morphological identification of the wild plant taxa, rbcL and matK regions were used in the study. The primer universality and discriminatory power of rbcL is 100%, while it is 35% for matK locus for these plant species. The sequences were submitted to GenBank; accession numbers were obtained for all the rbcL sequences and for 6 of matK sequences. We suggest rbcL as a promising barcode locus for the tested group of 51 plants. In the present study, an inexpensive, simple method of identification of rare desert plant taxa through rbcL barcode is being reported.

rbcL and matK Earn Two Thumbs Up as the Core DNA Barcode for Ferns

PubMed Central

Li, Fay-Wei; Kuo, Li-Yaung; Rothfels, Carl J.; Ebihara, Atsushi; Chiou, Wen-Liang; Windham, Michael D.; Pryer, Kathleen M.

2011-01-01

Background DNA barcoding will revolutionize our understanding of fern ecology, most especially because the accurate identification of the independent but cryptic gametophyte phase of the fern's life history—an endeavor previously impossible—will finally be feasible. In this study, we assess the discriminatory power of the core plant DNA barcode (rbcL and matK), as well as alternatively proposed fern barcodes (trnH-psbA and trnL-F), across all major fern lineages. We also present plastid barcode data for two genera in the hyperdiverse polypod clade—Deparia (Woodsiaceae) and the Cheilanthes marginata group (currently being segregated as a new genus of Pteridaceae)—to further evaluate the resolving power of these loci. Principal Findings Our results clearly demonstrate the value of matK data, previously unavailable in ferns because of difficulties in amplification due to a major rearrangement of the plastid genome. With its high sequence variation, matK complements rbcL to provide a two-locus barcode with strong resolving power. With sequence variation comparable to matK, trnL-F appears to be a suitable alternative barcode region in ferns, and perhaps should be added to the core barcode region if universal primer development for matK fails. In contrast, trnH-psbA shows dramatically reduced sequence variation for the majority of ferns. This is likely due to the translocation of this segment of the plastid genome into the inverted repeat regions, which are known to have a highly constrained substitution rate. Conclusions Our study provides the first endorsement of the two-locus barcode (rbcL+matK) in ferns, and favors trnL-F over trnH-psbA as a potential back-up locus. Future work should focus on gathering more fern matK sequence data to facilitate universal primer development. PMID:22028918

Testing the utility of matK and ITS DNA regions for discrimination of Allium species

USDA-ARS?s Scientific Manuscript database

Molecular phylogenetic analysis of the genus Allium L. has been mainly based on the nucleotide sequences of ITS region. In 2009 matK and rbcL were accepted as a two-locus DNA barcode to classify plant species by the Consortium for the Barcode of Life (CBOL) Plant Working Group. MatK region has been ...

Markers linked to vegetative incompatibility (vic) genes and a region of high heterogeneity and reduced recombination near the mating type locus (MAT) in Cryphonectria parasitica

Treesearch

Thomas L. Kubisiak; Michael g. Milgroom

2006-01-01

To find markers linked to vegetative incompatibility (vic) genes in the chestnut blight fungus, Cryphonectria parasitica, we constructed a preliminary linkage map. In general, this map is characterized by low levels of polymorphism, as evident from the more than 24 linkage groups observed, compared to seven expected from electrophoretic karyotyping....

Genetic diversity, QoI fungicide resistance, and mating type distribution of Cercospora sojina—Implications for the disease dynamics of frogeye leaf spot on soybean

PubMed Central

Shrestha, Sandesh Kumar; Cochran, Alicia; Mengistu, Alemu; Castro-Rocha, Arturo; Young-Kelly, Heather

2017-01-01

Frogeye leaf spot (FLS), caused by Cercospora sojina, causes significant damage to soybean in the U.S. One control strategy is the use of quinone outside inhibitor (QoI) fungicides. QoI resistant isolates were first reported in Tennessee (TN) in 2010. To investigate the disease dynamics of C. sojina, we collected 437 C. sojina isolates in 2015 from Jackson and Milan, TN and used 40 historical isolates collected from 2006–2009 from TN and ten additional states for comparison. A subset of 186 isolates, including historical isolates, were genotyped for 49 single nucleotide polymorphism (SNP) markers and the QoI resistance locus, revealing 35 unique genotypes. The genotypes clustered into three groups with two groups containing only sensitive isolates and the remaining group containing all resistant isolates and a dominant clonal lineage of 130 isolates. All 477 C. sojina isolates were genotyped for the QoI locus revealing 344 resistant and 133 sensitive isolates. All isolates collected prior to 2015 were QoI sensitive. Both mating type alleles (MAT1-1-1 and MAT1-2) were found in Jackson and Milan, TN and recovered from single lesions suggesting sexual recombination may play a role in the epidemiology of field populations. Analysis of C. sojina isolates using SNP markers proved useful to investigate population diversity and to elaborate on diversity as it relates to QoI resistance and mating type. PMID:28486517

Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids.

PubMed

Parveen, Iffat; Singh, Hemant K; Malik, Saloni; Raghuvanshi, Saurabh; Babbar, Shashi B

2017-08-01

Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand owing to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of effective identification methods, illicit trade of orchids continues unabated. Considering DNA barcoding as a potential identification tool, species discrimination capability of five loci, ITS, matK, rbcL, rpoB, and rpoC1, was tested in 393 accessions of 94 Indian orchid species belonging to 47 genera, including one listed in Appendix I of CITES and 26 medicinal species. ITS provided the highest species discrimination rate of 94.9%. While, among the chloroplast loci, matK provided the highest species discrimination rate of 85.7%. None of the tested loci individually discriminated 100% of the species. Therefore, multi-locus combinations of up to five loci were tested for their species resolution capability. Among two-locus combinations, the maximum species resolution (86.7%) was provided by ITS+matK. ITS and matK sequences of the medicinal orchids were species specific, thus providing unique molecular identification tags for their identification and detection. These observations emphasize the need for the inclusion of ITS in the core barcode for plants, whenever required and available.

Significant competitive advantage conferred by meiosis and syngamy in the yeast Saccharomyces cerevisiae.

PubMed Central

Birdsell, J; Wills, C

1996-01-01

The presumed advantages of genetic recombinations are difficult to demonstrate directly. To investigate the effects of recombination and background heterozygosity on competitive ability, we have performed serial-transfer competition experiments between isogenic sexual and asexual strains of the yeast Saccharomyces cerevisiae. The members of these diploid pairs of strains differed only in being heterozygous (sexual) or homozygous (asexual) at the mating type or MAT locus. Competing pairs had either a completely homozygous or a heterozygous genetic background, the latter being heterozygous at many different loci throughout the genome. A round of meiotic recombination (automixis) conferred a large and statistically significant enhancement of competitive ability on sexual strains with a heterozygous genetic background. By contrast, in homozygous background competitions, meiosis decreased the sexual strains' initial relative competitive ability. In all cases, however, the sexual strains outcompeted their isogenic asexual counterparts, whether meiotic recombination had occurred or not. In some genetic backgrounds, this was due in part to an overdominance effect on competitive advantage of heterozygosity at the MAT locus. The advantage of the sexual strains also increased significantly during the course of the homozygous background competitions, particularly when meiosis had occurred. This latter effect either did not occur or was very weak in heterozygous background competitions. Overall, sexual strains with heterozygous genetic backgrounds had a significantly higher initial relative competitive ability than those with homozygous backgrounds. The advantage of mating type heterozygosity in this organism extends far beyond the ability to recombine meiotically. PMID:8570658

A DNA barcode for land plants.

PubMed

2009-08-04

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

A DNA barcode for land plants

PubMed Central

Hollingsworth, Peter M.; Forrest, Laura L.; Spouge, John L.; Hajibabaei, Mehrdad; Ratnasingham, Sujeevan; van der Bank, Michelle; Chase, Mark W.; Cowan, Robyn S.; Erickson, David L.; Fazekas, Aron J.; Graham, Sean W.; James, Karen E.; Kim, Ki-Joong; Kress, W. John; Schneider, Harald; van AlphenStahl, Jonathan; Barrett, Spencer C.H.; van den Berg, Cassio; Bogarin, Diego; Burgess, Kevin S.; Cameron, Kenneth M.; Carine, Mark; Chacón, Juliana; Clark, Alexandra; Clarkson, James J.; Conrad, Ferozah; Devey, Dion S.; Ford, Caroline S.; Hedderson, Terry A.J.; Hollingsworth, Michelle L.; Husband, Brian C.; Kelly, Laura J.; Kesanakurti, Prasad R.; Kim, Jung Sung; Kim, Young-Dong; Lahaye, Renaud; Lee, Hae-Lim; Long, David G.; Madriñán, Santiago; Maurin, Olivier; Meusnier, Isabelle; Newmaster, Steven G.; Park, Chong-Wook; Percy, Diana M.; Petersen, Gitte; Richardson, James E.; Salazar, Gerardo A.; Savolainen, Vincent; Seberg, Ole; Wilkinson, Michael J.; Yi, Dong-Keun; Little, Damon P.

2009-01-01

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants. PMID:19666622

Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the filamentous Fungus Neurospora tetrasperma

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

Ellison, Christoper; Stajich, Jason; Jacobson, David

2011-05-16

A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility. The similarity of the N. tetrasperma mating chromosome to plant and animal sex chromosomes and its recent origin (5 MYA), combined with a long history of genetic and cytological research, make this fungus an ideal model for studying the evolutionary consequences of suppressed recombination. Here we compare genome sequences from two N. tetrasperma strains of opposite mating type to determine whether structural rearrangements are associated withmore » the nonrecombining region and to examine the effect of suppressed recombination for the evolution of the genes within it. We find a series of three inversions encompassing the majority of the region of suppressed recombination and provide evidence for two different types of rearrangement mechanisms: the recently proposed mechanism of inversion via staggered single-strand breaks as well as ectopic recombination between transposable elements. In addition, we show that the N. tetrasperma mat a mating-type region appears to be accumulating deleterious substitutions at a faster rate than the other mating type (mat A) and thus may be in the early stages of degeneration.« less

Alpha3, a transposable element that promotes host sexual reproduction.

PubMed

Barsoum, Emad; Martinez, Paula; Aström, Stefan U

2010-01-01

Theoretical models predict that selfish DNA elements require host sex to persist in a population. Therefore, a transposon that induces sex would strongly favor its own spread. We demonstrate that a protein homologous to transposases, called alpha3, was essential for mating type switch in Kluyveromyces lactis. Mutational analysis showed that amino acids conserved among transposases were essential for its function. During switching, sequences in the 5' and 3' flanking regions of the alpha3 gene were joined, forming a DNA circle, showing that alpha3 mobilized from the genome. The sequences encompassing the alpha3 gene circle junctions in the mating type alpha (MATalpha) locus were essential for switching from MATalpha to MATa, suggesting that alpha3 mobilization was a coupled event. Switching also required a DNA-binding protein, Mating type switch 1 (Mts1), whose binding sites in MATalpha were important. Expression of Mts1 was repressed in MATa/MATalpha diploids and by nutrients, limiting switching to haploids in low-nutrient conditions. A hairpin-capped DNA double-strand break (DSB) was observed in the MATa locus in mre11 mutant strains, indicating that mating type switch was induced by MAT-specific DSBs. This study provides empirical evidence for selfish DNA promoting host sexual reproduction by mediating mating type switch.

Influence of Molecular Resolution on Sequence-Based Discovery of Ecological Diversity among Synechococcus Populations in an Alkaline Siliceous Hot Spring Microbial Mat ▿ †

PubMed Central

Melendrez, Melanie C.; Lange, Rachel K.; Cohan, Frederick M.; Ward, David M.

2011-01-01

Previous research has shown that sequences of 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions may not have enough genetic resolution to define all ecologically distinct Synechococcus populations (ecotypes) inhabiting alkaline, siliceous hot spring microbial mats. To achieve higher molecular resolution, we studied sequence variation in three protein-encoding loci sampled by PCR from 60°C and 65°C sites in the Mushroom Spring mat (Yellowstone National Park, WY). Sequences were analyzed using the ecotype simulation (ES) and AdaptML algorithms to identify putative ecotypes. Between 4 and 14 times more putative ecotypes were predicted from variation in protein-encoding locus sequences than from variation in 16S rRNA and 16S-23S rRNA internal transcribed spacer sequences. The number of putative ecotypes predicted depended on the number of sequences sampled and the molecular resolution of the locus. Chao estimates of diversity indicated that few rare ecotypes were missed. Many ecotypes hypothesized by sequence analyses were different in their habitat specificities, suggesting different adaptations to temperature or other parameters that vary along the flow channel. PMID:21169433

A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago.

PubMed

Clerc-Blain, Jessica L E; Starr, Julian R; Bull, Roger D; Saarela, Jeffery M

2010-01-01

Previous research on barcoding sedges (Carex) suggested that basic searches within a global barcoding database would probably not resolve more than 60% of the world's some 2000 species. In this study, we take an alternative approach and explore the performance of plant DNA barcoding in the Carex lineage from an explicitly regional perspective. We characterize the utility of a subset of the proposed protein-coding and noncoding plastid barcoding regions (matK, rpoB, rpoC1, rbcL, atpF-atpH, psbK-psbI) for distinguishing species of Carex and Kobresia in the Canadian Arctic Archipelago, a clearly defined eco-geographical region representing 1% of the Earth's landmass. Our results show that matK resolves the greatest number of species of any single-locus (95%), and when combined in a two-locus barcode, it provides 100% species resolution in all but one combination (matK + atpFH) during unweighted pair-group method with arithmetic mean averages (UPGMA) analyses. Noncoding regions were equally or more variable than matK, but as single markers they resolve substantially fewer taxa than matK alone. When difficulties with sequencing and alignment due to microstructural variation in noncoding regions are also considered, our results support other studies in suggesting that protein-coding regions are more practical as barcoding markers. Plastid DNA barcodes are an effective identification tool for species of Carex and Kobresia in the Canadian Arctic Archipelago, a region where the number of co-existing closely related species is limited. We suggest that if a regional approach to plant DNA barcoding was applied on a global scale, it could provide a solution to the generally poor species resolution seen in previous barcoding studies. © 2009 Blackwell Publishing Ltd.

Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale

PubMed Central

Moore, Geromy G.; Elliott, Jacalyn L.; Singh, Rakhi; Horn, Bruce W.; Dorner, Joe W.; Stone, Eric A.; Chulze, Sofia N.; Barros, German G.; Naik, Manjunath K.; Wright, Graeme C.; Hell, Kerstin; Carbone, Ignazio

2013-01-01

Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B1 being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs). We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina (Córdoba), Australia (Queensland) and India (Karnataka). Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD) organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B1-dominant and G1-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of the population (more sexual versus more asexual) is predictive of aflatoxin chemotype diversity in these agriculturally important fungi. PMID:24009506

Evolution of hierarchical cytoplasmic inheritance in the plasmodial slime mold Physarum polycephalum.

PubMed

Iwanaga, Akiko; Sasaki, Akira

2004-04-01

A striking linear dominance relationship for uniparental mitochondrial transmission is known between many mating types of plasmodial slime mold Physarum polycephalum. We herein examine how such hierarchical cytoplasmic inheritance evolves in isogamous organisms with many self-incompatible mating types. We assume that a nuclear locus determines the mating type of gametes and that another nuclear locus controls the digestion of mitochondria DNAs (mtDNAs) of the recipient gamete after fusion. We then examine the coupled genetic dynamics for the evolution of self-incompatible mating types and biased mitochondrial transmission between them. In Physarum, a multiallelic nuclear locus matA controls both the mating type of the gametes and the selective elimination of the mtDNA in the zygotes. We theoretically examine two potential mechanisms that might be responsible for the preferential digestion of mitochondria in the zygote. In the first model, the preferential digestion of mitochondria is assumed to be the outcome of differential expression levels of a suppressor gene carried by each gamete (suppression-power model). In the second model (site-specific nuclease model), the digestion of mtDNAs is assumed to be due to their cleavage by a site-specific nuclease that cuts the mtDNA at unmethylated recognition sites. Also assumed is that the mtDNAs are methylated at the same recognition site prior to the fusion, thereby being protected against the nuclease of the same gamete, and that the suppressor alleles convey information for the recognition sequences of nuclease and methylase. In both models, we found that a linear dominance hierarchy evolves as a consequence of the buildup of a strong linkage disequilibrium between the mating-type locus and the suppressor locus, though it fails to evolve if the recombination rate between the two loci is larger than a threshold. This threshold recombination rate depends on the number of mating types and the degree of fitness reduction in the heteroplasmic zygotes. If the recombination rate is above the threshold, suppressor alleles are equally distributed in each mating type at evolutionary equilibrium. Based on the theoretical results of the site-specific nuclease model, we propose that a nested subsequence structure in the recognition sequence should underlie the linear dominance hierarchy of mitochondrial transmission.

Capsule null locus meningococci: typing of antigens used in an investigational multicomponent meningococcus serogroup B vaccine.

PubMed

Claus, Heike; Jördens, Markus S; Kriz, Pavla; Musilek, Martin; Jarva, Hanna; Pawlik, Marie-Christin; Meri, Seppo; Vogel, Ulrich

2012-01-05

The investigational multicomponent meningococcus serogroup B vaccine (4CMenB) targets the antigenetically variable population of serogroup B meningococci. Forty-one strains of capsule null locus (cnl) meningococci, which are frequent among healthy carriers, were selected from nine sequence types (ST), which belong to four clonal complexes (cc), and three countries. They were antigen sequence typed and analyzed for antigen expression to predict whether these strains harbor the genes and express the four vaccine antigens of 4CMenB as measured by the meningococcal antigen typing system (MATS). The PorA variant used in the vaccine was not found. The nadA gene was absent in all but one strain, which did not express the antigen in vitro. Only strains of clonal complex ST-198 harbored a factor H binding protein (FHBP) allele of the cross-reactive variant 1 family which is included in the vaccine. All these strains expressed the antigen. Five variants of the Neisserial heparin binding antigen (NHBA) gene were identified. Expression of NHBA was observed in all strains with highest levels in ST-198 cc and ST-845. The data suggest a potential impact of 4CMenB immunization at least on cnl meningococci of the ST-198 cc and ST-845. Copyright © 2011 Elsevier Ltd. All rights reserved.

Multigene assessment of the species boundaries and sexual status of the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales).

PubMed

Yurkov, Andrey; Guerreiro, Marco A; Sharma, Lav; Carvalho, Cláudia; Fonseca, Álvaro

2015-01-01

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful.

Multigene Assessment of the Species Boundaries and Sexual Status of the Basidiomycetous Yeasts Cryptococcus flavescens and C. terrestris (Tremellales)

PubMed Central

Sharma, Lav; Carvalho, Cláudia; Fonseca, Álvaro

2015-01-01

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful. PMID:25811603

Evaluating the capacity of plant DNA barcodes to discriminate species of cotton (Gossypium: Malvaceae).

PubMed

Ashfaq, Muhammad; Asif, Muhammad; Anjum, Zahid Iqbal; Zafar, Yusuf

2013-07-01

Although two plastid regions have been adopted as the standard markers for plant DNA barcoding, their limited resolution has provoked the consideration of other gene regions, especially in taxonomically diverse genera. The genus Gossypium (cotton) includes eight diploid genome groups (A-G, and K) and five allotetraploid species which are difficult to discriminate morphologically. In this study, we tested the effectiveness of three widely used markers (matK, rbcL, and ITS2) in the discrimination of 20 diploid and five tetraploid species of cotton. Sequences were analysed locus-wise and in combinations to determine the most effective strategy for species identification. Sequence recovery was high, ranging from 92% to 100% with mean pairwise interspecific distance highest for ITS2 (3.68%) and lowest for rbcL (0.43%). At a 0.5% threshold, the combination of matK+ITS2 produced the greatest number of species clusters. Based on 'best match' analysis, the combination of matK+ITS2 was best, while based on 'all species barcodes' analysis, ITS2 gave the highest percentage of correct species identifications (98.93%). The combination of sequences for all three markers produced the best resolved tree. The disparity index test based on matK+rbcL+ITS2 was significant (P < 0.05) for a higher number of species pairs than the individual gene sequences. Although all three barcodes separated the species with respect to their genome type, no single combination of barcodes could differentiate all the Gossypium species, and tetraploid species were particularly difficult. © 2013 John Wiley & Sons Ltd.

Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes.

PubMed

Valero-Jiménez, Claudio A; Faino, Luigi; Spring In't Veld, Daphne; Smit, Sandra; Zwaan, Bas J; van Kan, Jan A L

2016-12-01

Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence. A high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to the assemblies of the four other isolates. Whole genome analysis showed a high level of genetic diversity between the five isolates (2.85-16.8 SNPs/kb), which grouped into two distinct phylogenetic clusters. Mating type gene analysis revealed the presence of either the MAT1-1-1 or the MAT1-2-1 gene. Moreover, a putative new MAT gene (MAT1-2-8) was detected in the MAT1-2 locus. Comparative genome analysis revealed that Bb8028 contains 163 genes exclusive for this isolate. These unique genes have a tendency to cluster in the genome and to be often located near the telomeres. Among the genes unique to Bb8028 are a Non-Ribosomal Peptide Synthetase (NRPS) secondary metabolite gene cluster, a polyketide synthase (PKS) gene, and five genes with homology to bacterial toxins. A survey of candidate virulence genes for B. bassiana is presented. Our results indicate several genes and molecular processes that may underpin virulence towards mosquitoes. Thus, the genome sequences of five isolates of B. bassiana provide a better understanding of the natural variation in virulence and will offer a major resource for future research on this important biological control agent.

Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages.

PubMed

Leushkin, Evgeny V; Logacheva, Maria D; Penin, Aleksey A; Sutormin, Roman A; Gerasimov, Evgeny S; Kochkina, Galina A; Ivanushkina, Natalia E; Vasilenko, Oleg V; Kondrashov, Alexey S; Ozerskaya, Svetlana M

2015-05-21

Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50 Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100-10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.

Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L.

PubMed

Poovitha, Sundar; Stalin, Nithaniyal; Balaji, Raju; Parani, Madasamy

2016-12-01

The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%-9.6% with individual markers, which increased to 0%-12.5% and 0.8%-20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.

Metagenomic and metabolic profiling of nonlithifying and lithifying stromatolitic mats of Highborne Cay, The Bahamas.

PubMed

Khodadad, Christina L M; Foster, Jamie S

2012-01-01

Stromatolites are laminated carbonate build-ups formed by the metabolic activity of microbial mats and represent one of the oldest known ecosystems on Earth. In this study, we examined a living stromatolite located within the Exuma Sound, The Bahamas and profiled the metagenome and metabolic potential underlying these complex microbial communities. The metagenomes of the two dominant stromatolitic mat types, a nonlithifying (Type 1) and lithifying (Type 3) microbial mat, were partially sequenced and compared. This deep-sequencing approach was complemented by profiling the substrate utilization patterns of the mats using metabolic microarrays. Taxonomic assessment of the protein-encoding genes confirmed previous SSU rRNA analyses that bacteria dominate the metagenome of both mat types. Eukaryotes comprised less than 13% of the metagenomes and were rich in sequences associated with nematodes and heterotrophic protists. Comparative genomic analyses of the functional genes revealed extensive similarities in most of the subsystems between the nonlithifying and lithifying mat types. The one exception was an increase in the relative abundance of certain genes associated with carbohydrate metabolism in the lithifying Type 3 mats. Specifically, genes associated with the degradation of carbohydrates commonly found in exopolymeric substances, such as hexoses, deoxy- and acidic sugars were found. The genetic differences in carbohydrate metabolisms between the two mat types were confirmed using metabolic microarrays. Lithifying mats had a significant increase in diversity and utilization of carbon, nitrogen, phosphorus and sulfur substrates. The two stromatolitic mat types retained similar microbial communities, functional diversity and many genetic components within their metagenomes. However, there were major differences detected in the activity and genetic pathways of organic carbon utilization. These differences provide a strong link between the metagenome and the physiology of the mats, as well as new insights into the biological processes associated with carbonate precipitation in modern marine stromatolites.

Presence and Functionality of Mating Type Genes in the Supposedly Asexual Filamentous Fungus Aspergillus oryzae

PubMed Central

Wada, Ryuta; Maruyama, Jun-ichi; Yamaguchi, Haruka; Yamamoto, Nanase; Wagu, Yutaka; Paoletti, Mathieu; Archer, David B.; Dyer, Paul S.

2012-01-01

The potential for sexual reproduction in Aspergillus oryzae was assessed by investigating the presence and functionality of MAT genes. Previous genome studies had identified a MAT1-1 gene in the reference strain RIB40. We now report the existence of a complementary MAT1-2 gene and the sequencing of an idiomorphic region from A. oryzae strain AO6. This allowed the development of a PCR diagnostic assay, which detected isolates of the MAT1-1 and MAT1-2 genotypes among 180 strains assayed, including industrial tane-koji isolates. Strains used for sake and miso production showed a near-1:1 ratio of the MAT1-1 and MAT1-2 mating types, whereas strains used for soy sauce production showed a significant bias toward the MAT1-2 mating type. MAT1-1 and MAT1-2 isogenic strains were then created by genetic manipulation of the resident idiomorph, and gene expression was compared by DNA microarray and quantitative real-time PCR (qRT-PCR) methodologies under conditions in which MAT genes were expressed. Thirty-three genes were found to be upregulated more than 10-fold in either the MAT1-1 host strain or the MAT1-2 gene replacement strain relative to each other, showing that both the MAT1-1 and MAT1-2 genes functionally regulate gene expression in A. oryzae in a mating type-dependent manner, the first such report for a supposedly asexual fungus. MAT1-1 expression specifically upregulated an α-pheromone precursor gene, but the functions of most of the genes affected were unknown. The results are consistent with a heterothallic breeding system in A. oryzae, and prospects for the discovery of a sexual cycle are discussed. PMID:22327593

Marrow adipose tissue spectrum in obesity and type 2 diabetes mellitus.

PubMed

de Araújo, Iana M; Salmon, Carlos E G; Nahas, Andressa K; Nogueira-Barbosa, Marcello H; Elias, Jorge; de Paula, Francisco J A

2017-01-01

To assess the association of bone mass and marrow adipose tissue (MAT) with other fat depots, insulin resistance, bone remodeling markers, adipokines and glucose control in type 2 diabetes and obesity. The study groups comprised 24 controls (C), 26 obese (O) and 28 type 2 diabetes. Dual-energy X-ray absorptiometry was used to determine bone mineral density (BMD). Blood samples were collected for biochemical measurements. 1 H Magnetic resonance spectroscopy was used to assess MAT in the L3 vertebra, and abdominal magnetic resonance imaging was used to assess intrahepatic lipids in visceral (VAT) and subcutaneous adipose tissue. Regression analysis models were used to test the association between parameters. At all sites tested, BMD was higher in type 2 diabetes than in O and C subjects. The C group showed lower VAT values than the type 2 diabetes group and lower IHL than the O and type 2 diabetes groups. However, MAT was similar in the 3 groups. Osteocalcin and C-terminal telopeptide of type 1 collagen were lower in type 2 diabetes than those in C and O subjects. Moreover, at all sites, BMD was negatively associated with osteocalcin. No association was observed between MAT and VAT. No relationship was observed among MAT and HOMA-IR, leptin, adiponectin or Pref-1, but MAT was positively associated with glycated hemoglobin. MAT is not a niche for fat accumulation under conditions of energy surplus and type 2 diabetes, also is not associated with VAT or insulin resistance. MAT is associated with glycated hemoglobin. © 2017 European Society of Endocrinology.

Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles.

PubMed

Chen, Bingzhi; van Peer, Arend F; Yan, Junjie; Li, Xiao; Xie, Bin; Miao, Juan; Huang, Qianhui; Zhang, Lei; Wang, Wei; Fu, Junsheng; Zhang, Xiang; Zhang, Xiaoyin; Hu, Fengli; Kong, Qingfang; Sun, Xianyun; Zou, Feng; Zhang, Hanxing; Li, Shaojie; Xie, Baogui

2016-07-07

Volvariella volvacea is an important crop in Southeast Asia, but erratic fruiting presents a serious challenge for its production and breeding. Efforts to explain inconsistent fruiting have been complicated by the multinucleate nature, typical lack of clamp connections, and an incompletely identified sexual reproductive system. In this study, we addressed the life cycle of V. volvacea using whole genome sequencing, cloning of MAT loci, karyotyping of spores, and fruiting assays. Microscopy analysis of spores had previously indicated the possible coexistence of heterothallic and homothallic life cycles. Our analysis of the MAT loci showed that only MAT-A, and not MAT-B, controlled heterokaryotization. Thus, the heterothallic life cycle was bipolar. Karyotyping of single spore isolates (SSIs) using molecular markers supported the existence of heterokaryotic spores. However, most SSIs were clearly not heterokaryotic, yet contained structural variation (SV) markers relating to both alleles of both parents. Heterokaryons from crossed, self-sterile homokaryons could produce fruiting bodies, agreeing with bipolar heterothallism. Meanwhile, some SSIs with two different MAT-A loci also produced fruiting bodies, which supported secondary homothallism. Next, SSIs that clearly contained only one MAT-A locus (homothallism) were also able to fruit, demonstrating that self-fertile SSIs were not, per definition, secondary homothallic, and that a third life cycle or genetic mechanism must exist. Finally, recombination between SV markers was normal, yet 10 out of 24 SV markers showed 1:2 or 1:3 distributions in the spores, and large numbers of SSIs contained doubled SV markers. This indicated selfish genes, and possibly partial aneuploidy. Copyright © 2016 Chen et al.

Maternal Uniparental Disomy for Chromosome 20: Physical and Endocrinological Characteristics of Five Patients.

PubMed

Kawashima, Sayaka; Nakamura, Akie; Inoue, Takanobu; Matsubara, Keiko; Horikawa, Reiko; Wakui, Keiko; Takano, Kyoko; Fukushima, Yoshimitsu; Tatematsu, Toshi; Mizuno, Seiji; Tsubaki, Junko; Kure, Shigeo; Matsubara, Yoichi; Ogata, Tsutomu; Fukami, Maki; Kagami, Masayo

2018-06-01

Maternal uniparental disomy for chromosome 20 [UPD(20)mat], resulting in aberrant expression of imprinted transcripts at the GNAS locus, is a poorly characterized condition. These patients manifested a phenotype similar to that of Silver-Russell syndrome (SRS) and small for gestational age-short stature (SGA-SS); however, the etiological relationship between UPD(20)mat and SRS/SGA-SS remains unclear. Moreover, no report has described endocrinological assessment of UPD(20)mat patients, although paternal UPD(20), the mirror image entity of UPD(20)mat, is known to cause multiple hormone resistance reflecting reduced α-subunit of the stimulatory G protein expression. Patients 1 to 5 showed nonmosaic heterodisomy and/or isodisomy for the entire chromosome 20. Patients 1 to 3 and 4 were identified through UPD(20)mat screening for 55 patients with etiology-unknown SRS and 96 patients with SGA-SS, respectively. Patient 5 was identified through molecular analysis for patients with developmental defects. Patients 1 to 5 manifested postnatal growth failure and feeding problems, with or without developmental delay, and other clinical features. Patients 1 to 4 were born SGA. Patients 4 and 5 exhibited hypercalcemia and low or low-normal parathyroid hormone levels. Patient 1 showed constantly decreased thyroid-stimulating hormone (TSH) levels after 12 years of age, although she had a normal TSH level at 5.2 years of age. The results suggest that UPD(20)mat underlies growth failure and feeding problems with additional features and could account for >5% of etiology-unknown SRS and small percentages of SGA-SS. Most important, this study provides an indication that UPD(20)mat can be associated with hypersensitivity of hormone receptors, which may gradually develop with age.

Defects in a New Class of Sulfate/Anion Transporter Link Sulfur Acclimation Responses to Intracellular Glutathione Levels and Cell Cycle Control1[W][OPEN

PubMed Central

Fang, Su-Chiung; Chung, Chin-Lin; Chen, Chun-Han; Lopez-Paz, Cristina; Umen, James G.

2014-01-01

We previously identified a mutation, suppressor of mating type locus3 15-1 (smt15-1), that partially suppresses the cell cycle defects caused by loss of the retinoblastoma tumor suppressor-related protein encoded by the MAT3 gene in Chlamydomonas reinhardtii. smt15-1 single mutants were also found to have a cell cycle defect leading to a small-cell phenotype. SMT15 belongs to a previously uncharacterized subfamily of putative membrane-localized sulfate/anion transporters that contain a sulfate transporter domain and are found in a widely distributed subset of eukaryotes and bacteria. Although we observed that smt15-1 has a defect in acclimation to sulfur-limited growth conditions, sulfur acclimation (sac) mutants, which are more severely defective for acclimation to sulfur limitation, do not have cell cycle defects and cannot suppress mat3. Moreover, we found that smt15-1, but not sac mutants, overaccumulates glutathione. In wild-type cells, glutathione fluctuated during the cell cycle, with highest levels in mid G1 phase and lower levels during S and M phases, while in smt15-1, glutathione levels remained elevated during S and M. In addition to increased total glutathione levels, smt15-1 cells had an increased reduced-to-oxidized glutathione redox ratio throughout the cell cycle. These data suggest a role for SMT15 in maintaining glutathione homeostasis that impacts the cell cycle and sulfur acclimation responses. PMID:25361960

Assessment of mangroves from Goa, west coast India using DNA barcode.

PubMed

Saddhe, Ankush Ashok; Jamdade, Rahul Arvind; Kumar, Kundan

2016-01-01

Mangroves are salt-tolerant forest ecosystems of tropical and subtropical intertidal regions. They are among most productive, diverse, biologically important ecosystem and inclined toward threatened system. Identification of mangrove species is of critical importance in conserving and utilizing biodiversity, which apparently hindered by a lack of taxonomic expertise. In recent years, DNA barcoding using plastid markers rbcL and matK has been suggested as an effective method to enrich traditional taxonomic expertise for rapid species identification and biodiversity inventories. In the present study, we performed assessment of available 14 mangrove species of Goa, west coast India based on core DNA barcode markers, rbcL and matK. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in rbcL (97.7 %) and matK (95.5 %) region. The two candidate chloroplast barcoding regions (rbcL, matK) yielded barcode gaps. Our results clearly demonstrated that matK locus assigned highest correct identification rates (72.09 %) based on TaxonDNA Best Match criteria. The concatenated rbcL + matK loci were able to adequately discriminate all mangrove genera and species to some extent except those in Rhizophora, Sonneratia and Avicennia. Our study provides the first endorsement of the species resolution among mangroves using plastid genes with few exceptions. Our future work will be focused on evaluation of other barcode markers to delineate complete resolution of mangrove species and identification of putative hybrids.

Congenital cataracts and other abnormalities in a female with 46.X, del(X)(q26q28)mat: A new locus for X-linked congenital cataract?

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

Babul, R.; Chitayat, D.; Teshima, I.

1994-09-01

Three forms of X-linked congenital cataracts have been delineated: congenital cataract with posterior Y-sutural opacities in heterozygotes, congenital cataract and microcornea or microphthalmia and congenital cataract-dental syndrome (Nance-Horan syndrome). Of these, only the Nance-Horan syndrome has been mapped to Xp22.3-p21.1. However, Warburg has suggested that these different forms of X-linked congenital cataracts are due to deletions of varying sizes, placing them in the vicinity of the Nance-Horan syndrome region. We report on a female patient born to a 29-year-old primigravida woman who at birth was found to have hypotonia, dysmorphic facial features, hydrocephalus and dense white congenital bilateral cataracts. Othermore » ophthalmological findings included bilateral nystagmus and shallow orbits. Chromosome analysis revealed 46,X,del(X)(q26q28)mat. The mother, however, is phenotypically normal. Brain CT scan on the female infant revealed communicating hydrocephalus and a muscle biopsy showed congenital muscle fiber disproportion. An EMG and NCV were normal. At 4 years of age, her height and weight were below -3SD and her OFC was +2SD. Molecular studies using DNA markers located in Xq26-qter have revealed that the proximal breakpoint in the patient and her mother is defined by the HPRT locus while the distal breakpoint is defined by the locus DXS1108. This indicates that the deletion is not terminal but rather interstitial, retaining sequences proximal to the telomeric region. Other molecular studies are in progress to determine the X-inactivation status of the deleted chromosome in our patient and her mother as a possible explanation for the variation in the phenotype. These clinical and molecular findings suggest that another locus for X-linked congenital cataract exists at Xq26-28.« less

Cyanobacterial construction of hot spring siliceous stromatolites in Yellowstone National Park.

PubMed

Pepe-Ranney, Charles; Berelson, William M; Corsetti, Frank A; Treants, Merika; Spear, John R

2012-05-01

Living stromatolites growing in a hot spring in Yellowstone National Park are composed of silica-encrusted cyanobacterial mats. Two cyanobacterial mat types grow on the stromatolite surfaces and are preserved as two distinct lithofacies. One mat is present when the stromatolites are submerged or at the water-atmosphere interface and the other when stromatolites protrude from the hot spring. The lithofacies created by the encrustation of submerged mats constitutes the bulk of the stromatolites, is comprised of silica-encrusted filaments, and is distinctly laminated. To better understand the cyanobacterial membership and community structure differences between the mats, we collected mat samples from each type. Molecular methods revealed that submerged mat cyanobacteria were predominantly one novel phylotype while the exposed mats were predominantly heterocystous phylotypes (Chlorogloeopsis HTF and Fischerella). The cyanobacterium dominating the submerged mat type does not belong in any of the subphylum groups of cyanobacteria recognized by the Ribosomal Database Project and has also been found in association with travertine stromatolites in a Southwest Japan hot spring. Cyanobacterial membership profiles indicate that the heterocystous phylotypes are 'rare biosphere' members of the submerged mats. The heterocystous phylotypes likely emerge when the water level of the hot spring drops. Environmental pressures tied to water level such as sulfide exposure and possibly oxygen tension may inhibit the heterocystous types in submerged mats. These living stromatolites are finely laminated and therefore, in texture, may better represent similarly laminated ancient forms compared with more coarsely laminated living marine examples. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Establishment and Maintenance of a Heterochromatin Domain

NASA Astrophysics Data System (ADS)

Hall, Ira M.; Shankaranarayana, Gurumurthy D.; Noma, Ken-ichi; Ayoub, Nabieh; Cohen, Amikam; Grewal, Shiv I. S.

2002-09-01

The higher-order assembly of chromatin imposes structural organization on the genetic information of eukaryotes and is thought to be largely determined by posttranslational modification of histone tails. Here, we study a 20-kilobase silent domain at the mating-type region of fission yeast as a model for heterochromatin formation. We find that, although histone H3 methylated at lysine 9 (H3 Lys9) directly recruits heterochromatin protein Swi6/HP1, the critical determinant for H3 Lys9 methylation to spread in cis and to be inherited through mitosis and meiosis is Swi6 itself. We demonstrate that a centromere-homologous repeat (cenH) present at the silent mating-type region is sufficient for heterochromatin formation at an ectopic site, and that its repressive capacity is mediated by components of the RNA interference (RNAi) machinery. Moreover, cenH and the RNAi machinery cooperate to nucleate heterochromatin assembly at the endogenous mat locus but are dispensable for its subsequent inheritance. This work defines sequential requirements for the initiation and propagation of regional heterochromatic domains.

Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

PubMed

Pei, Nancai; Erickson, David L; Chen, Bufeng; Ge, Xuejun; Mi, Xiangcheng; Swenson, Nathan G; Zhang, Jin-Long; Jones, Frank A; Huang, Chun-Lin; Ye, Wanhui; Hao, Zhanqing; Hsieh, Chang-Fu; Lum, Shawn; Bourg, Norman A; Parker, John D; Zimmerman, Jess K; McShea, William J; Lopez, Ida C; Sun, I-Fang; Davies, Stuart J; Ma, Keping; Kress, W John

2015-10-12

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.

Mating-Type Genes and MAT Switching in Saccharomyces cerevisiae

PubMed Central

Haber, James E.

2012-01-01

Mating type in Saccharomyces cerevisiae is determined by two nonhomologous alleles, MATa and MATα. These sequences encode regulators of the two different haploid mating types and of the diploids formed by their conjugation. Analysis of the MATa1, MATα1, and MATα2 alleles provided one of the earliest models of cell-type specification by transcriptional activators and repressors. Remarkably, homothallic yeast cells can switch their mating type as often as every generation by a highly choreographed, site-specific homologous recombination event that replaces one MAT allele with different DNA sequences encoding the opposite MAT allele. This replacement process involves the participation of two intact but unexpressed copies of mating-type information at the heterochromatic loci, HMLα and HMRa, which are located at opposite ends of the same chromosome-encoding MAT. The study of MAT switching has yielded important insights into the control of cell lineage, the silencing of gene expression, the formation of heterochromatin, and the regulation of accessibility of the donor sequences. Real-time analysis of MAT switching has provided the most detailed description of the molecular events that occur during the homologous recombinational repair of a programmed double-strand chromosome break. PMID:22555442

Study on the Strength of GFRP/Stainless Steel Adhesive Joints Reinforced with Glass Mat

NASA Astrophysics Data System (ADS)

Iwasa, Masaaki

The adhesive strengths of glass fiber reinforced plastics/metal adhesive joints reinforced with glass mat under tensile shear loads and tensile loads were investigated analytically and experimentally. First, the stress singularity parameters of the bonding edges were analyzed by FEM for various types of adhesive joints reinforced with glass mat. The shear stress and normal stress distributions near the bonding edge can be expressed by two stress singularity parameters. Second, tensile shear tests were performed on taper lap joint and taper lap joint reinforced with glass mat and tensile tests were performed on T-type adhesive joint and T-type adhesive joint reinforced with glass mat. The relationships between the loads and the crosshead displacements were measured. We concluded that reinforcing adhesive joints has a greater effect on strength under tensile load than under tensile shear load. The adhesive joints strength reinforced with glass mat can be evaluated by using stress singularity parameters.

Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing.

PubMed

Mobberley, Jennifer M; Ortega, Maya C; Foster, Jamie S

2012-01-01

Thrombolites are unlaminated carbonate structures that form as a result of the metabolic interactions of complex microbial mat communities. Thrombolites have a long geological history; however, little is known regarding the microbes associated with modern structures. In this study, we use a barcoded 16S rRNA gene-pyrosequencing approach coupled with morphological analysis to assess the bacterial, cyanobacterial and archaeal diversity associated with actively forming thrombolites found in Highborne Cay, Bahamas. Analyses revealed four distinct microbial mat communities referred to as black, beige, pink and button mats on the surfaces of the thrombolites. At a coarse phylogenetic resolution, the domain bacterial sequence libraries from the four mats were similar, with Proteobacteria and Cyanobacteria being the most abundant. At the finer resolution of the rRNA gene sequences, significant differences in community structure were observed, with dramatically different cyanobacterial communities. Of the four mat types, the button mats contained the highest diversity of Cyanobacteria, and were dominated by two sequence clusters with high similarity to the genus Dichothrix, an organism associated with the deposition of carbonate. Archaeal diversity was low, but varied in all mat types, and the archaeal community was predominately composed of members of the Thaumarchaeota and Euryarchaeota. The morphological and genetic data support the hypothesis that the four mat types are distinctive thrombolitic mat communities. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Evaluating the Feasibility of Five Candidate DNA Barcoding Loci for Philippine Lasianthus Jack (Lasiantheae: Rubiaceae).

PubMed

Arshed, Muhammad Jefte C; Valdez, Marcos B; Alejandro, Grecebio Jonathan D

2017-01-01

The pantropical genus Lasianthus Jack is identified for high phenotypic plasticity making traditional taxonomic identification difficult. Having some members with important medicinal properties, a precise complimentary identification through DNA barcoding is needed for species delineation. In this study, 12 samples representing six Philippine Lasianthus species were used to determine the most efficient barcoding loci among the cpDNA markers ( mat K, rbc L, rps 16, and trn T-F) and nrDNA (ITS) based on the criteria of universality, discriminatory power, and resolution of species. The results revealed that ITS has the recommended primer universality, greatest interspecific divergences, and average resolution of species. Among the cpDNA markers, mat K and rbc L are recommended but with minimal resolution of species. While trn T-F showed moderate interspecific variations and resolution of Lasianthus species, rps 16 has the lowest interspecific divergence and resolution of species. Consequently, ITS is the potential ideal DNA barcode for Lasianthus species. ITS, mat K, and rps 16 markers have the excellent amplification and sequence qualityITS marker has the highest interspecific divergence with the maximum values, followed by mat K, rbc L, trn T-F, and rps 16, respectivelyAll markers except rps 16 yielded average resolution to Lasianthus speciesITS marker is the most ideal locus in terms of excellent universality, high interspecific discriminatory ability, and average species resolution. Abbreviations used: ITS: Internal Transcribe Spacer, mat K: maturase K, rbc L: ribulose-1,5-biphospahte-carboxylase, rps 16: ribosomal protein 16 small subunit gene.

Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.

PubMed

Chen, Shilin; Yao, Hui; Han, Jianping; Liu, Chang; Song, Jingyuan; Shi, Linchun; Zhu, Yingjie; Ma, Xinye; Gao, Ting; Pang, Xiaohui; Luo, Kun; Li, Ying; Li, Xiwen; Jia, Xiaocheng; Lin, Yulin; Leon, Christine

2010-01-07

The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

Effect of natural fiber types and sodium silicate coated on natural fiber mat/PLA composites: Tensile properties and rate of fire propagation

NASA Astrophysics Data System (ADS)

Thongpin, C.; Srimuk, J.; hipkam, N.; Wachirapong, P.

2015-07-01

In this study, 3 types of natural fibres, i.e. jute, sisal and abaca, were plain weaved to fibre mat. Before weaving, the fibres were treated with 5% NaOH to remove hemi cellulose and lignin. The weaving was performed by hand using square wooden block fit with nails for weaving using one and two types of natural fibres as weft and warp fibre to produce natural fibre mat. The fibre mat was also impregnated in sodium silicate solution extracted from rich husk ash. The pH of the solution was adjusted to pH 7 using H2SO4 before impregnation. After predetermined time, sodium silicate was gelled and deposited on the mat. The fabric mat and sodium silicate coated mat were then impregnated with PLA solution to produce prepreg. Dried pepreg was laminated with PLA sheet using compressing moulding machine to obtain natural fibre mat/PLA composite. The composite containing abaca aligned in longitudinal direction with respect to tension force enhanced Young's modulus more than 300%. Fibre mat composites with abaca aligned in longitudinal direction also showed tensile strength enhancement nearly 400% higher than neat PLA. After coating with sodium silicate, the tensile modulus of the composites was found slightly increased. The silicate coating was disadvantage on tensile strength of the composite due to the effect of sodium hydroxide solution that was used as solvent for silicate extraction from rice husk ash. However, sodium silicate could retard rate of fire propagation about 50%compare to neat PLA and about 10% reduction compared to fibre mat composites without sodium silicate coated fibre mat.

Mating Types and Optimum Culture Conditions for Sexual State Formation of Fusarium fujikuroi Isolates

PubMed Central

Kim, Jung-Mi; Hong, Sung Kee; Kim, Wan Gyu; Chun, Se-Chul; Yu, Seung-Hun

2009-01-01

Twenty-five isolates of Fusarium fujikuroi acquired from rice seeds and rice plants evidencing symptoms of Bakanae disease were evaluated to determine their mating types and characterize the formation of their sexual state. The mating types of the isolates were evaluated via multiplex PCR with the diagnostic primers of the mating-type (MAT) region: GFmat1a, GFmat1b, GFmat2c, and GFmat2d. Among the 25 isolates, 11 were identified as MAT-1 (male), and 14 as MAT-2 (female). Four MAT-1 isolates and three MAT-2 isolates were mated and cultured to evaluate the optimal culture conditions for the production of their sexual states. Among four tested media, 10% V8 juice agar proved optimal for the perithecial production of the isolates. The isolates also generated the largest numbers of perithecia when incubated at 23℃ in alternating cycles of 12 hr fluorescent light and NUV fluorescent light and 12 hr darkness. PMID:23983543

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing.

PubMed

Bolhuis, Henk; Stal, Lucas J

2011-11-01

Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.

Effect of concrete slats, three mat types and out-wintering pads on performance and welfare of finishing beef steers.

PubMed

Earley, Bernadette; McNamara, John D; Jerrams, Stephen J; O'Riordan, Edward G

2017-05-30

The objective was to investigate the effect of placing mats on concrete slatted floors on performance, behaviour, hoof condition, dirt scores, physiological and immunological variables of beef steers, and to compare responses with animals on out-wintering pads. Continental crossbred beef steers [n = 360; mean (±SD) initial live weight 539 kg (42.2)] were blocked by breed and live weight and randomly assigned to one of five treatments; (1) Concrete slats alone, (2) Mat 1 (Natural Rubber structure) (Durapak Rubber Products), (3) Mat 2 (Natural rubber structure) (EasyFix), (4) Mat 3 (modified ethylene vinyl acetate (EVA) foam structure) and (5) Out-wintering pads (OWP's). Animals on the OWPs had a greater (P < 0.05) live weight gain (P < 0.05) compared with the slat and Mat 2 treatments: results for Mat 1 and Mat 3 were the same (P > 0.05) as the other treatments. Animals on the OWPs had reduced lying percentage time compared with all the other treatments. Dry matter (DM) intake was greater for animals on the OWPs compared with all the other treatments. Carcass weight, kill out proportion, carcass fat score, carcass composition score, FCR and physiological responses were similar (P > 0.05) among treatments. No incidence of laminitis was observed among treatments. The number of hoof lesions was greater on all mat types (P < 0.05) compared with concrete slats and OWP treatments. Dirt scores were greater (P < 0.05) for animals on OWPs when measured on days 42, 84, 105, 126 and 150 compared with animals on slats. Under the conditions adopted for the present study, there was no evidence to suggest that animals housed on bare concrete slats were disadvantaged in respect of animal welfare compared with animals housed on other floor types. It is concluded that the welfare of steers was not adversely affected by slats compared with different mat types or OWPs.

The type of mat (Contact vs. Photocell) affects vertical jump height estimated from flight time.

PubMed

García-López, Juan; Morante, Juan C; Ogueta-Alday, Ana; Rodríguez-Marroyo, Jose A

2013-04-01

The purposes of this study were to analyze the validity and reliability of 2 photocell mats and to probe the possible influence of the type of mat (contact vs. photocell) on vertical jump height estimated from flight time. In 2 separate studies, 89 and 92 physical students performed 3 countermovement jumps that were simultaneously registered by a Force Plate (gold standard method), 2 photocell mats (SportJump System Pro and ErgoJump Plus), and a contact mat (SportJump-v1.0). The first study showed that the 2 photocell mats underestimated the vertical jump height (1.3 ± 0.2 cm and 5.9 ± 5.2 cm, respectively), but only SportJump System Pro showed a high correlation with the Force Plate (r = 0.999 and 0.676, respectively) and good intraday reliability (coefficient of variation = 2.98 and 15.94%, intraclass correlation coefficients = 0.95-0.97 and 0.45-0.57, respectively). The second study demonstrated a strong correlation (r = 0.994) between the 2 technologies (contact vs. photocell mats) with differences in vertical jump height of 2.0 ± 0.8 cm (95% confidence interval = 1.9-2.1 cm), which depended on both flight time and subjects' body mass. In conclusion, SportJump System Pro was a valid and reliable device. The new devices to measure vertical jump height from flight time should be validated. The type of mat (contact vs. photocell) affected approximately 6% the vertical jump height (approximately 2 cm in this study), which should be considered in further studies. The use of validated photocell mats instead of the contact mats was recommended.

Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete

PubMed Central

Sampaio, José Paulo; Gonçalves, Paula

2016-01-01

In fungi belonging to the phylum Basidiomycota, sexual compatibility is usually determined by two genetically unlinked MAT loci, one of which encodes one or more pheromone receptors (P/R) and pheromone precursors, and the other comprehends at least one pair of divergently transcribed genes encoding homeodomain (HD) transcription factors. Most species are heterothallic, meaning that sexual reproduction requires mating between two sexually compatible individuals harboring different alleles at both MAT loci. However, some species are known to be homothallic, one individual being capable of completing the sexual cycle without mating with a genetically distinct partner. While the molecular underpinnings of the heterothallic life cycles of several basidiomycete model species have been dissected in great detail, much less is known concerning the molecular basis for homothallism. Following the discovery in available draft genomes of the homothallic basidiomycetous yeast Phaffia rhodozyma of P/R and HD genes, we employed available genetic tools to determine their role in sexual development. Two P/R clusters, each harboring one pheromone receptor and one pheromone precursor gene were found in close vicinity of each other and were shown to form two redundant P/R pairs, each receptor being activated by the pheromone encoded by the most distal pheromone precursor gene. The HD locus is apparently genetically unlinked to the P/R locus and encodes a single pair of divergently transcribed HD1 and HD2 transcription factors, both required for normal completion of the sexual cycle. Given the genetic makeup of P. rhodozyma MAT loci, we postulate that it is a primarily homothallic organism and we propose a model for the interplay of molecular interactions required for sexual development in this species. Phaffia rhodozyma is considered one of the most promising microbial source of the carotenoid astaxanthin. Further development of this yeast as an industrial organism will benefit from new insights regarding its sexual reproduction system. PMID:27327578

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

NASA Astrophysics Data System (ADS)

Wong, Hon Lun; Smith, Daniela-Lee; Visscher, Pieter T.; Burns, Brendan P.

2015-10-01

Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.

The micromorphology of Younger Dryas-aged black mats from Nevada, Arizona, Texas and New Mexico

NASA Astrophysics Data System (ADS)

Harris-Parks, Erin

2016-01-01

Black mats are organic-rich sediments and soils that form in wet environments associated with spring discharge. Micromorphological and geochemical analyses of 25 black mats dating to the Younger Dryas Chronozone (12.9-11.7 ka) and early Holocene were conducted to determine their composition and depositional environment. Samples were collected from Arizona, New Mexico, Texas and Nevada. Micromorphological analyses were conducted on thin sections using polarized and blue fluorescent light. These analyses determined that black mats contain humic acids, fine (5-20 μm) plant fragments, diatoms, phytoliths, and gastropods. The dominant type of organic matter in black mats is derived from herbaceous plants, contradicting previous studies that supported algal or charcoal sources. Differences in the micromorphological characteristics of the samples revealed that black mats formed as three different types, organic horizons, moist soils and, ponded sediments, depending on their topographic position in relation to the water table. The microscopic evidence found in black mats supports the presence of widespread wet environments in Nevada and Arizona during the Younger Dryas Chronozone, clearly indicating a sustained period of greater effective moisture, optimal for spring discharge and black mat formation.

Sex-specific gene expression during asexual development of Neurospora crassa.

PubMed

Wang, Zheng; Kin, Koryu; López-Giráldez, Francesc; Johannesson, Hanna; Townsend, Jeffrey P

2012-07-01

The impact of loci that determine sexual identity upon the asexual, dominant stage of fungal life history has been well studied. To investigate their impact, expression differences between strains of different mating type during asexual development were assayed, with RNA sampled from otherwise largely isogenic mat A and mat a strains of Neurospora crassa at early, middle, and late clonal stages of development. We observed significant differences in overall gene expression between mating types across clonal development, especially at late development stages. The expression levels of mating-type genes and pheromone genes were assayed by reverse transcription and quantitative PCR, revealing expression of pheromone and receptor genes in strains of both mating types in all development stages, and revealing that mating type (mat) genes were increasingly expressed over the course of asexual development. Interestingly, among differentially expressed genes, the mat A genotype more frequently exhibited a higher expression level than mat a, and demonstrated greater transcriptional regulatory dynamism. Significant up-regulation of expression was observed for many late light-responsive genes at late asexual development stages. Further investigation of the impact of light and the roles of light response genes in asexual development of both mating types are warranted. Copyright © 2012 Elsevier Inc. All rights reserved.

Are floating algal mats a refuge from hypoxia for estuarine invertebrates?

PubMed Central

Knysh, Kyle M.; Theriault, Emma F.; Pater, Christina C.; Courtenay, Simon C.; van den Heuvel, Michael R.

2017-01-01

Eutrophic aquatic habitats are characterized by the proliferation of vegetation leading to a large standing biomass that upon decomposition may create hypoxic (low-oxygen) conditions. This is indeed the case in nutrient impacted estuaries of Prince Edward Island, Canada, where macroalgae, from the genus Ulva, form submerged ephemeral mats. Hydrological forces and gases released from photosynthesis and decomposition lead to these mats occasionally floating to the water’s surface, henceforth termed floating mats. Here, we explore the hypothesis that floating mats are refugia during periods of sustained hypoxia/anoxia and examine how the invertebrate community responds to it. Floating mats were not always present, so in the first year (2013) sampling was attempted monthly and limited to when both floating and submerged mats occurred. In the subsequent year sampling was weekly, but at only one estuary due to logistical constraints from increased sampling frequency, and was not limited to when both mat types occurred. Water temperature, salinity, and pH were monitored bi-weekly with dissolved oxygen concentration measured hourly. The floating and submerged assemblages shared many of the same taxa but were statistically distinct communities; submerged mats tended to have a greater proportion of benthic animals and floating mats had more mobile invertebrates and insects. In 2014, sampling happened to occur in the weeks before the onset of anoxia, during 113 consecutive hours of sustained anoxia, and for four weeks after normoxic conditions returned. The invertebrate community on floating mats appeared to be unaffected by anoxia, indicating that these mats may be refugia during times of oxygen stress. Conversely, there was a dramatic decrease in animal abundances that remained depressed on submerged mats for two weeks. Cluster analysis revealed that the submerged mat communities from before the onset of anoxia and four weeks after anoxia were highly similar to each other, indicating recovery. When mobile animals were considered alone, there was an exponential relationship between the percentage of animals on floating mats, relative to the total number on both mat types, and hypoxia. The occupation of floating mats by invertebrates at all times, and their dominance there during hypoxia/anoxia, provides support for the hypothesis that floating mats are refugia. PMID:28348927

Toxoplasmosis in Sand cats (Felis margarita) and other animals in the Breeding Centre for Endangered Arabian Wildlife in the United Arab Emirates and Al Wabra Wildlife Preservation, the State of Qatar.

PubMed

Dubey, J P; Pas, An; Rajendran, C; Kwok, O C H; Ferreira, L R; Martins, J; Hebel, C; Hammer, S; Su, C

2010-09-20

The Sand cat (Felis margarita) is a small-sized felid found in sand and stone deserts ranging from the north of Africa to Asia, with the Arabian Peninsula as its centre of distribution. The Sand cat captive breeding program at the Breeding Centre for Endangered Arabian Wildlife (BCEAW), Sharjah, UAE, has experienced high newborn mortality rates, and congenital toxoplasmosis was recently recognized as one of the causes of this mortality. In the present study, one 18-month-old Sand cat (FM019) died of acute toxoplasmosis-associated hepatitis and pneumonitis acquired after birth; Toxoplasma gondii was demonstrated in histological sections which reacted with T. gondii polyclonal antibodies by immunohistochemistry (IHC). T. gondii DNA was found by PCR of extracted DNA from liver and lung tissues of this cat. Antibodies to T. gondii were found in serum examined in 1:1600 dilution in the modified agglutination test (MAT); its 2-year-old cage mate seroconverted (MAT titer 1:3200) at the same time. Another Sand cat (FM017) was euthanized because of ill health when 3 years old; its MAT titer was >1:3200, and T. gondii tissue cysts were found in brain, heart, ocular muscles and skeletal muscle, confirmed by IHC. Viable T. gondii was isolated by bioassays in mice inoculated with tissues of another chronically infected Sand cat (FM002); T. gondii was not found in histological sections of this cat. T. gondii antibodies were found in several species of animals tested, notably in 49 of 57 wild felids at BCEAW. A 7-year-old Sand cat (3657) from Al Wabra Wildlife Preservation (AWWP), Doha, State of Qatar died of acute visceral toxoplasmosis with demonstrable T. gondii tachyzoites by IHC, and T. gondii DNA by PCR, and a MAT titer of >3200. T. gondii antibodies were found in 21 of 27 of wild felids at AWWP. PCR-RFLP genotyping at 10 genetic loci revealed that these T. gondii isolates from Sand cat (FM002 and FM019) at BCEAW have an atypical genotype, which was previously reported in T. gondii isolates of dogs from Sri Lanka. The genotype from the cat from AWWP (3657) is a genetic Type II strain with a Type I allele at locus Apico. This is the first report of genetic characterization of T. gondii isolates from Middle East.

Factors affecting stall use for different freestall bases.

PubMed

Wagner-Storch, A M; Palmer, R W; Kammel, D W

2003-06-01

The objective of this study was to compare stall use (stall occupancy and cow position) by barn side for factors affecting stall use. A closed circuit television system recorded stall use four times per day for a 9-mo period starting May 9, 2001. Six factors were analyzed: stall base, distance to water, stall location within stall base section, stall location within barn, inside barn temperature, and length of time cows were exposed to stall bases. Two barn sides with different stocking densities were analyzed: low (66%), with cows milked by robotic milker; and high (100%), with cows milked 2X in parlor. Six stall base types were tested: two mattresses, a waterbed, a rubber mat, concrete, and sand (high side only). The base types were grouped 3 to 7 stalls/section and randomly placed in each row. Cows spent more time in mattress-based stalls, but the highest percentage lying was in sand-based stalls. The following significant stall occupancy percentages were found: sand had the highest percentage of cows lying on the high stocking density side (69%), followed by mattress type 1 (65%) > mattress type 2 (57%) > waterbed (45%) > rubber mat (33%) > concrete (23%). Mattress type 1 had the highest percentage stalls occupied (88%), followed by mattress type 2 (84%) > sand (79%) > soft rubber mat (65%) > waterbed (62%) > concrete (39%). On the low stocking rate side, mattress type 1 had the highest percentage cows lying (45%) and occupied (59.6%), followed by mattress type 2 > waterbed > soft rubber mat > concrete. Cow lying and stalls occupied percentages were highest for stalls 1) not at the end of a section, and 2) on the outside row, and varied by base type for time cows exposed to stalls and inside barn temperature. Lying and occupied percentages were different for different mattress types. The percentage of stalls with cows standing was higher for mat and mattress-based stalls. Results show mattress type 1 and sand to be superior and rubber mats and concrete inferior stall bases.

Fossilization of Coniform (Phormidium) Stromatolites In Siliceous Thermal Springs, Yellowstone National Park

NASA Technical Reports Server (NTRS)

Farmer, Jack; Bebout, Brad; Jahnke, Linda; Chang, Sherwood (Technical Monitor)

1997-01-01

We have studied fossilization processes in well-developed cyanobacterial mats present in mid-terrace ponds of silica-precipitating thermal springs of Yellowstone National Park. These mats occur over temperatures of approx.35-60 C and are dominated by species of Phormidium. Within Bonded systems two end member environments have been distinguished based temperature, depth, and the stability of spring inflows, each differing substantially in the style of stromatolite morphogenesis and fossilization. Type 1 systems include shallow, ephemeral ponds where water flow and temperature fluctuates widely on a seasonal basis; mats typically secrete rapidly up to the air-water interface, forming exposed islands. Silicification occurs primarily by the wicking of water onto the surface of exposed mats, leading to the evaporative concentration of silica near the surface. pH microelectronic measurements in partially-exposed columns show strong gradients in pH with values exceeding 10.5 in the upper am of silicifying mats, decreasing to <9.0 a few mm below the surface. High oxygen concentrations lead to the rapid oxidation of most organic materials. In Type I systems, the tops of coniform and columnar stromatolites become silicified first, followed by the bases. This typically leads to extensive fragmentation during the initial stages of burial. Case 2 systems include deeper ponds where the water flow, temperature and depth are seasonally more stable, and where mats develop larger-scale tufts and columns. Alkalinity in permanently submerged mats increases into tuft interiors from approx.9.0 near the surface to >10.0 at depth. Moderate silicification is apparent throughout mat frameworks, although there is frequently a densely silicified core near the base. In Type 2 systems, preservation of the coniform and columnar architecture of stromatoilites is much more robust. Sub-fossil examples suggest minimal fragmentation prior to burial. Comparative rapid analysis of the phone zones of submerged and exposed (silicifying) mats demonstrated the recovery of comparable levels of esterified fatty acids in both types of mats. Membrane lipids apparently remain intact during the early stages of silicification, although their fate during early diagenesis is still being evaluated.

Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

PubMed Central

Chen, Shilin; Yao, Hui; Han, Jianping; Liu, Chang; Song, Jingyuan; Shi, Linchun; Zhu, Yingjie; Ma, Xinye; Gao, Ting; Pang, Xiaohui; Luo, Kun; Li, Ying; Li, Xiwen; Jia, Xiaocheng; Lin, Yulin; Leon, Christine

2010-01-01

Background The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL + matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Methodology/Principal Findings Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. Conclusions The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa. PMID:20062805

Evaluation of two multi-locus sequence typing schemes for commensal Escherichia coli from dairy cattle in Washington State.

PubMed

Ahmed, Sara; Besser, Thomas E; Call, Douglas R; Weissman, Scott J; Jones, Lisa P; Davis, Margaret A

2016-05-01

Multi-locus sequence typing (MLST) is a useful system for phylogenetic and epidemiological studies of multidrug-resistant Escherichiacoli. Most studies utilize a seven-locus MLST, but an alternate two-locus typing method (fumC and fimH; CH typing) has been proposed that may offer a similar degree of discrimination at lower cost. Herein, we compare CH typing to the standard seven-locus method for typing commensal E. coli isolates from dairy cattle. In addition, we evaluated alternative combinations of eight loci to identify combinations that maximize discrimination and congruence with standard seven-locus MLST among commensal E. coli while minimizing the cost. We also compared both methods when used for typing uropathogenic E. coli (UPEC). CH typing was less discriminatory for commensal E. coli than the standard seven-locus method (Simpson's Index of Diversity=0.933 [0.902-0.964] and 0.97 [0.96-0.979], respectively). Combining fimH with housekeeping gene loci improved discriminatory power for commensal E. coli from cattle but resulted in poor congruence with MLST. We found that a four-locus typing method including the housekeeping genes adk, purA, gyrB and recA could be used to minimize cost without sacrificing discriminatory power or congruence with Achtman seven-locus MLST when typing commensal E. coli. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic and biologic characteristics of Toxoplasma gondii isolates in free-range chickens from Colombia, South America.

PubMed

Dubey, J P; Gomez-Marin, Jorge E; Bedoya, Angela; Lora, Fabiana; Vianna, M C B; Hill, D; Kwok, O C H; Shen, S K; Marcet, P L; Lehmann, T

2005-11-25

The prevalence of Toxoplasma gondii in free-ranging chickens is a good indicator of the prevalence of T. gondii oocysts in the soil because chickens feed from the ground. The prevalence of T. gondii in 77 free-range chickens (Gallus domesticus) from Colombia, South America was determined. Antibodies to T. gondii were assayed by the modified agglutination test (MAT), and found in 32 (44.4%) of 72 chickens with titers of 1:5 in 4, 1:10 in 3, 1:20 in 1, 1:40 in 1, 1:80 in 8, 1:160 in 8, 1:320 in 3, and 1:640 or higher in 4. Hearts and brains of 31 seropositive chickens were pooled and bioassayed in mice. Tissues from 32 (16+16) seronegative chickens were pooled and fed to two, T. gondii-free cats, and tissues from nine chickens without matching sera were fed to one T. gondii-free cat. Feces of cats were examined for oocysts. T. gondii oocysts were excreted by a cat that was fed tissues of 16 seronegative chickens. T. gondii was isolated by bioassay in mice from 23 chickens with MAT titers of 1:20 or higher. All infected mice from 16 of the 23 isolates died of toxoplasmosis. Overall, 82 (81.1%) of 101 mice that became infected after inoculation with chicken tissues died of toxoplasmosis. Genotyping of these 24 isolates using polymorphisms at the SAG2 locus indicated that seven T. gondii isolates were Type I, 17 were Type III, and none was Type II. Phenotypically, T. gondii isolates from chickens from Colombia were similar to isolates from Brazil but different from the isolates from North America; most isolates from chickens from Brazil and Colombia were lethal for mice whereas isolates from North America did not kill inoculated mice. Genetically, none of the T. gondii isolates from Colombia and Brazil was SAG2 Type II, whereas most isolates from chickens from North America were Type II. This is the first report of genetic characterization of T. gondii isolates from Colombia, South America.

Comparative genomics of biotechnologically important yeasts

PubMed Central

Riley, Robert; Haridas, Sajeet; Wolfe, Kenneth H.; Lopes, Mariana R.; Hittinger, Chris Todd; Göker, Markus; Salamov, Asaf A.; Wisecaver, Jennifer H.; Long, Tanya M.; Aerts, Andrea L.; Barry, Kerrie W.; Choi, Cindy; Clum, Alicia; Coughlan, Aisling Y.; Deshpande, Shweta; Douglass, Alexander P.; Hanson, Sara J.; Klenk, Hans-Peter; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lipzen, Anna M.; Meier-Kolthoff, Jan P.; Ohm, Robin A.; Otillar, Robert P.; Pangilinan, Jasmyn L.; Peng, Yi; Rosa, Carlos A.; Scheuner, Carmen; Sibirny, Andriy A.; Slot, Jason C.; Stielow, J. Benjamin; Sun, Hui; Kurtzman, Cletus P.; Blackwell, Meredith; Grigoriev, Igor V.

2016-01-01

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation. PMID:27535936

Fiber webs

Treesearch

Roger M. Rowell; James S. Han; Von L. Byrd

2005-01-01

Wood fibers can be used to produce a wide variety of low-density three-dimensional webs, mats, and fiber-molded products. Short wood fibers blended with long fibers can be formed into flexible fiber mats, which can be made by physical entanglement, nonwoven needling, or thermoplastic fiber melt matrix technologies. The most common types of flexible mats are carded, air...

Mixed-reproductive strategies, competitive mating-type distribution and life cycle of fourteen black morel species.

PubMed

Du, Xi-Hui; Zhao, Qi; Xia, En-Hua; Gao, Li-Zhi; Richard, Franck; Yang, Zhu L

2017-05-04

Morchella species are well known world-round as popular and prized edible fungi due to their unique culinary flavor. Recently, several species have been successfully cultivated in China. However, their reproductive modes are still unknown, and their basic biology needs to be elucidated. Here, we use the morel genome information to investigate mating systems and life cycles of fourteen black morel species. Mating type-specific primers were developed to screen and genotype ascospores, hymenia and stipes from 223 ascocarps of the 14 species from Asia and Europe. Our data indicated that they are all heterothallic and their life cycles are predominantly haploid, but sterile haploid fruiting also exists. Ascospores in all species are mostly haploid, homokaryotic, and multinuclear, whereas aborted ascospores without any nuclei were also detected. Interestingly, we monitored divergent spatial distribution of both mating types in natural morel populations and cultivated sites, where the fertile tissue of fruiting bodies usually harbored both mating types, whereas sterile tissue of wild morels constantly had one MAT allele, while the sterile tissue of cultivated strains always exhibited both MAT alleles. Furthermore, MAT1-1-1 was detected significantly more commonly than MAT1-2-1 in natural populations, which strongly suggested a competitive advantage for MAT1-1 strains.

Preferences of dairy cows for three stall surface materials with small amounts of bedding.

PubMed

Norring, M; Manninen, E; de Passillé, A M; Rushen, J; Saloniemi, H

2010-01-01

Farmers' concerns about the economy, cost of labor, and hygiene have resulted in reduced use of organic bedding in stalls for dairy cows; however, the reduced use of organic bedding possibly impairs cow comfort. The effects of different stall surface materials were evaluated in an unheated building in which only a small amount of bedding was used. The lying time and preferences of 18 cows using 3 stall surface materials (concrete, soft rubber mat, and sand) were compared. All materials were lightly bedded with a small amount of straw, and the amount of straw added to each stall was measured. The cows only had access to stalls of one surface type while their lying time was observed. Lying times were longest on the rubber mats compared with other surfaces (rubber mat 768; concrete 727; sand 707+/-16 min/d). In a preference test, cows had access to 2 of the 3 types of stalls for 10 d and their stall preference was measured. Cows preferred stalls with rubber mats to stalls with a concrete floor (median 73 vs. 18 from a total of 160 observations per day; interquartile range was 27 and 12, respectively), but showed no preference for sand stalls compared with stalls with a concrete floor or with rubber mats. More straw was needed on sand stalls compared with concrete or mat (638+/-13 g/d on sand, 468+/-10 g/d on concrete, and 464+/-8 g/d on rubber mats). Lying times on bedded mats indicated that mats were comfortable for the cows. If availability or cost of bedding material requires limiting the amount of bedding used, rubber mats may help maintain cow comfort. Copyright 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Evaluation of six candidate DNA barcode loci for identification of five important invasive grasses in eastern Australia

PubMed Central

Wang, Aisuo; Gopurenko, David; Wu, Hanwen; Lepschi, Brendan

2017-01-01

Invasive grass weeds reduce farm productivity, threaten biodiversity, and increase weed control costs. Identification of invasive grasses from native grasses has generally relied on the morphological examination of grass floral material. DNA barcoding may provide an alternative means to identify co-occurring native and invasive grasses, particularly during early growth stages when floral characters are unavailable for analysis. However, there are no universal loci available for grass barcoding. We herein evaluated the utility of six candidate loci (atpF intron, matK, ndhK-ndhC, psbE—petL, ETS and ITS) for barcode identification of several economically important invasive grass species frequently found among native grasses in eastern Australia. We evaluated these loci in 66 specimens representing five invasive grass species (Chloris gayana, Eragrostis curvula, Hyparrhenia hirta, Nassella neesiana, Nassella trichotoma) and seven native grass species. Our results indicated that, while no single locus can be universally used as a DNA barcode for distinguishing the grass species examined in this study, two plastid loci (atpF and matK) showed good distinguishing power to separate most of the taxa examined, and could be used as a dual locus to distinguish several of the invasive from the native species. Low PCR success rates were evidenced among two nuclear loci (ETS and ITS), and few species were amplified at these loci, however ETS was able to genetically distinguish the two important invasive Nassella species. Multiple loci analyses also suggested that ETS played a crucial role in allowing identification of the two Nassella species in the multiple loci combinations. PMID:28399170

Evaluation of six candidate DNA barcode loci for identification of five important invasive grasses in eastern Australia.

PubMed

Wang, Aisuo; Gopurenko, David; Wu, Hanwen; Lepschi, Brendan

2017-01-01

Invasive grass weeds reduce farm productivity, threaten biodiversity, and increase weed control costs. Identification of invasive grasses from native grasses has generally relied on the morphological examination of grass floral material. DNA barcoding may provide an alternative means to identify co-occurring native and invasive grasses, particularly during early growth stages when floral characters are unavailable for analysis. However, there are no universal loci available for grass barcoding. We herein evaluated the utility of six candidate loci (atpF intron, matK, ndhK-ndhC, psbE-petL, ETS and ITS) for barcode identification of several economically important invasive grass species frequently found among native grasses in eastern Australia. We evaluated these loci in 66 specimens representing five invasive grass species (Chloris gayana, Eragrostis curvula, Hyparrhenia hirta, Nassella neesiana, Nassella trichotoma) and seven native grass species. Our results indicated that, while no single locus can be universally used as a DNA barcode for distinguishing the grass species examined in this study, two plastid loci (atpF and matK) showed good distinguishing power to separate most of the taxa examined, and could be used as a dual locus to distinguish several of the invasive from the native species. Low PCR success rates were evidenced among two nuclear loci (ETS and ITS), and few species were amplified at these loci, however ETS was able to genetically distinguish the two important invasive Nassella species. Multiple loci analyses also suggested that ETS played a crucial role in allowing identification of the two Nassella species in the multiple loci combinations.

Molecular Diversity of Cyanobacteria Inhabiting Coniform Structures and Surrounding Mat in a Yellowstone Hot Spring

NASA Astrophysics Data System (ADS)

Lau, Evan; Nash, Cody Z.; Vogler, Detlev R.; Cullings, K. W.

2005-02-01

Lithified coniform structures are common within cyanobacterial mats in Yellowstone National Park hot springs. It is unknown whether these structures and the mats from which they develop are inhabited by the same cyanobacterial populations. Denaturing gradient gel electrophoresis and sequencing and phylogenetic analysis of 16S rDNA was used to determine whether (1) three different morphological types of lithified coniform structures are inhabited by different cyanobacterial species, (2) these species are partitioned along a vertical gradient of these structures, and (3) lithified and non-lithified sections of mat are inhabited by different cyanobacterial species. Our results, based on multiple samplings, indicate that the cyanobacterial community compositions in the three lithified morphological types were identical and lacked any vertical differentiation. However, lithified and non-lithified portions of the same mat were inhabited by distinct and different populations of cyanobacteria. Cyanobacteria inhabiting lithified structures included at least one undefined Oscillatorialean taxon, which may represent the dominant cyanobacteria genus in lithified coniform stromatolites, Phormidium, three Synechococcus-like species, and two unknown cyanobacterial taxa. In contrast, the surrounding mats contained four closely related Synechococcus-like species. Our results indicate that the distribution of lithified coniform stromatolites may be dependent on the presence of one or more microorganisms, which are phylogenetically different from those inhabiting surrounding non-lithified mats.

Ultrafine polybenzimidazole (PBI) fibers. [separators for alkaline batteries and dfuel cells

NASA Technical Reports Server (NTRS)

Chenevey, E. C.

1979-01-01

Mats were made from ultrafine polybenzimidazole (PBI) fibers to provide an alternate to the use of asbestos as separators in fuel cells and alkaline batteries. To minimize distortion during mat drying, a process to provide a dry fibrid was developed. Two fibrid types were developed: one coarse, making mats for battery separators; the other fine, making low permeability matrices for fuel cells. Eventually, it was demonstrated that suitable mat fabrication techniques yielded fuel cell separators from the coarser alkaline battery fibrids. The stability of PBI mats to 45% KOH at 123 C can be increased by heat treatment at high temperatures. Weight loss data to 1000 hours exposure show the alkali resistance of the mats to be superior to that of asbestos.

Organization and evolution of mating-type genes in three Stagonosporopsis species causing gummy stem blight of cucurbits and leaf spot and dry rot of papaya.

PubMed

Li, Hao-Xi; Gottilla, Thomas M; Brewer, Marin Talbot

2017-10-01

Population divergence and speciation of closely related lineages can result from reproductive differences leading to genetic isolation. An increasing number of fungal diseases of plants and animals have been determined to be caused by morphologically indistinguishable species that are genetically distinct, thereby representing cryptic species. We were interested in identifying if mating systems among three Stagonosporopsis species (S. citrulli, S. cucurbitacearum, and S. caricae) causing gummy stem blight (GSB) of cucurbits or leaf spot and dry rot of papaya differed, possibly underlying species divergence. Additionally, we were interested in identifying evolutionary pressures acting on the genes controlling mating in these fungi. The mating-type loci (MAT1) of three isolates from each of the three species were identified in draft genome sequences. For the three species, MAT1 was structurally identical and contained both mating-type genes necessary for sexual reproduction, which suggests that all three species are homothallic. However, both MAT1-1-1 and MAT1-2-1 were divergent among species showing rapid evolution with a much greater number of amino acid-changing substitutions detected for the reproductive genes compared with genes flanking MAT1. Positive selection was detected in MAT1-2-1, especially in the highly conserved high mobility group (MATA_HMG-box) domain. Thus, the mating-type genes are rapidly evolving in GSB fungi, but a difference in mating systems among the three species does not underlie their divergence. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa.

PubMed

Vieira, Willie A S; Lima, Waléria G; Nascimento, Eduardo S; Michereff, Sami J; Câmara, Marcos P S; Doyle, Vinson P

2017-01-01

Developing a comprehensive and reliable taxonomy for the Colletotrichum gloeosporioides species complex will require adopting data standards on the basis of an understanding of how methodological choices impact morphological evaluations and phylogenetic inference. We explored the impact of methodological choices in a morphological and molecular evaluation of Colletotrichum species associated with banana in Brazil. The choice of alignment filtering algorithm has a significant impact on topological inference and the retention of phylogenetically informative sites. Similarly, the choice of phylogenetic marker affects the delimitation of species boundaries, particularly if low phylogenetic signal is confounded with strong discordance, and inference of the species tree from multiple-gene trees. According to both phylogenetic informativeness profiling and Bayesian concordance analyses, the most informative loci are DNA lyase (APN2), intergenic spacer (IGS) between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), calmodulin (CAL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), glutamine synthetase (GS), β-tubulin (TUB2), and a new marker, the intergenic spacer between GAPDH and an hypothetical protein (GAP2-IGS). Cornmeal agar minimizes the variance in conidial dimensions compared with potato dextrose agar and synthetic nutrient-poor agar, such that species are more readily distinguishable based on phenotypic differences. We apply these insights to investigate the diversity of Colletotrichum species associated with banana anthracnose in Brazil and report C. musae, C. tropicale, C. theobromicola, and C. siamense in association with banana anthracnose. One lineage did not cluster with any previously described species and is described here as C. chrysophilum.

Medication-assisted treatment in criminal justice agencies affiliated with the criminal justice-drug abuse treatment studies (CJ-DATS): availability, barriers, and intentions.

PubMed

Friedmann, Peter D; Hoskinson, Randall; Gordon, Michael; Schwartz, Robert; Kinlock, Timothy; Knight, Kevin; Flynn, Patrick M; Welsh, Wayne N; Stein, Lynda A R; Sacks, Stanley; O'Connell, Daniel J; Knudsen, Hannah K; Shafer, Michael S; Hall, Elizabeth; Frisman, Linda K

2012-01-01

Medication-assisted treatment (MAT) is underutilized in the treatment of drug-dependent, criminal justice populations. This study surveyed criminal justice agencies affiliated with the Criminal Justice Drug Abuse Treatment Studies (CJ-DATS) to assess use of MAT and factors influencing use of MAT. A convenience sample (N = 50) of criminal justice agency respondents (e.g., jails, prisons, parole/probation, and drug courts) completed a survey on MAT practices and attitudes. Pregnant women and individuals experiencing withdrawal were most likely to receive MAT for opiate dependence in jail or prison, whereas those reentering the community from jail or prison were the least likely to receive MAT. Factors influencing use of MAT included criminal justice preferences for drug-free treatment, limited knowledge of the benefits of MAT, security concerns, regulations prohibiting use of MAT for certain agencies, and lack of qualified medical staff. Differences across agency type in the factors influencing use and perceptions of MAT were also examined. MAT use is largely limited to detoxification and maintenance of pregnant women in criminal justice settings. Use of MAT during the community reentry period is minimal. Addressing inadequate knowledge and negative attitudes about MAT may increase its adoption, but better linkages to community pharmacotherapy during the reentry period might overcome other issues, including security, liability, staffing, and regulatory concerns. The CJ-DATS collaborative MAT implementation study to address inadequate knowledge, attitudes, and linkage will be described.

The Post-Dam System. Volume 4. Relational Data Base Management System (RDBMS)

DTIC Science & Technology

1992-10-01

15 THEN LOAD item FROM b15.mat ENDIF IF vfle EQ 16 THEN LOAD item FROM b16 .mat ENDIF IF vfle EQ 17 THEN LOAD item FROM b17.mat ENDIF IF vfle EQ 18...vple EQ 16 THEN LOAD reqet FROM bl6 .eqp ENDIF IF vple EQ 17 THEN LOAD reqet FROM bl7.eqp ENDIF IF vple EQ 18 THEN LOAD reqet FROM bl8.eqp ENDIF IF vple...b3.out ENDIF IF tWle EQ 14 THEN TYPE b14.out ENDIF IF tWle EQ 15 THEN 70 TYPE bIS.out ENDIF IF tfle EQ 16 THEN TYPE b16 .out ENDIF IF tfle EQ 17 THEN

Migration of the Antarctic Polar Front through the mid-Pleistocene transition: evidence and climatic implications

NASA Astrophysics Data System (ADS)

Kemp, A. E. S.; Grigorov, I.; Pearce, R. B.; Naveira Garabato, A. C.

2010-08-01

The Antarctic Polar Front is an important biogeochemical divider in the Southern Ocean. Laminated diatom mat deposits record episodes of massive flux of the diatom Thalassiothrix antarctica beneath the Antarctic Polar Front and provide a marker for tracking the migration of the Front through time. Ocean Drilling Program Sites 1091, 1093 and 1094 are the only deep piston cored record hitherto sampled from the sediments of the circumpolar biogenic opal belt. Mapping of diatom mat deposits between these sites indicates a glacial-interglacial front migration of up to 6 degrees of latitude in the early/mid Pleistocene. The mid-Pleistocene transition marks a stepwise minimum 7° northward migration of the locus of the Polar Front sustained for about 450 kyr until an abrupt southward return to a locus similar to its modern position and further south than any mid-Pleistocene locus. This interval from a "900 ka event" that saw major cooling of the oceans and a δ 13C minimum through to the 424 ka Mid-Brunhes Event at Termination V is also seemingly characterised by 1) sustained decreased carbonate in the sub-tropical south Atlantic, 2) reduced strength of Antarctic deep meridional circulation, 3) lower interglacial temperatures and lower interglacial atmospheric CO 2 levels (by some 30 per mil) than those of the last 400 kyr, evidencing less complete deglaciation. This evidence is consistent with a prolonged period lasting 450 kyr of only partial ventilation of the deep ocean during interglacials and suggests that the mechanisms highlighted by recent hypotheses linking mid-latitude atmospheric conditions to the extent of deep ocean ventilation and carbon sequestration over glacial-interglacial cycles are likely in operation during the longer time scale characteristic of the mid-Pleistocene transition. The cooling that initiated the "900 ka event" may have been driven by minima in insolation amplitude related to eccentricity modulation of precession that also affected low latitude climates as marked by threshold changes in the African monsoon system. The major thresholds in earth system behaviour through the mid-Pleistocene transition were likely governed by an interplay of the 100 kyr and 400 kyr eccentricity modulation of precession.

Influence of free-stall flooring on comfort and hygiene of dairy cows during warm climatic conditions.

PubMed

De Palo, P; Tateo, A; Zezza, F; Corrente, M; Centoducati, P

2006-12-01

An evaluation of behavioral and hygienic conditions was carried out with 4 materials used as free-stall flooring for dairy cows: polyethylene vinyl acetate (EVA) and polypropylene vinyl acetate (PVA) mats, wood shavings, and solid manure. The free-stall type selected by cows was evaluated in response to changes in environmental temperature and humidity. Two tests were used: 1) a preference test, in which 8 cows were housed in a pen with 32 free stalls and 4 types of flooring; and 2) an aversion test, in which 32 cows were placed in 4 pens, each with 8 free stalls. The free stalls in each pen had a single type of bedding material. These tests showed that the comfort of dairy cows was predominantly influenced by environmental conditions. The preference test for lying showed that cows preferred free-stall floors with EVA mats over those with PVA mats, wood shavings, and solid manure (332.4 +/- 24.0 vs. 130.8 +/- 6.2, 160.9 +/- 23.7, and 102.6 +/- 23.2 min/d, respectively), but under conditions of heat stress, with a temperature-humidity index > 80, they chose wood shavings and solid manure lying areas. These results were confirmed by the aversion test. In all experimental and environmental conditions, the PVA mats were the least suitable. The mats contaminated with organic manure and the free stalls bedded with wood shavings and organic solids did not differ in either the coliform load on the lying surfaces (EVA mats: 290 +/- 25; PVA mats: 306 +/- 33; wood shavings: 290 +/- 39; and solid manure: 305 +/- 23 log(10) cfu/mL) or the total bacterial count in the raw milk (EVA mats: 232 +/- 22; PVA mats: 233 + 24; wood shavings: 221 +/- 24; and solid manure: 220 +/- 25 log(10) cfu/mL). These results demonstrate that the comfort of dairy cows housed in barns with free stalls as resting areas does not depend only on the material used, but also on the value of the material in microenvironmental conditions.

Fe-oxidizing microbes are hydrothermal vent ecosystem engineers at the Loihi Seamount (Invited)

NASA Astrophysics Data System (ADS)

Chan, C. S.; McAllister, S.; Leavitt, A.; Emerson, D.; Moyer, C. L.; Glazer, B. T.

2013-12-01

Microaerophilic Fe-oxidizing microorganisms (FeOM) colonize gradients of Fe(II) and oxygen, taking advantage of the available chemical energy. Vast communities of FeOM proliferate at deep sea hydrothermal vents, forming mineralized mats that range from centimeters to meters thick. Because these mats structure the environment for both FeOM and the entire microbial community, the Fe-oxidizers are acting as ecosystem engineers. What organisms are responsible for initiating these mats, and how does the physical structure and community composition develop as the mats mature? By connecting structure, function, and ecology, we can better interpret modern mat structures, as well as ancient fossilized mats. We have been studying Fe microbial mats at Loihi Seamount in Hawaii, a long-term study site that has become a model for Fe oxidation in marine hydrothermal systems. Recent improvements in ROV imaging systems allow us to see a great range of mat textures and colors, which may represent diverse habitats and/or different stages of mat development. With improved imaging and sampling techniques, we have been able to obtain discrete, intact samples of these delicate microbial mats. Previous bulk sampling methods showed that mats consist of a mixture of Fe-mineralized morphologies. Our analyses of intact mats show that mats are initiated by one type of structure-former (either a stalk-former like Mariprofundus ferrooxydans or a Zetaproteobacterial sheath-former). These microbes may be the vanguard organisms that stabilize chemical gradients in this dynamic environment, allowing colonization by other organisms (evidenced by branching tubes, fibrillar nests, and other morphologies). We will show evidence of the composition and development of these mats, and discuss parallels between these marine Fe mats and their freshwater counterparts, supporting the idea that FeOM engineer environments favorable for growth.

Molecular manipulation of the mating-type system and development of a new approach for characterizing pathogen virulence in Pyrenophora tritici-repentis

USDA-ARS?s Scientific Manuscript database

The ascomycete Pyrenophora tritici-repentis (Ptr) is an important fungal pathogen worldwide that causes tan spot of wheat. The fungus is self-fertile because each isolate contains both mating type (MAT) idiomorphs. In this work, we developed knockouts of the MAT genes in Ptr and tested fertility of ...

A multiplex PCR assay for determination of mating type in isolates of the honey bee fungal pathogen, Ascosphaera apis

USDA-ARS?s Scientific Manuscript database

In this study we developed a multiplex PCR for identification of mating type idiomorphs in the filamentous fungus, Ascosphaera apis, the causative agent of chalkbrood disease in the honey bee (Apis melliffera). A combination of gene-specific primers was designed to amplify Mat1-1 and Mat1-2 gene fra...

Enhancement of the in-plane shear properties of carbon fiber composites containing carbon nanotube mats

NASA Astrophysics Data System (ADS)

Kim, Hansang

2015-01-01

The in-plane shear property of carbon fiber laminates is one of the most important structural features of aerospace and marine structures. Fiber-matrix debonding caused by in-plane shear loading is the major failure mode of carbon fiber composites because of the stress concentration at the interfaces. In this study, carbon nanotube mats (CNT mat) were incorporated in two different types of carbon fiber composites. For the case of woven fabric composites, mechanical interlocking between the CNTs and the carbon fibers increased resistance to shear failure. However, not much improvement was observed for the prepreg composites as a result of incorporation of the CNT mats. The reinforcement mechanism of the CNT mat layer was investigated by a fractographic study using scanning electron microscopy. In addition, the CNT mat was functionalized by three different methods and the effectiveness of the functionalization methods was determined and the most appropriate functionalization method for the CNT mat was air oxidation.

Carbonate mineralisation in sabkha microbial mats; a comparative study of field and laboratory systems

NASA Astrophysics Data System (ADS)

Dutton, Kirsten E.; Paul, Andreas; Lessa Andrade, Luiza; Sherry, Angela; Lokier, Stephen; Head, Ian M.; van der Land, Cees

2017-04-01

Microbial mats and their lithified counterparts are some of the earliest evidence of life on Earth. The coastal sabkha in Abu Dhabi, United Arab Emirates, is a modern setting where microbial mats flourish in a hypersaline and arid environment. These microbial communities are composed of microbes such as cyanobacteria, thermoplasmata and sulphate-reducing bacteria. The mats thrive as they are protected from predators, which are excluded by the extreme environmental conditions. Microbial mats are highly reactive to change, with their microbial communities and geochemistry varying on a millimetre scale, likely controlling mineralisation processes. Exact carbonate mineralisation rates within coastal sabkha microbial mats have not to date been quantified. Defining the mineralisation pathways and knowledge of precise mineralisation rates will help to explain how these organosedimentary structures are retained in the rock record. A fundamental understanding of the role of microbial mats in the formation of different carbonate phases is important, yet there are also other practical implications. For example, structures observed in core from the oil-bearing Arab Formation have been likened to modern microbial mats in terms of structure and mineralogy. The depositional configuration and primary mineralogy generated by microbial mats may control syndepositional lithification and later diagenesis thereby influencing reservoir porosity and permeability. In order to constrain factors effecting mineralisation and early lithification, experimentation in a controlled laboratory environment is required. Parameters for experimentation have been established during fieldwork and were applied to a tank-based laboratory simulation of sabkha microbial mats. These parameters include light, salinity and cation and anion water chemistry, gas production chemistry and vertical mat growth. Parameters were measured weekly with sampling for mineralogical and microbial community analysis on a biweekly basis. In addition to these parameter measurements already in place in current experiments, temperature and tidal cycle were monitored in the field. Over the course of the first three months, the microbial mat, which was submerged in an artificial seawater medium, grew vertically and developed a green surface at the top and sides. Thermogravimetric analysis has established that the top 1 mm surface mat biomass contains carbonate minerals, leading to an initial inferred carbonate mineralisation rate of approximately 0.5 g per 1 cm2 per year (approx. per 10 g surface mat material). This rate of mineralisation will become more accurate as more analysis is completed particularly comparing samples of mat, initially before they went in to the tank experiment and after incremental time periods, 3 months, 6 months etc. Further analysis of mat growth will establish the extent to which the precipitated carbonate minerals result from microbial activity and the types of minerals precipitated. The rate of mineralisation can be scaled-up to the km scale with the potential to isolate mineralisation rates promoted by different communities and in different types of microbial mat.

Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

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

Wong, Hon Lun; Visscher, Pieter T.; White, III, Richard Allen

Modern microbial mats provide remarkable insights into assembly, function and origin of complex microbial ecosystems. An excellent model of such systems is located in Shark Bay, Australia. Although bacteria have been extensively investigated in these communities, the role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of specific niches associated with this domain. In the present study, high throughput amplicon sequencing was undertaken in conjunction with key biogeochemical properties of two mat types (smooth and pustular). A total of 13,547,552 unfiltered sequences were obtained, and classified sequences weremore » affiliated to three archaeal and candidate phyla, Parvarchaeota, Euryarchaeota and Crenarchaeota. One way analysis of similarity tests (ANOSIM) indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1 %). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota, followed by Thermoplasmata, Class marine benthic group B and Halobacteria. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Conversely, pustular mats were enriched with Halobacteria and Parvarchaeota. The rates of oxygen production/consumption as well as sulphate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic part of mats and was up to seven-fold higher in smooth than in pustular mats. Metabolic cooperation in putative surface anoxic niches is proposed to be key in efficient cycling of key nutrients in these systems.« less

Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

DOE PAGES

Wong, Hon Lun; Visscher, Pieter T.; White, III, Richard Allen; ...

2017-04-11

Modern microbial mats provide remarkable insights into assembly, function and origin of complex microbial ecosystems. An excellent model of such systems is located in Shark Bay, Australia. Although bacteria have been extensively investigated in these communities, the role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of specific niches associated with this domain. In the present study, high throughput amplicon sequencing was undertaken in conjunction with key biogeochemical properties of two mat types (smooth and pustular). A total of 13,547,552 unfiltered sequences were obtained, and classified sequences weremore » affiliated to three archaeal and candidate phyla, Parvarchaeota, Euryarchaeota and Crenarchaeota. One way analysis of similarity tests (ANOSIM) indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1 %). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota, followed by Thermoplasmata, Class marine benthic group B and Halobacteria. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Conversely, pustular mats were enriched with Halobacteria and Parvarchaeota. The rates of oxygen production/consumption as well as sulphate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic part of mats and was up to seven-fold higher in smooth than in pustular mats. Metabolic cooperation in putative surface anoxic niches is proposed to be key in efficient cycling of key nutrients in these systems.« less

Modeling of process-induced residual stresses and resin flow behavior in resin transfer molded composites with woven fiber mats

NASA Astrophysics Data System (ADS)

Golestanian, Hossein

This research focuses on modeling Resin Transfer Molding process for manufacture of composite parts with woven fiber mats. Models are developed to determine cure dependent stiffness matrices for composites manufactured with two types of woven fiber mats. Five-harness carbon and eight-harness fiberglass mats with EPON 826 resin composites are considered. The models presented here take into account important material/process parameters with emphasis on; (1) The effects of cure-dependent resin mechanical properties, (2) Fiber undulation due to the weave of the fiber fill and warp bundles, and (3) Resin interaction with the fiber bundles at a microscopic scale. Cure-dependent mechanical properties were then used in numerical models to determine residual stresses and deformation in the composite parts. The complete cure cycle was modeled in these analyses. Also the cool down stage after the composite cure was analyzed. The effect of 5% resin shrinkage on residual stresses and deformations was also investigated. In the second part of the study, Finite Element models were developed to simulate mold filling in RTM processes. Resin flow in the fiber mats was modeled as flow through porous media. Physical models were also developed to investigate resin flow behavior into molds of rectangular and irregular shapes. Silicone fluids of 50 and 100 centistoke viscosities as well as EPON 826 epoxy resin were used in the mold filling experiments. The reinforcements consisted of several layers of woven fiberglass and carbon fiber mats. The effects of injection pressure, fluid viscosity, type of reinforcement, and mold geometry on mold filling times were investigated. Fiber mat permeabilities were determined experimentally for both types of reinforcements. Comparison of experimental and numerical resin front positions indicated the importance of edge effects in resin flow behavior in small cavities. The resin front positions agreed well for the rectangular mold geometry.

Self-Healing Nanofiber-Reinforced Polymer Composites. 1. Tensile Testing and Recovery of Mechanical Properties.

PubMed

Lee, Min Wook; An, Seongpil; Jo, Hong Seok; Yoon, Sam S; Yarin, Alexander L

2015-09-09

The present work aims at development of self-healing materials capable of partially restoring their mechanical properties under the conditions of prolonged periodic loading and unloading, which is characteristic, for example, of aerospace applications. Composite materials used in these and many other applications frequently reveal multiple defects stemming from their original inhomogeneity, which facilitates microcracking and delamination at ply interfaces. Self-healing nanofiber mats may effectively prevent such damage without compromising material integrity. Two types of core-shell nanofibers were simultaneously electrospun onto the same substrate in order to form a mutually entangled mat. The first type of core-shell fibers consisted of resin monomer (dimethylsiloxane) within the core and polyacrylonitrile within the shell. The second type of core-shell nanofibers consisted of cure (dimethyl-methyl hydrogen-siloxane) within the core and polyacrylonitrile within the shell. These mutually entangled nanofiber mats were used for tensile testing, and they were also encased in polydimethylsiloxane to form composites that were also subsequently subjected to tensile testing. During tensile tests, the nanofibers can be damaged in stretching up to the plastic regime of deformation. Then, the resin monomer and cure was released from the cores and the polydimethylsiloxane resin was polymerized, which might be expected to result in the self-healing properties of these materials. To reveal and evaluate the self-healing properties of the polyacrylonitrile-resin-cure nanofiber mats and their composites, the results were compared to the tensile test results of the monolithic polyacrylonitrile nanofiber mats or composites formed by encasing polyacrylonitrile nanofibers in a polydimethylsiloxane matrix. The latter do not possess self-healing properties, and indeed, do not recover their mechanical characteristics, in contrast to the polyacrylonitrile-resin-cure nanofiber mats and the composites reinforced by such mats. This is the first work, to the best of our knowledge, where self-healing nanofibers and composites based on them were developed, tested, and revealed restoration of mechanical properties (stiffness) in a 24 h rest period at room temperature.

Insights into the Processing of Carbon by Early Microbial Ecosystems

NASA Technical Reports Server (NTRS)

DesMarais, D.; Bebout, B.; Carpenter, S.; Discipulo, S.; Londry, K.; Habicht, K.; Turk, K.

2003-01-01

Interactions between Earth and the biosphere that were crucial for early biological evolution also influenced substantially the processes that circulate C between its reservoirs in the atmosphere, ocean, crust and mantle. The C-13 C-12 values of crustal carbonates and organics have recorded changes both in biological discrimination and in the relative rates of burial of organics and carbonates. A full interpretation of these patterns needs further isotopic studies of microbial ecosystems and individual anaerobes. Thus we measured carbon isotope discrimination during autotrophic and heterotrophic growth of pure cultures of sulfate-reducing bacteria and archaea (SRB and SRA). Discrimination during CO2 assimilation is significantly larger than during heterotrophic growth on lactate or acetate. SRB grown lithoautotrophically consumed less than 3% of available CO2 and exhibited substantial discrimination, as follows: Desulfobacterium autotrophicum (alpha 1.0100 to 1.0123), Desulfobacter hydrogenophilus (alpha = 0.0138), and Desulfotomuculum acetoxidans (alpha = 1.0310). Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO2 resulted in biomass with delta C-13 composition intermediate to that of the substrates. We have recently extended these experiments to include the thermophilic SRA Archeoglobus spp. Ecological forces also influence isotopic discrimination. Accordingly, we quantified the flow of C and other constituents in modern marine cyanobacterial mats, whose ancestry extends back billions of years. Such ecosystem processes shaped the biosignatures that entered sediments and atmospheres. At Guerrero Negro, BCS, Mexico, we examined mats dominated by Microcoleus (subtidal) and Lyngbya (intertidal to supratidal) cyanobacteria. During 24 hour cycles, we observed the exchange of O2 and dissolved inorganic C (DIC) between mats and the overlying water. Microcoleus mats assimilated near-equal amounts of DIC during the day as they released at night, but Lyngbya mats typically showed net uptake of DIC over the diel cycle. Patterns of O2 daytime release and nighttime uptake mirrored these DIC trends in both mat types. Nighttime DIC effluxes from Microcoleus mats were equivalent in the presence versus absence of O2, whereas nighttime DIC effluxes from Lyngbya mats dropped markedly in the absence of O2. Thus aerobic diagenesis was more important in Lyngbya mats than in Microcoleus mats, perhaps because trapped O2 bubbles persist only in Lyngbya mats at night and thus sustain populations of aerbes. In both mat types, effluxes of H2, CH4 and short-chain fatty acids were much greater at night in the absence of 02, emphasizing the importance of fermentation. Differences observed between Microcoleus versus Lyngbya mats forecast differences in their microbial populations and in their patterns of gene expression.

Post-eruption colonization and community succession of hydrothermal microbial mats

NASA Astrophysics Data System (ADS)

Moyer, C. L.; Hager, K. W.; Fullerton, H.

2015-12-01

T-RFLP fingerprint cluster analysis and qPCR of microbial mat communities from hydrothermal vent habitats among recent post-eruption sites exhibit similar communities containing Epsilonproteobacteria that are phylogenetically similar and capable of hydrogen-oxidation (e.g., Nitratiruptor, Caminibacter, Nautilia, Thioreductor, and/or Lebetimonas). This community is the first (Group I) of three community types that represent different stages in the transition from vapor-dominated to brine-dominated water-rock interactions (i.e., vent effluent geochemistry). We have now observed this similar transition from four hydrothermal regions from across the Pacific Ocean. The second type of mat community (Group II) that has been observed is characterized by the presence of another group of Epsilonproteobacteria; however, these are mostly sulfur-oxidizing phylotypes (e.g., Sulfurimonas, Sulfurovum, and/or Sulfuricurvum). Finally, once the transition from sulfur to iron is complete, then the third type (Group III) cluster together by the presence of Zetaproteobacteria, which are known to use iron-oxidation. Each of these community types are dominated by groups of microorganisms characterized by cultured isolates, all of which are strict chemolithoautotrophs capable of carbon fixation and are hypothesized as both ecosystem engineers and primary producers in these energy-rich ecosystems. We also consider the thermodynamic implications towards carbon fixation for each of the three groups of mat communities.

Silencers, silencing, and heritable transcriptional states.

PubMed Central

Laurenson, P; Rine, J

1992-01-01

Three copies of the mating-type genes, which determine cell type, are found in the budding yeast Saccharomyces cerevisiae. The copy at the MAT locus is transcriptionally active, whereas identical copies of the mating-type genes at the HML and HMR loci are transcriptionally silent. Hence, HML and HMR, also known as the silent mating-type loci, are subject to a position effect. Regulatory sequences flank the silent mating-type loci and mediate repression of HML and HMR. These regulatory sequences are called silencers for their ability to repress the transcription of nearby genes in a distance- and orientation-independent fashion. In addition, a number of proteins, including the four SIR proteins, histone H4, and an alpha-acetyltransferase, are required for the complete repression of HML and HMR. Because alterations in the amino-terminal domain of histone H4 result in the derepression of the silent mating-type loci, the mechanism of repression may involve the assembly of a specific chromatin structure. A number of additional clues permit insight into the nature of repression at HML and HMR. First, an S phase event is required for the establishment of repression. Second, at least one gene appears to play a role in the establishment mechanism yet is not essential for the stable propagation of repression through many rounds of cell division. Third, certain aspects of repression are linked to aspects of replication. The silent mating-type loci share many similarities with heterochromatin. Furthermore, regions of S. cerevisiae chromosomes, such as telomeres, which are known to be heterochromatic in other organisms, require a subset of SIR proteins for repression. Further analysis of the transcriptional repression at the silent mating-type loci may lend insight into heritable repression in other eukaryotes. PMID:1480108

Studies on Morphological and Physio-Ecological Variations of the Reniform Nematode, Rotylenchulus reniformis Linford and Oliveira, 1940 with an Emphasis on Differential Geographical Distribution of Amphimictic and Parthenogenetic Populations in Japan

PubMed Central

Nakasono, Kazutoshi

2004-01-01

The geographical distribution and polymorphism in morphological and biological characters of the reniform nematode, Rotylenchulus reniformis, in Japan were studied. The northern limit of habitat of this nematode was found on the 14 °C isothermal line of annual average-air temperature. Three morphologically different groups were ascertained which corresponded to three biological types based on male frequency. Incidence of males was consistent within populations and was not affected by environmental factors. Sexual attraction of males by females indicated reproductive isolation between the male-numerous type (MNT) and male-rare type (MRT) or male-absent type (MAT). Reproduction was amphimictic in the MNT and parthenogenetic in the MRT and MAT. Larval development in both MRT and MAT, but not that of MNT popula-tions, was inhibited at 34 °C. Differences in host preference were also observed among populations. PMID:19262821

Diversity, distribution and hydrocarbon biodegradation capabilities of microbial communities in oil-contaminated cyanobacterial mats from a constructed wetland.

PubMed

Abed, Raeid M M; Al-Kharusi, Samiha; Prigent, Stephane; Headley, Tom

2014-01-01

Various types of cyanobacterial mats were predominant in a wetland, constructed for the remediation of oil-polluted residual waters from an oil field in the desert of the south-eastern Arabian Peninsula, although such mats were rarely found in other wetland systems. There is scarce information on the bacterial diversity, spatial distribution and oil-biodegradation capabilities of freshwater wetland oil-polluted mats. Microbial community analysis by Automated Ribosomal Spacer Analysis (ARISA) showed that the different mats hosted distinct microbial communities. Average numbers of operational taxonomic units (OTUsARISA) were relatively lower in the mats with higher oil levels and the number of shared OTUsARISA between the mats was <60% in most cases. Multivariate analyses of fingerprinting profiles indicated that the bacterial communities in the wetland mats were influenced by oil and ammonia levels, but to a lesser extent by plant density. In addition to oil and ammonia, redundancy analysis (RDA) showed also a significant contribution of temperature, dissolved oxygen and sulfate concentration to the variations of the mats' microbial communities. Pyrosequencing yielded 282,706 reads with >90% of the sequences affiliated to Proteobacteria (41% of total sequences), Cyanobacteria (31%), Bacteriodetes (11.5%), Planctomycetes (7%) and Chloroflexi (3%). Known autotrophic (e.g. Rivularia) and heterotrophic (e.g. Azospira) nitrogen-fixing bacteria as well as purple sulfur and non-sulfur bacteria were frequently encountered in all mats. On the other hand, sequences of known sulfate-reducing bacteria (SRBs) were rarely found, indicating that SRBs in the wetland mats probably belong to yet-undescribed novel species. The wetland mats were able to degrade 53-100% of C12-C30 alkanes after 6 weeks of incubation under aerobic conditions. We conclude that oil and ammonia concentrations are the major key players in determining the spatial distribution of the wetland mats' microbial communities and that these mats contribute directly to the removal of hydrocarbons from oil field wastewaters.

The genetic structure of the A mating-type locus of Lentinula edodes.

PubMed

Au, Chun Hang; Wong, Man Chun; Bao, Dapeng; Zhang, Meiyan; Song, Chunyan; Song, Wenhua; Law, Patrick Tik Wan; Kües, Ursula; Kwan, Hoi Shan

2014-02-10

The Shiitake mushroom, Lentinula edodes (Berk.) Pegler is a tetrapolar basidiomycete with two unlinked mating-type loci, commonly called the A and B loci. Identifying the mating-types in shiitake is important for enhancing the breeding and cultivation of this economically-important edible mushroom. Here, we identified the A mating-type locus from the first draft genome sequence of L. edodes and characterized multiple alleles from different monokaryotic strains. Two intron-length polymorphism markers were developed to facilitate rapid molecular determination of A mating-type. L. edodes sequences were compared with those of known tetrapolar and bipolar basidiomycete species. The A mating-type genes are conserved at the homeodomain region across the order Agaricales. However, we observed unique genomic organization of the locus in L. edodes which exhibits atypical gene order and multiple repetitive elements around its A locus. To our knowledge, this is the first known exception among Homobasidiomycetes, in which the mitochondrial intermediate peptidase (mip) gene is not closely linked to A locus. Copyright © 2013 Elsevier B.V. All rights reserved.

Antimicrobial Activity of Silver Ions Released from Zeolites Immobilized on Cellulose Nanofiber Mats.

PubMed

Rieger, Katrina A; Cho, Hong Je; Yeung, Hiu Fai; Fan, Wei; Schiffman, Jessica D

2016-02-10

In this study, we exploit the high silver ion exchange capability of Linde Type A (LTA) zeolites and present, for the first time, electrospun nanofiber mats decorated with in-house synthesized silver (Ag(+)) ion exchanged zeolites that function as molecular delivery vehicles. LTA-Large zeolites with a particle size of 6.0 μm were grown on the surface of the cellulose nanofiber mats, whereas LTA-Small zeolites (0.2 μm) and three-dimensionally ordered mesoporous-imprinted (LTA-Meso) zeolites (0.5 μm) were attached to the surface of the cellulose nanofiber mats postsynthesis. After the three zeolite/nanofiber mat assemblies were ion-exchanged with Ag(+) ions, their ion release profiles and ability to inactivate Escherichia coli (E. coli) K12 were evaluated as a function of time. LTA-Large zeolites immobilized on the nanofiber mats displayed more than an 11 times greater E. coli K12 inactivation than the Ag-LTA-Large zeolites that were not immobilized on the nanofiber mats. This study demonstrates that by decorating nanometer to micrometer scale Ag(+) ion-exchanged zeolites on the surface of high porosity, hydrophilic cellulose nanofiber mats, we can achieve a tunable release of Ag(+) ions that inactivate bacteria faster and are more practical to use in applications over powder zeolites.

A Third Locus for Autosomal Dominant Cerebellar Ataxia Type 1 Maps to Chromosome 14q24.3-qter: Evidence for the Existence of a Fourth Locus

PubMed Central

Stevanin, Giovanni; Le Guern, Eric; Ravisé, Nicole; Chneiweiss, Hervé; Dürr, Alexandra; Cancel, Géraldine; Vignal, Alain; Boch, Anne-Laure; Ruberg, Merle; Penet, Christiane; Pothin, Yolaine; Lagroua, Isabelle; Haguenau, Michel; Rancurel, Gérald; Weissenbach, Jean; Agid, Yves; Brice, Alexis

1994-01-01

The autosomal dominant cerebellar ataxias (ADCA) type I are a group of neurological disorders that are clinically and genetically heterogeneous. Two genes implicated in the disease, SCA1 (spinal cerebellar ataxia 1) and SCA2, are already localized. We have mapped a third locus to chromosome 14q24.3-qter, by linkage analysis in a non-SCA1/non-SCA2 family and have confirmed its existence in a second such family. We suggest designating this new locus “SCA3.” Combined analysis of the two families restricted the SCA3 locus to a 15-cM interval between markers D14S67 and D14S81. The gene for Machado-Joseph disease (MJD), a clinically different form of ADCA type I, has been recently assigned to chromosome 14q24.3-q32. Although the SCA3 locus is within the MJD region, linkage analyses cannot yet demonstrate whether they result from mutations of the same gene. Linkage to all three loci (SCA1, SCA2, and SCA3) was excluded in another family, which indicates the existence of a fourth ADCA type I locus. PMID:8279460

Genetic Relatedness versus Biological Compatibility between Aspergillus fumigatus and Related Species

PubMed Central

Sugui, Janyce A.; Peterson, Stephen W.; Figat, Abigail; Hansen, Bryan; Samson, Robert A.; Mellado, Emilia; Cuenca-Estrella, Manuel

2014-01-01

Aspergillus section Fumigati contains 12 clinically relevant species. Among these Aspergillus species, A. fumigatus is the most frequent agent of invasive aspergillosis, followed by A. lentulus and A. viridinutans. Genealogical concordance and mating experiments were performed to examine the relationship between phylogenetic distance and mating success in these three heterothallic species. Analyses of 19 isolates from section Fumigati revealed the presence of three previously unrecognized species within the broadly circumscribed species A. viridinutans. A single mating type was found in the new species Aspergillus pseudofelis and Aspergillus pseudoviridinutans, but in Aspergillus parafelis, both mating types were present. Reciprocal interspecific pairings of all species in the study showed that the only successful crosses occurred with the MAT1-2 isolates of both A. parafelis and A. pseudofelis. The MAT1-2 isolate of A. parafelis was fertile when paired with the MAT1-1 isolates of A. fumigatus, A. viridinutans, A. felis, A. pseudoviridinutans, and A. wyomingensis but was not fertile with the MAT1-1 isolate of A. lentulus. The MAT1-2 isolates of A. pseudofelis were fertile when paired with the MAT1-1 isolate of A. felis but not with any of the other species. The general infertility in the interspecies crossings suggests that genetically unrelated species are also biologically incompatible, with the MAT1-2 isolates of A. parafelis and A. pseudofelis being the exception. Our findings underscore the importance of genealogical concordance analysis for species circumscription, as well as for accurate species identification, since misidentification of morphologically similar pathogens with differences in innate drug resistance may be of grave consequences for disease management. PMID:25100816

Organic geochemical studies of modern microbial mats from Shark Bay: Part I: Influence of depth and salinity on lipid biomarkers and their isotopic signatures.

PubMed

Pagès, A; Grice, K; Ertefai, T; Skrzypek, G; Jahnert, R; Greenwood, P

2014-09-01

The present study investigated the influence of abiotic conditions on microbial mat communities from Shark Bay, a World Heritage area well known for a diverse range of extant mats presenting structural similarities with ancient stromatolites. The distributions and stable carbon isotopic values of lipid biomarkers [aliphatic hydrocarbons and polar lipid fatty acids (PLFAs)] and bulk carbon and nitrogen isotope values of biomass were analysed in four different types of mats along a tidal flat gradient to characterize the microbial communities and systematically investigate the relationship of the above parameters with water depth. Cyanobacteria were dominant in all mats, as demonstrated by the presence of diagnostic hydrocarbons (e.g. n-C17 and n-C17:1). Several subtle but important differences in lipid composition across the littoral gradient were, however, evident. For instance, the shallower mats contained a higher diatom contribution, concordant with previous mat studies from other locations (e.g. Antarctica). Conversely, the organic matter (OM) of the deeper mats showed evidence for a higher seagrass contribution [high C/N, 13C-depleted long-chain n-alkanes]. The morphological structure of the mats may have influenced CO2 diffusion leading to more 13C-enriched lipids in the shallow mats. Alternatively, changes in CO2 fixation pathways, such as increase in the acetyl COA-pathway by sulphate-reducing bacteria, could have also caused the observed shifts in δ13C values of the mats. In addition, three smooth mats from different Shark Bay sites were analysed to investigate potential functional relationship of the microbial communities with differing salinity levels. The C25:1 HBI was identified in the high salinity mat only and a lower abundance of PLFAs associated with diatoms was observed in the less saline mats, suggesting a higher abundance of diatoms at the most saline site. Furthermore, it appeared that the most and least saline mats were dominated by autotrophic biomass using different CO2 fixation pathways. © 2014 John Wiley & Sons Ltd.

Using Intact Iron Microbial Mats to Gain Insights Into Mat Ecology and Geochemical Niche at the Microbial Scale

NASA Astrophysics Data System (ADS)

Glazer, B. T.; Chan, C. S. Y.; Mcallister, S.; Leavitt, A.; Emerson, D.

2015-12-01

Microbial mats are formed by microorganisms working in coordinated symbiosis, often benefitting the community by controlling the local geochemical or physical environment. Thus, the ecology of the mat depends on the individual roles of microbes organized into niches within a larger architecture. Chemolithotrophic Fe-oxidizing bacteria (FeOB) form distinctive Fe oxyhydroxide biominerals which constitute the building blocks of the mat. However, the majority of our progress has been in understanding the overall community structure. Understanding the physical mat structure on the microbial scale is important to unraveling FeOB evolution, the biogeochemistry and ecology of Fe-rich habitats, and ultimately interpreting FeOB biosignatures in the rock record. Mats in freshwater and marine environments contain strikingly similar biomineral morphologies, yet they are formed by phylogenetically distinct microorganisms. This suggests that the overall architecture and underlying genetics of freshwater and marine mats has evolved to serve particular roles specific to Fe oxidation. Thus, we conducted a comparative study of Fe seep freshwater mats and marine hydrothermal mats. We have developed a new approach to sampling Fe mats in order to preserve the delicate structure for analysis by confocal and scanning electron microscopy. Our analyses of these intact mats show that freshwater and marine mats are similarly initiated by a single type of structure-former. These ecosystem engineers form either a hollow sheath or a twisted stalk biomineral during mat formation, with a highly directional structure. These microbes appear to be the vanguard organisms that anchor the community within oxygen/Fe(II) gradients, further allowing for community succession in the mat interior as evidenced by other mineralized morphologies. Patterns in biomineral thickness and directionality were indicative of redox gradients and temporal changes in the geochemical environment. These observations show that the FeOB create the structure of the environment for the entire microbial community, acting as environmental engineers. Furthermore, they leave behind distinctive signatures of environmental conditions (e.g. presence of oxygen, hydrothermal pulsing), which can be recorded in the rock record.

Effect of salinity on nitrogenase activity and composition of the active diazotrophic community in intertidal microbial mats.

PubMed

Severin, Ina; Confurius-Guns, Veronique; Stal, Lucas J

2012-06-01

Microbial mats are often found in intertidal areas experiencing a large range of salinities. This study investigated the effect of changing salinities on nitrogenase activity and on the composition of the active diazotrophic community (nifH transcript libraries) of three types of microbial mats situated along a littoral gradient. All three mat types exhibited highest nitrogenase activity at salinities close to ambient seawater or lower. The response to lower or higher salinity was strongest in mats higher up in the littoral zone. Changes in nitrogenase activity as the result of exposure to different salinities were accompanied by changes in the active diazotrophic community. The two stations higher up in the littoral zone showed nifH expression by Cyanobacteria (Oscillatoriales and Chroococcales) and Proteobacteria (Gammaproteobacteria and Deltaproteobacteria). At these stations, a decrease in the relative contribution of Cyanobacteria to the nifH transcript libraries was observed at increasing salinity coinciding with a decrease in nitrogenase activity. The station at the low water mark showed low cyanobacterial contribution to nifH transcript libraries at all salinities but an increase in deltaproteobacterial nifH transcripts under hypersaline conditions. In conclusion, increased salinities caused decreased nitrogenase activity and were accompanied by a lower proportion of cyanobacterial nifH transcripts.

Association in Long-Evans hooded rats of red cell 2,3-diphosphoglycerate levels with hemoglobin types.

PubMed

Brewer, G; Gilman, J; Noble, N; Crews, V

1978-08-01

Two sublines of commercially available Long-Evans hooded rats have been developed by genetic selection. These sublines have widely differing levels of erythrocyte 2,3-diphosphoglycerate (DPG) due to different alleles at a single genetic locus. In the present work, it is shown that rats from the commercial population are also polymorphic at a hemoglobin locus, probably involving two alleles of the IIIbeta-globin chain locus. Particular hemoglobin types have been found to be strongly associated with certain DPG types, not only in the high-DPG and low-DPG lines but also in the commercial population. Two explanations for this association are considered. One is a single-locus hypothesis, with hemoglobin allelic variation causing DPG variation, and the other is a two-locus hypothesis, with marked linkage disequilibrium.

Development of a Single Locus Sequence Typing (SLST) Scheme for Typing Bacterial Species Directly from Complex Communities.

PubMed

Scholz, Christian F P; Jensen, Anders

2017-01-01

The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.

Lipids of recently-deposited algal mats at Laguna Mormona, Baja California

NASA Technical Reports Server (NTRS)

Cardoso, J.; Brooks, P. W.; Eglinton, G.; Goodfellow, R.; Maxwell, J. R.; Philp, R. P.

1976-01-01

A preliminary survey of the lipid composition of the core of a recently deposited algal mat of a subtropical, hypersaline coastal pond is described. Two layers of the core were examined: the upper, 2-cm-thick layer, comprising the fresh algal mat of predominantly the blue-green species Microcoleus chthonoplastes, and the black anaerobic algal ooze at a depth of 10 cm. About 75% of the n-alkanes in the mat were accounted for by n-C17, with smaller amounts of higher homologues maximizing at n-C27. The ooze was characterized by a bimodal distribution with maxima at n-C17 and n-C27. The n-alkanoic acids distributions were similar to the corresponding n-alkane distributions. A marked decrease in the ratio of monounsaturated to saturated acids in the ooze relative to the mat was observed, which indicates a preferential removal of unsaturated components. Certain triterpenes of the hopane skeletal type were present in the mat and ooze. The presence of stanols and sterenes in the ooze with similar carbon number distributions suggests a relationship between them.

Preparation and adsorption behavior of aminated electrospun polyacrylonitrile nanofiber mats for heavy metal ion removal.

PubMed

Kampalanonwat, Pimolpun; Supaphol, Pitt

2010-12-01

Polyacrylonitrile (PAN) nanofiber mats were prepared by electrospinning and they were further modified to contain amidino diethylenediamine chelating groups on their surface via heterogeneous reaction with diethylenetriamine (DETA). The obtained aminated PAN (APAN) nanofiber mats were evaluated for their chelating property with four types of metal ions, namely Cu(II), Ag(I), Fe(II), and Pb(II) ions. The amounts of the metal ions adsorbed onto the APAN nanofiber mats were influenced by the initial pH and the initial concentration of the metal ion solutions. Increasing the contact time also resulted in a monotonous increase in the adsorbed amounts of the metal ions, which finally reached equilibria at about 10 h for Cu(II) ions and about 5 h for Ag(I), Fe(II), and Pb(II) ions. The maximal adsorption capacities of the metal ions on the APAN nanofiber mats, as calculated from the Langmuir model, were 150.6, 155.5, 116.5, and 60.6 mg g(-1), respectively. Lastly, the spent APAN nanofiber mats could be facilely regenerated with a hydrochloric acid (HCl) aqueous solution.

Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus

PubMed Central

Mujic, Alija Bajro; Kuo, Alan; Tritt, Andrew; Lipzen, Anna; Chen, Cindy; Johnson, Jenifer; Sharma, Aditi; Barry, Kerrie; Grigoriev, Igor V.; Spatafora, Joseph W.

2017-01-01

Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species Rhizopogon vinicolor Smith and Zeller and R. vesiculosus Smith and Zeller (Basidiomycota, Boletales)—the first genomes available for Basidiomycota truffles—and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type A-locus as well as pheromone receptor and pheromone precursor homologs at the mating type B-locus. Comparison of Rhizopogon genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the A-locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the B-locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. Rhizopogon vinicolor possesses a greater number of B-locus pheromone receptor and precursor genes than R. vesiculosus, as well as a pair of isoprenyl cysteine methyltransferase genes flanking the B-locus compared to a single copy in R. vesiculosus. Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in R. vinicolor, consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with R. vinicolor possessing a B-locus region structure consistent with tetrapolar Boletales and R. vesiculosus possessing a B-locus region structure intermediate between bipolar and tetrapolar Boletales. PMID:28450370

Ecosystem carbon storage does not vary with mean annual temperature in Hawaiian tropical montane wet forests.

PubMed

Selmants, Paul C; Litton, Creighton M; Giardina, Christian P; Asner, Gregory P

2014-09-01

Theory and experiment agree that climate warming will increase carbon fluxes between terrestrial ecosystems and the atmosphere. The effect of this increased exchange on terrestrial carbon storage is less predictable, with important implications for potential feedbacks to the climate system. We quantified how increased mean annual temperature (MAT) affects ecosystem carbon storage in above- and belowground live biomass and detritus across a well-constrained 5.2 °C MAT gradient in tropical montane wet forests on the Island of Hawaii. This gradient does not systematically vary in biotic or abiotic factors other than MAT (i.e. dominant vegetation, substrate type and age, soil water balance, and disturbance history), allowing us to isolate the impact of MAT on ecosystem carbon storage. Live biomass carbon did not vary predictably as a function of MAT, while detrital carbon declined by ~14 Mg of carbon ha(-1) for each 1 °C rise in temperature - a trend driven entirely by coarse woody debris and litter. The largest detrital pool, soil organic carbon, was the most stable with MAT and averaged 48% of total ecosystem carbon across the MAT gradient. Total ecosystem carbon did not vary significantly with MAT, and the distribution of ecosystem carbon between live biomass and detritus remained relatively constant across the MAT gradient at ~44% and ~56%, respectively. These findings suggest that in the absence of alterations to precipitation or disturbance regimes, the size and distribution of carbon pools in tropical montane wet forests will be less sensitive to rising MAT than predicted by ecosystem models. This article also provides needed detail on how individual carbon pools and ecosystem-level carbon storage will respond to future warming. © 2014 John Wiley & Sons Ltd.

Temporal Changes in BEXSERO® Antigen Sequence Type Associated with Genetic Lineages of Neisseria meningitidis over a 15-Year Period in Western Australia

PubMed Central

Mowlaboccus, Shakeel; Perkins, Timothy T.; Smith, Helen; Sloots, Theo; Tozer, Sarah; Prempeh, Lydia-Jessica; Tay, Chin Yen; Peters, Fanny; Speers, David; Keil, Anthony D.; Kahler, Charlene M.

2016-01-01

Neisseria meningitidis is the causative agent of invasive meningococcal disease (IMD). The BEXSERO® vaccine which is used to prevent serogroup B disease is composed of four sub-capsular protein antigens supplemented with an outer membrane vesicle. Since the sub-capsular protein antigens are variably expressed and antigenically variable amongst meningococcal isolates, vaccine coverage can be estimated by the meningococcal antigen typing system (MATS) which measures the propensity of the strain to be killed by vaccinated sera. Whole genome sequencing (WGS) which identifies the alleles of the antigens that may be recognised by the antibody response could represent, in future, an alternative estimate of coverage. In this study, WGS of 278 meningococcal isolates responsible for 62% of IMD in Western Australia from 2000–2014 were analysed for association of genetic lineage (sequence type [ST], clonal complex [cc]) with BEXSERO® antigen sequence type (BAST) and MATS to predict the annual vaccine coverage. A hyper-endemic period of IMD between 2000–05 was caused by cc41/44 with the major sequence type of ST-146 which was not predicted by MATS or BAST to be covered by the vaccine. An increase in serogroup diversity was observed between 2010–14 with the emergence of cc11 serogroup W in the adolescent population and cc23 serogroup Y in the elderly. BASTs were statistically associated with clonal complex although individual antigens underwent antigenic drift from the major type. BAST and MATS predicted an annual range of 44–91% vaccine coverage. Periods of low vaccine coverage in years post-2005 were not a result of the resurgence of cc41/44:ST-146 but were characterised by increased diversity of clonal complexes expressing BASTs which were not predicted by MATS to be covered by the vaccine. The driving force behind the diversity of the clonal complex and BAST during these periods of low vaccine coverage is unknown, but could be due to immune selection and inter-strain competition with carriage of non-disease causing meningococci. PMID:27355628

MAT1A variants are associated with hypertension, stroke, and DNA damage and are modulated by vlasma vitamin B6 and folate concentration

USDA-ARS?s Scientific Manuscript database

Elevated plasma homocysteine is a cardiovascular disease (CVD) risk factor. However, the mechanism underlying this relationship is not understood. S-adenosylmethionine synthetase isoform type-1 (MAT1A) is a key enzyme in the metabolism of homocysteine, converting dietary methionine into S-adenosyl m...

Coconut matting bezoar identified by a combined analytical approach.

PubMed Central

Levison, D A; Crocker, P R; Boxall, T A; Randall, K J

1986-01-01

A rare type of bezoar composed of coconut matting was found in the stomach of a caucasian man. The exact identity of the fibres was established by scanning electron microscopy, x-ray energy spectroscopy, and microscopic infrared spectroscopy. This report illustrates the importance of these techniques for identifying the nature of foreign material. Images PMID:3950038

Halloysite nanotube-based electrospun ceramic nanofibre mat: a novel support for zeolite membranes

PubMed Central

Chen, Zhuwen; Zeng, Jiaying; Lv, Dong; Gao, Jinqiang; Zhang, Jian; Bai, Shan; Li, Ruili; Wu, Jingshen

2016-01-01

Some key parameters of supports such as porosity, pore shape and size are of great importance for fabrication and performance of zeolite membranes. In this study, we fabricated millimetre-thick, self-standing electrospun ceramic nanofibre mats and employed them as a novel support for zeolite membranes. The nanofibre mats were prepared by electrospinning a halloysite nanotubes/polyvinyl pyrrolidone composite followed by a programmed sintering process. The interwoven nanofibre mats possess up to 80% porosity, narrow pore size distribution, low pore tortuosity and highly interconnected pore structure. Compared with the commercial α-Al2O3 supports prepared by powder compaction and sintering, the halloysite nanotube-based mats (HNMs) show higher flux, better adsorption of zeolite seeds, adhesion of zeolite membranes and lower Al leaching. Four types of zeolite membranes supported on HNMs have been successfully synthesized with either in situ crystallization or a secondary growth method, demonstrating good universality of HNMs for supporting zeolite membranes. PMID:28083098

Halloysite nanotube-based electrospun ceramic nanofibre mat: a novel support for zeolite membranes

NASA Astrophysics Data System (ADS)

Chen, Zhuwen; Zeng, Jiaying; Lv, Dong; Gao, Jinqiang; Zhang, Jian; Bai, Shan; Li, Ruili; Hong, Mei; Wu, Jingshen

2016-12-01

Some key parameters of supports such as porosity, pore shape and size are of great importance for fabrication and performance of zeolite membranes. In this study, we fabricated millimetre-thick, self-standing electrospun ceramic nanofibre mats and employed them as a novel support for zeolite membranes. The nanofibre mats were prepared by electrospinning a halloysite nanotubes/polyvinyl pyrrolidone composite followed by a programmed sintering process. The interwoven nanofibre mats possess up to 80% porosity, narrow pore size distribution, low pore tortuosity and highly interconnected pore structure. Compared with the commercial α-Al2O3 supports prepared by powder compaction and sintering, the halloysite nanotube-based mats (HNMs) show higher flux, better adsorption of zeolite seeds, adhesion of zeolite membranes and lower Al leaching. Four types of zeolite membranes supported on HNMs have been successfully synthesized with either in situ crystallization or a secondary growth method, demonstrating good universality of HNMs for supporting zeolite membranes.

Mapping a major QTL responsible for dwarf architecture in Brassica napus using a single-nucleotide polymorphism marker approach.

PubMed

Wang, Yankun; Chen, Wenjing; Chu, Pu; Wan, Shubei; Yang, Mao; Wang, Mingming; Guan, Rongzhan

2016-08-18

Key genes related to plant type traits have played very important roles in the "green revolution" by increasing lodging resistance and elevating the harvest indices of crop cultivars. Although there have been numerous achievements in the development of dwarfism and plant type in Brassica napus breeding, exploring new materials conferring oilseed rape with efficient plant types that provide higher yields is still of significance in breeding, as well as in elucidating the mechanisms underlying plant development. Here, we report a new dwarf architecture with down-curved leaf mutant (Bndwf/dcl1) isolated from an ethyl methanesulphonate (EMS)-mutagenized B. napus line, together with its inheritance and gene mapping, and pleiotropic effects of the mapped locus on plant-type traits. We constructed a high-density single-nucleotide polymorphism (SNP) map using a backcross population derived from the Bndwf/dcl1 mutant and the canola cultivar 'zhongshuang11' ('ZS11') and mapped the dwarf architecture with the down-curved leaf dominant locus, BnDWF/DCL1, in a 6.58-cM interval between SNP marker bins M46180 and M49962 on the linkage group (LG) C05 of B. napus. Further mapping with other materials derived from Bndwf/dcl1 narrowed the interval harbouring BnDWF/DCL1 to 175 kb in length and this interval contained 16 annotated genes. Quantitative trait locus (QTL) mappings with the backcross population for plant type traits, including plant height, branching height, main raceme length and average branching interval, indicated that the mapped QTLs for plant type traits were located at the same position as the BnDWF/DCL1 locus. This study suggests that the BnDWF/DCL1 locus is a major pleiotropic locus/QTL in B. napus, which may reduce plant height, alter plant type traits and change leaf shape, and thus may lead to compact plant architecture. Accordingly, this locus may have substantial breeding potential for increasing planting density.

Implementation and validation of the extended Hill-type muscle model with robust routing capabilities in LS-DYNA for active human body models.

PubMed

Kleinbach, Christian; Martynenko, Oleksandr; Promies, Janik; Haeufle, Daniel F B; Fehr, Jörg; Schmitt, Syn

2017-09-02

In the state of the art finite element AHBMs for car crash analysis in the LS-DYNA software material named *MAT_MUSCLE (*MAT_156) is used for active muscles modeling. It has three elements in parallel configuration, which has several major drawbacks: restraint approximation of the physical reality, complicated parameterization and absence of the integrated activation dynamics. This study presents implementation of the extended four element Hill-type muscle model with serial damping and eccentric force-velocity relation including [Formula: see text] dependent activation dynamics and internal method for physiological muscle routing. Proposed model was implemented into the general-purpose finite element (FE) simulation software LSDYNA as a user material for truss elements. This material model is verified and validated with three different sets of mammalian experimental data, taken from the literature. It is compared to the *MAT_MUSCLE (*MAT_156) Hill-type muscle model already existing in LS-DYNA, which is currently used in finite element human body models (HBMs). An application example with an arm model extracted from the FE ViVA OpenHBM is given, taking into account physiological muscle paths. The simulation results show better material model accuracy, calculation robustness and improved muscle routing capability compared to *MAT_156. The FORTRAN source code for the user material subroutine dyn21.f and the muscle parameters for all simulations, conducted in the study, are given at https://zenodo.org/record/826209 under an open source license. This enables a quick application of the proposed material model in LS-DYNA, especially in active human body models (AHBMs) for applications in automotive safety.

Should Ballet Dancers Vary Postures and Underfoot Surfaces When Practicing Postural Balance?

PubMed

Steinberg, Nili; Waddington, Gordon; Adams, Roger; Karin, Janet; Tirosh, Oren

2018-01-01

Postural balance (PB) is an important component skill for professional dancers. However, the effects of different types of postures and different underfoot surfaces on PB have not adequately been addressed. The main aim of this study was to investigate the effect of different conditions of footwear, surfaces, and standing positions on static and dynamic PB ability of young ballet dancers. A total of 36 male and female young professional ballet dancers (aged 14-19 years) completed static and dynamic balance testing, measured by head and lumbar accelerometers, while standing on one leg in the turnout position, under six different conditions: (1) "relaxed" posture; (2) "ballet" posture; (3) barefoot; (4) ballet shoes with textured insoles; (5) barefoot on a textured mat; and (6) barefoot on a spiky mat. A condition effect was found for static and dynamic PB. Static PB was reduced when dancers stood in the ballet posture compared with standing in the relaxed posture and when standing on a textured mat and on a spiky mat (p < .05), and static PB in the relaxed posture was significantly better than PB in all the other five conditions tested. Dynamic PB was significantly better while standing in ballet shoes with textured insoles and when standing on a spiky mat compared with all other conditions (p < .05). The practical implications derived from this study are that both male and female dancers should try to be relaxed in their postural muscles when practicing a ballet aligned position, including dance practice on different types of floors and on different types of textured/spiky materials may result in skill transfer to practice on normal floor surfaces, and both static and dynamic PB exercises should be assessed and generalized into practical dance routines.

Short bowel syndrome: influence of nutritional therapy and incretin GLP1 on bone marrow adipose tissue.

PubMed

Parreiras-E-Silva, Luciana T; de Araújo, Iana M; Elias, Jorge; Nogueira-Barbosa, Marcello H; Suen, Vivian M M; Marchini, Julio S; Bonella, Jéssica; Nahas, Andressa K; Salmon, Carlos E G; de Paula, Francisco J A

2018-03-01

Energy deprivation leads to a decrease in white adipose tissue and bone mineral density (BMD), while simultaneously inducing the expansion of marrow adipose tissue (MAT). In short bowel syndrome (SBS), parenteral nutrition mitigates the deterioration of nutritional status, including decreases in MAT. Osteoporosis is, however, a frequent complication of SBS. The objective of our study here was to evaluate the association of fat deposit sites (subcutaneous and visceral adipose tissues: intrahepatic lipid (IHL) and MAT) and the incretin glucagon-like peptide 1 (GLP1) with BMD in individuals with SBS. MAT was negatively correlated with lumbar spine BMD in normal individuals, but not in those in the SBS group, who otherwise showed a positive correlation between MAT and GLP1. In addition, in individuals with SBS, IHL was negatively associated with lumbar spine BMD and positively associated with C-terminal telopeptide of type 1 collagen (a serum biomarker of bone turnover). Caloric maintenance in individuals with SBS, therefore, seems to positively affect the relationship between MAT and BMD, which may be modulated, at least in part, by GLP1. © 2018 New York Academy of Sciences.

Drug-loaded electrospun mats of poly(vinyl alcohol) fibres and their release characteristics of four model drugs

NASA Astrophysics Data System (ADS)

Taepaiboon, Pattama; Rungsardthong, Uracha; Supaphol, Pitt

2006-05-01

Mats of PVA nanofibres were successfully prepared by the electrospinning process and were developed as carriers of drugs for a transdermal drug delivery system. Four types of non-steroidal anti-inflammatory drug with varying water solubility property, i.e. sodium salicylate (freely soluble in water), diclofenac sodium (sparingly soluble in water), naproxen (NAP), and indomethacin (IND) (both insoluble in water), were selected as model drugs. The morphological appearance of the drug-loaded electrospun PVA mats depended on the nature of the model drugs. The 1H-nuclear magnetic resonance results confirmed that the electrospinning process did not affect the chemical integrity of the drugs. Thermal properties of the drug-loaded electrospun PVA mats were analysed by differential scanning calorimetry and thermogravimetric analysis. The molecular weight of the model drugs played a major role on both the rate and the total amount of drugs released from the as-prepared drug-loaded electrospun PVA mats, with the rate and the total amount of the drugs released decreasing with increasing molecular weight of the drugs. Lastly, the drug-loaded electrospun PVA mats exhibited much better release characteristics of the model drugs than drug-loaded as-cast films.

Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data.

PubMed

Schäfer, Christian; Schmidt, Alexander H; Sauter, Jürgen

2017-05-30

Knowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic stem cell donors, HLA haplotype frequencies of specific populations are used to optimize both donor searches for individual patients and strategic donor registry planning. However, the estimation of haplotype frequencies from HLA genotyping data is challenged by the large amount of genotype data, the complex HLA nomenclature, and the heterogeneous and ambiguous nature of typing records. To meet these challenges, we have developed the open-source software Hapl-o-Mat. It estimates haplotype frequencies from population data including an arbitrary number of loci using an expectation-maximization algorithm. Its key features are the processing of different HLA typing resolutions within a given population sample and the handling of ambiguities recorded via multiple allele codes or genotype list strings. Implemented in C++, Hapl-o-Mat facilitates efficient haplotype frequency estimation from large amounts of genotype data. We demonstrate its accuracy and performance on the basis of artificial and real genotype data. Hapl-o-Mat is a versatile and efficient software for HLA haplotype frequency estimation. Its capability of processing various forms of HLA genotype data allows for a straightforward haplotype frequency estimation from typing records usually found in stem cell donor registries.

A homozygous nonsense mutation in the gene for Tmem79, a component for the lamellar granule secretory system, produces spontaneous eczema in an experimental model of atopic dermatitis.

PubMed

Sasaki, Takashi; Shiohama, Aiko; Kubo, Akiharu; Kawasaki, Hiroshi; Ishida-Yamamoto, Akemi; Yamada, Taketo; Hachiya, Takayuki; Shimizu, Atsushi; Okano, Hideyuki; Kudoh, Jun; Amagai, Masayuki

2013-11-01

Flaky tail (ma/ma Flg(ft/ft)) mice have a frameshift mutation in the filaggrin (Flg(ft)) gene and are widely used as a model of human atopic dermatitis associated with FLG mutations. These mice possess another recessive hair mutation, matted (ma), and develop spontaneous dermatitis under specific pathogen-free conditions, whereas genetically engineered Flg(-/-) mice do not. We identified and characterized the gene responsible for the matted hair and dermatitis phenotype in flaky tail mice. We narrowed down the responsible region by backcrossing ma/ma mice with wild-type mice and identified the mutation using next-generation DNA sequencing. We attempted to rescue the matted phenotype by introducing the wild-type matted transgene. We characterized the responsible gene product by using whole-mount immunostaining of epidermal sheets. We demonstrated that ma, but not Flg(ft), was responsible for the dermatitis phenotype and corresponded to a Tmem79 gene nonsense mutation (c.840C>G, p.Y280*), which encoded a 5-transmembrane protein. Exogenous Tmem79 expression rescued the matted hair and dermatitis phenotype of Tmem79(ma/ma) mice. Tmem79 was mainly expressed in the trans-Golgi network in stratum granulosum cells in the epidermis in both mice and humans. The Tmem79(ma/ma) mutation impaired the lamellar granule secretory system, which resulted in altered stratum corneum formation and a subsequent spontaneous dermatitis phenotype. The Tmem79(ma/ma) mutation is responsible for the spontaneous dermatitis phenotype in matted mice, probably as a result of impaired lamellar granule secretory system and altered stratum corneum barrier function. Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

Characterization of Botrytis cinerea isolates collected on pepper in Southern Turkey by using molecular markers, fungicide resistance genes and virulence assay.

PubMed

Polat, İlknur; Baysal, Ömür; Mercati, Francesco; Gümrükcü, Emine; Sülü, Görkem; Kitapcı, Aytül; Araniti, Fabrizio; Carimi, Francesco

2018-06-01

Botrytis cinerea is a polyphagous fungal pathogen causing gray mold disease. Moreover, it is one of the most destructive infections of small fruit crops such as pepper (Capsicum annnum L.). C. sativum is a species belonging to the Solanaceae family and Turkey is one of the main producers in the World. In the present work, aiming to obtain information useful for pest management, fifty B. cinerea isolates collected from Turkey and a reference isolate (B05.10) were characterized using molecular markers and fungicide resistance genes. Morphological and molecular (ITS1-ITS4) identification of B. cinerea isolates, the degree of virulence and mating types were determined. Since one or several allelic mutations in the histidine kinase (Bos1) and β-tubulin genes generally confer the resistance to fungicides, the sequences of these target genes were investigated in the selected isolates, which allowed the identification of two different haplotypes. Mating types were also determined by PCR assays using primer specific for MAT1-1 alpha gene (MAT1-1-1) and MAT1-2 HMG (MAT1-2-1) of B. cinerea. Twenty-two out of 50 isolates (44%) were MAT1-2, while 38% were MAT1-1. Interestingly, out of whole studied samples, 9 isolates (18%) were heterokaryotic or mixed colonies. In addition, cluster and population structure analyses identified five main groups and two genetic pools, respectively, underlining a good level of variability in the analysed panel. The results highlighted the presence of remarkable genetic diversity in B. cinerea isolates collected in a crucial economical area for pepper cultivation in Turkey and the data will be beneficial in view of future gray mold disease management. Copyright © 2018 Elsevier B.V. All rights reserved.

Serotype and mating type characterization of Cryptococcus neoformans by multiplex PCR.

PubMed

Carvalho, Vívian Gonçalves; Terceti, Mateus Souza; Dias, Amanda Latercia Tranches; Paula, Claudete Rodrigues; Lyon, Juliana Pereira; de Siqueira, Antônio Martins; Franco, Marília Caixeta

2007-01-01

Cryptococcus neoformans is an encapsulated yeast, etiological agent of cryptococcosis. The species is commonly associated with pigeon droppings and plant materials. The aim of the present work was to verify the presence of the yeast in pigeon droppings, and to identify the isolates obtained in serotypes and mating types (MAT). Ten samples of pigeon droppings were collected in the rural area of the city of Alfenas, Brazil. Samples were inoculated in agar Niger medium for fungal isolation and 22 isolates with characteristics of C. neoformans were obtained. The serotypes and MAT were determined by multiplex PCR using specific primers. Serotypes were also determined by using the Kit Crypto Check. Among the 22 samples evaluated, eight were identified as C. neoformans by classic identification tests. These samples were characterized as serotype A by the Kit Crypto check and as serotype A MAT alpha by the multiplex PCR. The present study reinforces the evidence that pigeon droppings are a reservoir for C. neoformans and confirms the prevalence of C. neoformans var. grubii (A alpha) among environmental isolates. It also demonstrates that multiplex PCR is an acceptable alternative for serotype analysis because it reduces the costs for each reaction and analyses serotype and MAT simultaneously.

The diabetes type 1 locus Idd6 modulates activity of CD4+CD25+ regulatory T-cells.

PubMed

Rogner, Ute Christine; Lepault, Françoise; Gagnerault, Marie-Claude; Vallois, David; Morin, Joëlle; Avner, Philip; Boitard, Christian

2006-01-01

The genetic locus Idd6 confers susceptibility to the spontaneous development of type 1 diabetes in the NOD mouse. Our studies on disease resistance of the congenic mouse strain NOD.C3H 6.VIII showed that Idd6 influences T-cell activities in the peripheral immune system and suggest that a major mechanism by which the Idd6 locus modifies diabetes development is via modulation of regulatory T-cell activities. Our transfer experiments using total splenocytes and purified T-cells demonstrated that the locus specifically controls the efficiency of disease protection mediated by the regulatory CD4(+)CD25(+) T-cell subset. Our data also implicate the Idd6 locus in controlling the balance between infiltrating lymphocytes and antigen-presenting cells within the pancreatic islet.

Prevalence of toxin-producing Clostridium botulinum associated with the macroalga Cladophora in three Great Lakes: growth and management.

PubMed

Lan Chun, Chan; Kahn, Chase I; Borchert, Andrew J; Byappanahalli, Muruleedhara N; Whitman, Richard L; Peller, Julie; Pier, Christina; Lin, Guangyun; Johnson, Eric A; Sadowsky, Michael J

2015-04-01

The reemergence of avian botulism caused by Clostridium botulinum type E has been observed across the Great Lakes in recent years. Evidence suggests an association between the nuisance algae, Cladophora spp., and C. botulinum in nearshore areas of the Great Lakes. However, the nature of the association between Cladophora and C. botulinum is not fully understood due, in part, to the complex food web interactions in this disease etiology. In this study, we extensively evaluated their association by quantitatively examining population size and serotypes of C. botulinum in algal mats collected from wide geographic areas in lakes Michigan, Ontario, and Erie in 2011-2012 and comparing them with frequencies in other matrices such as sand and water. A high prevalence (96%) of C. botulinum type E was observed in Cladophora mats collected from shorelines of the Great Lakes in 2012. Among the algae samples containing detectable C. botulinum, the population size of C. Botulinum type E was 10(0)-10(4) MPN/g dried algae, which was much greater (up to 10(3) fold) than that found in sand or the water column, indicating that Cladophora mats are sources of this pathogen. Mouse toxinantitoxin bioassays confirmed that the putative C. botulinum belonged to the type E serotype. Steam treatment was effective in reducing or eliminating C. botulinum type E viable cells in Cladophora mats, thereby breaking the potential transmission route of toxin up to the food chain. Consequently, our data suggest that steam treatment incorporated with a beach cleaning machine may be an effective treatment of Cladophora-borne C. botulinum and may reduce bird mortality and human health risks. Copyright © 2014 Elsevier B.V. All rights reserved.

Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats

PubMed Central

Lee, Jackson Z.; Burow, Luke C.; Woebken, Dagmar; Everroad, R. Craig; Kubo, Mike D.; Spormann, Alfred M.; Weber, Peter K.; Pett-Ridge, Jennifer; Bebout, Brad M.; Hoehler, Tori M.

2013-01-01

Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB). However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico—permanently submerged Microcoleus microbial mat (GN-S), and intertidal Lyngbya microbial mat (GN-I)—were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H2 production occurred under dark anoxic conditions with simultaneous production of a suite of organic acids. H2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of DsrA phylotypes were responsible for H2 consumption. Incubation with 13C-acetate and NanoSIMS (secondary ion mass-spectrometry) indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen) was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi. PMID:24616716

Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats

DOE PAGES

Lee, Jackson Z.; Burow, Luke C.; Woebken, Dagmar; ...

2014-01-01

Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB). However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico$-$ permanently submerged Microcoleus microbial mat (GN-S), and intertidal Lyngbya microbial mat (GN-I)$-$were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H 2 production occurred under dark anoxic conditions with simultaneous production of a suitemore » of organic acids. H 2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO 2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of DsrA phylotypes were responsible for H 2 consumption. Incubation with 13C-acetate and NanoSIMS (secondary ion mass-spectrometry) indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen) was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi.« less

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817

Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat

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

Melendrez, Melanie C.; Becraft, Eric D.; Wood, Jason M.

Recent studies of bacterial speciation have claimed to support the biological species concept—that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B’) of Synechococcusmore » in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B’ lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B’ lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.« less

DNA barcoding the native flowering plants and conifers of Wales.

PubMed

de Vere, Natasha; Rich, Tim C G; Ford, Col R; Trinder, Sarah A; Long, Charlotte; Moore, Chris W; Satterthwaite, Danielle; Davies, Helena; Allainguillaume, Joel; Ronca, Sandra; Tatarinova, Tatiana; Garbett, Hannah; Walker, Kevin; Wilkinson, Mike J

2012-01-01

We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.

Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat

DOE PAGES

Melendrez, Melanie C.; Becraft, Eric D.; Wood, Jason M.; ...

2016-01-14

Recent studies of bacterial speciation have claimed to support the biological species concept—that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B’) of Synechococcusmore » in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B’ lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B’ lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.« less

DNA Barcoding the Native Flowering Plants and Conifers of Wales

PubMed Central

de Vere, Natasha; Rich, Tim C. G.; Ford, Col R.; Trinder, Sarah A.; Long, Charlotte; Moore, Chris W.; Satterthwaite, Danielle; Davies, Helena; Allainguillaume, Joel; Ronca, Sandra; Tatarinova, Tatiana; Garbett, Hannah; Walker, Kevin; Wilkinson, Mike J.

2012-01-01

We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification. PMID:22701588

A Study of Reward Preference in Taiwanese Gifted and Nongifted Students with Differential Locus of Control

ERIC Educational Resources Information Center

Wu, Su Chen; Elliott, Robert T.

2008-01-01

The purpose of the study was to investigate whether gifted and nongifted students' preferences for different types of reward were affected by differential locus of control. In total, 181 gifted and 107 nongifted junior high school students in Taiwan participated. The Nowicki-Strickland Locus of Control Scale was used as a measure of locus of…

Marrow Adipose Tissue Expansion Coincides with Insulin Resistance in MAGP1-Deficient Mice

PubMed Central

Walji, Tezin A.; Turecamo, Sarah E.; Sanchez, Alejandro Coca; Anthony, Bryan A.; Abou-Ezzi, Grazia; Scheller, Erica L.; Link, Daniel C.; Mecham, Robert P.; Craft, Clarissa S.

2016-01-01

Marrow adipose tissue (MAT) is an endocrine organ with the potential to influence skeletal remodeling and hematopoiesis. Pathologic MAT expansion has been studied in the context of severe metabolic challenge, including caloric restriction, high fat diet feeding, and leptin deficiency. However, the rapid change in peripheral fat and glucose metabolism associated with these models impedes our ability to examine which metabolic parameters precede or coincide with MAT expansion. Microfibril-associated glycoprotein-1 (MAGP1) is a matricellular protein that influences cellular processes by tethering signaling molecules to extracellular matrix structures. MAGP1-deficient (Mfap2−/−) mice display a progressive excess adiposity phenotype, which precedes insulin resistance and occurs without changes in caloric intake or ambulation. Mfap2−/− mice were, therefore, used as a model to associate parameters of metabolic disease, bone remodeling, and hematopoiesis with MAT expansion. Marrow adiposity was normal in Mfap2−/− mice until 6 months of age; however, by 10 months, marrow fat volume had increased fivefold relative to wild-type control at the same age. Increased gonadal fat pad mass and hyperglycemia were detectable in Mfap2−/− mice by 2 months, but peaked by 6 months. The development of insulin resistance coincided with MAT expansion. Longitudinal characterization of bone mass demonstrated a disconnection in MAT volume and bone volume. Specifically, Mfap2−/− mice had reduced trabecular bone volume by 2 months, but this phenotype did not progress with age or MAT expansion. Interestingly, MAT expansion in the 10-month-old Mfap2−/− mice was associated with modest alterations in basal hematopoiesis, including a shift from granulopoiesis to B lymphopoiesis. Together, these findings indicate MAT expansion is coincident with insulin resistance, but not excess peripheral adiposity or hyperglycemia in Mfap2−/− mice; and substantial MAT accumulation does not necessitate a proportional decrease in either bone mass or bone marrow cellularity. PMID:27445989

Two different types of double-strand breaks in Saccharomyces cerevisiae are repaired by similar RAD52-independent, nonhomologous recombination events.

PubMed Central

Kramer, K M; Brock, J A; Bloom, K; Moore, J K; Haber, J E

1994-01-01

In haploid rad52 Saccharomyces cerevisiae strains unable to undergo homologous recombination, a chromosomal double-strand break (DSB) can be repaired by imprecise rejoining of the broken chromosome ends. We have used two different strategies to generate broken chromosomes: (i) a site-specific DSB generated at the MAT locus by HO endonuclease cutting or (ii) a random DSB generated by mechanical rupture during mitotic segregation of a conditionally dicentric chromosome. Broken chromosomes were repaired by deletions that were highly variable in size, all of which removed more sequences than was required either to prevent subsequent HO cleavage or to eliminate a functional centromere, respectively. The junction of the deletions frequently occurred where complementary strands from the flanking DNA could anneal to form 1 to 5 bp, although 12% (4 of 34) of the events appear to have occurred by blunt-end ligation. These types of deletions are very similar to the junctions observed in the repair of DSBs by mammalian cells (D. B. Roth and J. H. Wilson, Mol. Cell. Biol. 6:4295-4304, 1986). When a high level of HO endonuclease, expressed in all phases of the cell cycle, was used to create DSBs, we also recovered a large class of very small (2- or 3-bp) insertions in the HO cleavage site. These insertions appear to represent still another mechanism of DSB repair, apparently by annealing and filling in the overhanging 3' ends of the cleavage site. These types of events have also been well documented for vertebrate cells. PMID:8289808

Quantification of metabolically active transient storage (MATS) in two reaches with contrasting transient storage and ecosystem respiration

Treesearch

Alba Argerich; Roy Haggerty; Eugènia Martí; Francesc Sabater; Jay Zarnetske

2011-01-01

Water transient storage zones are hotspots for metabolic activity in streams although the contribution of different types of transient storage zones to the whole�]reach metabolic activity is difficult to quantify. In this study we present a method to measure the fraction of the transient storage that is metabolically active (MATS) in two consecutive reaches...

Analysis of lipophilic pigments from a phototrophic microbial mat community by high performance liquid chromatography

NASA Technical Reports Server (NTRS)

Palmisano, A. C.; Cronin, S. E.; Des Marais, D. J.

1988-01-01

As assay for lipophilic pigments in phototrophic microbial mat communities using reverse phase-high performance liquid chromatography was developed which allows the separation of 15 carotenoids and chloropigments in a single 30 min program. Lipophilic pigments in a laminated mat from a commercial salina near Laguna Guerrero Negro, Baja California Sur, Mexico reflected their source organisms. Myxoxanthophyll, echinenone, canthaxanthin, and zeaxanthin were derived from cyanobacteria; chlorophyll c, and fucoxanthin from diatoms; chlorophyll a from cyanobacteria and diatoms; bacteriochlorophylls a and c, bacteriophaeophytin a, and gamma-carotene from Chloroflexus spp.; and beta-carotene from a variety of phototrophs. Sensitivity of detection was 0.6-6.1 ng for carotenoids and 1.7-12 ng for most chloropigments. This assay represents a significant improvement over previous analyses of lipophilic pigments in microbial mats and promises to have a wider application to other types of phototrophic communities.

The internal transcribed spacer (ITS) region and trnH-psbA [corrected] are suitable candidate loci for DNA barcoding of tropical tree species of India.

PubMed

Tripathi, Abhinandan Mani; Tyagi, Antariksh; Kumar, Anoop; Singh, Akanksha; Singh, Shivani; Chaudhary, Lal Babu; Roy, Sribash

2013-01-01

DNA barcoding as a tool for species identification has been successful in animals and other organisms, including certain groups of plants. The exploration of this new tool for species identification, particularly in tree species, is very scanty from biodiversity-rich countries like India. rbcL and matK are standard barcode loci while ITS, and trnH-psbA are considered as supplementary loci for plants. Plant barcode loci, namely, rbcL, matK, ITS, trnH-psbA, and the recently proposed ITS2, were tested for their efficacy as barcode loci using 300 accessions of tropical tree species. We tested these loci for PCR, sequencing success, and species discrimination ability using three methods. rbcL was the best locus as far as PCR and sequencing success rate were concerned, but not for the species discrimination ability of tropical tree species. ITS and trnH-psbA were the second best loci in PCR and sequencing success, respectively. The species discrimination ability of ITS ranged from 24.4 percent to 74.3 percent and that of trnH-psbA was 25.6 percent to 67.7 percent, depending upon the data set and the method used. matK provided the least PCR success, followed by ITS2 (59. 0%). Species resolution by ITS2 and rbcL ranged from 9.0 percent to 48.7 percent and 13.2 percent to 43.6 percent, respectively. Further, we observed that the NCBI nucleotide database is poorly represented by the sequences of barcode loci studied here for tree species. Although a conservative approach of a success rate of 60-70 percent by both ITS and trnH-psbA may not be considered as highly successful but would certainly help in large-scale biodiversity inventorization, particularly for tropical tree species, considering the standard success rate of plant DNA barcode program reported so far. The recommended matK and rbcL primers combination may not work in tropical tree species as barcode markers.

Demethylation and cleavage of dimethylsulfoniopropionate in marine intertidal sediments

USGS Publications Warehouse

Visscher, P.T.; Kiene, R.P.; Taylor, B.F.

1994-01-01

Demethylation and cleavage of dimethylsulfoniopropionate (DMSP) was measured in three different types of,intertidal marine sediments: a cyanobacterial mat, a diatom-covered tidal flat and a carbonate sediment. Consumption rates of added DMSP were highest in cyanobacterial mat slurries (59 ?? mol DMSP l-1 slurry h-1) and lower in slurries from a diatom mat and a carbonate tidal sediment (24 and 9 ??mol DMSP l-1 h-1, respectively). Dimethyl sulfide (DMS) and 3-mercaptopropionate (MPA) were produced simultaneously during DMSP consumption, indicating that cleavage and demethylation occurred at the same time. Viable counts of DMSP-utilizing bacteria revealed a population of 2 x 107 cells cm-3 sediment (90% of these cleaved DMSP to DMS, 10% demethylated DMSP to MPA) in the cyanobacterial mat, 7 x 105 cells cm-3 in the diatom mat (23% cleavers, 77% demethylators), and 9 x 104 cells cm-3 (20% cleavers and 80% demethylators) in the carbonate sediment. In slurries of the diatom mat, the rate of MPA production from added 3-methiolpropionate (MMPA) was 50% of the rate of MPA formation from DMSP. The presence of a large population of demethylating bacteria and the production of MPA from DMSP suggest that the demethylation pathway, in addition to cleavage, contributes significantly to DMSP consumption in coastal sediments.

Topographic control of mat-surface structures evolution: Examples from modern evaporitic carbonate (Abu Dhabi) and evaporitic siliciclastic (Tunisia) tidal flats.

NASA Astrophysics Data System (ADS)

Hafid Bouougri, El; Porada, Hubertus

2010-05-01

In terms of optimal light utilization, mat surfaces ideally are flat. In nature, however, flat mat surfaces are observed rarely or in restricted patches only. Rather they are shaped by a variety of linear and subcircular to irregular protrusions at various scales, including overgrown upturned crack margins, bulges (‘petees'), domes (‘blisters' and ‘pustules'), reticulate networks with tufts and pinnacles etc. These features are so characteristic that ‘mat types' have been established according to their prevalence, e.g., film, flat, smooth, crinkle, blister, tufted, cinder, mammilate, pustular and polygonal mats (Kendall and Skipwith, 1969; Logan et al., 1974). Responsible for the development of such mat surface features are environmental (physical and chemical) factors and, in reaction, the opportunistic growth behaviour of the participating bacterial taxa. Theoretically, a ‘juvenile' mat may be assumed as being flat, evolving into various forms with typical surface morphologies according to environmental impacts and respective bacterial reactions. Observations in the Abu Dhabi evaporitic carbonate tidal flats and Tunisian evaporitic siliciclastic tidal flats demonstrate that topography plays a fundamental role, both on the large scale of the tidal flat and on the small scale of mat surface morphology. It controls, together with related factors like, e.g., frequency of tidal flooding; duration of water cover; frequency and duration of subaerial exposure, the spatial distribution and the temporal evolution of mat surface structures. On the tidal flat scale, topographic differences result a priori from its seaward gradient and may arise additionally from physical processes which may modify the substrate surface and produce in the intertidal and lower supratidal zones narrow creeks and shallow depressions meandering perpendicular to the slope. Within a wide tidal flat without local topographic changes in the tidal zones, mat surface structures display a typical shore-parallel zonality. In contrast, in tidal flats with slight changes in topography, the typical shore-parallel zonality appears disturbed mainly along the intertidal and lower supratidal zones. The mat surface structures within each tidal zone show local and lateral transitions but all evolve from an incipient flat or polygonal mat. On the mat scale, microtopographic differences are created by the mats themselves, e.g., in the form of upturned crack margins, bulges and domes. All these are small-scale topographic highs that influence the distribution of microbial activity and mat growth dynamics. In the Abu Dhabi area it is observed that smooth or polygonal mats may grade temporally into mammilate, cinder or pustular and tufted mats along an evolutionary path controlled by preferred growth along bulges and upturned crack margins. A similar temporal evolution appears in the intertidal and supratidal zones in Tunisia where local changes on mat-surface induce a variety of mat-growth struc¬tures on and along upturned crack margins, gas domes and isolated to polygonal bulges and petee ridges. References Kendall C.G.St.C, Skipwith, P.A.d'E. (1968) Recent algal mats of a Persian gulf lagoon. J. Sedim. Res., 38, 1040-1058. Logan B.W. Hoffman P. Gebelein, C.D. (1974) Algal mats, cryptalgal fabrics, and structures, Hamelin Pool, Western Australia. AAPG Mem., 22, 140-194.

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

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

Kozubal, Mark; Romine, Margaret F.; Jennings, Ryan

Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicate that the replicate assemblies represent a newmore » phylum-level lineage referred to here as 'novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I CO dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogues active in YNP today.« less

USH1H, a novel locus for type I Usher syndrome, maps to chromosome 15q22-23.

PubMed

Ahmed, Z M; Riazuddin, S; Khan, S N; Friedman, P L; Riazuddin, S; Friedman, T B

2009-01-01

Usher syndrome (USH) is a hereditary disorder associated with sensorineural hearing impairment, progressive loss of vision attributable to retinitis pigmentosa (RP) and variable vestibular function. Three clinical types have been described with type I (USH1) being the most severe. To date, six USH1 loci have been reported. We ascertained two large Pakistani consanguineous families segregating profound hearing loss, vestibular dysfunction, and RP, the defining features of USH1. In these families, we excluded linkage of USH to the 11 known USH loci and subsequently performed a genome-wide linkage screen. We found a novel USH1 locus designated USH1H that mapped to chromosome 15q22-23 in a 4.92-cM interval. This locus overlaps the non-syndromic deafness locus DFNB48 raising the possibility that the two disorders may be caused by allelic mutations.

Reevaluating the serotype II capsular locus of Streptococcus agalactiae.

PubMed

Martins, E R; Melo-Cristino, J; Ramirez, M

2007-10-01

We report a novel sequence of the serotype II capsular locus of group B streptococcus that resolves inconsistencies among the results of various groups and the sequence in GenBank. This locus was found in diverse lineages and presents genes consistent with the complete synthesis of the type II polysaccharide.

Analysis techniques for multivariate root loci. [a tool in linear control systems

NASA Technical Reports Server (NTRS)

Thompson, P. M.; Stein, G.; Laub, A. J.

1980-01-01

Analysis and techniques are developed for the multivariable root locus and the multivariable optimal root locus. The generalized eigenvalue problem is used to compute angles and sensitivities for both types of loci, and an algorithm is presented that determines the asymptotic properties of the optimal root locus.

Intratypic variability of a tandem repeat locus within the DNA polymerase gene of human herpes simplex virus type 2.

PubMed

Sun, Yongjiang; Chan, Roy Kum Wah; Tan, Suat Hoon

2004-01-01

In this study, the irntratypic variability of a tandem repeat locus within the DNA polymerase (pol) gene of human herpes simplex virus type 2 (HSV2) was uncovered. The locus contained variable numbers of tandem dodecanucleotide (5'-GAC GAG GAC GGG-3') repetitive units. Our result showed that approximately 95% of analyzed HSV2 clinical isolates and the current GenBank HSV2 strains contained two copies of the repetitive units. From genital herpes specimens, three new HSV2 strains, which respectively contained 1, 3, and 4 copies of the repetitive units, were identified. This variable number of tandem repeat (VNTR) locus is absent in HSV1, and thus it also contributes to the intertypic variability of HSV1 and HSV2. The intratypic variability of the locus may be useful for HSV2 strain genotyping and this application is discussed.

The effect of woven and non-woven fiber structure on mechanical properties polyester composite reinforced kenaf

NASA Astrophysics Data System (ADS)

Ratim, S.; Bonnia, N. N.; Surip, S. N.

2012-07-01

The effects of woven and non-woven kenaf fiber on mechanical properties of polyester composites were studied at different types of perform structures. Composite polyester reinforced kenaf fiber has been prepared via hand lay-up process by varying fiber forms into plain weave, twill and mats structure. The reinforcing efficiency of different fiber structure was compared with control of unreinforced polyester sample. It was found that the strength and stiffness of the composites are largely affected by fiber structure. A maximum value for tensile strength of composite was obtained for twill weave pattern of fiber structure while no significant different for plain weave and mat structure. The elastic modulus of composite has shown some improvement on plain and twill weave pattern. Meanwhile, lower value of modulus elasticity achieved by mats structure composite as well as control sample. The modulus of rupture and impact resistance were also analyzed. The improvement of modulus of rupture value can be seen on plain and twill weave pattern. However impact resistance doesn't show significant improvement in all types of structure except for mat fiber. The mechanical properties of kenaf fiber reinforced polyester composite found to be increased with woven and non-woven fiber structures in composite.

Context, Biogeochemistry, and Morphology of Diverse and Spatially Extensive Microbial Mats, Little Ambergris Cay, Turks and Caicos Islands, B.W.I.

NASA Astrophysics Data System (ADS)

Present, T. M.; Trower, L.; Stein, N.; Alleon, J.; Bahniuk, A.; Gomes, M. L.; Lingappa, U.; Metcalfe, K.; Orzechowski, E. A.; Riedman, L. A.; Sanders, C. B.; Morris, D. K.; O'Reilly, S.; Sibert, E. C.; Thorpe, M.; Tarika, M.; Fischer, W. W.; Knoll, A. H.; Grotzinger, J. P.

2017-12-01

Little Ambergris Cay (21.3° N, 71.7° W) was the site of an integrated geobiological study conducted in July 2016 and August 2017. The cay ( 6 km x 1.6 km) is developed on a broad bank influenced by strong easterly trade winds (avg. 7.5 m/s), where convergent ooid shoals culminate in a linear shoal extending almost 25 km westward from the cay. Lithified upper shoreface to eolian ooid grainstones form a 2 m high bedrock rim that protects an extensive interior tidal marsh with well-developed microbial mats. Local breaches in the rim allow tidal flows to inundate interior bays floored by microbial mats. Three mat types were observed based on texture: dark toned "blister mat" that flanks the bays where they intersect with the bedrock rim; light-toned "polygonal mat" that covers broad tracts of the bay and is exposed at low tide; and lighter-toned "EPS mat" that is generally submerged even at low tide. The millimeter-to decimeter-thick layered mats overlie laterally extensive ooid sands, generally unlithified except for a few hardgrounds. The mats and underlying sediments were sampled by vibracoring, push coring, and piezometers. Biogeochemical analyses include groundwater salinity, pH, DIC, alkalinity, cation composition, DNA content, photosynthetic efficiency, C and S isotope composition, lipid biomarkers, and taphonomic state. Groundwater and interstitial water chemical analyses were integrated with hydrologic observations of tidal channels' level and flow. Visible light UAV images from 350 m standoff distance were processed to generate a 15 cm/pixel mosaic of the island that was used in combination with a DGPS survey, multispectral Landsat images (m-scale resolution) and Worldview satellite images (30 cm resolution) to map the island's topography, mats, and sedimentologic facies. A UAV-based VNIR hyperspectral camera was used to quantify pigment concentrations in the mats at cm-resolution over decameter scales. Sub-cm-scale bed textures, including those expressed by the different microbial mats, were quantified from images captured with 5-20 m standoff. The thickness of the Holocene sediment fill (0 to >2m) was estimated using core data and a depth probe. These data inform the preservation of microbial textures in grain-dominated carbonate facies and provide analogs for ancient microbial laminites.

Wrinkle structures—a critical review

NASA Astrophysics Data System (ADS)

Porada, Hubertus; Bouougri, El Hafid

2007-04-01

In this paper, a variety of so-called 'wrinkle structures' is reviewed in an attempt to help distinguish between crinkly decorations arising from physical processes that acted on siliciclastic bedding surfaces, and true microbially induced 'wrinkle structures'. Two types of small-scale, microbially induced sedimentary structures are prominent due to their distinct geometry and mode of occurrence: (1) 'elephant skin' textures, characterized by reticulate patterns of sharp-crested ridges forming mm- to cm-scale polygons, occurring on argillite or argillaceous veneers above fine-grained sandstone and likely reflecting growth structures of microbial, mats (2) 'Kinneyia' structures, characterized by mm-scale flat-topped, winding ridges and intervening troughs and pits, sometimes resembling small-scale interference ripples. 'Kinneyia' structures usually occur on upper surfaces of siltstone/sandstone beds, themselves frequently event deposits, and are thought to have formed beneath microbial mats. Additionally, more linear variations of mat growth structures, partly resembling small-scale 'α-petees' may be developed. Finally, some wrinkly structures resulting from tractional mat deformation or mat slumping are occasionally preserved. These may appear as arcuate belts of non-penetrative, small-scale folds or as wrinkled bulges on otherwise flat surfaces. 'Wrinkle structures' as indicators for the former presence of mats gain in importance if other mat-related structures are additionally observed in the same clastic succession, e.g. 'sand chips' (sandy intraclasts) or spindle-shaped or sinuously curved to circular sand cracks, frequently combined in networks. Furthermore, appropriate lithologies and facies are required. For instance, if compared with the distribution of modern cohesive microbial mats, laminated siltstone/argillite with intercalated siltstone/sandstone beds representing event deposits in tidal flat successions would be compatible with microbial mat development. Within a variety of physically induced small-scale wrinkly structures, miniature load structures may, above all, be misinterpreted as microbially induced 'wrinkle structures', due to their similar size and appearance, and their comparatively frequent occurrence.

Telomerase reverse transcriptase locus polymorphisms and cancer risk: a field synopsis and meta-analysis.

PubMed

Mocellin, Simone; Verdi, Daunia; Pooley, Karen A; Landi, Maria T; Egan, Kathleen M; Baird, Duncan M; Prescott, Jennifer; De Vivo, Immaculata; Nitti, Donato

2012-06-06

Several recent studies have provided evidence that polymorphisms in the telomerase reverse transcriptase (TERT) gene sequence are associated with cancer development, but a comprehensive synopsis is not available. We conducted a systematic review and meta-analysis of the available molecular epidemiology data regarding the association between TERT locus polymorphisms and predisposition to cancer. A systematic review of the English literature was conducted by searching PubMed, Embase, Cancerlit, Google Scholar, and ISI Web of Knowledge databases for studies on associations between TERT locus polymorphisms and cancer risk. Random-effects meta-analysis was performed to pool per-allele odds ratios for TERT locus polymorphisms and risk of cancer, and between-study heterogeneity and potential bias sources (eg, publication and chasing bias) were assessed. Because the TERT locus includes the cleft lip and palate transmembrane 1-like (CLPTM1L) gene, which is in linkage disequilibrium with TERT, CLPTM1L polymorphisms were also analyzed. Cumulative evidence for polymorphisms with statistically significant associations was graded as "strong," "moderate," and "weak" according to the Venice criteria. The joint population attributable risk was calculated for polymorphisms with strong evidence of association. Eighty-five studies enrolling 490 901 subjects and reporting on 494 allelic contrasts were retrieved. Data were available on 67 TERT locus polymorphisms and 24 tumor types, for a total of 221 unique combinations of polymorphisms and cancer types. Upon meta-analysis, a statistically significant association with the risk of any cancer type was found for 22 polymorphisms. Strong, moderate, and weak cumulative evidence for association with at least one tumor type was demonstrated for 11, 9, and 14 polymorphisms, respectively. For lung cancer, which was the most studied tumor type, the estimated joint population attributable risk for three polymorphisms (TERT rs2736100, intergenic rs4635969, and CLPTM1L rs402710) was 41%. Strong evidence for lack of association was identified for five polymorphisms in three tumor types. To our knowledge, this is the largest collection of data for associations between TERT locus polymorphisms and cancer risk. Our findings support the hypothesis that genetic variability in this genomic region can modulate cancer susceptibility in humans.

Genetics of the APM1 locus and its contribution to type 2 diabetes susceptibility in French Caucasians.

PubMed

Gibson, Fernando; Froguel, Philippe

2004-11-01

We have carried out a detailed reexamination of the genetics of the APM1 locus and its contribution to the genetic basis of type 2 diabetes susceptibility in the French Caucasian population. The G allele of single nucleotide polymorphism -11426 in the APM1 promoter showed modest association with type 2 diabetes (odds ratio 1.44 [95% CI 1.04-1.98]; P = 0.03), providing corroborative evidence that single nucleotide polymorphisms in the APM1 promoter region contribute to the genetic risk of type 2 diabetes. A "sliding window" analysis identified haplotypes 1-1-1, 1-1-1-1, and 1-1-1-1-1 as being strongly protective against type 2 diabetes (P

Three-dimensional multiexcitation magnetoacoustic tomography with magnetic induction

PubMed Central

Li, Xu; Mariappan, Leo; He, Bin

2010-01-01

Magnetoacoustic tomography with magnetic induction (MAT-MI) is a hybrid imaging modality proposed to image electrical conductivity contrast of biological tissue with high spatial resolution. This modality combines magnetic excitations with ultrasound detection through the Lorentz force based coupling mechanism. However, previous studies have shown that MAT-MI method with single type of magnetic excitation can only reconstruct the conductivity boundaries of a sample. In order to achieve more complete conductivity contrast reconstruction, we proposed a multiexcitation MAT-MI approach. In this approach, multiple magnetic excitations using different coil configurations are applied to the object sequentially and ultrasonic signals corresponding to each excitation are collected for conductivity image reconstruction. In this study, we validate the new multiexcitation MAT-MI method for three-dimensional (3D) conductivity imaging through both computer simulations and phantom experiments. 3D volume data are obtained by utilizing acoustic focusing and cylindrical scanning under each magnetic excitation. It is shown in our simulation and experiment results that with a common ultrasound probe that has limited bandwidth we are able to correctly reconstruct the 3D relative conductivity contrast of the imaging object. As compared to those conductivity boundary images generated by previous single-excitation MAT-MI, the new multiexcitation MAT-MI method provides more complete conductivity contrast reconstruction, and therefore, more valuable information in possible clinical and research applications. PMID:21267084

Quantifying Thin Mat Floating Marsh Strength and Interaction with Hydrodynamic Conditions

NASA Astrophysics Data System (ADS)

Collins, J. H., III; Sasser, C.; Willson, C. S.

2016-12-01

Louisiana possesses over 350,000 acres of unique floating vegetated systems known as floating marshes or flotants. Floating marshes make up 70% of the Terrebonne and Barataria basin wetlands and exist in several forms, mainly thick mat or thin mat. Salt-water intrusion, nutria grazing, and high-energy wave events are believed to be some contributing factors to the degradation of floating marshes; however, there has been little investigation into the hydrodynamic effects on their structural integrity. Due to their unique nature, floating marshes could be susceptible to changes in the hydrodynamic environment that may result from proposed river freshwater and sediment diversion projects introducing flow to areas that are typically somewhat isolated. This study aims to improve the understanding of how thin mat floating marshes respond to increased hydrodynamic stresses and, more specifically, how higher water velocities might increase the washout probability of this vegetation type. There are two major components of this research: 1) A thorough measurement of the material properties of the vegetative mats as a root-soil matrix composite material; and 2) An accurate numerical simulation of the hydrodynamics and forces imposed on the floating marsh mats by the flow. To achieve these goals, laboratory and field experiments were conducted using a customized device to measure the bulk properties of typical floating marshes. Additionally, Delft-3D FLOW and ANSYS FLUENT were used to simulate the flow around a series of simplified mat structures in order to estimate the hydrodynamic forcings on the mats. The hydrodynamic forcings are coupled with a material analysis, allowing for a thorough analysis of their interaction under various conditions. The 2-way Fluid Structure Interaction (F.S.I.) between the flow and the mat is achieved by coupling a Finite Element Analysis (F.E.A.) solver in ANSYS with FLUENT. The flow conditions necessary for the structural failure of the floating marshes are determined for a multitude of mat shapes and sizes, leading to a quantifiable critical velocity required for washout. Ultimately, through dimensional analysis, an equation for washout potential will be developed from the results, which could be used as a design guideline.

Spatiotemporal patterns in community structure of macroinvertebrates inhabiting calcareous periphyton mats

USGS Publications Warehouse

Liston, S.E.; Trexler, J.C.

2005-01-01

Calcareous floating periphyton mats in the southern Everglades provide habitat for a diverse macroinvertebrate community that has not been well characterized. Our study described this community in an oligotrophic marsh, compared it with the macroinvertebrate community associated with adjacent epiphytic algae attached to macrophytes in the water column, and detected spatial patterns in density and community structure. The floating periphyton mat (floating mat) and epiphytic algae in the water column (submerged epiphyton) were sampled at 4 sites (???1 km apart) in northern Shark River Slough, Everglades National Park (ENP), in the early (July) and late (November) wet season. Two perpendicular 90-m transects were established at each site and ???100 samples were taken in a nested design. Sites were located in wet-prairie spikerush-dominated sloughs with similar water depths and emergent macrophyte communities. Floating mats were sampled by taking cores (6-cm diameter) that were sorted under magnification to enumerate infauna retained on a 250-??m-mesh sieve and with a maximum dimension >1 mm. Our results showed that floating mats provide habitat for a macroinvertebrate community with higher densities (no. animals/g ash-free dry mass) of Hyalella azteca, Dasyhelea spp., and Cladocera, and lower densities of Chironomidae and Planorbella spp. than communities associated with submerged epiphyton. Densities of the most common taxa increased 3x to 15x from early to late wet season, and community differences between the 2 habitat types became more pronounced. Floating-mat coverage and estimated floating-mat biomass increased 20 to 30%, and 30 to 110%, respectively, at most sites in the late wet season. Some intersite variation was observed in individual taxa, but no consistent spatial pattern in any taxon was detected at any scale (from 0.2 m to 3 km). Floating mats and their resident macroinvertebrate communities are important components in the Everglades food web. This community should be included in environmental monitoring programs because degradation and eventual loss of the calcareous periphyton mat is associated with P enrichment in this ecosystem. ?? 2005 by The North American Benthological Society.

Morphological Survey of Microbial Mats Near Deep-Sea Thermal Vents †

PubMed Central

Jannasch, Holger W.; Wirsen, Carl O.

1981-01-01

A microscopic survey is presented of the most commonly observed and morphologically conspicuous microorganisms found attached to natural surfaces or to artificial materials deposited in the immediate vicinity of thermal submarine vents at the Galapagos Rift ocean spreading zone at a depth of 2,550 meters. Of special interest were the following findings: (i) all surfaces intermittently exposed to H2S-containing hydrothermal fluid were covered by layers, ca. 5 to 10 μm thick, of procaryotic, gram-negative cells interspaced with amorphous metal (Mn-Fe) deposits; (ii) although some of the cells were encased by dense metal deposits, there was little apparent correlation between metal deposition and the occurrence of microbial mats, (iii) highly differentiated forms appeared to be analogues of certain cyanobacteria, (iv) isolates from massive mats of a prosthecate bacterium could be identified as Hyphomicrobium spp., (v) intracellular membrane systems similar to those found in methylotrophic and nitrifying bacteria were observed in approximately 20% of the cells composing the mats, (vi) thiosulfate enrichments made from mat material resulted in isolations of different types of sulfur-oxidizing bacteria including the obligately chemolithotrophic genus Thiomicrospira. Images PMID:16345722

Processes of carbonate precipitation in modern microbial mats

NASA Astrophysics Data System (ADS)

Dupraz, Christophe; Reid, R. Pamela; Braissant, Olivier; Decho, Alan W.; Norman, R. Sean; Visscher, Pieter T.

2009-10-01

Microbial mats are ecosystems that arguably greatly affected the conditions of the biosphere on Earth through geological time. These laminated organosedimentary systems, which date back to > 3.4 Ga bp, are characterized by high metabolic rates, and coupled to this, rapid cycling of major elements on very small (mm-µm) scales. The activity of the mat communities has changed Earth's redox conditions (i.e. oxidation state) through oxygen and hydrogen production. Interpretation of fossil microbial mats and their potential role in alteration of the Earth's geochemical environment is challenging because these mats are generally not well preserved. Preservation of microbial mats in the fossil record can be enhanced through carbonate precipitation, resulting in the formation of lithified mats, or microbialites. Several types of microbially-mediated mineralization can be distinguished, including biologically-induced and biologically influenced mineralization. Biologically-induced mineralization results from the interaction between biological activity and the environment. Biologically-influenced mineralization is defined as passive mineralization of organic matter (biogenic or abiogenic in origin), whose properties influence crystal morphology and composition. We propose to use the term organomineralization sensu lato as an umbrella term encompassing biologically influenced and biologically induced mineralization. Key components of organomineralization sensu lato are the "alkalinity" engine (microbial metabolism and environmental conditions impacting the calcium carbonate saturation index) and an organic matrix comprised of extracellular polymeric substances (EPS), which may provide a template for carbonate nucleation. Here we review the specific role of microbes and the EPS matrix in various mineralization processes and discuss examples of modern aquatic (freshwater, marine and hypersaline) and terrestrial microbialites.

Prevalence of toxin-producing Clostridium botulinum associated with the macroalga Cladophora in three Great Lakes: growth and management

USGS Publications Warehouse

Chun, Chan Lan; Kahn, Chase I.; Borchert, Andrew J.; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Peller, Julie R.; Pier, Christina; Lin, Guangyun; Johnson, Eric A.; Sadowsky, Michael J.

2015-01-01

The reemergence of avian botulism caused by Clostridium botulinum type E has been observed across the Great Lakes in recent years. Evidence suggests an association between the nuisance algae, Cladophoraspp., and C. botulinum in nearshore areas of the Great Lakes. However, the nature of the association between Cladophora and C. botulinum is not fully understood due, in part, to the complex food web interactions in this disease etiology. In this study, we extensively evaluated their association by quantitatively examining population size and serotypes of C. botulinum in algal mats collected from wide geographic areas in lakes Michigan, Ontario, and Erie in 2011–2012 and comparing them with frequencies in other matrices such as sand and water. A high prevalence (96%) of C. botulinum type E was observed inCladophora mats collected from shorelines of the Great Lakes in 2012. Among the algae samples containing detectable C. botulinum, the population size of C. Botulinum type E was 100–104 MPN/g dried algae, which was much greater (up to 103 fold) than that found in sand or the water column, indicating thatCladophora mats are sources of this pathogen. Mouse toxinantitoxin bioassays confirmed that the putativeC. botulinum belonged to the type E serotype. Steam treatment was effective in reducing or eliminating C. botulinum type E viable cells in Cladophora mats, thereby breaking the potential transmission route of toxin up to the food chain. Consequently, our data suggest that steam treatment incorporated with a beach cleaning machine may be an effective treatment of Cladophora-borne C. botulinum and may reduce bird mortality and human health risks.

Analysis of meiotic segregation, using single-sperm typing: Meiotic drive at the myotonic dystrophy locus

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

Leeflang, E.P.; Arnheim, N.; McPeek, M.S.

Meiotic drive at the myotonic dystrophy (DM) locus has recently been suggested as being responsible for maintaining the frequency, in the human population, of DM chromosomes capable of expansion to the disease state. In order to test this hypothesis, we have studied samples of single sperm from three individuals heterozygous at the DM locus, each with one allele larger and one allele smaller than 19 CTG repeats. To guard against the possible problem of differential PCR amplification rates based on the lengths of the alleles, the sperm were also typed at another closely linked marker whose allele size was unrelatedmore » to the allele size at the DM locus. Using statistical models specifically designed to study single-sperm segregation data, we find no evidence of meiotic segregation distortion. The upper limit of the two-sided 95% confidence interval for the estimate of the common segregation probability for the three donors is at or below .515 for all models considered, and no statistically significant difference from .5 is detected in any of the models. This suggests that any greater amount of segregation distortion at the myotonic dystrophy locus must result from events following sperm ejaculation. The mathematical models developed make it possible to study segregation distortion with high resolution by using sperm-typing data from any locus. 26 refs., 1 fig., 8 tabs.« less

Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database.

PubMed

Garcia, Sònia; Kovařík, Ales; Leitch, Andrew R; Garnatje, Teresa

2017-03-01

The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S-type organisation (ancestral condition), the L-type arrangement has arisen independently several times during plant evolution. A non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single-locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid-like state over time. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Fatty Acid and Carbon Isotopic Evidence for type I Methanotrophs in Microbial Mats from a Shallow Marine Gas Seep, Coal Oil Point, CA.

NASA Astrophysics Data System (ADS)

Ding, H.; Valentine, D.

2005-12-01

To study the microbial community in a Southern California seep field, sediment and bacterial mat samples were collected from natural gas-bearing and gas-free surfaces at two distinct seeps in the Coal Oil Point seep field, offshore Santa Barbara. Fatty acids in these samples were extracted, analyzed and identified. Using gas chromatography (GC), more than 30 different fatty acids were separated. Generally, fatty acid concentrations in natural gas-bearing samples were about 5-fold higher compared to gas-free samples. Using gas chromatography mass sepctrometry (GC-MS), all separated fatty acids were identified in each sample. The major constituents included saturated 14:0, 16:0, 18:0, branched i-15, a-15 and unsaturated 16:1 and 18:1 series fatty acids. GC-IRMS (isotope ratio mass spectrometry) analysis provided the 13C of all major fatty acids and some 16:1 series fatty acids were found to be more depleted than -40% in samples associated with gas seepage. After treatment with dimethyl disufide (DMDS), the 16:1 series fatty acids were resolved into five distinct components, including common composition 16:1(7), bacterial specific i-16:1(7) and typical biomarkers of type I methnotrophs 16:1(8), 16(6) and 16:1(5), suggesting an important role for methnotrophs in seep sediments and microbial mats. These results provide evidence for the activity of type I methanotrophic bacteria in microbial mats and surficial sediments at the Coal Oil Point seep field, and have implications for methane cycling in this and other seep

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

PubMed Central

Kozubal, Mark A; Romine, Margaret; Jennings, Ryan deM; Jay, Zack J; Tringe, Susannah G; Rusch, Doug B; Beam, Jacob P; McCue, Lee Ann; Inskeep, William P

2013-01-01

Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron-oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as ‘Geoarchaeota' or ‘novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in the metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen-sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron-oxide mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogs active in YNP today. PMID:23151644

Hydroponic root mats for wastewater treatment-a review.

PubMed

Chen, Zhongbing; Cuervo, Diego Paredes; Müller, Jochen A; Wiessner, Arndt; Köser, Heinz; Vymazal, Jan; Kästner, Matthias; Kuschk, Peter

2016-08-01

Hydroponic root mats (HRMs) are ecotechnological wastewater treatment systems where aquatic vegetation forms buoyant filters by their dense interwoven roots and rhizomes, sometimes supported by rafts or other floating materials. A preferential hydraulic flow is created in the water zone between the plant root mat and the bottom of the treatment system. When the mat touches the bottom of the water body, such systems can also function as HRM filter; i.e. the hydraulic flow passes directly through the root zone. HRMs have been used for the treatment of various types of polluted water, including domestic wastewater; agricultural effluents; and polluted river, lake, stormwater and groundwater and even acid mine drainage. This article provides an overview on the concept of applying floating HRM and non-floating HRM filters for wastewater treatment. Exemplary performance data are presented, and the advantages and disadvantages of this technology are discussed in comparison to those of ponds, free-floating plant and soil-based constructed wetlands. Finally, suggestions are provided on the preferred scope of application of HRMs.

Énergie photovoltaïque : matériaux utilisés et perspectives

NASA Astrophysics Data System (ADS)

Marfaing, Y.

2002-04-01

Les matériaux pour la conversion photovoltaïque sont des semi-conducteurs dont la largeur de bande interdite peut se situer dans l'intervalle 1 - 1,8 eV. Les principes physiques de l'effet photovoltaïque sont d'abord rappelés afin de mettre en évidence les relations nécessaires entre les caractéristiques optiques et électroniques du semi-conducteur et l'épaisseur de la structure de conversion ou cellule. Les matériaux actuellement utilisés ou étudiés sont ensuite passés en revue en commençant par le silicium cristallin massif puis en décrivant le vaste secteur des couches minces : silicium amorphe, composés polycristallins, silicium cristallisé en film mince. Les développements attendus dans chacune de ces filières sont présentés ainsi que les recherches en cours sur d'autres types de matériaux et de structures.

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2007-07-01

Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia MacCollin, M.D. CONTRACTING ORGANIZATION: Massachusetts General Hospital...Identification of the Schwannomatosis Locus 5b. GRANT NUMBER DAMD17-03-1-0445 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Mia...Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Schwannomatosis is a recently recognized third major type of neurofibromatosis. Our

Developmental regulation of DNA replication timing at the human beta globin locus.

PubMed

Simon, I; Tenzen, T; Mostoslavsky, R; Fibach, E; Lande, L; Milot, E; Gribnau, J; Grosveld, F; Fraser, P; Cedar, H

2001-11-01

The human beta globin locus replicates late in most cell types, but becomes early replicating in erythroid cells. Using FISH to map DNA replication timing around the endogenous beta globin locus and by applying a genetic approach in transgenic mice, we have demonstrated that both the late and early replication states are controlled by regulatory elements within the locus control region. These results also show that the pattern of replication timing is set up by mechanisms that work independently of gene transcription.

DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia.

PubMed

Nevill, Paul G; Wallace, Mark J; Miller, Joseph T; Krauss, Siegfried L

2013-11-01

We used DNA barcoding to address an important conservation issue in the Midwest of Western Australia, working on Australia's largest genus of flowering plant. We tested whether or not currently recommended plant DNA barcoding regions (matK and rbcL) were able to discriminate Acacia taxa of varying phylogenetic distances, and ultimately identify an ambiguously labelled seed collection from a mine-site restoration project. Although matK successfully identified the unknown seed as the rare and conservation priority listed A. karina, and was able to resolve six of the eleven study species, this region was difficult to amplify and sequence. In contrast, rbcL was straightforward to recover and align, but could not determine the origin of the seed and only resolved 3 of the 11 species. Other chloroplast regions (rpl32-trnL, psbA-trnH, trnL-F and trnK) had mixed success resolving the studied taxa. In general, species were better resolved in multilocus data sets compared to single-locus data sets. We recommend using the formal barcoding regions supplemented with data from other plastid regions, particularly rpl32-trnL, for barcoding in Acacia. Our study demonstrates the novel use of DNA barcoding for seed identification and illustrates the practical potential of DNA barcoding for the growing discipline of restoration ecology. © 2013 John Wiley & Sons Ltd.

Quantitative Ultrasound Comparison of MAT and 4T1 Mammary Tumors in Mice and Rats Across Multiple Imaging Systems.

PubMed

Wirtzfeld, Lauren A; Ghoshal, Goutam; Rosado-Mendez, Ivan M; Nam, Kibo; Park, Yeonjoo; Pawlicki, Alexander D; Miller, Rita J; Simpson, Douglas G; Zagzebski, James A; Oelze, Michael L; Hall, Timothy J; O'Brien, William D

2015-08-01

Quantitative ultrasound estimates such as the frequency-dependent backscatter coefficient (BSC) have the potential to enhance noninvasive tissue characterization and to identify tumors better than traditional B-mode imaging. Thus, investigating system independence of BSC estimates from multiple imaging platforms is important for assessing their capabilities to detect tissue differences. Mouse and rat mammary tumor models, 4T1 and MAT, respectively, were used in a comparative experiment using 3 imaging systems (Siemens, Ultrasonix, and VisualSonics) with 5 different transducers covering a range of ultrasonic frequencies. Functional analysis of variance of the MAT and 4T1 BSC-versus-frequency curves revealed statistically significant differences between the two tumor types. Variations also were found among results from different transducers, attributable to frequency range effects. At 3 to 8 MHz, tumor BSC functions using different systems showed no differences between tumor type, but at 10 to 20 MHz, there were differences between 4T1 and MAT tumors. Fitting an average spline model to the combined BSC estimates (3-22 MHz) demonstrated that the BSC differences between tumors increased with increasing frequency, with the greatest separation above 15 MHz. Confining the analysis to larger tumors resulted in better discrimination over a wider bandwidth. Confining the comparison to higher ultrasonic frequencies or larger tumor sizes allowed for separation of BSC-versus-frequency curves from 4T1 and MAT tumors. These constraints ensure that a greater fraction of the backscattered signals originated from within the tumor, thus demonstrating that statistically significant tumor differences were detected. © 2015 by the American Institute of Ultrasound in Medicine.

HLA Haplotype Frequency Estimation from Real-Life Data with the Hapl-o-Mat Software.

PubMed

Sauter, Jürgen; Schäfer, Christian; Schmidt, Alexander H

2018-01-01

HLA haplotype frequencies are of use in a variety of settings. Such data is typically derived either from family pedigree data by targeted typing or statistical analysis of large population-specific genotype samples. As established tools for the latter approach lacked ability to treat the amount, ambiguity, and inhomogeneity found in genotype data in hematopoietic stem cell donor registries, we developed Hapl-o-Mat to alleviate these specific shortcomings.

LD Typing for Bone Marrow Transplantation.

DTIC Science & Technology

1977-06-15

LD ( HLA —D) locus is the least understood. Separate Navy contracts deal with development of knowledge regarding the specific antigens present at this...locus. This contract is directed to the problem of collecting homozygous typing cells which can be used for P . ,At ~i1&~ L!~Y ~~~~ •i~~•~ (LD ( HLA —D...therefore decided to examine this group with preliminary testing to see whether they could yield the type ef cells necessary for HLA —D typing. Because

Temperature-dependant shifts in a wet tropical Hawaiian forest ecosystem: impact on belowground carbon stocks, dynamics, and processes

NASA Astrophysics Data System (ADS)

Crow, S. E.; Litton, C. M.; Giardina, C. P.

2009-12-01

Global patterns suggest a positive correlation between temperature and total belowground carbon (C) flux and partitioning in temperate and tropical regions, but these relationships have yet to be tested within a given ecosystem type. We established a transect of nine permanent forest plots along an elevation gradient (800-1600 m) in native-dominated Metrosideros polymorpha / Acacia koa rainforest developed in volcanic ash soils along the windward slope of Mauna Kea, Hawaii. Along the transect parent material, bedrock age, species composition, and plant available water are nearly constant and only mean annual temperature (MAT) varies substantially (13°C-18°C). We hypothesized that warmer temperatures at lower elevations would drive greater C flux and partitioning to belowground, which represents a direct input of C into belowground stocks. Roots are often sources of stabilized soil organic matter, thus we expected that increased belowground flux and partitioning of C at higher MATs would increase soil C stocks within recalcitrant C pools, even if bulk soil C stock decreases overall. In fact, our data suggest non-linear relationships between temperature and the distribution of C among soil pools based on sequential density fractionation at 1.6 and 2.4 g mL-1, and radiocarbon-based estimates of mean residence time. The proportion of C recovered within the mineral-associated heavy fraction (>2.4 g mL-1) was greatest at the highest MAT (nearly 30% of total soil C), initially declined at the mid-MAT plots (~10% of total soil C), but then increased again at the lowest MAT plots (~25%). Although the proportion of soil C within the heavy fraction was lowest at the mid-MAT plots, the mean residence time of heavy fraction C was greatest in these plots (570-663 yr for the mid-MAT plots versus 120-220 yr for the highest MAT plots and 64-308 for the lowest MAT plots), suggesting that the mineral-associated C in the mid-MAT plots was the most stabilized. In contrast, the proportion of C recovered within the rapidly cycling light fraction (<1.6 g mL-1) initially increased as MAT decreased, from <10% to a peak of nearly 50% of total soil C in the mid-MAT plots, but then decreased again in the plots with lowest MAT. High temperature both directly and indirectly stimulates weathering in these soils-which are thought to be within the phase of maximum nutrient availability, productivity, and potential SOM stabilization during ecosystem development-through increased belowground activity. However, complex feedbacks between temperature, resource allocation, weathering rate, and carbon storage may be driving non-linear relationships between temperature and soil processes.

Identification and characterization of a locus which regulates multiple functions in Pseudomonas tolaasii, the cause of brown blotch disease of Agaricus bisporus.

PubMed Central

Grewal, S I; Han, B; Johnstone, K

1995-01-01

Pseudomonas tolaasii, the causal agent of brown blotch disease of Agaricus bisporus, spontaneously gives rise to morphologically distinct stable sectors, referred to as the phenotypic variant form, at the margins of the wild-type colonies. The phenotypic variant form is nonpathogenic and differs from the wild type in a range of biochemical and physiological characteristics. A genomic cosmid clone (pSISG29) from a wild-type P. tolaasii library was shown to be capable of restoring a range of characteristics of the phenotypic variant to those of the wild-type form, when present in trans. Subcloning and saturation mutagenesis analysis with Tn5lacZ localized a 3.0-kb region from pSISG29, designated the pheN locus, required for complementation of the phenotypic variant to the wild-type form. Marker exchange of the Tn5lacZ-mutagenized copy of the pheN locus into the wild-type strain demonstrated that a functional copy of the pheN gene is required to maintain the wild-type pathogenic phenotype and that loss of the pheN gene or its function results in conversion of the wild-type form to the phenotypic variant form. The pheN locus contained a 2,727-bp open reading frame encoding an 83-kDa protein. The predicted amino acid sequence of the PheN protein showed homology to the sensor and regulator domains of the conserved family of two component bacterial sensor regulator proteins. Southern hybridization analysis of pheN genes from the wild type and the phenotypic variant form revealed that DNA rearrangement occurs within the pheN locus during phenotypic variation. Analysis of pheN expression with a pheN::lacZ fusion demonstrated that expression is regulated by environmental factors. These results are related to a model for control for phenotypic variation in P. tolaasii. PMID:7642492

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2006-07-01

DAMD17-03-1-0445 TITLE: Molecular Identification of the Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia MacCollin, M.D...COVERED (From - To) 1 Jul 2005 – 30 Jun 2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Molecular Identification of the Schwannomatosis Locus 5b...Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Background: Schwannomatosis is a recently recognized third major type of

Advancing flexible volatile compound sensors using liquid crystals encapsulated in polymer fibers

NASA Astrophysics Data System (ADS)

Reyes, Catherine G.; Lagerwall, Jan P. F.

2018-02-01

Until recently, organic vapor sensors using liquid crystals (LCs) have employed rigid glass substrates for confining the LC, and bulky equipment for vapor detection. Previously, we demonstrated that coaxially electrospinning nematic LC within the core of polymer fibers provides an alternative and improved form factor for confinement. This enables ppm level sensitivity to harmful industrial organics, such as toluene, while giving the flexibility of textile-like sheets (imparted by polymer encapsulation). Moreover, toluene vapor responses of the LC-core fiber mats were visible macroscopically with the naked eye depending on the morphology of the fibers produced, and whether they were oriented in specific geometries (aligned, or random). We identified two types of responses: one corresponds to the LC transition from nematic to isotropic, and the other we suggest is due to an anchoring change at the LC-polymer interface that influences the alignment. While we need to study the presence that defects can have in more detail, we noted that fiber mat thickness is crucial in attempting to understand how and why we are able to visualize two responses in aligned LC-fiber mats. Ultimately, we noted that the response of the polymer sheath itself (softening) to organic vapor exposure affects the liquid crystal confinement in the core. From the microscopic point of view, this will influence the threshold concentration that fibers in a mat will overall respond to. In this paper we will discuss three findings the morphologies enabling LC-core fiber mat response to vapor seen both micro- and macroscopically, how thickness of the fiber mat can play a role in the visualization of the responses, and the effect that the polymer structure has in the mat's sensitivity threshold.

Mathematical simulation of the diel O, S, and C biogeochemistry of a hypersaline microbial mat

NASA Astrophysics Data System (ADS)

Decker, K.; Potter, C.

2003-12-01

The creation of a mathematical simulation model of photosynthetic microbial mats is an important step in our understanding of key biogeochemical cycles that may have altered the atmospheres of early Earth and of other terrestrial planets. A modeling investigation is presented here as a tool to utilize and integrate empirical results from research on hypersaline mats from Baja California, Mexico into a computational system that can be used to simulate biospheric inputs of trace gases to the atmosphere. An early version of our model calculates fluxes and cycling of oxygen, sulfide, and dissolved inorganic carbon (DIC) via abiotic components and via the major bacterial guilds: cyanobacteria (CYA), sulfur reducing bacteria (SRB), purple sulfur bacteria (PSB) and colorless sulfur bacteria (CSB). We used generalized monod-type equations that incorporate substrate and energy limits upon maximum rates of metabolic processes such as photosynthesis and sulfate reduction. We ran a simulation using temperature and irradiance inputs from data collected from a microbial mat in Guerrero Negro in Baja Mexico. Model oxygen, sulfide, and DIC results compared well with data collected in the field mats. A divergence from the field data was an initial large negative DIC flux early in the morning and little flux into the mat thereafter in the simulation. We hypothesize that this divergence will be reduced or eliminated if the salinity of the water surrounding the mat were used as an environmental input and as a limit to photosynthesis rates. Salinity levels, organic carbon, methane, methanogens and green nonsulfur bacteria will be added to this model before it is incorporated into a global model to simulate geological time scales.

Cyanobacterial life at low O(2): community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat.

PubMed

Voorhies, A A; Biddanda, B A; Kendall, S T; Jain, S; Marcus, D N; Nold, S C; Sheldon, N D; Dick, G J

2012-05-01

Cyanobacteria are renowned as the mediators of Earth's oxygenation. However, little is known about the cyanobacterial communities that flourished under the low-O(2) conditions that characterized most of their evolutionary history. Microbial mats in the submerged Middle Island Sinkhole of Lake Huron provide opportunities to investigate cyanobacteria under such persistent low-O(2) conditions. Here, venting groundwater rich in sulfate and low in O(2) supports a unique benthic ecosystem of purple-colored cyanobacterial mats. Beneath the mat is a layer of carbonate that is enriched in calcite and to a lesser extent dolomite. In situ benthic metabolism chambers revealed that the mats are net sinks for O(2), suggesting primary production mechanisms other than oxygenic photosynthesis. Indeed, (14)C-bicarbonate uptake studies of autotrophic production show variable contributions from oxygenic and anoxygenic photosynthesis and chemosynthesis, presumably because of supply of sulfide. These results suggest the presence of either facultatively anoxygenic cyanobacteria or a mix of oxygenic/anoxygenic types of cyanobacteria. Shotgun metagenomic sequencing revealed a remarkably low-diversity mat community dominated by just one genotype most closely related to the cyanobacterium Phormidium autumnale, for which an essentially complete genome was reconstructed. Also recovered were partial genomes from a second genotype of Phormidium and several Oscillatoria. Despite the taxonomic simplicity, diverse cyanobacterial genes putatively involved in sulfur oxidation were identified, suggesting a diversity of sulfide physiologies. The dominant Phormidium genome reflects versatile metabolism and physiology that is specialized for a communal lifestyle under fluctuating redox conditions and light availability. Overall, this study provides genomic and physiologic insights into low-O(2) cyanobacterial mat ecosystems that played crucial geobiological roles over long stretches of Earth history. © 2012 Blackwell Publishing Ltd.

Atmospheric exchange of carbon dioxide and methane of a small water body and a floating mat in the Luther Marsh peatland, Ontario, Canada

NASA Astrophysics Data System (ADS)

Burger, Magdalena; Berger, Sina; Blodau, Christian

2015-04-01

Recent investigations have suggested that small water bodies cover larger areas in northern peatlands than previously assumed. Their role in the carbon cycle and gas exchange rates are poorly constrained so far. To address this issue we measured CO2 and CH4 fluxes on a small water body (ca. 700 m2) and the surrounding floating mat in the Luther Marsh peatland in Ontario, Canada from July to September 2014. To this end we used closed chambers combined with a portable Los Gatos high-resolution trace gas analyzer at different water depths and distances from the shore on the pond and with different dominating plant types on the floating mat surrounding the pond. In addition, CO2 concentrations were recorded in high temporal resolution using an infrared sensor system during selected periods. Air and water temperature, humidity and temperature of the floating mat, wind speed and direction, photosynthetically active radiation, air pressure and relative humidity were also recorded as auxiliary data at the study site. The results show that pond and floating mat were sources of methane throughout the whole measuring period. Methane emissions via the ebullition pathway occurred predominantly near the shore and on the floating mat. During the daytime measurements the floating mat acted as a net sink and the pond as a net source of CO2. The dynamics of CO2 exchange was also strongly time dependent, as CO2 emissions from the pond strongly increased after mid-August. This suggests that photosynthesis was more affected by seasonal decline than respiration process in the pond and that the allochthonous component of the CO2 flux increased in relative importance towards fall.

The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

PubMed Central

Becraft, Eric D.; Wood, Jason M.; Rusch, Douglas B.; Kühl, Michael; Jensen, Sheila I.; Bryant, Donald A.; Roberts, David W.; Cohan, Frederick M.; Ward, David M.

2015-01-01

Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time. PMID:26157420

Strong association of common variants in the CDKN2A/CDKN2B region with type 2 diabetes in French Europids.

PubMed

Duesing, K; Fatemifar, G; Charpentier, G; Marre, M; Tichet, J; Hercberg, S; Balkau, B; Froguel, P; Gibson, F

2008-05-01

Genome-wide association studies (GWASs) recently identified common variants in the CDKN2A/CDKN2B region on chromosome 9p as being strongly associated with type 2 diabetes. Since these association signals were not picked up by the French-Canadian GWAS, we sought to replicate these findings in the French Europid population and to further characterise the susceptibility variants at this novel locus. We genotyped 20 single nucleotide polymorphisms (SNPs) spanning the CDKN2A/CDKN2B locus in our type 2 diabetes case-control cohort. The association between CDKN2A/CDKN2B SNPs and quantitative metabolic traits was also examined in the normoglycaemic participants comprising the control cohort. We report replication of the strong association of rs10811661 with type 2 diabetes found in the GWASs (P= 3.8 X 10(-7); OR 1.43 [95% CI 1.24-1.64]). The other CDKN2A/CDKN2B susceptibility variant, rs564398, did not attain statistical significance (p = 0.053; OR 1.11 [95% CI 1.00-1.24]) in the present study. We also obtained several additional nominal association signals (p < 0.05) at the CDKN2A/CDKN2B locus; however, only the rs3218018 result (p = 0.002) survived Bonferroni correction for multiple testing (adjusted p = 0.04). Our comprehensive association study of common variation spanning the CDKN2A/CDKN2B locus confirms the strong association between the distal susceptibility variant rs10811661 and type 2 diabetes in the French population. Further genetic and functional studies are required to identify the aetiological variants at this locus and determine the cellular and physiological mechanisms by which they act to modulate type 2 diabetes susceptibility.

Ancient sedimentary structures in the <3.7 Ga Gillespie Lake Member, Mars, that resemble macroscopic morphology, spatial associations, and temporal succession in terrestrial microbialites.

PubMed

Noffke, Nora

2015-02-01

Sandstone beds of the <3.7 Ga Gillespie Lake Member on Mars have been interpreted as evidence of an ancient playa lake environment. On Earth, such environments have been sites of colonization by microbial mats from the early Archean to the present time. Terrestrial microbial mats in playa lake environments form microbialites known as microbially induced sedimentary structures (MISS). On Mars, three lithofacies of the Gillespie Lake Member sandstone display centimeter- to meter-scale structures similar in macroscopic morphology to terrestrial MISS that include "erosional remnants and pockets," "mat chips," "roll-ups," "desiccation cracks," and "gas domes." The microbially induced sedimentary-like structures identified in Curiosity rover mission images do not have a random distribution. Rather, they were found to be arranged in spatial associations and temporal successions that indicate they changed over time. On Earth, if such MISS occurred with this type of spatial association and temporal succession, they would be interpreted as having recorded the growth of a microbially dominated ecosystem that thrived in pools that later dried completely: erosional pockets, mat chips, and roll-ups resulted from water eroding an ancient microbial mat-covered sedimentary surface; during the course of subsequent water recess, channels would have cut deep into the microbial mats, leaving erosional remnants behind; desiccation cracks and gas domes would have occurred during a final period of subaerial exposure of the microbial mats. In this paper, the similarities of the macroscopic morphologies, spatial associations, and temporal succession of sedimentary structures on Mars to MISS preserved on Earth has led to the following hypothesis: The sedimentary structures in the <3.7 Ga Gillespie Lake Member on Mars are ancient MISS produced by interactions between microbial mats and their environment. Proposed here is a strategy for detecting, identifying, confirming, and differentiating possible MISS during current and future Mars missions.

Telomerase Reverse Transcriptase Locus Polymorphisms and Cancer Risk: A Field Synopsis and Meta-Analysis

PubMed Central

Verdi, Daunia; Pooley, Karen A.; Landi, Maria T.; Egan, Kathleen M.; Baird, Duncan M.; Prescott, Jennifer; De Vivo, Immaculata; Nitti, Donato

2012-01-01

Background Several recent studies have provided evidence that polymorphisms in the telomerase reverse transcriptase (TERT) gene sequence are associated with cancer development, but a comprehensive synopsis is not available. We conducted a systematic review and meta-analysis of the available molecular epidemiology data regarding the association between TERT locus polymorphisms and predisposition to cancer. Methods A systematic review of the English literature was conducted by searching PubMed, Embase, Cancerlit, Google Scholar, and ISI Web of Knowledge databases for studies on associations between TERT locus polymorphisms and cancer risk. Random-effects meta-analysis was performed to pool per-allele odds ratios for TERT locus polymorphisms and risk of cancer, and between-study heterogeneity and potential bias sources (eg, publication and chasing bias) were assessed. Because the TERT locus includes the cleft lip and palate transmembrane 1-like (CLPTM1L) gene, which is in linkage disequilibrium with TERT, CLPTM1L polymorphisms were also analyzed. Cumulative evidence for polymorphisms with statistically significant associations was graded as “strong,” “moderate,” and “weak” according to the Venice criteria. The joint population attributable risk was calculated for polymorphisms with strong evidence of association. Results Eighty-five studies enrolling 490 901 subjects and reporting on 494 allelic contrasts were retrieved. Data were available on 67 TERT locus polymorphisms and 24 tumor types, for a total of 221 unique combinations of polymorphisms and cancer types. Upon meta-analysis, a statistically significant association with the risk of any cancer type was found for 22 polymorphisms. Strong, moderate, and weak cumulative evidence for association with at least one tumor type was demonstrated for 11, 9, and 14 polymorphisms, respectively. For lung cancer, which was the most studied tumor type, the estimated joint population attributable risk for three polymorphisms (TERT rs2736100, intergenic rs4635969, and CLPTM1L rs402710) was 41%. Strong evidence for lack of association was identified for five polymorphisms in three tumor types. Conclusions To our knowledge, this is the largest collection of data for associations between TERT locus polymorphisms and cancer risk. Our findings support the hypothesis that genetic variability in this genomic region can modulate cancer susceptibility in humans. PMID:22523397

A Genetic Locus Necessary for Rhamnose Uptake and Catabolism in Rhizobium leguminosarum bv. trifolii

PubMed Central

Richardson, Jason S.; Hynes, Michael F.; Oresnik, Ivan J.

2004-01-01

Rhizobium leguminosarum bv. trifolii mutants unable to catabolize the methyl-pentose rhamnose are unable to compete effectively for nodule occupancy. In this work we show that the locus responsible for the transport and catabolism of rhamnose spans 10,959 bp. Mutations in this region were generated by transposon mutagenesis, and representative mutants were characterized. The locus contains genes coding for an ABC-type transporter, a putative dehydrogenase, a probable isomerase, and a sugar kinase necessary for the transport and subsequent catabolism of rhamnose. The regulation of these genes, which are inducible by rhamnose, is carried out in part by a DeoR-type negative regulator (RhaR) that is encoded within the same transcript as the ABC-type transporter but is separated from the structural genes encoding the transporter by a terminator-like sequence. RNA dot blot analysis demonstrated that this terminator-like sequence is correlated with transcript attenuation only under noninducing conditions. Transport assays utilizing tritiated rhamnose demonstrated that uptake of rhamnose was inducible and dependent upon the presence of the ABC transporter at this locus. Phenotypic analyses of representative mutants from this locus provide genetic evidence that the catabolism of rhamnose differs from previously described methyl-pentose catabolic pathways. PMID:15576793

Multi-Excitation Magnetoacoustic Tomography with Magnetic Induction for Bioimpedance Imaging

PubMed Central

Li, Xu; He, Bin

2011-01-01

Magnetoacoustic tomography with magnetic induction (MAT-MI) is an imaging approach proposed to conduct non-invasive electrical conductivity imaging of biological tissue with high spatial resolution. In the present study, based on the analysis of the relationship between the conductivity distribution and the generated MAT-MI acoustic source, we propose a new multi-excitation MAT-MI approach and the corresponding reconstruction algorithms. In the proposed method, multiple magnetic excitations using different coil configurations are employed and ultrasound measurements corresponding to each excitation are collected to derive the conductivity distribution inside the sample. A modified reconstruction algorithm is also proposed for the multi-excitation MAT-MI imaging approach when only limited bandwidth acoustic measurements are available. Computer simulation and phantom experiment studies have been done to demonstrate the merits of the proposed method. It is shown that if unlimited bandwidth acoustic data is available, we can accurately reconstruct the internal conductivity contrast of an object using the proposed method. With limited bandwidth data and the use of the modified algorithm we can reconstruct the relative conductivity contrast of an object instead of only boundaries at the conductivity heterogeneity. Benefits that come with this new method include better differentiation of tissue types with conductivity contrast using the MAT-MI approach, specifically for potential breast cancer screening application in the future. PMID:20529729

Assessing the biological contribution to microbialite growth and morphogenesis utilizing lipid biomarkers

NASA Astrophysics Data System (ADS)

Beeler, S. R.; Gomez, F. J.; Bradley, A. S.

2016-12-01

Microbialites are sedimentary structures that arise from the interaction of microbial, geochemical, and physical processes. These structures are among the oldest evidence for life on Earth, and are abundant through much of the Proterozoic before declining in the Phanerozoic. Microbialites are of great importance geobiologically as they provide a record of microbial life and its interaction with the environment throughout Earth history. Yet, our capacity to use microbialites to reconstruct biological processes on ancient Earth is complicated by our lack of understanding of the mechanisms controlling the formation of these structures. The modern microbialites of Laguna Negra in northeastern Argentina [1] offer an opportunity to examine the biological and geochemical differences among microbialites displaying distinct morphological diversity in a single setting. Three broad types of microbialites are found at this site: oncoids, stromatolites, and laminar crusts. Each of these types of microbialites are associated with visually distinct microbial mats. We have examined the structural and isotopic composition of lipid biomarkers from each of these microbialite types, and their associated mats. Sterol profiles detected from microbial mats and microbialites showed abundant C27 to C29 sterols and indicate that primary producers are dominated by algae. Decreased abundances of more labile unsaturated fatty acids relative to more recalcitrant saturated fatty acids were observed in microbialites compared to extant mats suggesting preferential loss of these compounds during diagenesis. Among the three different microbialite morphologies, no statistically discernable differences in biomarker profiles were detected. This implies that morphological changes are due to either geochemical/physical changes across the zone of microbialite formation or changes in community structure that are not observable in the present biomarker set. [1] Gomez et al. (2014) Palaios 29, 233-249

Association of a new type of gliding, filamentous, purple phototrophic bacterium inside bundles of Microcoleus chthonoplastes in hypersaline cyanobacterial mats

NASA Technical Reports Server (NTRS)

D'Amelio, E. D.; Cohen, Y.; Des Marais, D. J.

1987-01-01

An unidentified filamentous purple bacterium, probably belonging to a new genus or even a new family, is found in close association with the filamentous, mat-forming cyanobacterium Microcoleus chthonoplastes in a hypersaline pond at Guerrero Negro, Baja California Sur, Mexico, and in Solar Lake, Sinai, Egypt. This organism is a gliding, segmented trichome, 0.8-0.9 micrometer wide. It contains intracytoplasmic stacked lamellae which are perpendicular and obliquely oriented to the cell wall, similar to those described for the purple sulfur bacteria Ectothiorhodospira. These bacteria are found inside the cyanobacterial bundle, enclosed by the cyanobacterial sheath. Detailed transmission electron microscopical analyses carried out in horizontal sections of the upper 1.5 mm of the cyanobacterial mat show this cyanobacterial-purple bacterial association at depths of 300-1200 micrometers, corresponding to the zone below that of maximal oxygenic photosynthesis. Sharp gradients of oxygen and sulfide are established during the day at this microzone in the two cyanobacterial mats studied. The close association, the distribution pattern of this association and preliminary physiological experiments suggest a co-metabolism of sulfur by the two-membered community. This probable new genus of purple bacteria may also grow photoheterotrophically using organic carbon excreted by the cyanobacterium. Since the chemical gradients in the entire photic zone fluctuate widely in a diurnal cycle, both types of metabolism probably take place. During the morning and afternoon, sulfide migrates up to the photic zone allowing photoautotrophic metabolism with sulfide as the electron donor. During the day the photic zone is highly oxygenated and the purple bacteria may either use oxidized species of sulfur such as elemental sulfur and thiosulfate in the photoautotrophic mode or grow photoheterotrophically using organic carbon excreted by M. chthonoplastes. The new type of filamentous purple sulfur bacteria is not available yet in pure culture, and its taxonomical position cannot be fully established. This organism is suggested to be a new type of gliding, filamentous, purple phototroph.

Comparison of semi-automated commercial rep-PCR fingerprinting, spoligotyping, 12-locus MIRU-VNTR typing and single nucleotide polymorphism analysis of the embB gene as molecular typing tools for Mycobacterium bovis.

PubMed

Armas, Federica; Camperio, Cristina; Coltella, Luana; Selvaggini, Serena; Boniotti, Maria Beatrice; Pacciarini, Maria Lodovica; Di Marco Lo Presti, Vincenzo; Marianelli, Cinzia

2017-08-04

Highly discriminatory genotyping strategies are essential in molecular epidemiological studies of tuberculosis. In this study we evaluated, for the first time, the efficacy of the repetitive sequence-based PCR (rep-PCR) DiversiLab Mycobacterium typing kit over spoligotyping, 12-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and embB single nucleotide polymorphism (SNP) analysis for Mycobacterium bovis typing. A total of 49 M. bovis animal isolates were used. DNA was extracted and genomic DNA was amplified using the DiversiLab Mycobacterium typing kit. The amplified fragments were separated and detected using a microfluidics chip with Agilent 2100. The resulting rep-PCR-based DNA fingerprints were uploaded to and analysed using web-based DiversiLab software through Pearson's correlation coefficient. Rep-PCR DiversiLab grouped M. bovis isolates into ten different clusters. Most isolates sharing identical spoligotype, MIRU-VNTR profile or embB gene polymorphism were grouped into different rep-PCR clusters. Rep-PCR DiversiLab displayed greater discriminatory power than spoligotyping and embB SNP analysis but a lower resolution power than the 12-locus MIRU-VNTR analysis. MIRU-VNTR confirmed that it is superior to the other PCR-based methods tested here. In combination with spoligotyping and 12-locus MIRU-VNTR analysis, rep-PCR improved the discriminatory power for M. bovis typing.

Effects of MAT9001 containing eicosapentaenoic acid and docosapentaenoic acid, compared to eicosapentaenoic acid ethyl esters, on triglycerides, lipoprotein cholesterol, and related variables.

PubMed

Maki, Kevin C; Bobotas, George; Dicklin, Mary R; Huebner, Margie; Keane, William F

Long-chain omega-3 fatty acid concentrate pharmaceuticals are used in the United States for treatment of severe hypertriglyceridemia (≥500 mg/dL) and are under investigation as adjuncts to statins for lowering cardiovascular risk in patients with high triglycerides (TGs; 200-499 mg/dL). To evaluate MAT9001, an investigational prescription-only omega-3 fatty acid agent containing predominantly eicosapentaenoic acid (EPA) and docosapentaenoic acid, in 42 men and women with fasting TG 200 to 400 mg/dL. In this open-label, crossover trial, subjects received MAT9001 and EPA ethyl esters (EPA-EE) in random order. They were housed in a clinical research unit for 2 14-day treatment periods, separated by a ≥35-day washout. Lipoprotein lipids, apolipoproteins (Apos) and proprotein convertase subtilisin kexin type 9 levels were measured before and at the end of each treatment period. MAT9001, compared with EPA-EE, resulted in significantly (P < .05) larger reductions from pretreatment levels for TG (-33.2% vs -10.5%), total cholesterol (-9.0% vs -6.2%), non-high-density lipoprotein cholesterol (-8.8% vs -4.6%), very low-density lipoprotein cholesterol (-32.5% vs -8.1%), Apo C3 (-25.5% vs -5.0%), and proprotein convertase subtilisin kexin type 9 (-12.3% vs +8.8%). MAT9001 also produced a significantly (P = .003) larger reduction in Apo A1 (-15.3% vs -10.2%), but responses for high-density lipoprotein cholesterol (-11.3% vs -11.1%), low-density lipoprotein cholesterol (-2.4% vs -4.3%), and Apo B (-3.8% vs -0.7%), respectively, were not significantly different relative to EPA-EE. MAT9001 produced significantly larger reductions than EPA-EE in several lipoprotein-related variables that would be expected to favorably alter cardiovascular disease risk in men and women with hypertriglyceridemia. Copyright © 2016 National Lipid Association. Published by Elsevier Inc. All rights reserved.

Biodiversity of the microbial mat of the Garga hot spring.

PubMed

Rozanov, Alexey Sergeevich; Bryanskaya, Alla Victorovna; Ivanisenko, Timofey Vladimirovich; Malup, Tatyana Konstantinovna; Peltek, Sergey Evgenievich

2017-12-28

Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.

Competition for sulfide among colorless and purple sulfur bacteria in cyanobacterial mats

NASA Technical Reports Server (NTRS)

Jorgensen, B. B.; Des Marais, D. J.

1986-01-01

The vertical zonation of light, O2, H2S, pH, and sulfur bacteria was studied in two benthic cyanobacterial mats from hypersaline ponds at Guerrero Negro, Baja California, Mexico. The physical-chemical gradients were analyzed in the upper few mm at < or = 100 micrometers spatial resolution by microelectrodes and by a fiber optic microprobe. In mats, where oxygen produced by photosynthesis diffused far below the depth of the photic zone, colorless sulfur bacteria (Beggiatoa sp.) were the dominant sulfide oxidizing organisms. In a mat, where the O2-H2S interface was close to the photic zone, but yet received no significant visible light, purple sulfur bacteria (Chromatium sp.) were the dominant sulfide oxidizers. Analysis of the spectral light distribution here showed that the penetration of only 1% of the incident near-IR light (800-900 nm) into the sulfide zone was sufficient for the mass development of Chromatium in a narrow band of 300 micromoles thickness. The balance between O2 and light penetration down into the sulfide zone thus determined in micro-scale which type of sulfur bacteria became dominant.

Sunlight-induced self-healing of a microcapsule-type protective coating.

PubMed

Song, Young-Kyu; Jo, Ye-Hyun; Lim, Ye-Ji; Cho, Sung-Youl; Yu, Hwan-Chul; Ryu, Byung-Cheol; Lee, Sang-In; Chung, Chan-Moon

2013-02-01

Photopolymerization behavior of a methacryloxypropyl-terminated polydimethylsiloxane (MAT-PDMS) healing agent was investigated in the presence of benzoin isobutyl ether (BIE) photoinitiator by Fourier transform infrared (FT-IR) spectroscopy. MAT-PDMS and BIE were microencapsulated with urea-formaldehyde polymer. The surface and shell morphology of the microcapsules was investigated by scanning electron microscopy (SEM). Mean diameter and size distribution of the microcapsules could be controlled by agitation rate. A coating matrix formulation was prepared by sol-gel reaction of tetraethyl orthosilicate (TEOS) in the presence of a polysiloxane and by subsequent addition of an adhesion promoter. The formulation and microcapsules were mixed to give a self-healing coating formulation, which was then sprayed to surface of cellulose-fiber-reinforced-cement (CRC) board or mortar. Contact angle measurements showed that both the polymerized MAT-PDMS and the prepared coating matrix are hydrophobic, and the coating matrix has good wettability with MAT-PDMS. It was confirmed by optical microscopy and SEM that, when the self-healing coating is damaged, the healing agent is released from ruptured microcapsules and fills the damaged region. The self-healing coating was evaluated as protective coating for mortar, and it was demonstrated by water permeability and chloride ion penetration tests that our system has sunlight-induced self-healing capability. Our self-healing coating is the first example of capsule-type photoinduced self-healing system, and offers the advantages of catalyst-free, environmentally friendly, inexpensive, practical healing.

Population genetic structure and mycotoxin potential of the wheat crown rot and head blight pathogen Fusarium culmorum in Algeria.

PubMed

Laraba, Imane; Boureghda, Houda; Abdallah, Nora; Bouaicha, Oussama; Obanor, Friday; Moretti, Antonio; Geiser, David M; Kim, Hye-Seon; McCormick, Susan P; Proctor, Robert H; Kelly, Amy C; Ward, Todd J; O'Donnell, Kerry

2017-06-01

Surveys for crown rot (FCR) and head blight (FHB) of Algerian wheat conducted during 2014 and 2015 revealed that Fusarium culmorum strains producing 3-acetyl-deoxynivalenol (3ADON) or nivalenol (NIV) were the causal agents of these important diseases. Morphological identification of the isolates (n FCR=110, n FHB=30) was confirmed by sequencing a portion of TEF1. To assess mating type idiomorph, trichothecene chemotype potential and global population structure, the Algerian strains were compared with preliminary sample of F. culmorum from Italy (n=27), Australia (n=30) and the United States (n=28). A PCR assay for MAT idiomorph revealed that MAT1-1 and MAT1-2 strains were segregating in nearly equal proportions, except within Algeria where two-thirds of the strains were MAT1-2. An allele-specific PCR assay indicated that the 3ADON trichothecene genotype was predominant globally (83.8% 3ADON) and in each of the four countries sampled. In vitro toxin analyses confirmed trichothecene genotype PCR data and demonstrated that most of the strains tested (77%) produced culmorin. Global population genetic structure of 191 strains was assessed using nine microsatellite markers (SSRs). AMOVA of the clone corrected data indicated that 89% of the variation was within populations. Bayesian analysis of the SSR data identified two globally distributed, sympatric populations within which both trichothecene chemotypes and mating types were represented. Copyright © 2017. Published by Elsevier Inc.

Characterisation of pks15/1 in clinical isolates of Mycobacterium tuberculosis from Mexico

PubMed Central

Zenteno-Cuevas, Roberto; Silva-Hernández, Francisco X; Mendoza-Damián, Fabiola; Ramírez-Hernández, Maria Dolores; Vázquez-Medina, Karen; Widrobo-García, Lorena; Cuellar-Sanchez, Aremy; Muñíz-Salazar, Raquel; Enciso-Moreno, Leonor; Pérez-Navarro, Lucia Monserrat; Enciso-Moreno, José Antonio

2013-01-01

Tuberculosis (TB) is an infectocontagious respiratory disease caused by members of the Mycobacterium tuberculosis complex. A 7 base pair (bp) deletion in the locus polyketide synthase (pks)15/1 is described as polymorphic among members of the M. tuberculosis complex, enabling the identification of Euro-American, Indo-Oceanic and Asian lineages. The aim of this study was to characterise this locus in TB isolates from Mexico. One hundred twenty clinical isolates were recovered from the states of Veracruz and Estado de Mexico. We determined the nucleotide sequence of a ± 400 bp fragment of the locus pks15/1, while genotypic characterisation was performed by spoligotyping. One hundred and fifty isolates contained the 7 bp deletion, while five had the wild type locus. Lineages X (22%), LAM (18%) and T (17%) were the most frequent; only three (2%) of the isolates were identified as Beijing and two (1%) EAI-Manila. The wild type pks15/1 locus was observed in all Asian lineage isolates tested. Our results confirm the utility of locus pks15/1 as a molecular marker for identifying Asian lineages of the M. tuberculosis complex. This marker could be of great value in the epidemiological surveillance of TB, especially in countries like Mexico, where the prevalence of such lineages is unknown. PMID:24037193

The Effects of Stroke Type, Locus, and Extent on Long-Term Outcome of Gait Rehabilitation: The LEAPS Experience.

PubMed

Nadeau, Stephen E; Dobkin, Bruce; Wu, Samuel S; Pei, Qinglin; Duncan, Pamela W

2016-08-01

Background Paresis in stroke is largely a result of damage to descending corticospinal and corticobulbar pathways. Recovery of paresis predominantly reflects the impact on the neural consequences of this white matter lesion by reactive neuroplasticity (mechanisms involved in spontaneous recovery) and experience-dependent neuroplasticity, driven by therapy and daily experience. However, both theoretical considerations and empirical data suggest that type of stroke (large vessel distribution/lacunar infarction, hemorrhage), locus and extent of infarction (basal ganglia, right-hemisphere cerebral cortex), and the presence of leukoaraiosis or prior stroke might influence long-term recovery of walking ability. In this secondary analysis based on the 408 participants in the Locomotor Experience Applied Post-Stroke (LEAPS) study database, we seek to address these possibilities. Methods Lesion type, locus, and extent were characterized by the 2 neurologists in the LEAPS trial on the basis of clinical computed tomography and magnetic resonance imaging scans. A series of regression models was used to test our hypotheses regarding the effects of lesion type, locus, extent, and laterality on 2- to 12-month change in gait speed, controlling for baseline gait speed, age, and Berg Balance Scale score. Results Gait speed change at 1 year was significantly reduced in participants with basal ganglia involvement and prior stroke. There was a trend toward reduction of gait speed change in participants with lacunar infarctions. The presence of right-hemisphere cortical involvement had no significant impact on outcome. Conclusions Type, locus, and extent of lesion, and the loss of substrate for neuroplastic effect as a result of prior stroke may affect long-term outcome of rehabilitation of hemiparetic gait. © The Author(s) 2015.

Photosynthesis below the surface in a cryptic microbial mat

NASA Astrophysics Data System (ADS)

Rothschild, Lynn J.; Giver, Lorraine J.

2002-10-01

The discovery of subsurface communities has encouraged speculation that such communities might be present on planetary bodies exposed to harsh surface conditions, including the early Earth. While the astrobiology community has focused on the deep subsurface, near-subsurface environments are unique in that they provide some protection while allowing partial access to photosynthetically active radiation. Previously we identified near-surface microbial communities based on photosynthesis. Here we assess the productivity of such an ecosystem by measuring in situ carbon fixation rates in an intertidal marine beach through a diurnal cycle, and find them surprisingly productive. Gross fixation along a transect (99×1 m) perpendicular to the shore was highly variable and depended on factors such as moisture and mat type, with a mean of ~41 mg C fixed m[minus sign]2 day[minus sign]1. In contrast, an adjacent well-established cyanobacterial mat dominated by Lyngbya aestuarii was ~12 times as productive (~500 mg C fixed m[minus sign]2 day[minus sign]1). Measurements made of the Lyngbya mat at several times per year revealed a correlation between total hours of daylight and gross daily production. From these data, annual gross fixation was estimated for the Lyngbya mat and yielded a value of ~1.3×105 g m[minus sign]2 yr[minus sign]1. An analysis of pulse-chase data obtained in the study in conjunction with published literature on similar ecosystems suggests that subsurface interstitial mats may be an overlooked endogenous source of organic carbon, mostly in the form of excreted fixed carbon.

30 CFR 816.68 - Use of explosives: Records of blasting operations.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (f) Type of material blasted. (g) Sketches of the blast pattern including number of holes, burden, spacing, decks, and delay pattern. (h) Diameter and depth of holes. (i) Types of explosives used. (j...-millisecond period. (l) Initiation system. (m) Type and length of stemming. (n) Mats or other protections used...

30 CFR 817.68 - Use of explosives: Records of blasting operations.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (f) Type of material blasted. (g) Sketches of the blast pattern including number of holes, burden, spacing, decks, and delay pattern. (h) Diameter and depth of holes. (i) Types of explosives used. (j...-millisecond period. (l) Initiation system. (m) Type and length of stemming. (n) Mats or other protections used...

30 CFR 817.68 - Use of explosives: Records of blasting operations.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (f) Type of material blasted. (g) Sketches of the blast pattern including number of holes, burden, spacing, decks, and delay pattern. (h) Diameter and depth of holes. (i) Types of explosives used. (j...-millisecond period. (l) Initiation system. (m) Type and length of stemming. (n) Mats or other protections used...

30 CFR 816.68 - Use of explosives: Records of blasting operations.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (f) Type of material blasted. (g) Sketches of the blast pattern including number of holes, burden, spacing, decks, and delay pattern. (h) Diameter and depth of holes. (i) Types of explosives used. (j...-millisecond period. (l) Initiation system. (m) Type and length of stemming. (n) Mats or other protections used...

Novel autosomal dominant mandibulofacial dysostosis with ptosis: clinical description and exclusion of TCOF1.

PubMed

Hedera, P; Toriello, H V; Petty, E M

2002-07-01

Treacher Collins syndrome (TCS), the most common type of mandibulofacial dysostosis (MFD), is genetically homogeneous. Other types of MFD are less common and, of these, only the Bauru type of MFD has an autosomal dominant (AD) mode of inheritance established. Here we report clinical features of a kindred with a unique AD MFD with the exclusion of linkage to the TCS locus (TCOF1) on chromosome 5q31-q32. Six affected family members underwent a complete medical genetics physical examination and two affected subjects had skeletal survey. All available medical records were reviewed. Linkage analysis using the markers spanning the TCOF1 locus was performed. One typically affected family member had a high resolution karyotype. Affected subjects had significant craniofacial abnormalities without any significant acral changes and thus had a phenotype consistent with a MFD variant. Distinctive features included hypoplasia of the zygomatic complex, micrognathia with malocclusion, auricular abnormalities with conductive hearing loss, and ptosis. Significantly negative two point lod scores were obtained for markers spanning the TCOF1 locus, excluding the possibility that the disease in our kindred is allelic with TCS. High resolution karyotype was normal. We report a kindred with a novel type of MFD that is not linked to the TCOF1 locus and is also clinically distinct from other types of AD MFD. Identification of additional families will facilitate identification of the gene causing this type of AD MFD and further characterisation of the clinical phenotype.

spa typing for epidemiological surveillance of Staphylococcus aureus.

PubMed

Hallin, Marie; Friedrich, Alexander W; Struelens, Marc J

2009-01-01

The spa typing method is based on sequencing of the polymorphic X region of the protein A gene (spa), present in all strains of Staphylococcus aureus. The X region is constituted of a variable number of 24-bp repeats flanked by well-conserved regions. This single-locus sequence-based typing method combines a number of technical advantages, such as rapidity, reproducibility, and portability. Moreover, due to its repeat structure, the spa locus simultaneously indexes micro- and macrovariations, enabling the use of spa typing in both local and global epidemiological studies. These studies are facilitated by the establishment of standardized spa type nomenclature and Internet shared databases.

Sperm FISH analysis of a 44,X,der(Y),t(Y;15)(q12;q10)pat,rob(13;14)(q10;q10)mat complex chromosome rearrangement.

PubMed

Ferfouri, F; Boitrelle, F; Clement, P; Molina Gomes, D; Selva, J; Vialard, F

2014-06-01

Complex chromosome rearrangements (CCR) with two independent chromosome rearrangements are rare. Although CCRs lead to high unbalanced gamete rates, data on meiotic segregation in this context are scarce. A male patient was referred to our clinic as part of a family screening programme prompted by the observation of a 44,X,der(Y),t(Y;15)(q12;q10)pat,rob(13;14)(q10;q10)mat karyotype in his brother. Karyotyping identified the same CCR. Sperm FISH (with locus-specific probes for the segments involved in the translocations and nine chromosomes not involved in both rearrangements) was used to investigate the rearrangements meiotic segregation products and establish whether or not an inter-chromosomal effect was present. Sperm nuclear DNA fragmentation was also evaluated. For rob(13;14) and der(Y), the proportions of unbalanced products were, respectively, 26.4% and 60.6%. Overall, 70.3% of the meiotic segregation products were unbalanced. No evidence of an inter-chromosomal effect was found, and the sperm nuclear DNA fragmentation rate was similar to our laboratory's normal cut-off value. In view of previously published sperm FISH analyses of Robertsonian translocations (and even though the mechanism is still unknown), we hypothesise that cosegregation of der(Y) and rob(13;14) could modify rob(13;14) meiotic segregation. © 2013 Blackwell Verlag GmbH.

DNA barcoding of Rhodiola (crassulaceae): a case study on a group of recently diversified medicinal plants from the Qinghai-Tibetan Plateau.

PubMed

Zhang, Jian-Qiang; Meng, Shi-Yong; Wen, Jun; Rao, Guang-Yuan

2015-01-01

DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences - rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) - for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau.

Composition, variation, expression and evolution of low-molecular-weight glutenin subunit genes in Triticum urartu.

PubMed

Luo, Guangbin; Zhang, Xiaofei; Zhang, Yanlin; Yang, Wenlong; Li, Yiwen; Sun, Jiazhu; Zhan, Kehui; Zhang, Aimin; Liu, Dongcheng

2015-02-28

Wheat (AABBDD, 2n = 6x = 42) is a major dietary component for many populations across the world. Bread-making quality of wheat is mainly determined by glutenin subunits, but it remains challenging to elucidate the composition and variation of low-molecular-weight glutenin subunits (LMW-GS) genes, the major components for glutenin subunits in hexaploid wheat. This problem, however, can be greatly simplified by characterizing the LMW-GS genes in Triticum urartu, the A-genome donor of hexaploid wheat. In the present study, we exploited the high-throughput molecular marker system, gene cloning, proteomic methods and molecular evolutionary genetic analysis to reveal the composition, variation, expression and evolution of LMW-GS genes in a T. urartu population from the Fertile Crescent region. Eight LMW-GS genes, including four m-type, one s-type and three i-type, were characterized in the T. urartu population. Six or seven genes, the highest number at the Glu-A3 locus, were detected in each accession. Three i-type genes, each containing more than six allelic variants, were tightly linked because of their co-segregation in every accession. Only 2-3 allelic variants were detected for each m- and s-type gene. The m-type gene, TuA3-385, for which homologs were previously characterized only at Glu-D3 locus in common wheat and Aegilops tauschii, was detected at Glu-A3 locus in T. urartu. TuA3-460 was the first s-type gene identified at Glu-A3 locus. Proteomic analysis showed 1-4 genes, mainly i-type, expressed in individual accessions. About 62% accessions had three active i-type genes, rather than one or two in common wheat. Southeastern Turkey might be the center of origin and diversity for T. urartu due to its abundance of LMW-GS genes/genotypes. Phylogenetic reconstruction demonstrated that the characterized T. urartu might be the direct donor of the Glu-A3 locus in common wheat varieties. Compared with the Glu-A3 locus in common wheat, a large number of highly diverse LMW-GS genes and active genes were characterized in T. urartu, demonstrating that this progenitor might provide valuable genetic resources for LMW-GS genes to improve the quality of common wheat. The phylogenetic analysis provided molecular evidence and confirmed that T. urartu was the A-genome donor of hexaploid wheat.

Transcriptional activation of the tad type IVb pilus operon by PypB in Yersinia enterocolitica.

PubMed

Schilling, Jennifer; Wagner, Karin; Seekircher, Stephanie; Greune, Lilo; Humberg, Verena; Schmidt, M Alexander; Heusipp, Gerhard

2010-07-01

Type IV pili are virulence factors in various bacteria and mediate, among other functions, the colonization of diverse surfaces. Various subclasses of type IV pili have been identified, but information on pilus expression, biogenesis, and the associated phenotypes is sparse for the genus Yersinia. We recently described the identification of PypB as a transcriptional regulator in Yersinia enterocolitica. Here we show that the pypB gene is associated with the tad locus, a genomic island that is widespread among bacterial and archaeal species. The genetic linkage of pypB with the tad locus is conserved throughout the yersiniae but is not found among other bacteria carrying the tad locus. We show that the genes of the tad locus form an operon in Y. enterocolitica that is controlled by PypB and that pypB is part of this operon. The tad genes encode functions necessary for the biogenesis of the Flp subfamily of type IVb pili initially described for Aggregatibacter actinomycetemcomitans to mediate a tight-adherence phenotype. In Y. enterocolitica, the Flp pilin protein shows some peculiarities in its amino acid sequence that imply similarities as well as differences compared to typical motifs found in the Flp subtype of type IVb pili. Flp is expressed and processed after PypB overproduction, resulting in microcolony formation but not in increased adherence to biotic or abiotic surfaces. Our data describe the transcriptional regulation of the tad type IVb pilus operon by PypB in Y. enterocolitica but fail to show most previously described phenotypes associated with this type of pilus in other bacteria.

Experimental Studies on Geocells and Mat Systems for Stabilization of Unpaved Shoulders and Temporary Roads

NASA Astrophysics Data System (ADS)

Guo, Jun

Geosynthetics have been used to improve the performance of geomaterials, especially when weak soil exists in roadway applications. In this study, two types of geosynthetic materials, geocell and a mat system, were studied for their applications for unpaved roads and shoulders. The study of geocell was focused on its application for unpaved shoulders. The ability of geocell to improve different geomaterials over intermediate strength subgrade and its possible effect on vegetation were investigated. The study of the mat system was focused on investigating the performance of the mat system over soft and intermediate subgrade with different strengths under cyclic loading to simulate temporary roadway conditions. In the study of geocell for the application for unpaved shoulders, six large scale plate loading tests were conducted on a single type of geocell on target 5% CBR subgrade to investigate the benefits of geocell reinforcement on different base course and topsoil combinations. Different base course and topsoil combinations were investigated including: 200-mm thick unreinforced aggregate, 200-mm thick soil-aggregate mixture (50% aggregate and 50% top soil) with and without geocell reinforcement, 200-mm thick geocell-reinforced topsoil, 50-mm thick aggregate over 150-mm soil-aggregate mixture (50% aggregate and 50% top soil), and 50-mm thick top soil over 150-mm thick geocell-reinforced soil-aggregate mixture (50% aggregate and 50% top soil). Earth pressure cells were install at the interface between subgrade and base course to monitor the load distribution. The cyclic plate loading tests showed that geocell effectively reduced the permanent deformation and the geocell-reinforced soil-aggregate mixture slightly outperformed the unreinforced aggregate at the same thickness. The plate loading tests also suggested the topsoil cover resulted in large permanent deformations. A one-year long outdoor field vegetation test was conducted on base courses with different combinations of aggregate and topsoil including: 200-mm thick unreinforced topsoil, 200-mm thick soil-aggregate mixture (50% aggregate and 50% topsoil), 50-mm thick aggregate over 150-mm soil-aggregate mixture (50% aggregate and 50% topsoil), and 50-mm thick topsoil over 150-mm reinforced soil-aggregate mixture (50% aggregate and 50% topsoil) to investigate the possible effect of geocell on shoulder vegetation established mainly by tall fescue grass and perennial ryegrass. One control (unreinforced) section and one geocell-reinforced section were prepared for each base course combination with a surface area of 1.5 m by 1.5 m. During the one-year test period, soil moisture temperature and volumetric moisture content were monitored. Weather data, such as precipitation and air temperature, were obtain from the nearby weather station at the Lawrence airport. Vegetation growth was evaluated by grass leaf blade length, root length, and grass density. Vegetation biomass was obtained at the end of the test. The test results showed no definite evidence of geocell influencing the vegetation in unpaved shoulders. In the study of the mat system, six large-scale cyclic plate loading tests were conducted on a single type of polyethylene mat system with anchorage to study its performance over soft and intermediate subgrade with the CBR ranging from 1% to 4%. For the comparison purposes, test sections with and without the mat system were prepared and evaluated. For the test section with 1% CBR subgrade, an aggregate base course was used for the test section without the mat system to enable the cyclic plate loading test. The size of the mat system under the investigation was 1.92 m by 1.92 m. A cyclic load at the magnitude of 40 kN was applied through a 300 mm diameter loading plate with a thin rubber pad to simulate a vehicle tire. Earth pressure cells were installed at the interface between the mat system and the subgrade to monitor the load distribution. Loading plate displacements were measured by the displacement transducer inside the actuator. Test results concluded that the mat system was more effective over the intermediate subgrade than the soft subgrade and when large permanent deformations were allowed.

A silent allele in the locus D5S818 contained within the PowerPlex®21 PCR Amplification Kit.

PubMed

Chen, Ling; Tai, Yunchun; Qiu, Pingming; Du, Weian; Liu, Chao

2015-11-01

Three paternity tests cases were found with a single locus mismatch at the locus D5S818 with PowerPlex®21 PCR Amplification Kit (Promega). Forward and reverse primers were redesigned to type the samples again and to evaluate if there were alleles dropped out. The results showed the existence of a silent allele 12 in all the three families, due to a point mutation that changed cytosine to adenine at 90 nucleotides upstream from the 5' end of the AGAT repeat sequences in all the six individuals. A single locus mismatch due to a silent allele may occur in any locus using any kit. Therefore, we recommend using multiple kits to confirm the results in paternity testing cases with mismatches, especially when there is a single locus mismatch with homozygote involved. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Association of toxin-producing Clostridium botulinum with the macroalga Cladophora in the Great Lakes.

PubMed

Chun, Chan Lan; Ochsner, Urs; Byappanahalli, Muruleedhara N; Whitman, Richard L; Tepp, William H; Lin, Guangyun; Johnson, Eric A; Peller, Julie; Sadowsky, Michael J

2013-03-19

Avian botulism, a paralytic disease of birds, often occurs on a yearly cycle and is increasingly becoming more common in the Great Lakes. Outbreaks are caused by bird ingestion of neurotoxins produced by Clostridium botulinum, a spore-forming, gram-positive, anaerobe. The nuisance, macrophytic, green alga Cladophora (Chlorophyta; mostly Cladophora glomerata L.) is a potential habitat for the growth of C. botulinum. A high incidence of botulism in shoreline birds at Sleeping Bear Dunes National Lakeshore (SLBE) in Lake Michigan coincides with increasingly massive accumulations of Cladophora in nearshore waters. In this study, free-floating algal mats were collected from SLBE and other shorelines of the Great Lakes between June and October 2011. The abundance of C. botulinum in algal mats was quantified and the type of botulism neurotoxin (bont) genes associated with this organism were determined by using most-probable-number PCR (MPN-PCR) and five distinct bont gene-specific primers (A, B, C, E, and F). The MPN-PCR results showed that 16 of 22 (73%) algal mats from the SLBE and 23 of 31(74%) algal mats from other shorelines of the Great Lakes contained the bont type E (bont/E) gene. C. botulinum was present up to 15000 MPN per gram dried algae based on gene copies of bont/E. In addition, genes for bont/A and bont/B, which are commonly associated with human diseases, were detected in a few algal samples. Moreover, C. botulinum was present as vegetative cells rather than as dormant spores in Cladophora mats. Mouse toxin assays done using supernatants from enrichment of Cladophora containing high densities of C. botulinum (>1000 MPN/g dried algae) showed that Cladophora-borne C. botulinum were toxin-producing species (BoNT/E). Our results indicate that Cladophora provides a habitat for C. botulinum, warranting additional studies to better understand the relationship between this bacterium and the alga, and how this interaction potentially contributes to botulism outbreaks in birds.

Association of toxin-producing Clostridium botulinum with the macroalga Cladophora in the Great Lakes

USGS Publications Warehouse

Chun, Chan Lan; Ochsner, Urs; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Tepp, William H.; Lin, Guangyun; Johnson, Eric A.; Peller, Julie; Sadowsky, Michael J.

2013-01-01

Avian botulism, a paralytic disease of birds, often occurs on a yearly cycle and is increasingly becoming more common in the Great Lakes. Outbreaks are caused by bird ingestion of neurotoxins produced by Clostridium botulinum, a spore-forming, gram-positive, anaerobe. The nuisance, macrophytic, green alga Cladophora (Chlorophyta; mostly Cladophora glomerata L.) is a potential habitat for the growth of C. botulinum. A high incidence of botulism in shoreline birds at Sleeping Bear Dunes National Lakeshore (SLBE) in Lake Michigan coincides with increasingly massive accumulations of Cladophora in nearshore waters. In this study, free-floating algal mats were collected from SLBE and other shorelines of the Great Lakes between June and October 2011. The abundance of C. botulinum in algal mats was quantified and the type of botulism neurotoxin (bont) genes associated with this organism were determined by using most-probable-number PCR (MPN-PCR) and five distinct bont gene-specific primers (A, B, C, E, and F). The MPN-PCR results showed that 16 of 22 (73%) algal mats from the SLBE and 23 of 31(74%) algal mats from other shorelines of the Great Lakes contained the bont type E (bont/E) gene. C. botulinum was present up to 15 000 MPN per gram dried algae based on gene copies of bont/E. In addition, genes for bont/A and bont/B, which are commonly associated with human diseases, were detected in a few algal samples. Moreover, C. botulinum was present as vegetative cells rather than as dormant spores in Cladophora mats. Mouse toxin assays done using supernatants from enrichment of Cladophora containing high densities of C. botulinum (>1000 MPN/g dried algae) showed that Cladophora-borne C. botulinum were toxin-producing species (BoNT/E). Our results indicate that Cladophora provides a habitat for C. botulinum, warranting additional studies to better understand the relationship between this bacterium and the alga, and how this interaction potentially contributes to botulism outbreaks in birds.

Influence of health locus of control and fear of hypoglycaemia on glycaemic control and treatment satisfaction in people with Type 1 diabetes on insulin pump therapy.

PubMed

Indelicato, L; Mariano, V; Galasso, S; Boscari, F; Cipponeri, E; Negri, C; Frigo, A; Avogaro, A; Bonora, E; Trombetta, M; Bruttomesso, D

2017-05-01

To assess the influence of health locus of control and fear of hypoglycaemia on metabolic control and treatment satisfaction in people with Type 1 diabetes mellitus on continuous subcutaneous insulin infusion. People with Type 1 diabetes on continuous subcutaneous insulin infusion for at least 1 year, sub-classified as an 'acceptable glucose control' group [HbA 1c ≤ 58 mmol/mol (7.5%)] and a 'suboptimum glucose control' group [HbA 1c > 58 mmol/mol (7.5%)], were consecutively enrolled in a multicentre cross-sectional study. Questionnaires were administered to assess health locus of control [Multidimensional Health Locus of Control (MHLC) scale, with internal and external subscales], fear of hypoglycaemia [Hypoglycaemia Fear Survey II (HFS-II)] and treatment satisfaction [Diabetes Treatment Satisfaction Questionnaire (DTSQ)]. We enrolled 214 participants (mean ± sd age 43.4 ± 12.1 years). The suboptimum glucose control group (n = 127) had lower mean ± sd internal MHLC and DTSQ scores than the acceptable glucose control group (19.6 ± 5.2 vs 21.0 ± 5.0, P = 0.04 and 28.8 ± 4.8 vs 30.9 ± 4.5, P < 0.001). HFS-II scores did not differ between the two groups. Internal MHLC score was negatively associated with HbA 1c (r = -0.15, P < 0.05) and positively associated with the number of mild and severe hypoglycaemic episodes (r = 0.16, P < 0.05 and r = 0.18, P < 0.001, respectively) and with DTSQ score (r = 0.17, P < 0.05). HFS-II score was negatively associated with DTSQ score (r = -0.18, P < 0.05) and positively with number of severe hypoglycaemic episodes (r = 0.16, P < 0.5). In adults with Type 1 diabetes receiving continuous subcutaneous insulin infusion, high internal locus represents the most important locus of control pattern for achieving good metabolic control. © 2017 Diabetes UK.

Molecular Characterization and Phylogenetic Analysis of Pseudomonas aeruginosa Isolates Recovered from Greek Aquatic Habitats Implementing the Double-Locus Sequence Typing Scheme.

PubMed

Pappa, Olga; Beloukas, Apostolos; Vantarakis, Apostolos; Mavridou, Athena; Kefala, Anastasia-Maria; Galanis, Alex

2017-07-01

The recently described double-locus sequence typing (DLST) scheme implemented to deeply characterize the genetic profiles of 52 resistant environmental Pseudomonas aeruginosa isolates deriving from aquatic habitats of Greece. DLST scheme was able not only to assign an already known allelic profile to the majority of the isolates but also to recognize two new ones (ms217-190, ms217-191) with high discriminatory power. A third locus (oprD) was also used for the molecular typing, which has been found to be fundamental for the phylogenetic analysis of environmental isolates given the resulted increased discrimination between the isolates. Additionally, the circulation of acquired resistant mechanisms in the aquatic habitats according to their genetic profiles was proved to be more extent. Hereby, we suggest that the combination of the DLST to oprD typing can discriminate phenotypically and genetically related environmental P. aeruginosa isolates providing reliable phylogenetic analysis at a local level.

Personality correlates of the Five-Factor Model for a sample of business owners/managers: associations with scores on Self-Monitoring, Type A Behavior, Locus of Control, and Subjective Well-being.

PubMed

Morrison, K A

1997-02-01

Bivariate relationships were examined between scores on the Five-Factor Model of personality and four personality dimensions including Self-monitoring, Locus of Control, Type A Behavior, and Subjective Well-being. Data were collected from 307 franchise business owner/managers from four different industries. Scores for Self-monitoring were positively related to those on Extraversion; Self-monitoring was the only personality measure significantly correlated with scores on Openness to Experience. Scores for Type A Behavior, measured by the Jenkins Activity Survey, were negatively correlated with Agreeableness and positively correlated with those for Extraversion. Somewhat surprisingly, the score for Type A Behavior had a relatively low correlation with the score for Conscientiousness. Scores for Subjective Well-being and Locus of Control were most strongly correlated with the positive pole of Neuroticism (Emotional Stability), Conscientiousness, and Extraversion. Possible explanations for the observed relationships are discussed.

Molecular typing of Chinese Streptococcus pyogenes isolates.

PubMed

You, Yuanhai; Wang, Haibin; Bi, Zhenwang; Walker, Mark; Peng, Xianhui; Hu, Bin; Zhou, Haijian; Song, Yanyan; Tao, Xiaoxia; Kou, Zengqiang; Meng, Fanliang; Zhang, Menghan; Bi, Zhenqiang; Luo, Fengji; Zhang, Jianzhong

2015-06-01

Streptococcus pyogenes causes human infections ranging from mild pharyngitis and impetigo to serious diseases including necrotizing fasciitis and streptococcal toxic shock syndrome. The objective of this study was to compare molecular emm typing and pulsed field gel electrophoresis (PFGE) with multiple-locus variable-number tandem-repeat analysis (MLVA) for genotyping of Chinese S. pyogenes isolates. Molecular emm typing and PFGE were performed using standard protocols. Seven variable number tandem repeat (VNTR) loci reported in a previous study were used to genotype 169 S. pyogenes geographically-diverse isolates from China isolated from a variety of disease syndromes. Multiple-locus variable-number tandem-repeat analysis provided greater discrimination between isolates when compared to emm typing and PFGE. Removal of a single VNTR locus (Spy2) reduced the sensitivity by only 0.7%, which suggests that Spy2 was not informative for the isolates screened. The results presented support the use of MLVA as a powerful epidemiological tool for genotyping S. pyogenes clinical isolates. Copyright © 2015 Elsevier Ltd. All rights reserved.

Leaf litter decomposition rates increase with rising mean annual temperature in Hawaiian tropical montane wet forests

PubMed Central

Bothwell, Lori D.; Giardina, Christian P.; Litton, Creighton M.

2014-01-01

Decomposing litter in forest ecosystems supplies nutrients to plants, carbon to heterotrophic soil microorganisms and is a large source of CO2 to the atmosphere. Despite its essential role in carbon and nutrient cycling, the temperature sensitivity of leaf litter decay in tropical forest ecosystems remains poorly resolved, especially in tropical montane wet forests where the warming trend may be amplified compared to tropical wet forests at lower elevations. We quantified leaf litter decomposition rates along a highly constrained 5.2 °C mean annual temperature (MAT) gradient in tropical montane wet forests on the Island of Hawaii. Dominant vegetation, substrate type and age, soil moisture, and disturbance history are all nearly constant across this gradient, allowing us to isolate the effect of rising MAT on leaf litter decomposition and nutrient release. Leaf litter decomposition rates were a positive linear function of MAT, causing the residence time of leaf litter on the forest floor to decline by ∼31 days for each 1 °C increase in MAT. Our estimate of the Q10 temperature coefficient for leaf litter decomposition was 2.17, within the commonly reported range for heterotrophic organic matter decomposition (1.5–2.5) across a broad range of ecosystems. The percentage of leaf litter nitrogen (N) remaining after six months declined linearly with increasing MAT from ∼88% of initial N at the coolest site to ∼74% at the warmest site. The lack of net N immobilization during all three litter collection periods at all MAT plots indicates that N was not limiting to leaf litter decomposition, regardless of temperature. These results suggest that leaf litter decay in tropical montane wet forests may be more sensitive to rising MAT than in tropical lowland wet forests, and that increased rates of N release from decomposing litter could delay or prevent progressive N limitation to net primary productivity with climate warming. PMID:25493213

Proposal of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat Loci for Subtyping of Mycobacterium tuberculosis Beijing Isolates

PubMed Central

Allix-Béguec, Caroline; Wahl, Céline; Hanekom, Madeleine; Nikolayevskyy, Vladyslav; Drobniewski, Francis; Maeda, Shinji; Campos-Herrero, Isolina; Mokrousov, Igor; Niemann, Stefan; Kontsevaya, Irina; Rastogi, Nalin; Samper, Sofia; Sng, Li-Hwei; Warren, Robin M.

2014-01-01

Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multidrug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing lacks resolution power for accurately discriminating closely related clones that often compose Beijing strain populations. Therefore, we evaluated a set of 7 additional, hypervariable MIRU-VNTR loci for better resolution and tracing of such strains, using a collection of 535 Beijing isolates from six world regions where these strains are known to be prevalent. The typeability and interlaboratory reproducibility of these hypervariable loci were lower than those of the 24 standard loci. Three loci (2163a, 3155, and 3336) were excluded because of their redundant variability and/or more frequent noninterpretable results compared to the 4 other markers. The use of the remaining 4-locus set (1982, 3232, 3820, and 4120) increased the number of types by 52% (from 223 to 340) and reduced the clustering rate from 58.3 to 36.6%, when combined with the use of the standard 24-locus set. Known major clonal complexes/24-locus-based clusters were all subdivided, although the degree of subdivision varied depending on the complex. Only five single-locus variations were detected among the hypervariable loci of an additional panel of 92 isolates, representing 15 years of clonal spread of a single Beijing strain in a geographically restricted setting. On this calibrated basis, we propose this 4-locus set as a consensus for subtyping Beijing clonal complexes and clusters, after standard typing. PMID:24172154

Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat loci for subtyping of Mycobacterium tuberculosis Beijing isolates.

PubMed

Allix-Béguec, Caroline; Wahl, Céline; Hanekom, Madeleine; Nikolayevskyy, Vladyslav; Drobniewski, Francis; Maeda, Shinji; Campos-Herrero, Isolina; Mokrousov, Igor; Niemann, Stefan; Kontsevaya, Irina; Rastogi, Nalin; Samper, Sofia; Sng, Li-Hwei; Warren, Robin M; Supply, Philip

2014-01-01

Mycobacterium tuberculosis Beijing strains represent targets of special importance for molecular surveillance of tuberculosis (TB), especially because they are associated with spread of multidrug resistance in some world regions. Standard 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing lacks resolution power for accurately discriminating closely related clones that often compose Beijing strain populations. Therefore, we evaluated a set of 7 additional, hypervariable MIRU-VNTR loci for better resolution and tracing of such strains, using a collection of 535 Beijing isolates from six world regions where these strains are known to be prevalent. The typeability and interlaboratory reproducibility of these hypervariable loci were lower than those of the 24 standard loci. Three loci (2163a, 3155, and 3336) were excluded because of their redundant variability and/or more frequent noninterpretable results compared to the 4 other markers. The use of the remaining 4-locus set (1982, 3232, 3820, and 4120) increased the number of types by 52% (from 223 to 340) and reduced the clustering rate from 58.3 to 36.6%, when combined with the use of the standard 24-locus set. Known major clonal complexes/24-locus-based clusters were all subdivided, although the degree of subdivision varied depending on the complex. Only five single-locus variations were detected among the hypervariable loci of an additional panel of 92 isolates, representing 15 years of clonal spread of a single Beijing strain in a geographically restricted setting. On this calibrated basis, we propose this 4-locus set as a consensus for subtyping Beijing clonal complexes and clusters, after standard typing.

Heterogeneity analysis in 40 X-linked retinitis pigmentosa families

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

Teague, P.W.; Aldred, M.A.; Dempster, M.

1994-07-01

Analysis of genetic heterogeneity in 40 kindreds with X-linked retinitis pigmentosa (XLRP), with 20 polymorphic markers, showed that significant heterogeneity is present (P=.001) and that 56% of kindreds are of RP3 type and that 26% are of RP2 type. The location of the RP3 locus was found to be 0.4 cM distal to OTC in the Xp21.1 region, and that of the RP2 locus was 6.5 cM proximal to DXS7 in Xp11.2-p11.3. Bayesian probabilities of linkage to RP2, RP3, or to neither locus were calculated. This showed that 20 of 40 kindreds could be assigned to one or the othermore » locus, with a probability >.70 (14 kindreds with RP3 and 6 kindreds with RP2 disease). A further three kindreds were found to be unlinked to either locus, with a probability >.8. The remaining 17 kindreds could not be classified unambiguously. This highlights the difficulty of classifying families in the presence of genetic heterogeneity, where two loci are separated by an estimated 16 cM. 34 refs., 1 fig., 4 tabs.« less

Interaction between transposable phages: cip locus of prophage D3112, responsible for inhibition of integration and transposition of the related phage B39 of Pseudomonas aeruginosa

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

Gerasimov, V.A.; Yanenko, A.S.; Akhverdyan, V.Z.

1986-04-01

Bacteriophage D3112 forms two types of PA01 (D3112) lysogens: those that partially, or completely, limit the growth of the related heteroimmune phage B39. DNA/DNA hybridization has shown that the lysogens of the first type always contain one copy of prophage D3112 (monolysogens), and the lysogens of the second type contain two or more copies of prophage D3112. Limitation of the growth of phage B39 on PA01 (D3112) lysogens is associated with the functioning of the locus of prophage D3112, designated as cip (control of interaction of phages). Using deletion derivatives of plasmid RP4::D3112, the cip locus was mapped at anmore » interval of 1.3-2.45 kb of the D3112 genome. The expression of the cip locus occurs only if the D3112 genome is at the prophage state. The function of the Cip prophage of D3112 exerts an influence on early stages of development of phage B39, decreasing the efficiency of the integration and transposition processes of phage B39.« less

Microbialite Biosignature Analysis by Mesoscale X-ray Fluorescence (μXRF) Mapping

NASA Astrophysics Data System (ADS)

Tice, Michael M.; Quezergue, Kimbra; Pope, Michael C.

2017-11-01

As part of its biosignature detection package, the Mars 2020 rover will carry PIXL, the Planetary Instrument for X-ray Lithochemistry, a spatially resolved X-ray fluorescence (μXRF) spectrometer. Understanding the types of biosignatures detectable by μXRF and the rock types μXRF is most effective at analyzing is therefore an important goal in preparation for in situ Mars 2020 science and sample selection. We tested mesoscale chemical mapping for biosignature interpretation in microbialites. In particular, we used μXRF to identify spatial distributions and associations between various elements ("fluorescence microfacies") to infer the physical, biological, and chemical processes that produced the observed compositional distributions. As a test case, elemental distributions from μXRF scans of stromatolites from the Mesoarchean Nsuze Group (2.98 Ga) were analyzed. We included five fluorescence microfacies: laminated dolostone, laminated chert, clotted dolostone and chert, stromatolite clast breccia, and cavity fill. Laminated dolostone was formed primarily by microbial mats that trapped and bound loose sediment and likely precipitated carbonate mud at a shallow depth below the mat surface. Laminated chert was produced by the secondary silicification of microbial mats. Clotted dolostone and chert grew as cauliform, cryptically laminated mounds similar to younger thrombolites and was likely formed by a combination of mat growth and patchy precipitation of early-formed carbonate. Stromatolite clast breccias formed as lag deposits filling erosional scours and interstromatolite spaces. Cavities were filled by microquartz, Mn-rich dolomite, and partially dolomitized calcite. Overall, we concluded that μXRF is effective for inferring genetic processes and identifying biosignatures in compositionally heterogeneous rocks.

On the Effects of the Evolution of Microbial Mats and Land Plants on the Earth as a Planet. Photometric and Spectroscopic Light Curves of Paleo-Earths

NASA Astrophysics Data System (ADS)

Sanromá, E.; Pallé, E.; García Munõz, A.

2013-04-01

Understanding the spectral and photometric variability of the Earth and the rest of the solar system planets has become of utmost importance for the future characterization of rocky exoplanets. As this is not only interesting at present times but also along the planetary evolution, we studied the effect that the evolution of microbial mats and plants over land has had on the way our planet looks from afar. As life evolved, continental surfaces changed gradually and non-uniformly from deserts through microbial mats to land plants, modifying the reflective properties of the ground and most likely the distribution of moisture and cloudiness. Here, we used a radiative transfer model of the Earth, together with geological paleo-records of the continental distribution and a reconstructed cloud distribution, to simulate the visible and near-IR radiation reflected by our planet as a function of Earth's rotation. We found that the evolution from deserts to microbial mats and to land plants produces detectable changes in the globally averaged Earth's reflectance. The variability of each surface type is located in different bands and can induce reflectance changes of up to 40% in period of hours. We conclude that by using photometric observations of an Earth-like planet at different photometric bands it would be possible to discriminate between different surface types. While recent literature proposes the red-edge feature of vegetation near 0.7 μm as a signature for land plants, observations in near-IR bands can be equally or even better suited for this purpose.

Clostridium botulinum type E occurs and grows in the alga Cladophora glomerata

USGS Publications Warehouse

Byappanahalli, M.N.; Whitman, R.L.

2009-01-01

In recent years, massive avian die-offs from Clostridium botulinum type E infection have occurred in the Sleeping Bear Dunes National Lakeshore (SLBE) area of Lake Michigan. These outbreaks have been coincidental with massive blooms of the green algae Cladophora, mostly Cladophora glomerata. We tested the hypothesis that Clostridium botulinum type E can grow under suitable conditions in these algal mats. In a lab mesocosm study, Cladophora from four outbreak-impacted beaches from SLBE were compared with four unimpacted beaches in the Milwaukee–Racine area for bontE gene of Clostridium botulinum. Frequency of the bontE gene was higher after incubation (25 °C for up to 6 weeks) of Cladophora from impacted vs. the unimpacted area. Since no type E gene was detected initially in Cladophora from any of the eight locations, we infer that the increased occurrence of type E gene arose from spore germination or vegetative Clostridium growth within the existing algal mats of SLBE. Moreover, we found that the congener Clostridium perfringens readily grows in mesocosms containing Cladophora.

Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools.

PubMed

Koo, Hyunmin; Hakim, Joseph A; Fisher, Phillip R E; Grueneberg, Alexander; Andersen, Dale T; Bej, Asim K

2016-01-01

In this study, we report the distribution and abundance of cold-adaptation proteins in microbial mat communities in the perennially ice-covered Lake Joyce, located in the McMurdo Dry Valleys, Antarctica. We have used MG-RAST and R code bioinformatics tools on Illumina HiSeq2000 shotgun metagenomic data and compared the filtering efficacy of these two methods on cold-adaptation proteins. Overall, the abundance of cold-shock DEAD-box protein A (CSDA), antifreeze proteins (AFPs), fatty acid desaturase (FAD), trehalose synthase (TS), and cold-shock family of proteins (CSPs) were present in all mat samples at high, moderate, or low levels, whereas the ice nucleation protein (INP) was present only in the ice and bulbous mat samples at insignificant levels. Considering the near homogeneous temperature profile of Lake Joyce (0.08-0.29 °C), the distribution and abundance of these proteins across various mat samples predictively correlated with known functional attributes necessary for microbial communities to thrive in this ecosystem. The comparison of the MG-RAST and the R code methods showed dissimilar occurrences of the cold-adaptation protein sequences, though with insignificant ANOSIM (R = 0.357; p-value = 0.012), ADONIS (R(2) = 0.274; p-value = 0.03) and STAMP (p-values = 0.521-0.984) statistical analyses. Furthermore, filtering targeted sequences using the R code accounted for taxonomic groups by avoiding sequence redundancies, whereas the MG-RAST provided total counts resulting in a higher sequence output. The results from this study revealed for the first time the distribution of cold-adaptation proteins in six different types of microbial mats in Lake Joyce, while suggesting a simpler and more manageable user-defined method of R code, as compared to a web-based MG-RAST pipeline.

Generation of selectable marker-free transgenic eggplant resistant to Alternaria solani using the R/RS site-specific recombination system.

PubMed

Darwish, Nader Ahmed; Khan, Raham Sher; Ntui, Valentine Otang; Nakamura, Ikuo; Mii, Masahiro

2014-03-01

Marker-free transgenic eggplants, exhibiting enhanced resistance to Alternaria solani , can be generated on plant growth regulators (PGRs)- and antibiotic-free MS medium employing the multi-auto-transformation (MAT) vector, pMAT21 - wasabi defensin , wherein isopentenyl transferase ( ipt ) gene is used as a positive selection marker. Use of the selection marker genes conferring antibiotic or herbicide resistance in transgenic plants has been considered a serious problem for environment and the public. Multi-auto-transformation (MAT) vector system has been one of the tools to excise the selection marker gene and produce marker-free transgenic plants. Ipt gene was used as a selection marker gene. Wasabi defensin gene, isolated from Wasabia japonica (a Japanese horseradish which has been a potential source of antimicrobial proteins), was used as a gene of interest. Wasabi defensin gene was cloned from the binary vector, pEKH-WD, to an ipt-type MAT vector, pMAT21, by gateway cloning technology and transferred to Agrobacterium tumefaciens strain EHA105. Infected cotyledon explants of eggplant were cultured on PGRs- and antibiotic-free MS medium. Extreme shooty phenotype/ipt shoots were produced by the explants infected with the pMAT21-wasabi defensin (WD). The same PGRs- and antibiotic-free MS medium was used in subcultures of the ipt shoots. Subsequently, morphologically normal shoots emerged from the Ipt shoots. Molecular analyses of genomic DNA from transgenic plants confirmed the integration of the WD gene and excision of the selection marker (ipt gene). Expression of the WD gene was confirmed by RT-PCR and Northern blot analyses. In vitro whole plant and detached leaf assay of the marker-free transgenic plants exhibited enhanced resistance against Alternaria solani.

Evolution of the Bipolar Mating System of the Mushroom Coprinellus disseminatus From Its Tetrapolar Ancestors Involves Loss of Mating-Type-Specific Pheromone Receptor Function

PubMed Central

James, Timothy Y.; Srivilai, Prayook; Kües, Ursula; Vilgalys, Rytas

2006-01-01

Mating incompatibility in mushroom fungi is controlled by the mating-type loci. In tetrapolar species, two unlinked mating-type loci exist (A and B), whereas in bipolar species there is only one locus. The A and B mating-type loci encode homeodomain transcription factors and pheromones and pheromone receptors, respectively. Most mushroom species have a tetrapolar mating system, but numerous transitions to bipolar mating systems have occurred. Here we determined the genes controlling mating type in the bipolar mushroom Coprinellus disseminatus. Through positional cloning and degenerate PCR, we sequenced both the transcription factor and pheromone receptor mating-type gene homologs from C. disseminatus. Only the transcription factor genes segregate with mating type, discounting the hypothesis of genetic linkage between the A and B mating-type loci as the causal origin of bipolar mating behavior. The mating-type locus of C. disseminatus is similar to the A mating-type locus of the model species Coprinopsis cinerea and encodes two tightly linked pairs of homeodomain transcription factor genes. When transformed into C. cinerea, the C. disseminatus A and B homologs elicited sexual reactions like native mating-type genes. Although mating type in C. disseminatus is controlled by only the transcription factor genes, cellular functions appear to be conserved for both groups of genes. PMID:16461425

The motor locus of no-go backward crosstalk.

PubMed

Durst, Moritz; Janczyk, Markus

2018-04-23

A frequent observation in dual-task studies is the backward crosstalk effect (BCE), meaning that aspects of a secondary Task 2 influence Task 1 performance. Up to this point, 2 major types of the BCE were investigated: a BCE based on dimensional overlap between both stimuli and/or responses (the compatibility-based BCE), and a BCE based on whether Task 2 is a go or no-go task (the no-go BCE). Recent evidence suggests that the compatibility-based BCE has its locus inside the response selection stage. The available evidence for the locus of the no-go BCE is still mixed, however. To this end, the 3 experiments reported in the present study used an extended psychological refractory period (PRP) paradigm with 3 subsequent tasks. Applying the locus of slack logic in Experiment 1, the no-go BCE was not absorbed into the cognitive slack and, thus, a locus before response selection could be ruled out. Subsequently applying the effect propagation logic in Experiment 2 and 3, the no-go BCE arising in Task 1 was even inverted in Task 3. Because no propagation of the no-go BCE was observed, a locus before or in response selection could be ruled out. Thus, we conclude that the no-go BCE has its locus during motor execution. Because the no-go BCE and the compatibility-based BCE are located in different stages, we suggest that both types of the BCE do not share a common underlying mechanism. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Iron microbial mats in modern and phanerozoic environments

NASA Astrophysics Data System (ADS)

Baele, Jean-Marc; Bouvain, Frédéric; De Jong, Jeroen; Matielli, Nadine; Papier, Séverine; Préat, Alain

2008-08-01

The recognition of iron microbial mats in terrestrial environments is of great relevance for the search for extraterrestrial life, especially on mars where significant iron minerals were identified in the subsurface. Most researches focused on very ancient microbial mats (e.g. BIFs) since they formed on Earth at a time where similar conditions are supposed to have prevailed on Mars too. However, environmental proxies are often difficult to use for these deposits on Earth which, in addition, may be heavily transformed due to diagenesis or even metamorphism. Here we present modern and phanerozoic iron microbial mats occurrences illustrating the wide variety of environments in which they form, including many marine settings, ponds, creeks, caves, volcanoes, etc. Contrarily to their Precambrian counterparts, Modern and Phanerozoic deposits are usually less affected by diagenesis and the environmental conditions likely to be better constrained. Therefore, their investigation may help for the search for morphological and geochemical biosignatures (e.g. iron isotopes) in ancient iron microbial occurrences on Earth but also on other Planets. In particular, many of the case studies presented here show that microstromatolithe-like morphologies may be valuable targets for screening potential biosignatures in various rock types.

Regulation of electron transfer processes affects phototrophic mat structure and activity

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

Ha, Phuc T.; Renslow, Ryan S.; Atci, Erhan

Phototrophic microbial mats are among the most diverse ecosystems in nature. These systems undergo daily cycles in redox potential caused by variations in light energy input and metabolic interactions among the microbial species. In this work, solid electrodes with controlled potentials were placed under mats to study the electron transfer processes between the electrode and the microbial mat. The phototrophic microbial mat was harvested from Hot Lake, a hypersaline, epsomitic lake located near Oroville (Washington, USA). We operated two reactors: graphite electrodes were polarized at potentials of -700 mV Ag/AgCl [cathodic (CAT) mat system] and +300 mV Ag/AgCl [anodic (AN)more » mat system] and the electron transfer rates between the electrode and mat were monitored. We observed a diel cycle of electron transfer rates for both AN and CAT mat systems. Interestingly, the CAT mats generated the highest reducing current at the same time points that the AN mats showed the highest oxidizing current. To characterize the physicochemical factors influencing electron transfer processes, we measured depth profiles of dissolved oxygen (DO) and sulfide in the mats using microelectrodes. We further demonstrated that the mat-to-electrode and electrode-to-mat electron transfer rates were light- and temperature-dependent. Using nuclear magnetic resonance (NMR) imaging, we determined that the electrode potential regulated the diffusivity and porosity of the microbial mats. Both porosity and diffusivity were higher in the CAT mats than in the AN mats. We also used NMR spectroscopy for high-resolution quantitative metabolite analysis and found that the CAT mats had significantly higher concentrations of osmoprotectants such as betaine and trehalose. Subsequently, we performed amplicon sequencing across the V4 region of the 16S rRNA gene of incubated mats to understand the impact of electrode potential on microbial community structure. In conclusion, these data suggested that variation in the electrochemical conditions under which mats were generated significantly impacted the relative abundances of mat members and mat metabolism.« less

Regulation of electron transfer processes affects phototrophic mat structure and activity

DOE PAGES

Ha, Phuc T.; Renslow, Ryan S.; Atci, Erhan; ...

2015-09-03

Phototrophic microbial mats are among the most diverse ecosystems in nature. These systems undergo daily cycles in redox potential caused by variations in light energy input and metabolic interactions among the microbial species. In this work, solid electrodes with controlled potentials were placed under mats to study the electron transfer processes between the electrode and the microbial mat. The phototrophic microbial mat was harvested from Hot Lake, a hypersaline, epsomitic lake located near Oroville (Washington, USA). We operated two reactors: graphite electrodes were polarized at potentials of -700 mV Ag/AgCl [cathodic (CAT) mat system] and +300 mV Ag/AgCl [anodic (AN)more » mat system] and the electron transfer rates between the electrode and mat were monitored. We observed a diel cycle of electron transfer rates for both AN and CAT mat systems. Interestingly, the CAT mats generated the highest reducing current at the same time points that the AN mats showed the highest oxidizing current. To characterize the physicochemical factors influencing electron transfer processes, we measured depth profiles of dissolved oxygen (DO) and sulfide in the mats using microelectrodes. We further demonstrated that the mat-to-electrode and electrode-to-mat electron transfer rates were light- and temperature-dependent. Using nuclear magnetic resonance (NMR) imaging, we determined that the electrode potential regulated the diffusivity and porosity of the microbial mats. Both porosity and diffusivity were higher in the CAT mats than in the AN mats. We also used NMR spectroscopy for high-resolution quantitative metabolite analysis and found that the CAT mats had significantly higher concentrations of osmoprotectants such as betaine and trehalose. Subsequently, we performed amplicon sequencing across the V4 region of the 16S rRNA gene of incubated mats to understand the impact of electrode potential on microbial community structure. In conclusion, these data suggested that variation in the electrochemical conditions under which mats were generated significantly impacted the relative abundances of mat members and mat metabolism.« less

Fraud, Ethics, and the Disciplinary Contexts of Science and Scholarship.

ERIC Educational Resources Information Center

Fox, Mary Frank

1990-01-01

Posits the disciplinary context is the locus of legitimate and illegitimate activity in science and scholarship. Compares structural features of sciences and social sciences that influence malpractice rates, type, and detection. These features include research activity, replication and replicability, coauthorship, plagiarism, locus of creativity…

High prevalence and genotypes of Toxoplasma gondii isolated from organic pigs in northern USA.

PubMed

Dubey, J P; Hill, D E; Rozeboom, D W; Rajendran, C; Choudhary, S; Ferreira, L R; Kwok, O C H; Su, C

2012-08-13

The ingestion of undercooked pork infected with Toxoplasma gondii is considered an important source of transmission of this parasite. While T. gondii infection in confinement raised market pigs (market pigs are typically used for fresh, unprocessed pork products) in the USA has decreased significantly over the last 20 years, infection levels in pigs with access to the outdoors can be quite high. An upsurge in consumer demand for 'organically raised', 'humanely raised' and 'free range' pork products has resulted in increasing numbers of hogs being raised in non-confinement systems. To determine T. gondii infection rate in these organic pigs, prevalence of T. gondii in organically raised pigs in two establishments (Farm 1, Farm 2) in Michigan was investigated. Serum and tissue samples from 33 pigs on the farm were available for T. gondii evaluation at slaughter. Serological testing was performed using both ELISA and the modified agglutination test (MAT). Antibodies to T. gondii were detected by both ELISA and MAT in 30 of 33 animals with MAT titers of 1:25 in three, 1:50 in six, 1:100 in seven, 1:200 in 13, and 1:400 in one. Hearts of all 33 pigs were bioassayed for T. gondii in mice; T. gondii was isolated from 17 pigs including one from a seronegative (both ELISA and MAT) pig. Genetic typing of 16 of the 17 T. gondii isolates using the SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico loci revealed clonal Type II from Farm 1 and clonal Type III on Farm 2. These results revealed very high prevalence of T. gondii in organic pigs for the first time in USA, indicating potentially increased health risk of consuming organic swine products. Published by Elsevier B.V.

Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments.

PubMed

Vaishampayan, Parag; Moissl-Eichinger, Christine; Pukall, Rüdiger; Schumann, Peter; Spröer, Cathrin; Augustus, Angela; Roberts, Anne Hayden; Namba, Greg; Cisneros, Jessica; Salmassi, Tina; Venkateswaran, Kasthuri

2013-07-01

Two strains of aerobic, non-motile, Gram-reaction-positive cocci were independently isolated from geographically distinct spacecraft assembly clean room facilities (Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana). A polyphasic study was carried out to delineate the taxonomic identity of these two isolates (1P05MA(T) and KO_PS43). The 16S rRNA gene sequences exhibited a high similarity when compared to each other (100 %) and lower than 96.7 % relatedness with Arthrobacter crystallopoietes ATCC 15481(T), Arthrobacter luteolus ATCC BAA-272(T), Arthrobacter tumbae DSM 16406(T) and Arthrobacter subterraneus DSM 17585(T). In contrast with previously described Arthrobacter species, the novel isolates maintained their coccidal morphology throughout their growth and did not exhibit the rod-coccus life cycle typically observed in nearly all Arthrobacter species, except A. agilis. The distinct taxonomic identity of the novel isolates was confirmed based on their unique cell-wall peptidoglycan type (A.11.20; Lys-Ser-Ala2) and polar lipid profile (presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and two unknown glycolipids). The G+C content of the genomic DNA was 70.6 mol%. The novel strains revealed MK-9(H2) and MK-8(H2) as dominant menaquinones and exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and moderate amounts of iso-C15 : 0 discriminating them again from closely related Arthrobacter species. Based on these observations, the authors propose that strains 1P05MA(T) and KO_PS43 be assigned into a separate genus Tersicoccus gen. nov. For this new taxon, comprising strains 1P05MA(T) and KO_PS43, we propose the name Tersicoccus phoenicis gen. nov., sp. nov. (the type species of Tersicoccus), represented by the type strain Tersicoccus phoenicis 1P05MA(T) ( = NRRL B-59547(T) = DSM 30849(T)).

Identification of a novel locus for a USH3 like syndrome combined with congenital cataract.

PubMed

Dad, S; Østergaard, E; Thykjaer, T; Albrectsen, A; Ravn, K; Rosenberg, T; Møller, L B

2010-10-01

Usher syndrome (USH) is the most common genetic disease that causes both deafness and blindness. USH is divided into three types, USH1, USH2 and USH3, depending on the age of onset, the course of the disease, and on the degree of vestibular dysfunction. By homozygosity mapping of a consanguineous Danish family of Dutch descent, we have identified a novel locus for a rare USH3-like syndrome. The affected family members have a unique association of retinitis pigmentosa, progressive hearing impairment, vestibular dysfunction, and congenital cataract. The phenotype is similar, but not identical to that of USH3 patients, as congenital cataract has not been reported for USH3. By homozygosity mapping, we identified a 7.3 Mb locus on chromosome 15q22.2-23 with a maximum multipoint LOD score of 2.0. The locus partially overlaps with the USH1 locus, USH1H, a novel unnamed USH2 locus, and the non-syndromic deafness locus DFNB48. © 2010 John Wiley & Sons A/S.

Pressure load on specific body areas of gestating sows lying on rubber mats with different softness.

PubMed

Schubbert, A; Hartung, E; Schrader, L

2014-08-01

Rubber mats offer a possibility to increase lying comfort for sows with positive effects on sow lying behavior and health. However, until now, no information has been reported about the relationship between the softness of rubber mats and the pressure load on certain body areas of sows. We used a total of 68 (40 multiparous, 28 primiparous) German Landrace × German Landrace sows with a BW within the range of 90 to 330 kg (divided in 3 weight classes) to measure peak force and distribution of pressure during lying in the sternal and half recumbent position. Measures were done in an experimental pen that was equipped with a pressure sensor map system (5400 NTL; Tekscan Inc., Boston, MA). Three rubber mats differing in softness (penetration depth: hard mat, 4.0 mm [HM]; soft mat, 14.6 mm [SM]; very soft mat, 43.0 mm [VSM]) were tested and compared to concrete floor (CF) as a reference. Pressure load was analyzed in the sternal position for the sternum, belly, and ham body regions and also in the half recumbent position for the shoulder. For each lying position we determined the body region with the highest pressure load and analyzed the peak force (PF) and the contact area (CA) using a mixed model ANOVA (MIXED procedure of SAS Enterprise, version 4.3., SAS Inst. Inc., Cary, NC) with floor type, weight class of sows, and their interaction as fixed factors. Overall, the highest values for PF in the sternal position were found on the sternum (median: 1.62 N/cm(2)) and in the half recumbent position on the shoulder (median: 2.72 N/cm(2)). In the sternal position PF on the sternum was lower on VSM compared to CF (P = 0.001). In the half-recumbent position PF on the shoulder was lower on VSM compared to CF (P = 0.013) and compared to HM (P = 0.011). The weight of the sows affected PF on the sternum in the sternal position, with lower values in weight class 1 compared to weight class 2 (P = 0.001) and weight class 3 (P = 0.002). Contact area under the sternum was larger on SM (P = 0.016) and VSM (P = 0.008) compared to CF in the sternal position, and this was affected by weight class (P = 0.0002). In the half-recumbent position floor type did not affect CA under the shoulder, but CA was larger in weight classes 2 and 3 compared to weight class 1 (all P < 0.05). Assuming that a reduced PF in combination with pressure distributed over a larger area will increase lying comfort, hard rubber mats do not seem to offer a high lying comfort with regard to pressure load on debited body regions such as the sternum or shoulder.

Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco

PubMed Central

Bouklata, Nada; Supply, Philip; Jaouhari, Sanae; Charof, Reda; Seghrouchni, Fouad; Sadki, Khalid; El Achhab, Youness; Nejjari, Chakib; Filali-Maltouf, Abdelkarim

2015-01-01

Background Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community. Methodology During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTRplus database. Principal Findings Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6). Conclusions 24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context. PMID:26285026

Financial factors and the implementation of medications for treating opioid use disorders.

PubMed

Knudsen, Hannah K; Roman, Paul M

2012-12-01

Despite the established effectiveness of pharmacotherapies for treating opioid use disorders, implementation of medications for addiction treatment (MAT) by specialty treatment programs is limited. This research examined relationships between organizational factors and the program-level implementation of MAT, with attention paid to specific sources of funding, organizational structure, and workforce resources. Face-to-face structured interviews were conducted in 2008 to 2009 with administrators of 154 community-based treatment programs affiliated with the National Institute on Drug Abuse's Clinical Trials Network; none of these programs exclusively dispensed methadone without offering other levels of care. Implementation of MAT was measured by summing the percentages of opioid patients receiving buprenorphine maintenance, methadone maintenance, and tablet naltrexone. Financial factors included the percentages of revenues received from Medicaid, private insurance, criminal justice, the Federal block grant, state government, and county government. Organizational structure and workforce characteristics were also measured. Implementation of MAT for opioid use disorders was low. Greater reliance on Medicaid was positively associated with implementation after controlling for organizational structure and workforce measures, whereas the association for reliance on criminal justice revenues was negative. The implementation of MAT for opioid use disorders by specialty addiction treatment programs may be facilitated by Medicaid but may be impeded by reliance on funding from the criminal justice system. These findings point to the need for additional research that considers the impact of organizational dependence on different types of funding on patterns of addiction treatment practice.

Effects of Mat Pilates training and habitual physical activity on thoracoabdominal expansion during quiet and vital capacity breathing in healthy women.

PubMed

Campos, Jeniffer L; Vancini, Rodrigo L; Zanoni, Graziely R; Barbosa DE Lira, Claudio A; Santos Andrade, Marilia; Sarro, Karine J

2017-10-27

Pilates is a body/mind method that requires different types of exercise (balance, endurance, strength, and flexibility) and attention to muscle control, posture, and breathing. The aim of the present study was to investigate the effects of 12 weeks of Mat Pilates training and habitual physical activity on thoracoabdominal motion of healthy and physically active women. Thirty-five women without experience in Pilates exercise, aged between 18 and 35 years, participated in the study (habitual physical activity group, n=14; and Mat Pilates group, n=21). Three- dimensional kinematic analysis was used to evaluate total and separate thoracoabdominal compartments' expansion (superior and inferior thorax and abdomen), contribution of each compartment to total thoracoabdominal expansion, and coordination between thoracoabdominal compartments. After 12 weeks of Mat Pilates training, thoracoabdominal expansion during quiet breathing was improved by increasing the expansion of abdomen by about 33% (P=0.01). Moreover, expansion of superior (P=0.04) and inferior thorax (P=0.02) and abdomen (P=0.01) was also improved in Pilates (35%, 33% and 37%, respectively) compared to the habitual physical activity group, after the experimental protocol. Finally, the habitual physical activity group presented a decrease of 13% in the expansion of abdomen (P = 0.002). The results suggest the capability of Mat Pilates in improving the action of respiratory and abdominal muscles during breathing and, thus, its benefits to breathing mechanics.

The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

PubMed Central

Chan, Clara S.; McAllister, Sean M.; Leavitt, Anna H.; Glazer, Brian T.; Krepski, Sean T.; Emerson, David

2016-01-01

Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe oxidation, including (1) removing Fe oxyhydroxide waste without entombing cells or clogging flow paths through the mat and (2) colonizing niches where Fe(II) and O2 overlap. This work improves our understanding of Fe mat developmental history and how mat morphology links to metabolism. We can use these results to interpret biogenicity, metabolism, and paleoenvironmental conditions of Fe microfossil mats, which would give us insight into Earth's Fe and O2 history. PMID:27313567

Influence of board density, mat construction, and chip type on performance of particleboard made from eastern redcedar

Treesearch

Zhiyong Cai; Qinglin Wu; Jong N. Lee; Salim Hiziroglu

2004-01-01

The purpose of this study was to investigate mechanical and physical performances of particleboard made from low-value eastern redcedar trees. The properties evaluated included bending strength and stiffness, swelling, surface hardness, and screw holding capacity as a function of processing variables (i.e., density, chip type, and board construction). Two types of...

Pleiotropic effects of methionine adenosyltransferases deregulation as determinants of liver cancer progression and prognosis.

PubMed

Frau, Maddalena; Feo, Francesco; Pascale, Rosa M

2013-10-01

Downregulation of liver-specific MAT1A gene, encoding S-adenosylmethionine (SAM) synthesizing isozymes MATI/III, and upregulation of widely expressed MAT2A, encoding MATII isozyme, known as MAT1A:MAT2A switch, occurs in hepatocellular carcinoma (HCC). Being inhibited by its reaction product, MATII isoform upregulation cannot compensate for MATI/III decrease. Therefore, MAT1A:MAT2A switch contributes to decrease in SAM level in rodent and human hepatocarcinogenesis. SAM administration to carcinogen-treated rats prevents hepatocarcinogenesis, whereas MAT1A-KO mice, characterized by chronic SAM deficiency, exhibit macrovesicular steatosis, mononuclear cell infiltration in periportal areas, and HCC development. This review focuses upon the pleiotropic changes, induced by MAT1A/MAT2A switch, associated with HCC development. Epigenetic control of MATs expression occurs at transcriptional and post-transcriptional levels. In HCC cells, MAT1A/MAT2A switch is associated with global DNA hypomethylation, decrease in DNA repair, genomic instability, and signaling deregulation including c-MYC overexpression, rise in polyamine synthesis, upregulation of RAS/ERK, IKK/NF-kB, PI3K/AKT, and LKB1/AMPK axis. Furthermore, decrease in MAT1A expression and SAM levels results in increased HCC cell proliferation, cell survival, and microvascularization. All of these changes are reversed by SAM treatment in vivo or forced MAT1A overexpression or MAT2A inhibition in cultured HCC cells. In human HCC, MAT1A:MAT2A and MATI/III:MATII ratios correlate negatively with cell proliferation and genomic instability, and positively with apoptosis and global DNA methylation. This suggests that SAM decrease and MATs deregulation represent potential therapeutic targets for HCC. Finally, MATI/III:MATII ratio strongly predicts patients' survival length suggesting that MAT1A:MAT2A expression ratio is a putative prognostic marker for human HCC. Copyright © 2013 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Effect of HLA-C and DQ matching on Pediatric Heart Transplant Graft Survival

PubMed Central

Butts, Ryan J.; Savage, Andrew J.; Nietert, Paul J.; Kavarana, Minoo; Moussa, Omar; Burnette, Ali L.; Atz, Andrew M.

2014-01-01

Background Higher degree of HLA matching at the A, B, and DR-loci has been associated with improved long-term survival after pediatric heart transplantation in multiple ISHLT registry reports. The aim of this study was to investigate the association of HLA matching at the C and DQ loci with pediatric graft survival. Methods The UNOS database was queried for isolated heart transplants that occurred from 1988 to 2012 with a recipient age of 17 or less and at least one postoperative follow up encounter. When analyzing HLA matching at the C or DQ loci, only those transplants with complete typing of donor and recipient at the respective loci were included. Transplants were divided into patients with at least one match at the C-locus (C-match) versus no match (C-no), and at least one match at the DQ locus versus no match (DQ-match versus DQ-no). Primary outcome was graft loss. Univariate analysis was performed with log-rank test. Cox regression analysis was performed with following patient factors included in the model: recipient age, ischemic time; recipient on ventilator, ECMO, ventricular assist device or inotropes at transplant; recipient serum bilirubin and creatinine closest to transplant, donor-recipient weight ratio, underlying cardiac diagnosis, crossmatch results, transplant year, and HLA matching at the A, B, and DR loci. Results Complete typing at the C-locus occurred in 2429/4731 (51%) transplants and 3498/4731 (74%) transplants had complete typing at the DQ locus. C-match did not differ from C-no with respect to patient factors, except for year of transplant; [C-match median year 2007 (IQR 1997–2010) vs. C-no median year 2005 (IQR 1996–2009), p=0.03] and degree of HLA matching at A, B, and DR loci (11.9% of C-match with high level of HLA matching v. 3% of C-no, p<0.01). Matching at the C-locus was not associated with decreased risk of graft loss [C-no median graft survival 13.1 yrs (95%CI 11.5–14.8) vs. C-match 15.1 yrs (95%CI 13.5–16.6) p=0.44, log-rank, hazard ratio 0.93 (95%CI 0.76–1.15, p=0.52)]. DQ-match did not differ from DQ-no in any of the above-mentioned patient factors, except DQ-match was more likely to have high degree of matching at the A, B, and DR loci versus DQ-no (9.8% v. 3.2%, p<0.01). Matching at the DQ-locus was not associated with decreased risk of graft loss [DQ-no median graft survival 13.1yrs (95%CI 11.7–14.6) vs. DQ-match 13.0 yrs (11.4–14.6) p=0.80, log rank, hazard ratio 0.95 (0.81–1.1), p=0.51]. Conclusion Complete typing at the C-locus of both donor and recipient occurs less often then typing at the DQ locus. A higher degree of donor-recipient HLA matching at the C-locus or the DQ-locus appears not to confer any graft survival advantage. PMID:25128416

Effect of human leukocyte antigen-C and -DQ matching on pediatric heart transplant graft survival.

PubMed

Butts, Ryan J; Savage, Andrew J; Nietert, Paul J; Kavarana, Minoo; Moussa, Omar; Burnette, Ali L; Atz, Andrew M

2014-12-01

A higher degree of human leukocyte antigen (HLA) matching at the A, B, and DR loci has been associated with improved long-term survival after pediatric heart transplantation in multiple International Society for Heart and Lung Transplantation registry reports. The aim of this study was to investigate the association of HLA matching at the C and DQ loci with pediatric graft survival. The United Network of Organ Sharing database was queried for isolated heart transplants that occurred from 1988 to 2012 with a recipient age of 17 or younger and at least 1 postoperative follow-up encounter. When HLA matching at the C or DQ loci were analyzed, only transplants with complete typing of donor and recipient at the respective loci were included. Transplants were divided into patients with at least 1 match at the C locus (C-match) vs no match (C-no), and at least 1 match at the DQ (DQ-match) locus vs no match (DQ-no). Primary outcome was graft loss. Univariate analysis was performed with the log-rank test. Cox regression analysis was performed with the following patient factors included in the model: recipient age, ischemic time; recipient on ventilator, extracorporeal membrane oxygenation, ventricular assist device, or inotropes at transplant; recipient serum bilirubin and creatinine closest to transplant, ratio of donor weight to recipient weight, underlying cardiac diagnosis, crossmatch results, transplant year, and HLA matching at the A, B, and DR loci. Complete typing at the C locus occurred in 2,429 of 4,731 transplants (51%), and complete typing at the DQ locus occurred in 3,498 of 4,731 transplants (74%). Patient factors were similar in C-match and C-no, except for year of transplant (median year, 2007 [interquartile range, 1997-2010] vs year 2005 [interquartile range, 1996-2009], respectively; p = 0.03) and the degree of HLA matching at the A, B, and DR loci (high level of HLA matching in 11.9% vs 3%, respectively; p < 0.01). Matching at the C locus was not associated with a decreased risk of graft loss (median graft survival: 13.1 years [95% confidence interval {CI}, 11.5-14.8] in C-no vs 15.1 years [95% CI, 13.5-16.6) in C-match, p = 0.44 log-rank; hazard ratio, 0.93; 95% CI, 0.76-1.15; p = 0.52). DQ-match did not differ from DQ-no in any of the analyzed patient factors, except DQ-match was more likely to have high degree of matching at the A, B, and DR loci vs DQ-no (9.8% vs 3.2%, p < 0.01). Matching at the DQ locus was not associated with decreased risk of graft loss (median graft survival: DQ-no, 13.1 years [95% CI, 11.7-14.6) vs DQ-match, 13.0 years [95% CI, 11.4-14.6], p = 0.80, log-rank; hazard ratio, 0.95; 95% CI, 0.81-1.1; p = 0.51. Complete typing at the C locus of both donor and recipient occurs less often then typing at the DQ locus. A higher degree of donor-recipient HLA matching at the C locus or the DQ locus appears not to confer any graft survival advantage. Copyright © 2014 International Society for Heart and Lung Transplantation. Published by Elsevier Inc. All rights reserved.

Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A

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

Quinlan, Casey L.; Kaiser, Stephen E.; Bolaños, Ben

S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzymemore » turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.« less

Chemogenetic locus coeruleus activation restores reversal learning in a rat model of Alzheimer's disease.

PubMed

Rorabaugh, Jacki M; Chalermpalanupap, Termpanit; Botz-Zapp, Christian A; Fu, Vanessa M; Lembeck, Natalie A; Cohen, Robert M; Weinshenker, David

2017-11-01

See Grinberg and Heinsen (doi:10.1093/brain/awx261) for a scientific commentary on this article. Clinical evidence suggests that aberrant tau accumulation in the locus coeruleus and noradrenergic dysfunction may be a critical early step in Alzheimer’s disease progression. Yet, an accurate preclinical model of these phenotypes that includes early pretangle tau accrual in the locus coeruleus, loss of locus coeruleus innervation and deficits locus coeruleus/norepinephrine modulated behaviours, does not exist, hampering the identification of underlying mechanisms and the development of locus coeruleus-based therapies. Here, a transgenic rat (TgF344-AD) expressing disease-causing mutant amyloid precursor protein (APPsw) and presenilin-1 (PS1ΔE9) was characterized for histological and behavioural signs of locus coeruleus dysfunction reminiscent of mild cognitive impairment/early Alzheimer’s disease. In TgF344-AD rats, hyperphosphorylated tau was detected in the locus coeruleus prior to accrual in the medial entorhinal cortex or hippocampus, and tau pathology in the locus coeruleus was negatively correlated with noradrenergic innervation in the medial entorhinal cortex. Likewise, TgF344-AD rats displayed progressive loss of hippocampal norepinephrine levels and locus coeruleus fibres in the medial entorhinal cortex and dentate gyrus, with no frank noradrenergic cell body loss. Cultured mouse locus coeruleus neurons expressing hyperphosphorylation-prone mutant human tau had shorter neurites than control neurons, but similar cell viability, suggesting a causal link between pretangle tau accrual and altered locus coeruleus fibre morphology. TgF344-AD rats had impaired reversal learning in the Morris water maze compared to their wild-type littermates, which was rescued by chemogenetic locus coeruleus activation via designer receptors exclusively activated by designer drugs (DREADDs). Our results indicate that TgF344-AD rats uniquely meet several key criteria for a suitable model of locus coeruleus pathology and dysfunction early in Alzheimer’s disease progression, and suggest that a substantial window of opportunity for locus coeruleus/ norepinephrine-based therapeutics exists.

Polyamine and methionine adenosyltransferase 2A crosstalk in human colon and liver cancer

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

Tomasi, Maria Lauda; USC Research Center for Liver Diseases, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033; The Southern California Research Center for Alcoholic and Pancreatic Diseases and Cirrhosis, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033

Methionine adenosyltransferase (MAT) is an essential enzyme that is responsible for the biosynthesis of S-adenosylmethionine (SAMe), the principal methyl donor and precursor of polyamines. MAT1A is expressed in normal liver and MAT2A is expressed in all extrahepatic tissues. MAT2A expression is increased in human colon cancer and in colon cancer cells treated with mitogens, whereas silencing MAT2A resulted in apoptosis. The aim of the current work was to examine the mechanism responsible for MAT2A-dependent growth and apoptosis. We found that in RKO (human adenocarcinoma cell line) cells, MAT2A siRNA treatment lowered cellular SAMe and putrescine levels by 70–75%, increased apoptosismore » and inhibited growth. Putrescine supplementation blunted significantly MAT2A siRNA-induced apoptosis and growth suppression. Putrescine treatment (100 pmol/L) raised MAT2A mRNA level to 4.3-fold of control, increased the expression of c-Jun and c-Fos and binding to an AP-1 site in the human MAT2A promoter and the promoter activity. In human colon cancer specimens, the expression levels of MAT2A, ornithine decarboxylase (ODC), c-Jun and c-Fos are all elevated as compared to adjacent non-tumorous tissues. Overexpression of ODC in RKO cells also raised MAT2A mRNA level and MAT2A promoter activity. ODC and MAT2A are also overexpressed in liver cancer and consistently, similar MAT2A-ODC-putrescine interactions and effects on growth and apoptosis were observed in HepG2 cells. In conclusion, there is a crosstalk between polyamines and MAT2A. Increased MAT2A expression provides more SAMe for polyamines biosynthesis; increased polyamine (putrescine in this case) can activate MAT2A at the transcriptional level. This along with increased ODC expression in cancer all feed forward to further enhance the proliferative capacity of the cancer cell. -- Highlights: • MAT2A knockdown depletes putrescine and leads to apoptosis. • Putrescine attenuates MAT2A knockdown-induced apoptosis and growth suppression. • Putrescine induces AP-1, which activates MAT2A promoter to increase its expression. • Putrescine increases ornithine decarboxylase expression, which induce MAT2A promoter. • Expression of MAT2A correlates with that of ornithine decarboxylase in colon cancer.« less

Population-specific variation in haplotype composition and heterozygosity at the POLB locus.

PubMed

Yamtich, Jennifer; Speed, William C; Straka, Eva; Kidd, Judith R; Sweasy, Joann B; Kidd, Kenneth K

2009-05-01

DNA polymerase beta plays a central role in base excision repair (BER), which removes large numbers of endogenous DNA lesions from each cell on a daily basis. Little is currently known about germline polymorphisms within the POLB locus, making it difficult to study the association of variants at this locus with human diseases such as cancer. Yet, approximately thirty percent of human tumor types show variants of DNA polymerase beta. We have assessed the global frequency distributions of coding and common non-coding SNPs in and flanking the POLB gene for a total of 14 sites typed in approximately 2400 individuals from anthropologically defined human populations worldwide. We have found a marked difference between haplotype frequencies in African populations and in non-African populations.

Microbial Biosignatures in High Iron Thermal Springs

NASA Astrophysics Data System (ADS)

Parenteau, M. N.; Embaye, T.; Jahnke, L. L.; Cady, S. L.

2003-12-01

The emerging anoxic source waters at Chocolate Pots hot springs in Yellowstone National Park contain 2.6 to 11.2 mg/L Fe(II) and are 51-54° C and pH 5.5-6.0. These waters flow down the accumulating iron deposits and over three major phototrophic mat communities: Synechococcus/Chloroflexus at 51-54° C, Pseudanabaena at 51-54° C, and a narrow Oscillatoria at 36-45° C. We are assessing the contribution of the phototrophs to biosignature formation in this high iron system. These biosignatures can be used to assess the biological contribution to ancient iron deposits on Earth (e.g. Precambrian Banded Iron Formations) and, potentially, to those found on Mars. Most studies to date have focused on chemotrophic iron-oxidizing communities; however, recent research has demonstrated that phototrophs have a significant physiological impact on these iron thermal springs (Pierson et al. 1999, Pierson and Parenteau 2000, and Trouwborst et al., 2003). We completed a survey of the microfossils, biominerals, biofabrics, and lipid biomarkers in the phototrophic mats and stromatolitic iron deposits using scanning and transmission electron microscopy (SEM and TEM), energy dispersive spectrometry (EDS), powder X-ray diffraction (XRD), and gas chromatography-mass spectroscopy (GC-MS). The Synechococcus/Chloroflexus mat was heavily encrusted with iron silicates while the narrow Oscillatoria mat was encrusted primarily with iron oxides. Encrustation of the cells increased with depth in the mats. Amorphous 2-line ferrihydrite is the primary precipitate in the spring and the only iron oxide mineral associated with the mats. Goethite, hematite, and siderite were detected in dry sediment samples on the face of the main iron deposit. Analysis of polar lipid fatty acid methyl esters (FAME) generated a suite of lipid biomarkers. The Synechococcus/Chloroflexus mat contained two mono-unsaturated isomers of n-C18:1 with smaller amounts of polyunsaturated n-C18:2, characteristic of cyanobacteria. The mat also contained abundant n,n-wax esters of C32 to C37, characteristic of Chloroflexus. 10-Methyl-C16 was also detected, indicative of sulfate reducing bacteria (SRB). The narrow Oscillatoria mat was dominated by the aforementioned cyanobacterial biomarkers as well as iso-C17:1, a biomarker for some groups of SRB. Unusual dimethyl fatty acids were also detected. The goal of this research is to provide an initial dataset that will illustrate the maximum amount of paleobiological and paleoenvironmental information expected to form in these types of iron deposits. Insights from our research may help elucidate the role of phototrophs in the deposition of BIFs on Earth, and may assist in the search for evidence of fossilized microbial life in iron deposits on Mars. Pierson, B.K., M.N. Parenteau, and B.M. Griffin, Phototrophs in high-iron-concentration microbial mats: Ecology of phototrophs in an iron-depositing hot spring, Appl. Environ. Microbiol., 65, 5474-5483, 1999. Pierson, B.K., and M.N. Parenteau, Phototrophs in high iron microbial mats: Microstructure of mats in iron-depositing hot springs, FEMS Microbiology Ecology 32, 181-196, 2000. Trouwborst, R., G. Koch, G. Luther, and B.K. Pierson, Photosynthesis and iron in hot spring microbial mats (abstract), NAI General Meeting, Astrobiology 2(4), 206, 2003.

Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode.

PubMed

Afzal, Ahmed J; Srour, Ali; Saini, Navinder; Hemmati, Naghmeh; El Shemy, Hany A; Lightfoot, David A

2012-04-01

Host resistance to "yellow dwarf" or "moonlight" disease cause by any population (Hg type) of Heterodera glycines I., the soybean cyst nematode (SCN), requires a functional allele at rhg1. The host resistance encoded appears to mimic an apoptotic response in the giant cells formed at the nematode feeding site about 24-48 h after nematode feeding commences. Little is known about how the host response to infection is mediated but a linked set of 3 genes has been identified within the rhg1 locus. This study aimed to identify the role of the genes within the locus that includes a receptor-like kinase (RLK), a laccase and an ion antiporter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles, gene-based markers, and a new Hg type 0 and new recombination events. A syntenic gene cluster on Lg B1 was found. The effectiveness of SNP probes from the RLK for distinguishing homolog sequence variants on LgB1 from alleles at the rhg1 locus on LgG was shown. The resistant allele of the rhg1 locus was shown to be dominant in NILs. None of the recombination events were within the cluster of the three candidate genes. Finally, rhg1 was shown to reduce the plant root development. A model for rhg1 as a dominant multi-gene resistance locus based on the developmental control was inferred.

Measuring salt retention.

DOT National Transportation Integrated Search

2013-03-01

This research developed and completed a field evaluation of salt distribution equipment. The evaluation provides a direct comparison of three different types of salt spreaders at three different truck speeds and brine rates. A rubber mat was divided ...

7 CFR 1437.309 - Turfgrass sod.

Code of Federal Regulations, 2011 CFR

2011-01-01

... stratum of soil bound by mature grass and plant roots into a thick mat produced in commercial quantities for sale. (b) Specific species, types or varieties of grass intended for turfgrass sod will be...

7 CFR 1437.309 - Turfgrass sod.

Code of Federal Regulations, 2010 CFR

2010-01-01

... stratum of soil bound by mature grass and plant roots into a thick mat produced in commercial quantities for sale. (b) Specific species, types or varieties of grass intended for turfgrass sod will be...

Short communication: Flooring preferences of dairy cows at calving.

PubMed

Campler, M; Munksgaard, L; Jensen, M B; Weary, D M; von Keyserlingk, M A G

2014-02-01

The present study investigated the flooring preference during the 30 h before parturition in Holstein dairy cows housed individually in a maternity pen. Seventeen multiparous cows were moved, on average, 2 d before expected calving date into an individual maternity pen with 3 different flooring surfaces: 10 cm of sand, pebble-top rubber mats, or concrete flooring, each covered with 15 cm of straw. Calving location, lying time, and total time and number of lying bouts on each of the floor types were recorded during 2 periods: precalving (24 to 29 h before calving) and at calving (0 to 5h before calving). Ten cows calved on sand, 6 on concrete, and 1 on the rubber mat. Lying bouts increased during the hours closest to calving, regardless of flooring. The number of lying bouts did not differ between flooring types precalving but cows had more lying bouts on sand and concrete compared with rubber at calving. Cows spent more time lying down on sand and concrete compared with rubber precalving, but lying times did not differ between treatments at calving. Cows that calved on sand spent more time lying on sand at calving compared with the other 2 flooring types. Cows that calved on concrete did not show a flooring preference at calving. These results indicate that rubber mats are the least preferred by dairy cows in the maternity pens, even when covered with a deep layer of straw. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Recent hybridization between Taenia asiatica and Taenia saginata.

PubMed

Yamane, Kanako; Suzuki, Yumi; Tachi, Eiko; Li, Tiaoying; Chen, Xingwang; Nakao, Minoru; Nkouawa, Agathe; Yanagida, Testuya; Sako, Yasuhito; Ito, Akira; Sato, Hiroshi; Okamoto, Munehiro

2012-06-01

Five Taenia tapeworms collected from humans in Tibetan Plateau, Sichuan, China, where three species of human Taenia are sympatrically endemic, were examined for the mitochondrial cox1 gene and two nuclear genes, ef1 and elp. Phylogenetic analyses of these genes revealed that two adult worms showed nuclear-mitochondrial discordance, suggesting that they originated from hybridization between Taenia saginata and Taenia asiatica. One of two worms had T. asiatica-type mtDNA, whereas another worm had T. saginata-type mtDNA, indicating that reciprocal hybridization between T. saginata and T. asiatica could occur. The worm having T. asiatica-type mtDNA was heterozygous at both nuclear loci with T. saginata-type alleles and T. asiatica-type alleles. In another worm, the ef1 locus was heterozygous with a T. saginata-type alleles and T. asiatica-type alleles, while the elp locus was homozygous with T. saginata-type alleles. Self-fertilization is the main reproductive method of the genus Taenia. Since self-fertilization represents a type of inbreeding, each locus in the offspring would become homozygous over generations with genetic drift. The fact that some nuclear loci are still heterozygous means that hybridization might have occurred recently. Hybridization between T. asiatica and T. saginata is probably an ongoing event in many areas in which they are sympatrically endemic. Crown Copyright © 2012. Published by Elsevier Ireland Ltd. All rights reserved.

Ancient roots for polymorphism at the HLA-DQ. alpha. locus in primates

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

Gyllensten, U.B.; Erlich, H.A.

1989-12-01

The genes encoding the human histocompatibility antigens (HLA) exhibit a remarkable degree of polymorphism as revealed by immunologic and molecular analyses. This extensive sequence polymorphism either may have been generated during the lifetime of the human species or could have arisen before speciation and been maintained in the contemporary human population by selection or, possibly, by genetic drift. These two hypotheses were examined using the polymerase chain reaction method to amplify polymorphic sequences from the DQ{alpha} locus, as well as the DX{alpha} locus, an homologous but nonexpressed locus, in a series of primates that diverged at known times. In general,more » the amino acid sequence of a specific human DQ{alpha} allelic type is more closely related to its chimpanzee or gorilla counterpart than to other human DQ{alpha} alleles. Phylogenetic analysis of the silent nucleotide position changes shows that the similarity of allelic types between species is due to common ancestry rather than convergent evolution. Thus, most of the polymorphism at the DQ{alpha} locus in the human species was already present at least 5 million years ago in the ancestral species that gave rise to the chimpanzee, gorilla, and human lineages. However, one of the DQ{alpha} alleles may have arisen after speciation by recombination between two ancestral alleles.« less

Spatial and Temporal Variability in Microbial Communities from Pre- and Post-Eruption Microbial Mats Collected from Loihi Seamount, Hawaii: An Update

NASA Astrophysics Data System (ADS)

Moyer, C. L.; Davis, R. E.; Curtis, A. C.; Rassa, A. C.

2007-12-01

Loihi Seamount is an active submarine volcano that marks the southernmost extent of the Hawaiian hotspot. Loihi rises over 3000 meters from the seafloor and summits nearly 1000 meters below sea level. Hydrothermal activity was discovered at Loihi in 1987, yielding diffuse vent effluent (Tmax 37°C) with associated high CO2 and Fe(II) concentrations and luxuriant microbial mats located near the summit of the volcano. Loihi erupted most recently in 1996 forming a new 300 meter deep caldera (Pele's Pit) with hydrothermal venting up to 200°C. Pele's Pit has cooled and now contains multiple hydrothermal vents with hydrothermal fluids ranging from 8-58°C with concentrations of Fe(II) remaining between 50 and 750 μM. Community fingerprints from over 75 microbial mat samples have now been collected from Loihi Seamount from 1993 to 2006, with temperatures ranging from ambient (~4°C) up to nearly ~200°C. These samples were analyzed using Pearson product-moment coupled with UPGMA cluster analysis of terminal- restriction fragment length polymorphisms (T-RFLP) coupled with traditional clone library and sequence analysis to identify the primary populations within each community. These mat samples form two distinct community clusters (Loihi Cluster Group 1 and Group 2) representing a combined 90% of all mat samples collected. Loihi Cluster Group 1 is by far the largest group (n = 45) and contains the most mat samples collected over time. Group 1 is dominated by phylotypes closely related to the recently described zeta- Proteobacteria that includes the type strain Mariprofundus ferrooxydans, an obligately lithotrophic, Fe-oxidizing bacterium. Loihi Cluster Group 2 is comprised of only post-eruption communities (n = 18) that generally contain greater diversity (in terms of richness) than Group 1 communities. Group 2 communities are primarily dominated by a unique array of phylotypes belonging to the Nitrospira division and by the class epsilon- Proteobacteria, including many putative sulphur-oxidizing bacteria. Interestingly, we have recently witnessed a shift away from the Group 2 communities back to the Group 1 communities. Only 2 of 11 microbial mat samples collected in 2004 exhibited the Group 2 community structure. All 10 of the mat samples collected in 2006 from multiple locations exhibited the Group 1 community structure, indicating a reduced overall diversity within Pele's Pit and a return to the microbial mats being dominated by Fe-oxidizing bacteria.

Molecular typing of Sporothrix schenckii isolates from cats in Malaysia.

PubMed

Kano, Rui; Okubo, Miki; Siew, Han Hock; Kamata, Hiroshi; Hasegawa, Atsuhiko

2015-04-01

Epidemiological data on the aetiologic agents of feline sporotrichosis in Malaysia have not been reported, though human sporotrichosis in Malaysia is reported to be transmitted primarily via cat scratch. To the best of our knowledge, the present report is the first study of the molecular epidemiology of Sporothrix schenckii isolates from cats with sporotrichosis in Malaysia. In the present work, we characterised 18 clinical isolates from cats in Malaysia based on molecular properties, including sequence analyses of the calmodulin gene and the rDNA ITS region and selective PCR of mating type (MAT) loci. In this study, isolates from feline sporotrichosis were identified as a S. schenckii sensu stricto by sequence analyses of the calmodulin gene and the internal transcribed spacer (ITS) region. Notably, phylogenetic analysis of the ITS confirmed assignment to clinical clade D (and not C) of S. schenckii sensu stricto. Therefore, clinical clade D of S. schenckii sensu stricto appeared to be the prevailing source of feline sporotrichosis in Malaysia. The ratio of MAT1-1-1:MAT1-2-1 in these Malaysian isolates was found to be 1 : 0. This result suggested that a clonal strain of S. schenckii is the prevailing causative agent of feline sporotrichosis in Malaysia. © 2015 Blackwell Verlag GmbH.

Prevalence of Flp Pili-Encoding Plasmids in Cutibacterium acnes Isolates Obtained from Prostatic Tissue

PubMed Central

Davidsson, Sabina; Carlsson, Jessica; Mölling, Paula; Gashi, Natyra; Andrén, Ove; Andersson, Swen-Olof; Brzuszkiewicz, Elzbieta; Poehlein, Anja; Al-Zeer, Munir A.; Brinkmann, Volker; Scavenius, Carsten; Nazipi, Seven; Söderquist, Bo; Brüggemann, Holger

2017-01-01

Inflammation is one of the hallmarks of prostate cancer. The origin of inflammation is unknown, but microbial infections are suspected to play a role. In previous studies, the Gram-positive, low virulent bacterium Cutibacterium (formerly Propionibacterium) acnes was frequently isolated from prostatic tissue. It is unclear if the presence of the bacterium represents a true infection or a contamination. Here we investigated Cutibacterium acnes type II, also called subspecies defendens, which is the most prevalent type among prostatic C. acnes isolates. Genome sequencing of type II isolates identified large plasmids in several genomes. The plasmids are highly similar to previously identified linear plasmids of type I C. acnes strains associated with acne vulgaris. A PCR-based analysis revealed that 28.4% (21 out of 74) of all type II strains isolated from cancerous prostates carry a plasmid. The plasmid shows signatures for conjugative transfer. In addition, it contains a gene locus for tight adherence (tad) that is predicted to encode adhesive Flp (fimbrial low-molecular weight protein) pili. In subsequent experiments a tad locus-encoded putative pilin subunit was identified in the surface-exposed protein fraction of plasmid-positive C. acnes type II strains by mass spectrometry, indicating that the tad locus is functional. Additional plasmid-encoded proteins were detected in the secreted protein fraction, including two signal peptide-harboring proteins; the corresponding genes are specific for type II C. acnes, thus lacking from plasmid-positive type I C. acnes strains. Further support for the presence of Flp pili in C. acnes type II was provided by electron microscopy, revealing cell appendages in tad locus-positive strains. Our study provides new insight in the most prevalent prostatic subspecies of C. acnes, subsp. defendens, and indicates the existence of Flp pili in plasmid-positive strains. Such pili may support colonization and persistent infection of human prostates by C. acnes. PMID:29201018

Where's the dust? Characterizing locations of azinphos-methyl residues in house and vehicle dust among farmworkers with young children.

PubMed

Coronado, Gloria D; Griffith, William C; Vigoren, Eric M; Faustman, Elaine M; Thompson, Beti

2010-12-01

Organophosphate pesticides are commonly used in the United States, and farmworkers are at risk for chronic exposure. Using data from a community randomized trial to interrupt the take-home pathway of pesticide exposure, we examined the association between floor surface type (smooth floor, thin carpet, and thick carpet) and rooms in which dust samples were collected (living room vs. non-living room) and concentrations of azinphos-methyl residues in home environments. We also examined the association between vehicle type (truck, auto, or other) and footwell floor surfaces (carpeted, smooth surface, or no mat) and concentrations of azinphos-methyl in vehicle dust samples. Dust samples were collected from 203 and 179 households and vehicles, respectively. All households had at least one child aged 2-6. Vehicle dust samples were collected from footwells of the vehicle used for commuting to and from work. A total of 183 samples were collected from living rooms, and 20 were collected from other rooms in the home. Forty-two samples were collected from thick carpets, 130 from thin carpets, and 27 from smooth floor surfaces. Thick and thin carpets had a significantly greater dust mass than smooth floor surfaces (6.0 g/m(2) for thick carpets, 7.8 g/m(2) for thin carpets, and 1.5 g/m(2) for smooth surfaces). Of the 179 vehicle samples, 113 were from cars, 34 from trucks, and 32 from other vehicles. Vehicles with no mats had a significantly higher mass of dust (21.3 g) than those with hard mats (9.3 g) but did not differ from vehicles with plush mats (12.0 g). Further research is needed to characterize the environment in which children may be exposed to pesticides.

Where’s the Dust? Characterizing Locations of Azinphos-Methyl Residues in House and Vehicle Dust Among Farmworkers with Young Children

PubMed Central

Coronado, Gloria D.; Griffith, William C.; Vigoren, Eric M.; Faustman, Elaine M.; Thompson, Beti

2010-01-01

Organophosphate pesticides (OPs) are commonly used in the United States, and farm workers are at risk for chronic exposure. Using data from a community randomized trial to interrupt the take-home pathway of pesticide exposure, we examined the association between floor surface type (smooth floor, thin carpet, and thick carpet) and rooms in which dust samples were collected (living room vs. non-living room) and concentrations of azinphos-methyl residues in home environments. We also examined the association between vehicle type (truck, auto, or other) and footwell floor surfaces (carpeted, smooth surface, or no mat) and concentrations of azinphos-methyl in vehicle dust samples. Dust samples were collected from 203 and 179 households and vehicles, respectively. All households had at least one child aged 2–6. Vehicle dust samples were collected from footwells of the vehicle used for commuting to and from work. A total of 183 samples were collected from living rooms, and 20 were collected from other rooms in the home. Forty-two samples were collected from thick carpets, 130 from thin carpets, and 27 from smooth floor surfaces. Thick and thin carpets had a significantly greater dust mass than smooth floor surfaces (6.0 g/m2 for thick carpets, 7.8 g/m2 for thin carpets, and 1.5 g/m2 for smooth surfaces). Of the 179 vehicle samples, 113 were from cars, 34 from trucks, and 32 from other vehicles. Vehicles with no mats had a significantly higher mass of dust (21.3 g) than those with hard mats (9.3 g) but did not differ from vehicles with plush mats (12.0g). Further research is needed to characterize the environment in which children may be exposed to pesticides. PMID:20945243

Microbialite Biosignature Analysis by Mesoscale X-ray Fluorescence (μXRF) Mapping.

PubMed

Tice, Michael M; Quezergue, Kimbra; Pope, Michael C

2017-11-01

As part of its biosignature detection package, the Mars 2020 rover will carry PIXL, the Planetary Instrument for X-ray Lithochemistry, a spatially resolved X-ray fluorescence (μXRF) spectrometer. Understanding the types of biosignatures detectable by μXRF and the rock types μXRF is most effective at analyzing is therefore an important goal in preparation for in situ Mars 2020 science and sample selection. We tested mesoscale chemical mapping for biosignature interpretation in microbialites. In particular, we used μXRF to identify spatial distributions and associations between various elements ("fluorescence microfacies") to infer the physical, biological, and chemical processes that produced the observed compositional distributions. As a test case, elemental distributions from μXRF scans of stromatolites from the Mesoarchean Nsuze Group (2.98 Ga) were analyzed. We included five fluorescence microfacies: laminated dolostone, laminated chert, clotted dolostone and chert, stromatolite clast breccia, and cavity fill. Laminated dolostone was formed primarily by microbial mats that trapped and bound loose sediment and likely precipitated carbonate mud at a shallow depth below the mat surface. Laminated chert was produced by the secondary silicification of microbial mats. Clotted dolostone and chert grew as cauliform, cryptically laminated mounds similar to younger thrombolites and was likely formed by a combination of mat growth and patchy precipitation of early-formed carbonate. Stromatolite clast breccias formed as lag deposits filling erosional scours and interstromatolite spaces. Cavities were filled by microquartz, Mn-rich dolomite, and partially dolomitized calcite. Overall, we concluded that μXRF is effective for inferring genetic processes and identifying biosignatures in compositionally heterogeneous rocks. Key Words: Stromatolites-Biosignatures-Spectroscopy-Archean. Astrobiology 17, 1161-1172.

Linkage of a gene for macular corneal dystrophy to chromosome 16.

PubMed Central

Vance, J. M.; Jonasson, F.; Lennon, F.; Sarrica, J.; Damji, K. F.; Stauffer, J.; Pericak-Vance, M. A.; Klintworth, G. K.

1996-01-01

Autosomal recessive macular corneal dystrophy (MCD) is a heterogeneous disorder leading to visual impairment. Sixteen American and Icelandic families (11 type I and 5 type II) were analyzed for linkage, by use of 208 polymorphic microsatellite markers. A significant maximum LOD score Zmax of 7.82 at a maximum recombination fraction (thetamax) of .06 was found with the 16q22 locus D16S518 for MCD type I. In addition, a peak LOD score of 2.50 at a recombination fraction of .00 was obtained for the MCD type II families, by use of the identical marker. These findings raise the possibility that MCD type II may be due to the same genetic locus that is involved in MCD type I. PMID:8644739

Sequence Elements Upstream of the Core Promoter Are Necessary for Full Transcription of the Capsule Gene Operon in Streptococcus pneumoniae Strain D39

PubMed Central

Wen, Zhensong; Sertil, Odeniel; Cheng, Yongxin; Zhang, Shanshan; Liu, Xue; Wang, Wen-Ching

2015-01-01

Streptococcus pneumoniae is a major bacterial pathogen in humans. Its polysaccharide capsule is a key virulence factor that promotes bacterial evasion of human phagocytic killing. While S. pneumoniae produces at least 94 antigenically different types of capsule, the genes for biosynthesis of almost all capsular types are arranged in the same locus. The transcription of the capsular polysaccharide (cps) locus is not well understood. This study determined the transcriptional features of the cps locus in the type 2 virulent strain D39. The initial analysis revealed that the cps genes are cotranscribed from a major transcription start site at the −25 nucleotide (G) upstream of cps2A, the first gene in the locus. Using unmarked chromosomal truncations and a luciferase-based transcriptional reporter, we showed that the full transcription of the cps genes not only depends on the core promoter immediately upstream of cps2A, but also requires additional elements upstream of the core promoter, particularly a 59-bp sequence immediately upstream of the core promoter. Unmarked deletions of these promoter elements in the D39 genome also led to significant reduction in CPS production and virulence in mice. Lastly, common cps gene (cps2ABCD) mutants did not show significant abnormality in cps transcription, although they produced significantly less CPS, indicating that the CpsABCD proteins are involved in the encapsulation of S. pneumoniae in a posttranscriptional manner. This study has yielded important information on the transcriptional characteristics of the cps locus in S. pneumoniae. PMID:25733517

Fast releasing oral electrospun PVP/CD nanofiber mats of taste-masked meloxicam.

PubMed

Samprasit, Wipada; Akkaramongkolporn, Prasert; Ngawhirunpat, Tanasait; Rojanarata, Theerasak; Kaomongkolgit, Ruchadaporn; Opanasopit, Praneet

2015-06-20

Fast release and taste masking of meloxicam (MX)-loaded polyvinylpyrrolidone (PVP)/cyclodextrin (CD) nanofiber mats were developed using an electrospinning process. CDs were blended to improve the stability of the mats. The morphology and diameter of the mats were determined using scanning electron microscopy (SEM); physical and mechanical properties were also studied. The MX content, disintegration time, MX release and cytotoxicity of the mats were investigated. In vivo studies were also performed in healthy human volunteers. The results indicated that the mats were successfully prepared with fiber in the nanometer range. MX was well incorporated into the mats, with an amorphous form. The mats showed suitable tensile strength. CDs improved the physical stability by their cage-like supramolecular structure to protect from humidity and moisture, and create bead free nanofiber mats. The nanofiber mats with CDs were physically stable without any hygroscopicity and fusion. A fast disintegration and release of MX was achieved. Moreover, this mat released MX faster than the MX powder and commercial tablets. The cytotoxicity test revealed that mats were safe for a 5-min incubation. The disintegration studies indicated that in vivo disintegration agreed with the in vitro studies; the mat rapidly disintegrated in the mouth. The less bitter of MX was occurred in the mats that incorporated CD, menthol and aspartame. In addition, this mat was physical stable for 6 months. The results suggest that these mats may be a good candidate for fast dissolving drug delivery systems of bitter drugs to increase the palatability of dosage forms. Copyright © 2015 Elsevier B.V. All rights reserved.

A novel locus for dilated cardiomyopathy maps to canine chromosome 8.

PubMed

Werner, Petra; Raducha, Michael G; Prociuk, Ulana; Sleeper, Meg M; Van Winkle, Thomas J; Henthorn, Paula S

2008-06-01

Dilated cardiomyopathy (DCM), the most common form of cardiomyopathy, often leads to heart failure and sudden death. While a substantial proportion of DCMs are inherited, mutations responsible for the majority of DCMs remain unidentified. A genome-wide linkage study was performed to identify the locus responsible for an autosomal recessive inherited form of juvenile DCM (JDCM) in Portuguese water dogs using 16 families segregating the disease. Results link the JDCM locus to canine chromosome 8 with two-point and multipoint lod scores of 10.8 and 14, respectively. The locus maps to a 3.9-Mb region, with complete syntenic homology to human chromosome 14, that contains no genes or loci known to be involved in the development of any type of cardiomyopathy. This discovery of a DCM locus with a previously unknown etiology will provide a new gene to examine in human DCM patients and a model for testing therapeutic approaches for heart failure.

Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding.

PubMed

Ghahramanzadeh, R; Esselink, G; Kodde, L P; Duistermaat, H; van Valkenburg, J L C H; Marashi, S H; Smulders, M J M; van de Wiel, C C M

2013-01-01

Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH-psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics. © 2012 Blackwell Publishing Ltd.

Evaluation of candidate barcoding markers in Orinus (Poaceae).

PubMed

Su, X; Liu, Y P; Chen, Z; Chen, K L

2016-04-26

Orinus is an alpine endemic genus of Poaceae. Because of the imperfect specimens, high level of intraspecific morphological variability, and homoplasies of morphological characters, it is relatively difficult to delimitate species of Orinus by using morphology alone. To this end, the DNA barcoding has shown great potential in identifying species. The present study is the first attempt to test the feasibility of four proposed DNA barcoding markers (matK, rbcL, trnH-psbA, and ITS) in identifying four currently revised species of Orinus from the Qinghai-Tibetan Plateau (QTP). Among all the single-barcode candidates, the differentiation power was the highest for the nuclear internal transcribed spacer (ITS), while the chloroplast barcodes matK (M), rbcL (R), and trnH-psbA (H) could not identify the species. Meanwhile, the differentiation efficiency of the nuclear ITS (I) was also higher than any two- or three-locus combination of chloroplast barcodes, or even a combination of ITS and any chloroplast barcode except H + I and R + I. All the combinations of chloroplast barcodes plus the nuclear ITS, H + I, and R + I differentiated the highest portion of species. The highest differentiation rate for the barcodes or barcode combinations examined here was 100% (H + I and R + I). In summary, this case study showed that the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions in differentiating Orinus species from the QTP. Moreover, combining the ITS region with chloroplast regions may improve the barcoding success rate.

Detection of plant-based adulterants in turmeric powder using DNA barcoding.

PubMed

Parvathy, V A; Swetha, V P; Sheeja, T E; Sasikumar, B

2015-01-01

In its powdered form, turmeric [Curcuma longa L. (Zingiberaceae)], a spice of medical importance, is often adulterated lowering its quality. The study sought to detect plant-based adulterants in traded turmeric powder using DNA barcoding. Accessions of Curcuma longa L., Curcuma zedoaria Rosc. (Zingiberaceae), and cassava starch served as reference samples. Three barcoding loci, namely ITS, rbcL, and matK, were used for PCR amplification of the reference samples and commercial samples representing 10 different companies. PCR success rate, sequencing efficiency, occurrence of SNPs, and BLAST analysis were used to assess the potential of the barcoding loci in authenticating the traded samples of turmeric. The PCR and sequencing success of the loci rbcL and ITS were found to be 100%, whereas matK showed no amplification. ITS proved to be the ideal locus because it showed greater variability than rbcL in discriminating the Curcuma species. The presence of C. zedoaria could be detected in one of the samples whereas cassava starch, wheat, barley, and rye in other two samples although the label claimed nothing other than turmeric powder in the samples. Unlabeled materials in turmeric powder are considered as adulterants or fillers, added to increase the bulk weight and starch content of the commodity for economic gains. These adulterants pose potential health hazards to consumers who are allergic to these plants, lowering the product's medicinal value and belying the claim that the product is gluten free. The study proved DNA barcoding as an efficient tool for testing the integrity and the authenticity of commercial products of turmeric.

DNA Barcoding of Rhodiola (Crassulaceae): A Case Study on a Group of Recently Diversified Medicinal Plants from the Qinghai-Tibetan Plateau

PubMed Central

Zhang, Jian-Qiang; Meng, Shi-Yong; Wen, Jun; Rao, Guang-Yuan

2015-01-01

DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences — rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) — for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau. PMID:25774915

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

Petrash, Daniel A.; Lalonde, Stefan V.; González-Arismendi, Gabriela

The formation of dolomite in modern peritidal environments is linked to the degradation of buried microbial mats, with complexation of Ca and Mg by extracellular polymeric substances (EPSs) and alkalinity generation through organic carbon respiration facilitating the nucleation of dolomite precursors. In the past two decades, microbial sulfate reduction, methanogenesis, and methanotrophy have all been considered as potential drivers of the nucleation process, but it remains unclear why dolomite formation could not also occur in suboxic sediments where abundant alkalinity is produced by processes linked to Mn(IV) and/or Fe(III) reduction coupled with the diffusion and reoxidation of reduced sulfur species.more » Here we report the interstitial occurrence of spheroidal aggregates of nanometer-scale Ca-rich dolomite rhombohedra within suboxic sediments associated with remnant microbial mats that developed in the peritidal zone of the Archipelago Los Roques, Venezuela. Multiple analytical tools, including EPMA, ICP-MS, synchrotron-based XRF and XRD, and spatially resolved XANES microanalyses, show that the dolomite-cemented interval exhibits depleted bulk iron concentrations, but is interstitially enriched in Mn and elemental sulfur (S⁰). Manganese occurs in several oxidation states, indicating that the dolomite-cemented interval was the locus of complex biological redox transformations characterized by coupled Mn and S cycling. The tight correspondence between sedimentary Mn and MgCO₃ concentrations further hints at a direct role for Mn during dolomitization. While additional studies are required to confirm its relevance in natural settings, we propose a model by which coupled Mn–S redox cycling may promote alkalinity generation and thus dolomite formation in manner similar to, or even more efficiently, than bacterial sulfate reduction alone.« less

The Effects of Advisement and Locus of Control on Achievement in Learner-Controlled Instruction.

ERIC Educational Resources Information Center

Santiago, Rowena S.; Okey, James R.

1992-01-01

Describes a study of undergraduate preservice teachers that investigated three types of advisement--adaptive, evaluative, and combined--and their effects in learner-controlled computer-based instruction for learners with varying locus of control orientations. Posttest results are reported, and it is concluded that there is no significant…

Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS (NRRL) Culture Collection using multi-locus sequence analysis

USDA-ARS?s Scientific Manuscript database

Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 str...

Archean Microbial Mat Communities

NASA Astrophysics Data System (ADS)

Tice, Michael M.; Thornton, Daniel C. O.; Pope, Michael C.; Olszewski, Thomas D.; Gong, Jian

2011-05-01

Much of the Archean record of microbial communities consists of fossil mats and stromatolites. Critical physical emergent properties governing the evolution of large-scale (centimeters to meters) topographic relief on the mat landscape are (a) mat surface roughness relative to the laminar sublayer and (b) cohesion. These properties can be estimated for fossil samples under many circumstances. A preliminary analysis of Archean mat cohesion suggests that mats growing in shallow marine environments from throughout this time had cohesions similar to those of modern shallow marine mats. There may have been a significant increase in mat strength at the end of the Archean.

Single-gene deletions that restore mating competence to diploid yeast.

PubMed

Schmidlin, Tom; Kaeberlein, Matt; Kudlow, Brian A; MacKay, Vivian; Lockshon, Daniel; Kennedy, Brian K

2008-03-01

Using the Saccharomyces cerevisiae MATa/MATalpha ORF deletion collection, homozygous deletion strains were identified that undergo mating with MATa or MATalpha haploids. Seven homozygous deletions were identified that confer enhanced mating. Three of these, lacking CTF8, CTF18, and DCC1, mate at a low frequency with either MATa or MATalpha haploids. The products of these genes form a complex involved in sister chromatid cohesion. Each of these strains also exhibits increased chromosome loss rates, and mating likely occurs due to loss of one copy of chromosome III, which bears the MAT locus. Three other homozygous diploid deletion strains, ylr193cDelta/ylr193cDelta, yor305wDelta/yor305wDelta, and ypr170cDelta/ypr170cDelta, mate at very low frequencies with haploids of either or both mating types. However, an ist3Delta/ist3Delta strain mates only with MATa haploids. It is shown that IST3, previously linked to splicing, is required for efficient processing of the MATa1 message, particularly the first intron. As a result, the ist3Delta/ist3Delta strain expresses unbalanced ratios of Matalpha to Mata proteins and therefore mates with MATa haploids. Accordingly, mating in this diploid can be repressed by introduction of a MATa1 cDNA. In summary, this study underscores and elaborates upon predicted pathways by which mutations restore mating function to yeast diploids and identifies new mutants warranting further study.

Using metatranscriptomics to understand the roles of Fe(II)-oxidizing microbes in marine hydrothermal vents

NASA Astrophysics Data System (ADS)

Glazer, B. T.; Mcallister, S.; Polson, S. W.; Chan, C. S. Y.

2015-12-01

Fe(II)-oxidizing microbes (FeOM) are thought to be key players in marine Fe cycling, particularly at hydrothermal vents. However, we do not have tools to track their activity, largely because we do not know the genes involved in neutrophilic chemolithotrophic Fe oxidation. Researchers have used gene homology between FeOM isolates to suggest several genes that may be involved in Fe(II) oxidation, including the Fe oxidase cyc2 found in the Zetaproteobacteria type strain Mariprofundus ferrooxydans, as well as all other known neutrophilic microaerophilic FeOM. Although many Zetaproteobacteria are found within natural Fe mats, close relatives of Fe(II)-oxidizing isolates are rarely present. Therefore, one goal of this study was to determine the activity of putative Fe(II) oxidation genes in dominant OTUs found in natural environments. We collected Fe mats from hydrothermal vents at Loihi Seamount, Hawaii, preserving RNA in situ. By analyzing metatranscriptomes of different Fe mat niches, we were able to determine the OTUs involved and the gene expression patterns associated with Fe(II) oxidation in the marine environment. Analysis of metatranscriptomic data confirms that the Zetaproteobacteria express the various genes necessary to support the Fe mat community through chemoautotrophic growth. Globally ubiquitous and even some rare species of the Zetaproteobacteria were active, with different relative abundances depending on Fe mat niches defined by fluid flow and geochemistry. Initial results show that genes thought to be involved in the electron transport pathway from Fe(II) to O2, including cyc2, are some of the most highly expressed genes in marine Fe microbial mats. Species-specific variants of these genes suggest that many of the Zetaproteobacteria species, spanning the breadth of the diversity of the class, are expressing genes necessary for Fe(II) oxidation within natural Fe mat niches. Understanding the differential expression of these genes in different niches will enable us to quantify the activity of marine FeOM and their effect on Fe and associated element cycling within deep and coastal marine systems.

Neutral monosaccharides from a hypersaline tropical environment: Applications to the characterization of modern and ancient ecosystems

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

Moers, M.E.C.; Larter, S.R.

1993-07-01

Surficial and buried sediment samples from a hypersaline lagoon-sabkha system (Abu Dhabi, United Arab Emirates) were analyzed for carbohydrates (as neutral monosaccharides) to distinguish and characterize various types of recent and ancient tropical ecosystems on a molecular level. The samples consisted of surficial and buried microbial mats, lagoonal sediments containing seagrass (Halodule uninervis), and mangrove (Avicennia marine) paleosoils and handpicked mangrove leaves, ranging in age from contemporary to ca. 6000 yr BP. Analysis of quantitative neutral monosaccharide data by multivariate techniques shows that various groups can be distinguished: intact vascular plant material (mangrove leaf) contains high amounts of arabinose andmore » glucose and hardly any partially methylated monosaccharides, whereas microbial mats in general and lagoonal seagrass sediments show high contributions of fucose, ribose, mannose, galactose, and partially methylated monosaccharides. Moreover, surficial microbial mats consisting of filamentous cyanobacteria (Microcoleus chtonoplastes, Lyngbya aestuarii) can be distinguished from other mats and sediments containing coccoid cyanobacteria (Entophysalis major) and/or fermenting, sulphate reducing, and methanogenic bacteria on the basis of high contributions of specific groups of partially methylated monosaccharides and other [open quotes]minor[close quotes] saccharides. The neutral monosaccharides present in mangrove paleosoils are for a substantial part derived from microorganisms. 22 refs., 4 figs., 4 tabs.« less

Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats.

PubMed

Jay, Zackary J; Beam, Jacob P; Dlakić, Mensur; Rusch, Douglas B; Kozubal, Mark A; Inskeep, William P

2018-05-14

The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and characterization of a phylum-level archaeal lineage proposed and herein referred to as the 'Marsarchaeota', after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50-80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcriptional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III). Phylogenomic analyses of replicate assemblies corresponding to two groups of Marsarchaeota indicate that they branch between the Crenarchaeota and all other major archaeal lineages. Transcriptomic analyses of several Fe(III) oxide mat communities reveal that these organisms were actively transcribing two different terminal oxidase complexes in situ and genes comprising an F 420 -dependent butanal catabolism. The broad distribution of Marsarchaeota in geothermal, microaerobic Fe(III) oxide mats suggests that similar habitat types probably played an important role in the evolution of archaea.

Dissecting variation in biomass conversion factors across China's forests: implications for biomass and carbon accounting.

PubMed

Luo, Yunjian; Zhang, Xiaoquan; Wang, Xiaoke; Ren, Yin

2014-01-01

Biomass conversion factors (BCFs, defined as the ratios of tree components (i.e. stem, branch, foliage and root), as well as aboveground and whole biomass of trees to growing stock volume, Mg m-3) are considered as important parameters in large-scale forest biomass carbon estimation. To date, knowledge of possible sources of the variation in BCFs is still limited at large scales. Using our compiled forest biomass dataset of China, we presented forest type-specific values of BCFs, and examined the variation in BCFs in relation to forest type, stand development and environmental factors (climate and soil fertility). BCFs exhibited remarkable variation across forest types, and also were significantly related to stand development (especially growing stock volume). BCFs (except Stem BCF) had significant relationships with mean annual temperature (MAT) and mean annual precipitation (MAP) (P<0.001). Climatic data (MAT and MAP) collectively explained 10.0-25.0% of the variation in BCFs (except Stem BCFs). Moreover, stronger climatic effects were found on BCFs for functional components (i.e. branch, foliage and root) than BCFs for combined components (i.e. aboveground section and whole trees). A general trend for BCFs was observed to decrease and then increase from low to high soil fertility. When qualitative soil fertility and climatic data (MAT and MAP) were combined, they explained 14.1-29.7% of the variation in in BCFs (except Stem BCFs), adding only 4.1-4.9% than climatic data used. Therefore, to reduce the uncertainty induced by BCFs in forest carbon estimates, we should apply values of BCFs for a specified forest type, and also consider climatic and edaphic effects, especially climatic effect, in developing predictive models of BCFs (except Stem BCF).

Dissecting Variation in Biomass Conversion Factors across China’s Forests: Implications for Biomass and Carbon Accounting

PubMed Central

Wang, Xiaoke; Ren, Yin

2014-01-01

Biomass conversion factors (BCFs, defined as the ratios of tree components (i.e. stem, branch, foliage and root), as well as aboveground and whole biomass of trees to growing stock volume, Mg m−3) are considered as important parameters in large-scale forest biomass carbon estimation. To date, knowledge of possible sources of the variation in BCFs is still limited at large scales. Using our compiled forest biomass dataset of China, we presented forest type-specific values of BCFs, and examined the variation in BCFs in relation to forest type, stand development and environmental factors (climate and soil fertility). BCFs exhibited remarkable variation across forest types, and also were significantly related to stand development (especially growing stock volume). BCFs (except Stem BCF) had significant relationships with mean annual temperature (MAT) and mean annual precipitation (MAP) (P<0.001). Climatic data (MAT and MAP) collectively explained 10.0–25.0% of the variation in BCFs (except Stem BCFs). Moreover, stronger climatic effects were found on BCFs for functional components (i.e. branch, foliage and root) than BCFs for combined components (i.e. aboveground section and whole trees). A general trend for BCFs was observed to decrease and then increase from low to high soil fertility. When qualitative soil fertility and climatic data (MAT and MAP) were combined, they explained 14.1–29.7% of the variation in in BCFs (except Stem BCFs), adding only 4.1–4.9% than climatic data used. Therefore, to reduce the uncertainty induced by BCFs in forest carbon estimates, we should apply values of BCFs for a specified forest type, and also consider climatic and edaphic effects, especially climatic effect, in developing predictive models of BCFs (except Stem BCF). PMID:24728222

Power conditioning using dynamic voltage restorers under different voltage sag types.

PubMed

Saeed, Ahmed M; Abdel Aleem, Shady H E; Ibrahim, Ahmed M; Balci, Murat E; El-Zahab, Essam E A

2016-01-01

Voltage sags can be symmetrical or unsymmetrical depending on the causes of the sag. At the present time, one of the most common procedures for mitigating voltage sags is by the use of dynamic voltage restorers (DVRs). By definition, a DVR is a controlled voltage source inserted between the network and a sensitive load through a booster transformer injecting voltage into the network in order to correct any disturbance affecting a sensitive load voltage. In this paper, modelling of DVR for voltage correction using MatLab software is presented. The performance of the device under different voltage sag types is described, where the voltage sag types are introduced using the different types of short-circuit faults included in the environment of the MatLab/Simulink package. The robustness of the proposed device is evaluated using the common voltage sag indices, while taking into account voltage and current unbalance percentages, where maintaining the total harmonic distortion percentage of the load voltage within a specified range is desired. Finally, several simulation results are shown in order to highlight that the DVR is capable of effective correction of the voltage sag while minimizing the grid voltage unbalance and distortion, regardless of the fault type.

Power conditioning using dynamic voltage restorers under different voltage sag types

PubMed Central

Saeed, Ahmed M.; Abdel Aleem, Shady H.E.; Ibrahim, Ahmed M.; Balci, Murat E.; El-Zahab, Essam E.A.

2015-01-01

Voltage sags can be symmetrical or unsymmetrical depending on the causes of the sag. At the present time, one of the most common procedures for mitigating voltage sags is by the use of dynamic voltage restorers (DVRs). By definition, a DVR is a controlled voltage source inserted between the network and a sensitive load through a booster transformer injecting voltage into the network in order to correct any disturbance affecting a sensitive load voltage. In this paper, modelling of DVR for voltage correction using MatLab software is presented. The performance of the device under different voltage sag types is described, where the voltage sag types are introduced using the different types of short-circuit faults included in the environment of the MatLab/Simulink package. The robustness of the proposed device is evaluated using the common voltage sag indices, while taking into account voltage and current unbalance percentages, where maintaining the total harmonic distortion percentage of the load voltage within a specified range is desired. Finally, several simulation results are shown in order to highlight that the DVR is capable of effective correction of the voltage sag while minimizing the grid voltage unbalance and distortion, regardless of the fault type. PMID:26843975

Study on hydraulic property models for water retention and unsaturated hydraulic conductivity in MATSIRO with representation of water table dynamics

NASA Astrophysics Data System (ADS)

Yoshida, N.; Oki, T.

2016-12-01

Appropriate initial condition of soil moisture and water table depth are important factors to reduce uncertainty in hydrological simulations. Approaches to determine the initial water table depth have been developed because of difficulty to get information on global water table depth and soil moisture distributions. However, how is equilibrium soil moisture determined by climate conditions? We try to discuss this issue by using land surface model with representation of water table dynamics (MAT-GW). First, the global pattern of water table depth at equilibrium soil moisture in MAT-GW was verified. The water table depth in MAT-GW was deeper than the previous one at fundamentally arid region because the negative recharge and continuous baseflow made water table depth deeper. It indicated that the hydraulic conductivity used for estimating recharge and baseflow need to be reassessed in MAT-GW. In soil physics field, it is revealed that proper hydraulic property models for water retention and unsaturated hydraulic conductivity should be selected for each soil type. So, the effect of selecting hydraulic property models on terrestrial soil moisture and water table depth were examined.Clapp and Hornburger equation(CH eq.) and Van Genuchten equation(VG eq.) were used as representative hydraulic property models. Those models were integrated on MAT-GW and equilibrium soil moisture and water table depth with using each model were compared. The water table depth and soil moisture at grids which reached equilibrium in both simulations were analyzed. The equilibrium water table depth were deeper in VG eq. than CH eq. in most grids due to shape of hydraulic property models. Then, total soil moisture were smaller in VG eq. than CH eq. at almost all grids which water table depth reached equilibrium. It is interesting that spatial patterns which water table depth reached equilibrium or not were basically similar in both simulations but reverse patterns were shown in east and west part of America. Selection of each hydraulic property model based on soil types may compensate characteristic of models in initialization.

Macrofaunal communities associated with chemosynthetic habitats from the U.S. Atlantic margin: A comparison among depth and habitat types

USGS Publications Warehouse

Bourque, Jill R.; Robertson, Craig M.; Brooke, Sandra; Demopoulos, Amanda W.J.

2016-01-01

Hydrocarbon seeps support distinct benthic communities capable of tolerating extreme environmental conditions and utilizing reduced chemical compounds for nutrition. In recent years, several locations of methane seepage have been mapped along the U.S. Atlantic continental slope. In 2012 and 2013, two newly discovered seeps were investigated in this region: a shallow site near Baltimore Canyon (BCS, 366–412 m) and a deep site near Norfolk Canyon (NCS, 1467–1602 m), with both sites containing extensive chemosynthetic mussel bed and microbial mat habitats. Sediment push cores, suction samples, and Ekman box cores were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 μm) in mussel beds, mats, and slope habitats at both sites. Community data from the deep site were also assessed in relation to the associated sediment environment (organic carbon and nitrogen, stable carbon and nitrogen isotopes, grain size, and depth). Infaunal assemblages and densities differed both between depths and among habitat types. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments and were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in BCS microbial mat habitats, but higher in mussel and slope sediments compared to NCS habitats. Multivariate statistical analysis revealed specific sediment properties as important for distinguishing the macrofaunal communities, including larger grain sizes present within NCS microbial mat habitats and depleted stable carbon isotopes (δ13C) in sediments present at mussel beds. These results suggest that habitat differences in the quality and source of organic matter are driving the observed patterns in the infaunal assemblages, including high β diversity and high variability in the macrofaunal community composition. This study is the first investigation of seep infauna along the U.S. Atlantic slope north of the Blake Ridge Diapir and provides a baseline for future regional comparisons to other seep habitats along the Atlantic margin.

Macrofaunal communities associated with chemosynthetic habitats from the U.S. Atlantic margin: A comparison among depth and habitat types

NASA Astrophysics Data System (ADS)

Bourque, Jill R.; Robertson, Craig M.; Brooke, Sandra; Demopoulos, Amanda W. J.

2017-03-01

Hydrocarbon seeps support distinct benthic communities capable of tolerating extreme environmental conditions and utilizing reduced chemical compounds for nutrition. In recent years, several locations of methane seepage have been mapped along the U.S. Atlantic continental slope. In 2012 and 2013, two newly discovered seeps were investigated in this region: a shallow site near Baltimore Canyon (BCS, 366-412 m) and a deep site near Norfolk Canyon (NCS, 1467-1602 m), with both sites containing extensive chemosynthetic mussel bed and microbial mat habitats. Sediment push cores, suction samples, and Ekman box cores were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 μm) in mussel beds, mats, and slope habitats at both sites. Community data from the deep site were also assessed in relation to the associated sediment environment (organic carbon and nitrogen, stable carbon and nitrogen isotopes, grain size, and depth). Infaunal assemblages and densities differed both between depths and among habitat types. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments and were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in BCS microbial mat habitats, but higher in mussel and slope sediments compared to NCS habitats. Multivariate statistical analysis revealed specific sediment properties as important for distinguishing the macrofaunal communities, including larger grain sizes present within NCS microbial mat habitats and depleted stable carbon isotopes (δ13C) in sediments present at mussel beds. These results suggest that habitat differences in the quality and source of organic matter are driving the observed patterns in the infaunal assemblages, including high β diversity and high variability in the macrofaunal community composition. This study is the first investigation of seep infauna along the U.S. Atlantic slope north of the Blake Ridge Diapir and provides a baseline for future regional comparisons to other seep habitats along the Atlantic margin.

Urinary Concentrations of Polycyclic Aromatic Hydrocarbon Metabolites in Maté Drinkers in Rio Grande do Sul, Brazil

PubMed Central

Lopes, Antonio Barros; Metzdorf, Marcela; Metzdorf, Luiza; Ramalho, Marcos Paulo; Kavalco, Caroline; Etemadi, Arash; Pritchett, Natalie R.; Murphy, Gwen; Calafat, Antonia M.; Abnet, Christian C.; Dawsey, Sanford M.; Fagundes, Renato Borges

2017-01-01

Background Consumption of maté, an infusion of the herb Ilex paraguariensis (yerba maté), is associated with increased risk of esophageal squamous cell carcinoma (ESCC), but the carcinogenic mechanism is unclear. Commercial brands of yerba maté contain high levels of carcinogenic polycyclic aromatic hydrocarbons (PAHs), which are acquired during the traditional drying process. The purpose of this study was to characterize exposure to PAHs in maté drinkers over a wide range of maté consumption. Methods We recruited 244 adults who answered a questionnaire and collected a fasting spot urine specimen. We quantified urinary concentrations of seven PAH metabolites, and assessed associations between self-reported recent maté consumption and urinary PAH metabolites by multivariate regression. Results Recent maté consumption showed a significant dose-response association with 6 of 7 PAH metabolites in unadjusted models (p-for-trend <0.05). After adjustment for creatinine and potential confounders, concentrations of 2-naphthol, 1-hydroxyphenanthrene, and the sum of 2- and 3-hydroxyphenanthrene remained significantly associated with recent maté intake. The sum of the urinary concentrations of the phenanthrene metabolites was similar or higher among maté drinkers who did not smoke than among smokers who did not drink maté. Conclusions Urinary concentrations of PAH metabolites were significantly associated with self-reported amount of recent maté intake, and drinking maté increased urinary concentrations of some PAH metabolites as much as smoking cigarettes. Impact Drinking maté is a source of exposure to potentially carcinogenic PAHs, consistent with the hypothesis that the PAH content of maté may contribute to the increased risk of ESCC in maté drinkers. PMID:29263183

Urinary Concentrations of Polycyclic Aromatic Hydrocarbon Metabolites in Maté Drinkers in Rio Grande do Sul, Brazil.

PubMed

Lopes, Antonio Barros; Metzdorf, Marcela; Metzdorf, Luiza; Sousa, Marcos Paulo Ramalho; Kavalco, Caroline; Etemadi, Arash; Pritchett, Natalie R; Murphy, Gwen; Calafat, Antonia M; Abnet, Christian C; Dawsey, Sanford M; Fagundes, Renato Borges

2018-03-01

Background: Consumption of maté , an infusion of the herb Ilex paraguariensis (yerba maté) , is associated with increased risk of esophageal squamous cell carcinoma (ESCC), but the carcinogenic mechanism is unclear. Commercial brands of yerba maté contain high levels of carcinogenic polycyclic aromatic hydrocarbons (PAHs), which are acquired during the traditional drying process. The purpose of this study was to characterize exposure to PAHs in maté drinkers over a wide range of maté consumption. Methods: We recruited 244 adults who answered a questionnaire and collected a fasting spot urine specimen. We quantified urinary concentrations of seven PAH metabolites and assessed associations between self-reported recent maté consumption and urinary PAH metabolites by multivariate regression. Results: Recent maté consumption showed a significant dose-response association with 6 of 7 PAH metabolites in unadjusted models ( P trend < 0.05). After adjustment for creatinine and potential confounders, concentrations of 2-naphthol, 1-hydroxyphenanthrene, and the sum of 2- and 3-hydroxyphenanthrene remained significantly associated with recent maté intake. The sum of the urinary concentrations of the phenanthrene metabolites was similar or higher among maté drinkers who did not smoke than among smokers who did not drink maté Conclusions: Urinary concentrations of PAH metabolites were significantly associated with self-reported amounts of recent maté intake, and drinking maté increased urinary concentrations of some PAH metabolites as much as smoking cigarettes. Impact: Drinking maté is a source of exposure to potentially carcinogenic PAHs, consistent with the hypothesis that the PAH content of maté may contribute to the increased risk of ESCC in maté drinkers. Cancer Epidemiol Biomarkers Prev; 27(3); 331-7. ©2017 AACR . ©2017 American Association for Cancer Research.

MatLab Script and Functional Programming

NASA Technical Reports Server (NTRS)

Shaykhian, Gholam Ali

2007-01-01

MatLab Script and Functional Programming: MatLab is one of the most widely used very high level programming languages for scientific and engineering computations. It is very user-friendly and needs practically no formal programming knowledge. Presented here are MatLab programming aspects and not just the MatLab commands for scientists and engineers who do not have formal programming training and also have no significant time to spare for learning programming to solve their real world problems. Specifically provided are programs for visualization. The MatLab seminar covers the functional and script programming aspect of MatLab language. Specific expectations are: a) Recognize MatLab commands, script and function. b) Create, and run a MatLab function. c) Read, recognize, and describe MatLab syntax. d) Recognize decisions, loops and matrix operators. e) Evaluate scope among multiple files, and multiple functions within a file. f) Declare, define and use scalar variables, vectors and matrices.

Ice Shelf Microbial Ecosystems in the High Arctic and Implications for Life on Snowball Earth

NASA Astrophysics Data System (ADS)

Vincent, W. F.; Gibson, J. A. E.; Pienitz, R.; Villeneuve, V.; Broady, P. A.; Hamilton, P. B.; Howard-Williams, C.

The Ward Hunt Ice Shelf (83°N, 74°W) is the largest remaining section of thick (>10m) landfast sea ice along the northern coastline of Ellesmere Island, Canada. Extensive meltwater lakes and streams occur on the surface of the ice and are colonized by photosynthetic microbial mat communities. This High Arctic cryo-ecosystem is similar in several of its physical, biological and geochemical features to the McMurdo Ice Shelf in Antarctica. The ice-mats in both polar regions are dominated by filamentous cyanobacteria but also contain diatoms, chlorophytes, flagellates, ciliates, nematodes, tardigrades and rotifers. The luxuriant Ward Hunt consortia also contain high concentrations (107-108cm-2) of viruses and heterotrophic bacteria. During periods of extensive ice cover, such as glaciations during the Proterozoic, cryotolerant mats of the type now found in these polar ice shelf ecosystems would have provided refugia for the survival, growth and evolution of a variety of organisms, including multicellular eukaryotes.

A novel methanol sensor based on gas-penetration through a porous polypyrrole-coated polyacrylonitrile nanofiber mat.

PubMed

Jun, Tae-Sun; Ho, Thi Anh; Rashid, Muhammad; Kim, Yong Shin

2013-09-01

In this work, we propose a novel chemoresistive gas sensor operated under a vertical analyte flow passing through a permeable sensing membrane. Such a configuration is different from the use of a planar sensor implemented under a conventional horizontal flow. A highly porous core-shell polyacrylonitrile-polypyrrole (PAN@PPy) nanofiber mat was prepared as the sensing element via electrospinning and two-step vapor-phase polymerization (VPP). Various analysis methods such as SEM, TEM, FT-IR and XPS measurements were employed in order to characterize structural features of the porous sensing mat. These analyses confirmed that very thin (ca. 10 nm) conductive PPy sheath layers were deposited by VPP on electrospun PAN nanofibers with an average diameter of 258 nm. Preliminary results revealed that the gas penetration-type PAN@PPy sensor had a higher sensor response and shorter detection and recovery times upon exposure to methanol analyte when compared with a conventional horizontal flow sensor due to efficient and fast analyte transfer into the sensing layer.

Synthetic-rubber extrusions form low cost roll-on solar collector

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

Smay, V.E.

1979-06-01

Synthetic rubber extrusions composed of ethylene propylene diene monomer (EPDM) have been developed in 4.4-inch-wide mats as solar absorbers that are light weight and simple to install. The mats, which come in rolls up to 600 ft long, have 6 small tubes alternating with thin webbing. EPDM has a lifespan of 30-50 yrs and maintains its flexibility within a temperature range of -80 to 375/sup 0/F. The mats are laid over rigid insulation and covered with glazing, detailed assembly instructions are provided. EPDM is not subject to corrosion and is not damaged by freezing water, a second EPDM extrusion ismore » used for glazed solar collectors. The efficiency of the design is attributed to the greater surface-to-mass ratio, permitting more heat collection, and the smaller mass of the synthetic rubber, which allows faster heat-up. The total cost for a complete, installed solar heating system of this type, including pumps, tanks, and plumbing, is about $12/ft/sup 2/.« less

Effect of free stall surface on daily activity patterns in dairy cows with relevance to lameness prevalence.

PubMed

Cook, N B; Bennett, T B; Nordlund, K V

2004-09-01

Differences in behavior of nonlame cows, slightly lame cows, and moderately lame cows in 6 free stall barns with sand bedding (SAND) vs. 6 free stall barns with rubber-crumb geotextile mattress surfaces (MAT) were documented in Wisconsin dairy herds. All lactating cows in the 12 herds were observed and given a locomotion score based on a 4-point scale: 1 = nonlame, 2 = slightly lame, 3 = moderately lame, and 4 = severely lame. Herd least square means +/-SE for prevalence of clinical lameness (locomotion scores = 3 and 4) were 11.1 vs. 24.0 +/- 1.7% for herds using SAND vs. MAT surfaces, respectively. Subsets of 10 cows per herd with locomotion scores of 1 to 3 were observed via video cameras for 24-h periods. Cows in MAT herds spent more time standing in free stalls per day than cows in SAND herds. Differences in standing times were 0.73 h/d for cows that were not lame, 2.32 h/d for cows that were slightly lame, and 4.31 h/d for cows that were moderately lame in MAT herds compared with equivalent cows in SAND herds. In MAT herds, the increase in time spent standing in the stall in moderately lame cows was associated with a significant reduction in stall use sessions per day, which impacted daily lying time. Although cause and effect are not clear, these findings have implications for housing, comfort, and care of cows in dairy herds with different types of free stall surfaces.

Fabrication and In Vitro/In Vivo Performance of Mucoadhesive Electrospun Nanofiber Mats Containing α-Mangostin.

PubMed

Samprasit, Wipada; Rojanarata, Theerasak; Akkaramongkolporn, Prasert; Ngawhirunpat, Tanasait; Kaomongkolgit, Ruchadaporn; Opanasopit, Praneet

2015-10-01

This study aimed to fabricate mucoadhesive electrospun nanofiber mats containing α-mangostin for the maintenance of oral hygiene and reduction of the bacterial growth that causes dental caries. Synthesized thiolated chitosan (CS-SH) blended with polyvinyl alcohol (PVA) was selected as the mucoadhesive polymer. α-Mangostin was incorporated into the CS-SH/PVA solution and electrospun to obtain nanofiber mats. Scanning electron microscopy, differential scanning calorimetry, X-ray diffraction, and tensile strength testing were used to characterize the mats. The swelling degree and mucoadhesion were also determined. The nanofiber mats were further evaluated regarding their α-mangostin content, in vitro α-mangostin release, antibacterial activity, cytotoxicity, in vivo performance, and stability. The results indicated that the mats were in the nanometer range. The α-mangostin was well incorporated into the mats, with an amorphous form. The mats showed suitable tensile strength, swelling, and mucoadhesive properties. The loading capacity increased when the initial amount of α-mangostin was increased. Rapid release of α-mangostin from the mats was achieved. Additionally, a fast bacterial killing rate occurred at the lowest concentration of nanofiber mats when α-mangostin was added to the mats. The mats were less cytotoxic after use for 72 h. Moreover, in vivo testing indicated that the mats could reduce the number of oral bacteria, with a good mouth feel. The mats maintained the amount of α-mangostin for 6 months. The results suggest that α-mangostin-loaded mucoadhesive electrospun nanofiber mats may be a promising material for oral care and the prevention of dental caries.

ERB master archival tape specification no. T 134081 ERB MAT, revision 1

NASA Technical Reports Server (NTRS)

1984-01-01

The Earth radiation budget (ERB)MAT tapes are generated by the ERB MATGEN software using the IBM 3081 computer system operated by the Science and Applications Computer Center at Goddard Space Flight Center. All MAT's are 9-track and MAT data are in ascending time order. The gross tape format for NIMBUS year-1 and year-2 MAT's is different from the format of MAT's starting with year-3. The MATs from the first two years are to contain one day's worth of data while all other MATs are to contain multiple day's worth of data stacked onto the tapes.

Kobresia pygmaea pasture degradation and its response to increasing N deposition

NASA Astrophysics Data System (ADS)

Liu, Shibin; Schleuss, Per-Marten; Kuzyakov, Yakov

2016-04-01

Kobresia pygmaea is a dominant plant species on the Tibetan Plateau covering ca. one fifth of the total area. Severe degradation by overgrazing is ongoing at K. pygmaea pastures in recent decades. Nitrogen (N) deposition is also increasingly exacerbated across the Tibetan Plateau. Up to now the response of K. pygmaea pastures with increasing degradation to N deposition is unclear. We aimed at: (1) evaluating the effect of pasture degradation on carbon (C) and N contents of soil, root, microbial biomass and leachate, (2) determining N allocation to plant, soil and microbial biomass after N addition and (3) making an estimation of N storage and loss in Kobresia pasture. We used three Kobresia root mat types varying in their degradation stages: (1) living root mats, (2) dying root mats and (3) dead root mats. We also added two levels of 15NH415NO3 solution to simulate N deposition (control: 2.5 kg N/ha; deposition 50.9 kg N/ha) and traced the 15N in the soil-plant system. Leaching of NH4+, NO3- and DON were detected by homogeneously adding distilled water to each sample and collecting the leachate afterwards. Total N content lost by leaching increased 6.5 times following the degradation from living to dead root mats. This indicated that living Kobresia effectively decreased N loss from leaching due to N uptake by plants. The microbial biomass C to N (MBC/MBN) ratio narrowed from 10.2 to 7.5 and then to 5.0 for living, dying and dead root mats, respectively. This shows the degradation K. pygmaea shift the ecosystem from a N-limited to a C-limited status for microbes. Nitrogen addition increased above-ground plant biomass (AGB) as well as its total N content in living root mat while MBC and MBN were not affected. This shows K. pygmaea is more sensitive to N addition than microorganisms. N allocation (% of total N added) by AGB, below-ground plant biomass and soil in living root mats were 22.1%, 22.7% and 17.6%, respectively. No significant effect between these parameters was identified indicating that N allocation was independent to the giving amount of N. Up to 1.86 Mg N/ha were stored in living root mat (0-5 cm). In contrast, dead and dying root mats maintained about 2.0 Mg N/ha and 2.1 Mg N/ha, respectively. N loss in leachate of living root mat regarding a precipitation of 355 mm during growing season (equal to 85% of annual precipitation) was estimated to be around 3.6 kg N/ha (3.4 kg DON and 0.2 kg NH4-N). This amount was up to 6.5 times higher in dead root mat (23.6 kg N/ha with 19.1 kg NO3-N, 4 kg DON and 0.5 kg NH4-N). Therefore, degradation of K. pygmaea significantly increased N loss via leaching, especially NO3-N loss. We conclude N deposition facilitates the growth of K. pygmaea, which may positively affect plant productivity as well as C sequestration. In the absence of K. pygmaea, however, N deposition will lead to high N loss. Key words: Nitrogen allocation, Kobresia pygmaea, above-ground biomass, microbial biomass carbon and nitrogen

[Preparation of carbon fiber reinforced fluid type resin denture (author's transl)].

PubMed

Kasuga, H; Sato, H; Nakabayashi, N

1980-01-01

Transverse strength of cured fluid resins is weaker than that of the heat cured. We have studied to improve the mechanical strength of self-cured acrylic resin by application of carbon fibers as reinforcement and simple methods which must be acceptable for technicians are proposed. A cloth type carbon fiber was the best reinforcement among studied carbon fibers such as chopped or mat. The chopped fibers were difficult to mix homogeneously with fluid resins and effectiveness of the reinforcement was low. Breaking often occurred at the interface between the reinforcement and resin in the cases of mat which gave defects to the test specimens. To prepare reinforced denture, the cloth was trimmed on the master cast after removal of wax and the prepreg was formed with the alginate impression on the cast by Palapress and the cloth. Other steps were same as the usual fluid resin.

Electrospun polymeric dressings functionalized with antimicrobial peptides and collagen type I for enhanced wound healing

NASA Astrophysics Data System (ADS)

Felgueiras, H. P.; Amorim, M. T. P.

2017-10-01

Modern wound dressings combine medical textiles with active compounds that stimulate wound healing while protecting against infection. Electrospun wound dressings have been extensively studied and the electrospinning technique recognized as an efficient approach for the production of nanoscale fibrous mats. The unique diverse function and architecture of antimicrobial peptides (AMPs) has attracted considerable attention as a tool for the design of new anti-infective drugs. Functionalizing electrospun wound dressings with these AMPs is nowadays being researched. In the present work, we explore these new systems by highlighting the most important characteristics of electropsun wound dressings, revealing the importance of AMPs to wound healing, and the methods available to functionalize the electrospun mats with these molecules. The combined therapeutic potential of collagen type I and these AMP functionalized dressings will be highlighted as well; the significance of these new strategies for the future of wound healing will be clarified.

MatMRI and MatHIFU: software toolboxes for real-time monitoring and control of MR-guided HIFU

PubMed Central

2013-01-01

Background The availability of open and versatile software tools is a key feature to facilitate pre-clinical research for magnetic resonance imaging (MRI) and magnetic resonance-guided high-intensity focused ultrasound (MR-HIFU) and expedite clinical translation of diagnostic and therapeutic medical applications. In the present study, two customizable software tools that were developed at the Thunder Bay Regional Research Institute are presented for use with both MRI and MR-HIFU. Both tools operate in a MATLAB®; environment. The first tool is named MatMRI and enables real-time, dynamic acquisition of MR images with a Philips MRI scanner. The second tool is named MatHIFU and enables the execution and dynamic modification of user-defined treatment protocols with the Philips Sonalleve MR-HIFU therapy system to perform ultrasound exposures in MR-HIFU therapy applications. Methods MatMRI requires four basic steps: initiate communication, subscribe to MRI data, query for new images, and unsubscribe. MatMRI can also pause/resume the imaging and perform real-time updates of the location and orientation of images. MatHIFU requires four basic steps: initiate communication, prepare treatment protocol, and execute treatment protocol. MatHIFU can monitor the state of execution and, if required, modify the protocol in real time. Results Four applications were developed to showcase the capabilities of MatMRI and MatHIFU to perform pre-clinical research. Firstly, MatMRI was integrated with an existing small animal MR-HIFU system (FUS Instruments, Toronto, Ontario, Canada) to provide real-time temperature measurements. Secondly, MatMRI was used to perform T2-based MR thermometry in the bone marrow. Thirdly, MatHIFU was used to automate acoustic hydrophone measurements on a per-element basis of the 256-element transducer of the Sonalleve system. Finally, MatMRI and MatHIFU were combined to produce and image a heating pattern that recreates the word ‘HIFU’ in a tissue-mimicking heating phantom. Conclusions MatMRI and MatHIFU leverage existing MRI and MR-HIFU clinical platforms to facilitate pre-clinical research. MatMRI substantially simplifies the real-time acquisition and processing of MR data. MatHIFU facilitates the testing and characterization of new therapy applications using the Philips Sonalleve clinical MR-HIFU system. Under coordination with Philips Healthcare, both MatMRI and MatHIFU are intended to be freely available as open-source software packages to other research groups. PMID:25512856

A new experimental material for modeling relief dynamics and interactions between tectonics and surface processes

NASA Astrophysics Data System (ADS)

Graveleau, F.; Hurtrez, J.-E.; Dominguez, S.; Malavieille, J.

2011-12-01

We developed a new granular material (MatIV) to study experimentally landscape evolution in active mountain belt piedmonts. Its composition and related physical properties have been determined using empirical criteria derived from the scaling of deformation, erosion-transport and sedimentation natural processes. MatIV is a water-saturated composite material made up with 4 granular components (silica powder, glass microbeads, plastic powder and graphite) whose physical, mechanical and erosion-related properties were measured with different laboratory tests. Mechanical measurements were made on a modified Hubbert-type direct shear apparatus. Erosion-related properties were determined using an experimental set-up that allows quantifying the erosion/sedimentation budget from tilted relaxation topographies. For MatIV, we also investigated the evolution of mean erosion rates and stream power erosion law exponents in 1D as a function of slope. Our results indicate that MatIV satisfies most of the defined criteria. It deforms brittlely according to the linear Mohr-Coulomb failure criterion and localizes deformation along discrete faults. Its erosion pattern is characterized by realistic hillslope and channelized processes (slope diffusion, mass wasting, channel incision). During transport, eroded particles are sorted depending on their density and shape, which results in stratified alluvial deposits displaying lateral facies variations. To evaluate the degree of similitude between model and nature, we used a new experimental device that combines accretionary wedge deformation mechanisms and surface runoff erosion processes. Results indicate that MatIV succeeded in producing detailed morphological and sedimentological features (drainage basin, channel network, terrace, syntectonic alluvial fan). Geometric, kinematic and dynamic similarity criteria have been investigated to compare precisely model to nature. Although scaling is incomplete, it yields particularly informative orders of magnitude. With all these characteristics, MatIV appears as a very promising material to investigate experimentally a wide range of scientific questions dealing with relief dynamics and interactions between tectonics, erosion and sedimentation processes.

Benthic Community Structure and Sediment Geochemical Properties at Hydrocarbon Seeps Along the Continental Slope of the Western North Atlantic

NASA Astrophysics Data System (ADS)

Demopoulos, A. W.; Bourque, J. R.; Brooke, S.

2015-12-01

Hydrocarbon seeps support distinct benthic communities capable of utilizing reduced chemical compounds for nutrition. In recent years, methane seepage has been increasingly documented along the continental slope of the U.S. Atlantic margin. In 2012 and 2013, two seeps were investigated in this region: a shallow site near Baltimore Canyon (410-450 m) and a deep site near Norfolk Canyon (1600 m). Both sites contain extensive mussel beds and microbial mats. Sediment cores and grab samples were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 mm) in relationship to the associated sediment environment (organic carbon and nitrogen, stable isotopes 13C and 15N, grain size, and depth) of mussel beds, mats, and slope habitats. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments. Macrofaunal communities were distinctly different both between depths and among habitat types. Specifically, microbial mat sediments were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in Baltimore microbial mat habitats, but higher in mussel and slope sediments compared to Norfolk seep habitats found at deeper depths. Multivariate statistical analysis identified sediment carbon:nitrogen (C:N) ratios and 13C values as important variables for structuring the macrofaunal communities. Higher C:N ratios were present within microbial mat habitats and depleted 13C values occurred in sediments adjacent to mussel beds found in Norfolk Canyon seeps. Differences in the quality and source of organic matter present in the seep habitats are known to be important drivers in macrofaunal community structure and associated food webs. The multivariate analysis provides new insight into the relative importance of the seep sediment quality in supporting dense macrofaunal communities compared to other seeps found throughout the region.

Brucite-carbonate chimneys found at the Shinkai Seep Field, a serpentine-hosted vent system in the Southern Mariana Forearc

NASA Astrophysics Data System (ADS)

Okumura, T.; Ohara, Y.; Stern, R. J.; Yamanaka, T.; Onishi, Y.; Watanabe, H.; Chen, C.; Bloomer, S. H.; Pujana, I.; Sakai, S.; Ishii, T.; Takai, K.

2016-12-01

Brucite-carbonate chimneys have been discovered from the Shinkai Seep Field (SSF) in the southernmost Mariana forearc, on the landward trench slope to the northeast of the Challenger Deep. SSF is the deepest known ( 5700 mbsl) serpentinization-hosted cold seep and associated ecosystem. Explorations of SSF over the past six years led to the discovery of eleven vesicomyid clam colony sites and four chimney sites occurring within an area of 500 square meters. Observations and geochemical analysis reveal three types (I-III) of chimneys, formed by the precipitation and dissolution of constitutive minerals. Type I chimneys are bright white to light yellow, have a spiky crystalline and wrinkled surface with active microbial mats, and are mostly brucite; these formed by rapid precipitation from vent fluid under high fluid flux conditions. Type II chimneys are white to dull brown, show tuberous textures like vascular bundles, and are covered with grayish microbial mats and dense populations of the polychaete Phyllochaetopterus. This type of chimney contains more carbonate than type I chimney because of precipitation under lower fluid flux conditions and re-equilibration with seawater. Type III chimneys are ivory colored with surface depressions and lack living microbial mats or animals. This type of chimney is mostly carbonate and is actively dissolving. Stable carbon isotope compositions of carbonates in the two types (I and II) of active chimneys are extremely enriched in δ13C (up to +24.1‰), likely reflecting microbial consumption of 12C from extremely low concentration of dissolved inorganic carbon in the serpentinization-driven alkaline fluid. The active SSF chimneys are also unique in that they sustain abundant endo- and epi-lithic Phyllochaetopterus populations. The geochemical and geobiological features of the SSF chimney are distinct from those in the Lost City hydrothermal field near Mid-Atlantic Ridge, another serpentinization-driven hydrothermal system. Our findings shed light on the variability of subseafloor and seafloor geochemical and geobiological processes in the global deep-sea serpentinite-hosted fluid discharge systems.

Genetic diversity among sea otter isolates of Toxoplasma gondii

USGS Publications Warehouse

Sundar, N.; Cole, Rebecca A.; Thomas, N.J.; Majumdar, D.; Dubey, J.P.; Su, C.

2008-01-01

Sea otters (Enhydra lutris) have been reported to become infected with Toxoplasma gondiiand at times succumb to clinical disease. Here, we determined genotypes of 39 T. gondiiisolates from 37 sea otters in two geographically distant locations (25 from California and 12 from Washington). Six genotypes were identified using 10 PCR-RFLP genetic markers including SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico, and by DNA sequencing of loci SAG1 and GRA6 in 13 isolates. Of these 39 isolates, 13 (33%) were clonal Type II which can be further divided into two groups at the locus Apico. Two of the 39 isolates had Type II alleles at all loci except a Type I allele at locus L358. One isolate had Type II alleles at all loci except the Type I alleles at loci L358 and Apico. One isolate had Type III alleles at all loci except Type II alleles at SAG2 and Apico. Two sea otter isolates had a mixed infection. Twenty-one (54%) isolates had an unique allele at SAG1 locus. Further genotyping or DNA sequence analysis for 18 of these 21 isolates at loci SAG1 and GRA6 revealed that there were two different genotypes, including the previously identified Type X (four isolates) and a new genotype named Type A (14 isolates). The results from this study suggest that the sea otter isolates are genetically diverse.

Locus of Control and Sex Differences in Performance on an Instructional Task.

ERIC Educational Resources Information Center

Holloway, Richard L.; Robinson, Beatrice

1979-01-01

Used locus of control, ability, sex, task selection, task structure, and recall in a regression model to predict affective response to type of instruction of 104 high school seniors. Results showed a main effect for recall, and interaction effects for recall x sex and recall x ability. References are listed. (Author/JEG)

Effects of Locus of Control and Learner-Control on Web-Based Language Learning

ERIC Educational Resources Information Center

Chang, Mei-Mei; Ho, Chiung-Mei

2009-01-01

The study explored the effects of students' locus of control and types of control over instruction on their self-efficacy and performance in a web-based language learning environment. A web-based interactive instructional program focusing on the comprehension of news articles for English language learners was developed in two versions: learner-…

Locus of Control as a Function of Family Type and Age at Onset of Father Absence.

ERIC Educational Resources Information Center

Parish, Thomas S.; Nunn, Gerald D.

1983-01-01

American undergraduate students (n = 644) completed the Rather Internality-Externality Scale and provided information on their family background. Subjects were grouped according to father absence, cause of this absence, and their age at the time this event occurred. Results indicated locus of control varied markedly as a function of these…

The Effects of Low Sulfate Concentrations on Modern Microbial Mat Communities: A Long Term Manipulation

NASA Technical Reports Server (NTRS)

Bebout, Brad; Carpenter, Steve; DesMarais, David J.; Discipulo, Mykell; Hogan, Mary; Turk, Kendra

2002-01-01

Microbial mats were widespread during the first ca. 2 Ga. of our biosphere's history. To better understand microbial ecosystems and their biomarkers under the low sulfate levels present in early oceans, we attempted a long-term (ca. 1 year) manipulation of sulfate in modem mats. Mats collected from salt ponds at Guerrero Negro, Baja Calif. Sur were incubated in a Greenhouse "Collaboratory" at Ames. Mats were maintained in artificial seawater brine containing either: 1) sulfate levels normal for these mats (70 mM), or 2) brine in which sulfate was replaced by chloride. Sulfate concentrations in the "low sulfate" brine gradually approached their lowest (to date) value of 0. 1 mM as sulfate was consumed and/or diffused out of the mat over a period of ca. 4 months. During that period of time, a number of differences between the treatments emerged. Relative to the "low sulfate" mats, "normal sulfate" mats had: 1) lower consumption of oxygen in the lower levels of the mat, 2) higher efficiencies of oxygenic photosynthesis, and 3) higher rates of nitrogen fixation. Rates of methane production by the mats increased greatly as sulfate concentrations fell below ca. 0.2 mM. In contrast, "low" and "normal" sulfate mats had similar net rates of exchange of O2 and dissolved inorganic C between the mats and overlying water. Reduced sulfate levels have diverse impacts upon these ecosystems.

Flight Test of Advanced Digital Control Concepts.

DTIC Science & Technology

1982-03-01

34 equations, and this result is then compared against the "model" equations. OPTION :::CREATrE ,CIEY, COFPY, MAT ,AMAT, COIP-YUMAT, BMAT , 74 COPFY, CMAT...BMATY .-COPY, NMAT, AMAT ,72 ,COPY, GMAT, RMA, COP:Y, (MAT, BMA’TCOFY, MA T ,AMAT >74, COPY, CMA’TsmA, PCOPY, RMAT, BmAT , pCOPYVMiAT , AMAo.T 72...COP’Y, MAT, AMAT, >75, COPY , MAtT, BMAT , COPY, ZMAT, AMAT, 74 ,COP’Y, MAT, TMAT, COPY, VMAT, AMAT, .:COPY ,RMAiT, MAT,73,COPW GMAT, E4MAT, COP-"YTMAT

Cell Specific eQTL Analysis without Sorting Cells

PubMed Central

Esko, Tõnu; Peters, Marjolein J.; Schurmann, Claudia; Schramm, Katharina; Kettunen, Johannes; Yaghootkar, Hanieh; Fairfax, Benjamin P.; Andiappan, Anand Kumar; Li, Yang; Fu, Jingyuan; Karjalainen, Juha; Platteel, Mathieu; Visschedijk, Marijn; Weersma, Rinse K.; Kasela, Silva; Milani, Lili; Tserel, Liina; Peterson, Pärt; Reinmaa, Eva; Hofman, Albert; Uitterlinden, André G.; Rivadeneira, Fernando; Homuth, Georg; Petersmann, Astrid; Lorbeer, Roberto; Prokisch, Holger; Meitinger, Thomas; Herder, Christian; Roden, Michael; Grallert, Harald; Ripatti, Samuli; Perola, Markus; Wood, Andrew R.; Melzer, David; Ferrucci, Luigi; Singleton, Andrew B.; Hernandez, Dena G.; Knight, Julian C.; Melchiotti, Rossella; Lee, Bernett; Poidinger, Michael; Zolezzi, Francesca; Larbi, Anis; Wang, De Yun; van den Berg, Leonard H.; Veldink, Jan H.; Rotzschke, Olaf; Makino, Seiko; Salomaa, Veikko; Strauch, Konstantin; Völker, Uwe; van Meurs, Joyce B. J.; Metspalu, Andres; Wijmenga, Cisca; Jansen, Ritsert C.; Franke, Lude

2015-01-01

The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn’s disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus. PMID:25955312

Genetic heterogeneity in psoriasis vulgaris based on linkage analyses of a large family material

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

Wahlstroem, J.; Swanbeck, G.; Inerot, A.

1994-09-01

Information on psoriasis among parents and siblings in 14,008 families has been collected. On the basis of this material, evidence for monogenetic autosomal recessive inheritance of psoriasis has recently been presented. Indications from more than one type of non-pustular psoriasis has been obtained from the population genetic data. Molecular genetic linkage analysis of psoriasis to a number of polymorphic genetic markers for a large number of families has been made. It is apparent that there is genetic heterogeneity in a psoriasis population with regard to psoriasis genes. Using the computer program Linkage 5.0 and a formula for heterogeneity, a lodscoremore » over 3.0 for one locus has been obtained. This locus has further been confirmed by several other markers in the vicinity. The locus found is linked to slightly over half of the families, indicating that there are more genetically independent types of psoriasis. The age at onset of those families that are apparently linked to this locus have a slightly higher age at onset than those not linked to that locus but with a considerable overlap. In spite of close coverage of the whole chromosomes number 6 and 17, no linkage has been found in this regions. This indicates that neither the HLA region nor the region earlier found to be involved in one family with psoriasis are primarily involved in our families.« less

One year nationwide evaluation of 24-locus MIRU-VNTR genotyping on Slovenian Mycobacterium tuberculosis isolates.

PubMed

Bidovec-Stojkovic, Urska; Zolnir-Dovc, Manca; Supply, Philip

2011-10-01

Slovenia is one of the few countries where IS6110 RFLP is applied for genotyping M. tuberculosis at a nationwide level, which has been in effect since 2000. Based on S6110 RFLP clustering, typical risk factors and routes of M. tuberculosis transmission were identified, such as alcohol abuse, homelessness, and bars. However, IS6110 RFLP typing suffers from important limitations including a long wait for results, which reduces the potential benefit of molecular-guided tuberculosis (TB) control. PCR-based 24-locus MIRU-VNTR typing combined with spoligotyping has recently emerged as a potential alternative for faster, large-scale genotyping of M. tuberculosis. We compared these genotyping methods for analyzing 196 Slovenian Mycobacterium tuberculosis isolates representing 97.5% of all culture-positive cases included in the Slovenian TB Registry in 2008. IS6110 RFLP and 24-locus MIRU-VNTR typing combined with spoligotyping identified 157 and 155 distinct profiles, 135 and 125 unique isolates, and 61 and 71 clustered isolates grouped into 22 and 29 clusters, respectively. The discriminatory indexes were very close, at 0.9963 and 0.9965, respectively. The majority of the molecular clusters defined by either of the two methods were identical, including in the few cases for which epidemiological links were available. The differences frequently consisted of single-band changes in IS6170-RFLP profiles subdividing a MIRU-VNTR/spoligotype-based cluster. Our one-year nationwide study showed that the results of 24-locus MIRU-VNTR typing combined with spoligotyping reached a high level of concordance with those obtained from IS6110 RFLP typing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Foam-mat drying technology: A review.

PubMed

Hardy, Z; Jideani, V A

2017-08-13

This article reviews various aspects of foam-mat drying such as foam-mat drying processing technique, main additives used for foam-mat drying, foam-mat drying of liquid and solid foods, quality characteristics of foam-mat dried foods, and economic and technical benefits for employing foam-mat drying. Foam-mat drying process is an alternative method that allows the removal of water from liquid materials and pureed materials. In this drying process, a liquid material is converted into foam that is stable by being whipped after adding an edible foaming agent. The stable foam is then spread out in sheet or mat and dried by using hot air (40-90°C) at atmospheric pressure. Methyl cellulose (0.25-2%), egg white (3-20%), maltodextrin (0.5-05%), and gum Arabic (2-9%) are the commonly utilized additives for the foam-mat drying process at the given range, either combined together for their effectiveness or individual effect. The foam-mat drying process is suitable for heat sensitive, viscous, and sticky products that cannot be dried using other forms of drying methods such as spray drying because of the state of product. More interest has developed for foam-mat drying because of the simplicity, cost effectiveness, high speed drying, and improved product quality it provides.

Comparison of double-locus sequence typing (DLST) and multilocus sequence typing (MLST) for the investigation of Pseudomonas aeruginosa populations.

PubMed

Cholley, Pascal; Stojanov, Milos; Hocquet, Didier; Thouverez, Michelle; Bertrand, Xavier; Blanc, Dominique S

2015-08-01

Reliable molecular typing methods are necessary to investigate the epidemiology of bacterial pathogens. Reference methods such as multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) are costly and time consuming. Here, we compared our newly developed double-locus sequence typing (DLST) method for Pseudomonas aeruginosa to MLST and PFGE on a collection of 281 isolates. DLST was as discriminatory as MLST and was able to recognize "high-risk" epidemic clones. Both methods were highly congruent. Not surprisingly, a higher discriminatory power was observed with PFGE. In conclusion, being a simple method (single-strand sequencing of only 2 loci), DLST is valuable as a first-line typing tool for epidemiological investigations of P. aeruginosa. Coupled to a more discriminant method like PFGE or whole genome sequencing, it might represent an efficient typing strategy to investigate or prevent outbreaks. Copyright © 2015 Elsevier Inc. All rights reserved.

Effective application of multiple locus variable number of tandem repeats analysis to tracing Staphylococcus aureus in food-processing environment.

PubMed

Rešková, Z; Koreňová, J; Kuchta, T

2014-04-01

A total of 256 isolates of Staphylococcus aureus were isolated from 98 samples (34 swabs and 64 food samples) obtained from small or medium meat- and cheese-processing plants in Slovakia. The strains were genotypically characterized by multiple locus variable number of tandem repeats analysis (MLVA), involving multiplex polymerase chain reaction (PCR) with subsequent separation of the amplified DNA fragments by an automated flow-through gel electrophoresis. With the panel of isolates, MLVA produced 31 profile types, which was a sufficient discrimination to facilitate the description of spatial and temporal aspects of contamination. Further data on MLVA discrimination were obtained by typing a subpanel of strains by multiple locus sequence typing (MLST). MLVA coupled to automated electrophoresis proved to be an effective, comparatively fast and inexpensive method for tracing S. aureus contamination of food-processing factories. Subspecies genotyping of microbial contaminants in food-processing factories may facilitate identification of spatial and temporal aspects of the contamination. This may help to properly manage the process hygiene. With S. aureus, multiple locus variable number of tandem repeats analysis (MLVA) proved to be an effective method for the purpose, being sufficiently discriminative, yet comparatively fast and inexpensive. The application of automated flow-through gel electrophoresis to separation of DNA fragments produced by multiplex PCR helped to improve the accuracy and speed of the method. © 2013 The Society for Applied Microbiology.

Refinement of a locus for autosomal dominant hereditary motor and sensory neuropathy with proximal dominancy (HMSN-P) and genetic heterogeneity.

PubMed

Maeda, Kouji; Kaji, Ryuji; Yasuno, Katsuhito; Jambaldorj, Jamiyansuren; Nodera, Hiroyuki; Takashima, Hiroshi; Nakagawa, Masanori; Makino, Satoshi; Tamiya, Gen

2007-01-01

Hereditary motor and sensory neuropathy with proximal dominancy (HMSN-P) is an adult-onset peripheral neurodegenerative disorder which has been reported only in the Okinawa Islands, Japan. The disease locus of "Okinawa-type" HMSN-P has been previously mapped to 3q13.1, with all affected individuals sharing an identical haplotype around the locus, suggesting that the undiscovered causative mutation in HMSN-P originated from a single founder. We have newly found two large families from the western part of Japan within which multiple members developed symptoms similar to those exhibited by HMSN-P patients from Okinawa, with no record of affinal connection between the islands. Using these pedigrees with "Kansai-type" HMSN-P, we carried out a linkage study utilizing eight microsatellite markers and identified a candidate region on 3q13.1 cosegregating with the disease (maximum two-point LOD score of 8.44 at theta=0.0) overlapping with the Okinawa-type HMSN-P locus. However, the disease haplotype shared among all affected members in these families was different from that in the Okinawa kindred, suggesting allelic heterogeneity. Such allelic variation should aid in the identification of the disease-causative gene. Moreover, the allelic heterogeneity of HMSN-P in the Japanese population suggests that HMSN-P may be more common across other ethnic groups, but classified into other disease categories.

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.).

PubMed

Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

2015-06-01

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding.

Serological investigation of Leptospira infection and its circulation in one intensive-type water buffalo farm in the Philippines.

PubMed

Villanueva, Marvin A; Mingala, Claro N; Gloriani, Nina G; Yanagihara, Yasutake; Isoda, Norikazu; Nakajima, Chie; Suzuki, Yasuhiko; Koizumi, Nobuo

2016-02-01

Water buffalo is an indispensable livestock in the Philippines. Leptospirosis is a serious zoonosis that can be fatal to humans and cause reproductive problems in livestock. Leptospirosis has been reported in some countries where water buffaloes are commercially raised, highlighting the Leptospira prevalence in this farming system, but information on leptospirosis in water buffalo farms in the Philippines is limited. In this study, we collected blood samples from rats (n = 21), and water buffaloes (n = 170) from different groups and locations in one intensive-type buffalo farm in the Philippines. Serum was analyzed by microscopic agglutination test (MAT). Anti-Leptospira antibodies reacting with serogroups Canicola, Icterohaemorrhagiae and Pomona were found in sera of 30% tested rats, and 48% of water buffalo sera tested positive for at least one Leptospira strain, in which serogroups Mini, Hebdomadis, Tarassovi and Pyrogenes were predominantly agglutinated. The number of seropositive young water buffaloes (< 1 year-old) was lower than that of older seropositive ones. Furthermore, sera from younger water buffaloes were reactive with single serotypes with low MAT titers, but older animals were reactive with multiple Leptospira strains with variable MAT titers. In addition, antibodies against serogroups Icterohaemorrhagiae and Pomona were detected in both animals. Finally, Leptospira infection was found associated with age and animal grouping, highlighting the impact of management in the persistence of leptospirosis at intensive-type buffalo farm settings in the Philippines. Further investigation and appropriate control strategies are required to prevent leptospirosis from causing risks to public health and economic losses to the water buffalo farming industry.

Novel insights into the composition, variation, organization, and expression of the low-molecular-weight glutenin subunit gene family in common wheat

PubMed Central

Zhang, Xiaofei; Liu, Dongcheng; Zhang, Jianghua; Jiang, Wei; Luo, Guangbin; Yang, Wenlong; Sun, Jiazhu; Tong, Yiping; Cui, Dangqun; Zhang, Aimin

2013-01-01

Low-molecular-weight glutenin subunits (LMW-GS), encoded by a complex multigene family, play an important role in the processing quality of wheat flour. Although members of this gene family have been identified in several wheat varieties, the allelic variation and composition of LMW-GS genes in common wheat are not well understood. In the present study, using the LMW-GS gene molecular marker system and the full-length gene cloning method, a comprehensive molecular analysis of LMW-GS genes was conducted in a representative population, the micro-core collections (MCC) of Chinese wheat germplasm. Generally, >15 LMW-GS genes were identified from individual MCC accessions, of which 4–6 were located at the Glu-A3 locus, 3–5 at the Glu-B3 locus, and eight at the Glu-D3 locus. LMW-GS genes at the Glu-A3 locus showed the highest allelic diversity, followed by the Glu-B3 genes, while the Glu-D3 genes were extremely conserved among MCC accessions. Expression and sequence analysis showed that 9–13 active LMW-GS genes were present in each accession. Sequence identity analysis showed that all i-type genes present at the Glu-A3 locus formed a single group, the s-type genes located at Glu-B3 and Glu-D3 loci comprised a unique group, while high-diversity m-type genes were classified into four groups and detected in all Glu-3 loci. These results contribute to the functional analysis of LMW-GS genes and facilitate improvement of bread-making quality by wheat molecular breeding programmes. PMID:23536608

Ecophysiological Changes in Microbial Mats Incubated in a Greenhouse Collaboratory

NASA Technical Reports Server (NTRS)

Bebout, Brad; DesMarais, David J.; GarciaPichel, Ferran; Hogan, Mary; Jahnke, Linda; Keller, Richard M.; Miller, Scott R.

2001-01-01

Microbial mats are modern examples of the earliest microbial communities known. Among the best studied are microbial mats growing in hypersaline ponds managed for the production of salt by Exportadora de Sal, S.A. de C.V., Guerrero Negro, Baja California Sur, Mexico. In May, 2001, we collected mats from Ponds 4 and 5 in this system and returned them to Ames Research Center, where they have been maintained for a period of over nine months. We report here on both the ecophysiological changes occurring in the mats over that period of time as well as the facility in which they were incubated. Mats (approximately 1 sq. meter total area) were incubated in a greenhouse facility modified to provide the mats with natural levels of visible and ultraviolet radiation as well as constantly flowing, temperature-controlled water. Two replicated treatments were maintained, a 'high salinity' treatment (about 120 ppt) and a 'low salinity' treatment (about 90 ppt). Rates of net biological activity (e.g., photosynthesis, respiration, trace gas production) in the mats were relatively constant over the several months, and were similar to rates of activity measured in the field. However, over the course of the incubation, mats in both treatments changed in physical appearance. The most obvious change was that mats in the higher salinity treatments developed a higher proportion of carotenoid pigments (relative to chlorophyll), resulting in a noticeably orange color in the high salinity mats. This trend is also seen in the natural salinity gradient present at the field site. Changes in the community composition of the mats, as assayed by denaturing gradient gel electrophoresis (DGGE), as well as biomarker compounds produced in the mats were also monitored. The degree to which the mats kept in the greenhouse changed from the originally collected mats, as well as differences between high and low salinity mats will be discussed. Additional information is contained in the original extended abstract.

Marked Phenotypic Heterogeneity Associated with Expansion of a CAG Repeat Sequence at the Spinocerebellar Ataxia 3/Machado-Joseph Disease Locus

PubMed Central

Cancel, Géraldine; Abbas, Nacer; Stevanin, Giovanni; Dürr, Alexandra; Chneiweiss, Hervé; Néri, Christian; Duyckaerts, Charles; Penet, Christiane; Cann, Howard M.; Agid, Yves; Brice, Alexis

1995-01-01

The spinocerebellar ataxia 3 locus (SCA3) for type I autosomal dominant cerebellar ataxia (ADCA type I), a clinically and genetically heterogeneous group of neuro-degenerative disorders, has been mapped to chromosome 14q32.1. ADCA type I patients from families segregating SCA3 share clinical features in common with those with Machado-Joseph disease (MJD), the gene of which maps to the same region. We show here that the disease gene segregating in each of three French ADCA type I kindreds and in a French family with neuropatho-logical findings suggesting the ataxochoreic form of dentatorubropallidoluysian atrophy carries an expanded CAG repeat sequence located at the same locus as that for MJD. Analysis of the mutation in these families shows a strong negative correlation between size of the expanded CAG repeat and age at onset of clinical disease. Instability of the expanded triplet repeat was not found to be affected by sex of the parent transmitting the mutation. Evidence was found for somatic and gonadal mosaicism for alleles carrying expanded trinucleotide repeats. ImagesFigure 3Figure 5 PMID:7573040

Organization and PprB-dependent control of the Pseudomonas aeruginosa tad Locus, involved in Flp pilus biology.

PubMed

Bernard, Christophe S; Bordi, Christophe; Termine, Elise; Filloux, Alain; de Bentzmann, Sophie

2009-03-01

Bacterial attachment to the substratum involves several cell surface organelles, including various types of pili. The Pseudomonas aeruginosa Tad machine assembles type IVb pili, which are required for adhesion to abiotic surfaces and to eukaryotic cells. Type IVb pili consist of a major subunit, the Flp pilin, processed by the FppA prepilin peptidase. In this study, we investigated the regulatory mechanism of the tad locus. We showed that the flp gene is expressed late in the stationary growth phase in aerobic conditions. We also showed that the tad locus was composed of five independent transcriptional units. We used transcriptional fusions to show that tad gene expression was positively controlled by the PprB response regulator. We subsequently showed that PprB bound to the promoter regions, directly controlling the expression of these genes. We then evaluated the contribution of two genes, tadF and rcpC, to type IVb pilus assembly. The deletion of these two genes had no effect on Flp production, pilus assembly, or Flp-mediated adhesion to abiotic surfaces in our conditions. However, our results suggest that the putative RcpC protein modifies the Flp pilin, thereby promoting Flp-dependent adhesion to eukaryotic cells.

Effects of short-term repeated exposure to different flooring surfaces on the behavior and physiology of dairy cattle.

PubMed

Schütz, K E; Cox, N R

2014-05-01

Dairy cattle managed in some pasture-based systems such as in New Zealand are predominantly kept outdoors all year around, but are often taken off pasture for periods of time in wet weather to avoid soil damage. It is common to keep cattle on concrete surfaces during such "stand-off" practices and we investigated whether the addition of rubber matting onto concrete areas improves the welfare of dairy cattle. Sixteen groups of 5 cows (4 groups/treatment, 5 cows/group) were allocated to 1 of 4 treatments (concrete, 12-mm-thick rubber mat, 24-mm-thick rubber mat, or deep-bedded wood chips) and kept on these surfaces for 18 h/24h for 4 consecutive days (6h on pasture/24h). Each 4-d stand-off period was repeated 4 times (with 7 d of recovery between periods) to study the accumulated effects of repeated stand-off. Lying behavior was recorded continuously during the experiment. Gait score, stride length, hygiene score, live weight, and blood samples for cortisol analysis were recorded immediately before and after each stand-off period. Cows on wood chips spent the most time lying, and cows on concrete spent the least time lying compared with those on other surfaces [wood chips: 10.8h, 24-mm rubber mat: 7.3h, 12-mm rubber mat: 6.0 h, and concrete: 2.8h/18 h, standard error of the difference (SED): 0.71 h]. Cows on concrete spent more time lying during the 6h on pasture, likely compensating for the reduced lying during the stand-off period. Similarly, cows on concrete spent more time lying on pasture between stand-off periods (concrete: 12.1h, 12-mm rubber mat: 11.1h, 24-mm rubber mat: 11.2h, and wood chips: 10.7h/24h, SED: 0.28 h). Cows on concrete had higher gait score and shorter stride length after the 4-d stand-off period compared with cows on the other surface types, suggesting a change in gait pattern caused by discomfort. Cows on rubber mats were almost 3 times dirtier than cows on concrete or wood chips. Cortisol and live weight decreased for all treatment groups during the stand-off period. We observed no major effect of the repeated stand-off exposure. In summary, adding rubber matting onto concrete surfaces for stand-off purposes is beneficial for animal welfare. A well-managed wood chip surface offered the best welfare for dairy cows removed from pasture, and the findings of this study confirm that a concrete surface decreases the welfare of cows removed from pasture. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A locus problem solved by using a mechanism with three dyads and two leading elements

NASA Astrophysics Data System (ADS)

Popescu, I.; Sass, L.; Romanescu, A. E.

2016-11-01

In Geometry there are many types of loci, solved by means of classic geometrical considerations and yielding lines and arcs of circles or conics. Yet more complicated locus can be solved by means of the Theory of Mechanisms. Our research starts from a locus and provides a solution based on the Theory of Mechanisms, finding the equivalent mechanism. The structural and cinematic analysis of the mechanism is made, determining the trajectory of a point representing the locus which presents interest. The mechanism has three dyads and two leading elements, for which the movements were correlated by means of a coefficient q. For various values of q different loci were obtained, similar for close values of q but different for significantly different values of q.

Genetic sex determination and extinction.

PubMed

Hedrick, Philip W; Gadau, Jürgen; Page, Robert E

2006-02-01

Genetic factors can affect the probability of extinction either by increasing the effect of detrimental variants or by decreasing the potential for future adaptive responses. In a recent paper, Zayed and Packer demonstrate that low variation at a specific locus, the complementary sex determination (csd) locus in Hymenoptera (ants, bees and wasps), can result in a sharply increased probability of extinction. Their findings illustrate situations in which there is a feedback process between decreased genetic variation at the csd locus owing to genetic drift and decreased population growth, resulting in an extreme type of extinction vortex for these ecologically important organisms.

HLA Type Inference via Haplotypes Identical by Descent

NASA Astrophysics Data System (ADS)

Setty, Manu N.; Gusev, Alexander; Pe'Er, Itsik

The Human Leukocyte Antigen (HLA) genes play a major role in adaptive immune response and are used to differentiate self antigens from non self ones. HLA genes are hyper variable with nearly every locus harboring over a dozen alleles. This variation plays an important role in susceptibility to multiple autoimmune diseases and needs to be matched on for organ transplantation. Unfortunately, HLA typing by serological methods is time consuming and expensive compared to high throughput Single Nucleotide Polymorphism (SNP) data. We present a new computational method to infer per-locus HLA types using shared segments Identical By Descent (IBD), inferred from SNP genotype data. IBD information is modeled as graph where shared haplotypes are explored among clusters of individuals with known and unknown HLA types to identify the latter. We analyze performance of the method in a previously typed subset of the HapMap population, achieving accuracy of 96% in HLA-A, 94% in HLA-B, 95% in HLA-C, 77% in HLA-DR1, 93% in HLA-DQA1 and 90% in HLA-DQB1 genes. We compare our method to a tag SNP based approach and demonstrate higher sensitivity and specificity. Our method demonstrates the power of using shared haplotype segments for large-scale imputation at the HLA locus.

Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

NASA Astrophysics Data System (ADS)

Wong, Hon Lun; Visscher, Pieter T.; White, Richard Allen, III; Smith, Daniela-Lee; Patterson, Molly M.; Burns, Brendan P.

2017-04-01

The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.

Rare Sequence Variation in the Genome Flanking a Short Tandem Repeat Locus Can Lead to a Question of “Nonmaternity”

PubMed Central

Deucher, Anne; Chiang, Tsoyu; Schrijver, Iris

2010-01-01

Typing of STR (short tandem repeat) alleles is used in a variety of applications in clinical molecular pathology, including evaluations for maternal cell contamination. Using a commercially available STR typing assay for maternal cell contamination performed in conjunction with prenatal diagnostic testing, we were posed with apparent nonmaternity when the two fetal samples did not demonstrate the expected maternal allele at one locus. By designing primers external to the region amplified by the primers from the commercial assay and by performing direct sequencing of the resulting amplicon, we were able to determine that a guanine to adenine sequence variation led to primer mismatch and allele dropout. This explained the apparent null allele shared between the maternal and fetal samples. Therefore, although rare, allele dropout must be considered whenever unexplained homozygosity at an STR locus is observed. PMID:20203001

Molecular Ecological and Stable Isotopic Studies of Nitrogen Fixation in Modern Microbial Mats

NASA Technical Reports Server (NTRS)

Bebout, B. M.; Crumbliss, L. L.; DesMarais, D. J.; Hogan, M. E.; Omoregie, E.; Turk, K. A.; Zehr, J. P.

2003-01-01

Nitrogen is usually the element limiting biological productivity in the marine environment. Microbial mats, laminated microbial communities analogous to some of the oldest forms of life on Earth, are often the sites of high rates of N fixation (the energetically expensive conversion of atmospheric dinitrogen into a biologically useful form). The N fixing enzyme nitrogenase is generally considered to be of ancient origin, and is widely distributed throughout the Bacterial and Archaeal domains of life, indicating an important role for this process over evolutionary time. The stable isotopic signature of N fixation is purportedly recognizable in organic matter (ancient kerogens as well as present-day microbial mats) as a delta (15)N(sub organic) near zero. We studied two microbial mats exhibiting different rates of N fixation in order to better understand the impact of N fixation on the delta (15)N (sub organic) of the mats, as well as what organisms are important in this process. Mats dominated by the cyanobacterium Microcoleus chthonoplastes grow in permanently submerged hypersaline salterns, and exhibit low rates of N fixation, whereas mats dominated by the cyanobacterium Lyngbya spp grow in an intertidal area, and exhibit rates of N fixation an order of magnitude higher. To examine successional stages in mat growth, both developing and established mats at each location were sampled. PCR and RT-PCR based approaches were used to identify, respectively, the organisms containing nifH (one of the genes that encode nitrogenase) as well as those expressing nifH in these mats. Both mats exhibited a distinct diel cycle of N fixation, with highest rates occurring at night. The delta (15)N(sub organic) of the subtidal Microcoleus mats is near zero whereas the delta (15)N(sub organic) is slightly more positive (+ 2-3%), in the intertidal Lyngbya mats, an interesting difference in view of the fact that overall rates of activity in the intertidal mats are much higher that those in the submerged hypersaline mats. Developing mats in both the subtidal and intertidal locations had delta (15)N(sub organic) values very near those of the established mats. Further work is necessary in order to determine the importance of other transformations of nitrogen on the delta (15)N(sub organic) signature of the mats.

Flow-induced Development of Unicellular Cyanobacterial Mats

NASA Astrophysics Data System (ADS)

Gong, J.; Tice, M. M.

2011-12-01

Microbial mats/biofilms are abundant microbial growth structures throughout the history of life on Earth. Understanding the mechanisms for their morphogenesis and interactions with physical sedimentary forces are important topics that allow deeper understanding of related records. When subjected to hydrodynamic influences, mats are known to vary in morphology and structure in response to fluid shear, yet mechanistically, the underlying cellular architecture due to interactions with flow remain unexplained. Moreover, mats are found to emerge larger scale roughness elements and modified cohesive strength growing under flow. It is a mystery how and why these mat-community-level features are linked in association with modified boundary layers at the mats surface. We examined unicellular cyanobacterium Synechocystis sp. PCC 6803 in a circular flow bioreactor designed to maintain a fixed set of hydrodynamic conditions. The use of monoculture strains and unidirectional currents, while not replicating natural mat systems (almost certainly multi-species and often multi-directional currents under complex wind or tidal wave actions), helps to simplify these systems and allows for specific testing of hypotheses regarding how mats evolve distinctive morphologies induced by flow. The unique design of the reactor also makes measurements such as critical erosional shear stress of the mats possible, in addition to microscopic, macroscopic imaging and weeks of continuous mats growth monitoring. We report the finding that linear chains, filament-like cell groups were present from unicellular cyanobacterial mats growing under flow (~1-5 cm/s) and these structures are organized within ~1-3mm size streamers and ~0.5-1mm size nodular macrostructures. Ultra-small, sub-micron thick EPS strings are observed under TEM and are likely the cohesive architectural elements in mats across different fluid regimes. Mat cohesion generally grows with and adapts to increasing flow shear stress within certain limits. Overall topological roughness of the mats were analyzed and estimated in terms of the skin friction of the mats surfaces interacting with flow. Then, together with the critical erosional cohesive strength of the mats estimated, we present a theoretical physical model linking morphology and material strength of mats to overlying fluid flow. If this model were further tested true, it suggests that physical flows may very well have a controlling effect on the properties of mats growing within it.

Calcium-dependent protein kinase CPK28 targets the methionine adenosyltransferases for degradation by the 26S proteasome and affects ethylene biosynthesis and lignin deposition in Arabidopsis.

PubMed

Jin, Yu; Ye, Nenghui; Zhu, Fuyuan; Li, Haoxuan; Wang, Juan; Jiang, Liwen; Zhang, Jianhua

2017-04-01

S-adenosylmethionine (AdoMet) is synthesized by methionine adenosyltransferase (MAT), and plays an essential role in ethylene biosynthesis and other methylation reactions. Despite increasing knowledge of MAT regulation at transcriptional levels, how MAT is post-translationally regulated remains unknown in plant cells. Phosphorylation is an important post-translational modification for regulating the activity of enzymes, protein function and signaling transduction. Using molecular and biochemical approaches, we have identified the phosphorylation of MAT proteins by calcium-dependent protein kinase (CPK28). Phenotypically, both MAT2-overexpressing transgenic plants and cpk28 mutants display short hypocotyls and ectopic lignifications. Their shortened hypocotyl phenotypes are caused by ethylene overproduction and rescued by ethylene biosynthesis inhibitor aminoethoxyvinylglycine treatment. Genetic evidence reveals that MAT2 mutation restores the phenotype of ectopic lignification in CPK28-deficient plants. We find that total MAT proteins and AdoMet are increased in cpk28 mutants, but decreased in CPK28-overexpressing seedlings. We also find that MATs in OE::CPK28 are degraded through the 26S proteasome pathway. Our work suggests that CPK28 targets MATs (MAT1, MAT2 and MAT3) for degradation by the 26S proteasome pathway, and thus affects ethylene biosynthesis and lignin deposition in Arabidopsis. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat

NASA Technical Reports Server (NTRS)

Canfield, Donald E.; Des Marais, David J.

1993-01-01

Complete budgets for carbon and oxygen have been constructed for cyanobacterial mats dominated by Microcoleus chthonoplastes from the evaporating ponds of a salt works. We infer from the data the various sinks for O2 as well as the sources of carbon for primary production. Although seasonal variability exists, a major percentage of the O2 produced during the day did not diffuse out of the mat but was used within the mat to oxidize both organic carbon and the sulfide produced by sulfate reduction. At night, most of the O2 that diffused into the mat was used to oxidize sulfide, with O2 respiration of minor importance. During the day, the internal mat processes of sulfate reduction and O2 respiration generated as much or more inorganic carbon (DIC) for primary production as diffusion into the mat. Oxygenic photosynthesis was the most important process of carbon fixation. At night, the DIC lost from the mat was mostly from sulfate reduction. Elemental fluxes across the mat/brine interface indicated that carbon with an oxidation state of greater than zero was taken up by the mat during the day and liberated from the mat at night. Overall, carbon with an average oxidation state of near zero accumulated in the mat. Both carbon fixation and carbon oxidation rates varied with temperature by a similar amount.

A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation.

PubMed

Tomita, Saori; Abdalla, Mohamed Osama Ali; Fujiwara, Saori; Matsumori, Haruka; Maehara, Kazumitsu; Ohkawa, Yasuyuki; Iwase, Hirotaka; Saitoh, Noriko; Nakao, Mitsuyoshi

2015-04-29

Estrogen receptor-α (ER)-positive breast cancer cells undergo hormone-independent proliferation after deprivation of oestrogen, leading to endocrine therapy resistance. Up-regulation of the ER gene (ESR1) is critical for this process, but the underlying mechanisms remain unclear. Here we show that the combination of transcriptome and fluorescence in situ hybridization analyses revealed that oestrogen deprivation induced a cluster of noncoding RNAs that defined a large chromatin domain containing the ESR1 locus. We termed these RNAs as Eleanors (ESR1 locus enhancing and activating noncoding RNAs). Eleanors were present in ER-positive breast cancer tissues and localized at the transcriptionally active ESR1 locus to form RNA foci. Depletion of one Eleanor, upstream (u)-Eleanor, impaired cell growth and transcription of intragenic Eleanors and ESR1 mRNA, indicating that Eleanors cis-activate the ESR1 gene. Eleanor-mediated gene activation represents a new type of locus control mechanism and plays an essential role in the adaptation of breast cancer cells.

A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation

PubMed Central

Tomita, Saori; Abdalla, Mohamed Osama Ali; Fujiwara, Saori; Matsumori, Haruka; Maehara, Kazumitsu; Ohkawa, Yasuyuki; Iwase, Hirotaka; Saitoh, Noriko; Nakao, Mitsuyoshi

2015-01-01

Estrogen receptor-α (ER)-positive breast cancer cells undergo hormone-independent proliferation after deprivation of oestrogen, leading to endocrine therapy resistance. Up-regulation of the ER gene (ESR1) is critical for this process, but the underlying mechanisms remain unclear. Here we show that the combination of transcriptome and fluorescence in situ hybridization analyses revealed that oestrogen deprivation induced a cluster of noncoding RNAs that defined a large chromatin domain containing the ESR1 locus. We termed these RNAs as Eleanors (ESR1 locus enhancing and activating noncoding RNAs). Eleanors were present in ER-positive breast cancer tissues and localized at the transcriptionally active ESR1 locus to form RNA foci. Depletion of one Eleanor, upstream (u)-Eleanor, impaired cell growth and transcription of intragenic Eleanors and ESR1 mRNA, indicating that Eleanors cis-activate the ESR1 gene. Eleanor-mediated gene activation represents a new type of locus control mechanism and plays an essential role in the adaptation of breast cancer cells. PMID:25923108

Analysis of an "off-ladder" allele at the Penta D short tandem repeat locus.

PubMed

Yang, Y L; Wang, J G; Wang, D X; Zhang, W Y; Liu, X J; Cao, J; Yang, S L

2015-11-25

Kinship testing of a father and his son from Guangxi, China, the location of the Zhuang minority people, was performed using the PowerPlex® 18D System with a short tandem repeat typing kit. The results indicated that both the father and his son had an off-ladder allele at the Penta D locus, with a genetic size larger than that of the maximal standard allelic ladder. To further identify this locus, monogenic amplification, gene cloning, and genetic sequencing were performed. Sequencing analysis demonstrated that the fragment size of the Penta D-OL locus was 469 bp and the core sequence was [AAAGA]21, also called Penta D-21. The rare Penta D-21 allele was found to be distributed among the Zhuang population from the Guangxi Zhuang Autonomous Region of China; therefore, this study improved the range of DNA data available for this locus and enhanced our ability for individual identification of gene loci.

A Novel Locus For Dilated Cardiomyopathy Maps to Canine Chromosome 8

PubMed Central

Werner, Petra; Raducha, Michael G.; Prociuk, Ulana; Sleeper, Meg M.; Henthorn, Paula S.

2008-01-01

Dilated cardiomyopathy (DCM), the most common form of cardiomyopathy, often leads to heart failure and sudden death. While a substantial proportion of DCMs are inherited, mutations responsible for the majority of DCMs remain unidentified. A genome-wide linkage study was performed to identify the locus responsible for an autosomal recessive inherited form of juvenile DCM (JDCM) in Portuguese water dogs using 16 families segregating the disease. Results link the JDCM locus to canine chromosome 8 with two-point and multipoint LOD scores of 10.8 and 14, respectively. The locus maps to a 3.9 Mb region, with complete syntenic homology to human chromosome 14, that contains no genes or loci known to be involved in the development of any type of cardiomyopathy. This discovery of a DCM locus with a previously unknown etiology will provide a new gene to examine in human DCM patients and a model for testing therapeutic approaches for heart failure. PMID:18442891

Biophysical controls on accretion and elevation change in Caribbean mangrove ecosystems

USGS Publications Warehouse

McKee, K.L.

2011-01-01

Habitat stability of coastal ecosystems, such as marshes and mangroves, depends on maintenance of soil elevations relative to sea level. Many such systems are characterized by limited mineral sedimentation and/or rapid subsidence and are consequently dependent upon accumulation of organic matter to maintain elevations. However, little field information exists regarding the contribution of specific biological processes to vertical accretion and elevation change. This study used biogenic mangrove systems in carbonate settings in Belize (BZ) and southwest Florida (FL) to examine biophysical controls on elevation change. Rates of elevation change, vertical accretion, benthic mat formation, and belowground root accumulation were measured in fringe, basin, scrub, and dwarf forest types plus a restored forest. Elevation change rates (mm yr-1) measured with Surface Elevation Tables varied widely: BZ-Dwarf (-3.7), BZ-Scrub (-1.1), FL-Fringe (0.6), FL-Basin (2.1), BZ-Fringe (4.1), and FL-Restored (9.9). Root mass accumulation varied across sites (82-739 g m-2 yr-1) and was positively correlated with elevation change. Root volumetric contribution to vertical change (mm yr-1) was lowest in BZ-Dwarf (1.2) and FL-Fringe (2.4), intermediate in FL-Basin (4.1) and BZ-Scrub (4.3), and highest in BZ-Fringe (8.8) and FL-Restored (11.8) sites. Surface growth of turf-forming algae, microbial mats, or accumulation of leaf litter and detritus also made significant contributions to vertical accretion. Turf algal mats in fringe and scrub forests accreted faster (2.7 mm yr-1) than leaf litter mats in basin forests (1.9 mm yr-1), but similarly to microbial mats in dwarf forests (2.1 mm yr-1). Surface accretion of mineral material accounted for only 0.2-3.3% of total vertical change. Those sites with high root contributions and/or rapid growth of living mats exhibited an elevation surplus (+2 to +8 mm yr-1), whereas those with low root inputs and low (or non-living) mat accumulation showed an elevation deficit (-1 to -5.7 mm yr-1). This study indicates that biotic processes of root production and benthic mat formation are important controls on accretion and elevation change in mangrove ecosystems common to the Caribbean Region. Quantification of specific biological controls on elevation provides better insight into how sustainability of such systems might be influenced by global (e.g., climate, atmospheric CO2) and local (e.g., nutrients, disturbance) factors affecting organic matter accumulation, in addition to relative sea-level rise. ?? 2010.

Biophysical controls on accretion and elevation change in Caribbean mangrove ecosystems

NASA Astrophysics Data System (ADS)

McKee, Karen L.

2011-03-01

Habitat stability of coastal ecosystems, such as marshes and mangroves, depends on maintenance of soil elevations relative to sea level. Many such systems are characterized by limited mineral sedimentation and/or rapid subsidence and are consequently dependent upon accumulation of organic matter to maintain elevations. However, little field information exists regarding the contribution of specific biological processes to vertical accretion and elevation change. This study used biogenic mangrove systems in carbonate settings in Belize (BZ) and southwest Florida (FL) to examine biophysical controls on elevation change. Rates of elevation change, vertical accretion, benthic mat formation, and belowground root accumulation were measured in fringe, basin, scrub, and dwarf forest types plus a restored forest. Elevation change rates (mm yr -1) measured with Surface Elevation Tables varied widely: BZ-Dwarf (-3.7), BZ-Scrub (-1.1), FL-Fringe (0.6), FL-Basin (2.1), BZ-Fringe (4.1), and FL-Restored (9.9). Root mass accumulation varied across sites (82-739 g m -2 yr -1) and was positively correlated with elevation change. Root volumetric contribution to vertical change (mm yr -1) was lowest in BZ-Dwarf (1.2) and FL-Fringe (2.4), intermediate in FL-Basin (4.1) and BZ-Scrub (4.3), and highest in BZ-Fringe (8.8) and FL-Restored (11.8) sites. Surface growth of turf-forming algae, microbial mats, or accumulation of leaf litter and detritus also made significant contributions to vertical accretion. Turf algal mats in fringe and scrub forests accreted faster (2.7 mm yr -1) than leaf litter mats in basin forests (1.9 mm yr -1), but similarly to microbial mats in dwarf forests (2.1 mm yr -1). Surface accretion of mineral material accounted for only 0.2-3.3% of total vertical change. Those sites with high root contributions and/or rapid growth of living mats exhibited an elevation surplus (+2 to +8 mm yr -1), whereas those with low root inputs and low (or non-living) mat accumulation showed an elevation deficit (-1 to -5.7 mm yr -1). This study indicates that biotic processes of root production and benthic mat formation are important controls on accretion and elevation change in mangrove ecosystems common to the Caribbean Region. Quantification of specific biological controls on elevation provides better insight into how sustainability of such systems might be influenced by global (e.g., climate, atmospheric CO 2) and local (e.g., nutrients, disturbance) factors affecting organic matter accumulation, in addition to relative sea-level rise.

Effects of medication assisted treatment (MAT) for opioid use disorder on functional outcomes: A systematic review.

PubMed

Maglione, Margaret A; Raaen, Laura; Chen, Christine; Azhar, Gulrez; Shahidinia, Nima; Shen, Mimi; Maksabedian, Ervant; Shanman, Roberta M; Newberry, Sydne; Hempel, Susanne

2018-06-01

This systematic review synthesizes evidence on the effects of Medication-Assisted Treatment (MAT) for opioid use disorder (OUD) on functional outcomes, including cognitive (e.g., memory), physical (e.g., fatigue), occupational (e.g., return to work), social/behavioral (e.g., criminal activity), and neurological (e.g., balance) function. Five databases were searched from inception to July 2017 to identify English-language controlled trials, case control studies, and cohort comparisons of one or more groups; cross-sectional studies were excluded. Two independent reviewers screened identified literature, abstracted study-level information, and assessed the quality of included studies. Meta-analyses used the Hartung-Knapp method for random-effects models. The quality of evidence was assessed using the GRADE approach. A comprehensive search followed by 1411 full text publication screenings yielded 30 randomized controlled trials (RCTs) and 10 observational studies meeting inclusion criteria. The studies reported highly diverse functional outcome measures. Only one RCT was rated as high quality, but several methodologically sound observational studies were identified. The statistical power to detect differences in functional outcomes was unclear in most studies. When compared with matched "healthy" controls with no history of substance use disorder (SUD), in two studies MAT patients had significantly poorer working memory and cognitive speed. One study found MAT patients scored worse in aggressive responding than did "healthy" controls. A large observational study found that MAT users had twice the odds of involvement in an injurious traffic accident as non-users. When compared with persons with OUD not on MAT, one cohort study found lower fatigue rates among buprenorphine-treated OUD patients. No differences were reported for occupational outcomes and results for criminal activity and other social/behavioral areas were mixed. There were few differences among MAT drug types. A pooled analysis of three RCTs found a significantly lower prevalence of fatigue with buprenorphine compared to methadone, while a meta-analysis of the same RCTs found no statistical difference in insomnia prevalence. Three RCTs that focused on cognitive function compared the effects of buprenorphine to methadone; no statistically significant differences in memory, cognitive speed and flexibility, attention, or vision were reported. The quality of evidence for most functional outcomes was rated low or very low. In sum, weaknesses in the body of evidence prevent strong conclusions about the effects of MAT for opioid use disorder on functional outcomes. Rigorous studies of functional effects would strengthen the body of literature. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

75 FR 55360 - In the Matter of Mattingly Testing Services, Inc. Molt, MT; Order Revoking License (Effective...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-10

... radiation safety officer, and due to expire on February 28, 2016. The license authorizes Mattingly to... effectiveness of Mattingly's radiation safety and compliance programs by commencing an assessment of Mattingly's radiation safety program within 30 days of NRC's approval of the consultant; by reviewing Mattingly's...

Community structure of free-floating filamentous cyanobacterial mats from the Wonder Lake geothermal springs in the Philippines.

PubMed

Lacap, Donnabella C; Smith, Gavin J D; Warren-Rhodes, Kimberley; Pointing, Stephen B

2005-07-01

Cyanobacterial mats were characterized from pools of 45-60 degrees C in near-neutral pH, low-sulphide geothermal springs in the Philippines. Mat structure did not vary with temperature. All mats possessed highly ordered layers of airspaces at both the macroscopic and microscopic level, and these appear to be an adaptation to a free-floating growth habit. Upper mat layers supported biomass with elevated carotenoid:chlorophyll a ratios and an as yet uncharacterized waxy layer on the dorsal surface. Microscopic examination revealed mats comprised a single Fischerella morphotype, with abundant heterocysts throughout mats at all temperatures. Molecular analysis of mat community structure only partly matched morphological identification. All samples supported greater 16S rDNA-defined diversity than morphology suggested, with a progressive loss in the number of genotypes with increasing temperature. Fischerella-like sequences were recovered from mats occurring at all temperatures, but some mats also yielded Oscillatoria-like sequences, although corresponding phenotypes were not observed. Phylogenetic analysis revealed that Fischerella-like sequences were most closely affiliated with Fischerella major and the Oscillatoria-like sequences with Oscillatoria amphigranulata.

Novel autosomal dominant mandibulofacial dysostosis with ptosis: clinical description and exclusion of TCOF1

PubMed Central

Hedera, P; Toriello, H; Petty, E

2002-01-01

Methods: Six affected family members underwent a complete medical genetics physical examination and two affected subjects had skeletal survey. All available medical records were reviewed. Linkage analysis using the markers spanning the TCOF1 locus was performed. One typically affected family member had a high resolution karyotype. Results: Affected subjects had significant craniofacial abnormalities without any significant acral changes and thus had a phenotype consistent with a MFD variant. Distinctive features included hypoplasia of the zygomatic complex, micrognathia with malocclusion, auricular abnormalities with conductive hearing loss, and ptosis. Significantly negative two point lod scores were obtained for markers spanning the TCOF1 locus, excluding the possibility that the disease in our kindred is allelic with TCS. High resolution karyotype was normal. Conclusions: We report a kindred with a novel type of MFD that is not linked to the TCOF1 locus and is also clinically distinct from other types of AD MFD. Identification of additional families will facilitate identification of the gene causing this type of AD MFD and further characterisation of the clinical phenotype. PMID:12114479

Development of a Ballistics Range for the Assessment of Small Arms Ammunition

DTIC Science & Technology

1991-02-01

within the stop butt. Best results are obtained using Agfa-Gevart intensifying screens, type Curvix MR 800, and Kodak XO-MAT type XRP -5 film. These are...conditions for flash radiographs which use Kodak XRP -5 film and Agfa MR 800 intensifying screens are 4 min at 24°C with nitrogen agitation for 5 s

Volatile organic compound hot-press emissions from southern pine furnish as a function of adhesive type

Treesearch

Wenlong Wang; Douglas J. Gardner; Melissa G. D. Baumann

1999-01-01

Three types of adhesives, urea-formaldehyde (UF) resin, phenol-formaldehyde (PF) resin, and polymeric methylene bis(phenyl isocyanate) (pMDI), were used for investigating the effect of pressing variables on volatile organic compound (VOC) emissions. The variables examined included press temperature and time, mat moisture content and resin content, and board density....

Accuracy of Jump-Mat Systems for Measuring Jump Height.

PubMed

Pueo, Basilio; Lipinska, Patrycja; Jiménez-Olmedo, José M; Zmijewski, Piotr; Hopkins, Will G

2017-08-01

Vertical-jump tests are commonly used to evaluate lower-limb power of athletes and nonathletes. Several types of equipment are available for this purpose. To compare the error of measurement of 2 jump-mat systems (Chronojump-Boscosystem and Globus Ergo Tester) with that of a motion-capture system as a criterion and to determine the modifying effect of foot length on jump height. Thirty-one young adult men alternated 4 countermovement jumps with 4 squat jumps. Mean jump height and standard deviations representing technical error of measurement arising from each device and variability arising from the subjects themselves were estimated with a novel mixed model and evaluated via standardization and magnitude-based inference. The jump-mat systems produced nearly identical measures of jump height (differences in means and in technical errors of measurement ≤1 mm). Countermovement and squat-jump height were both 13.6 cm higher with motion capture (90% confidence limits ±0.3 cm), but this very large difference was reduced to small unclear differences when adjusted to a foot length of zero. Variability in countermovement and squat-jump height arising from the subjects was small (1.1 and 1.5 cm, respectively, 90% confidence limits ±0.3 cm); technical error of motion capture was similar in magnitude (1.7 and 1.6 cm, ±0.3 and ±0.4 cm), and that of the jump mats was similar or smaller (1.2 and 0.3 cm, ±0.5 and ±0.9 cm). The jump-mat systems provide trustworthy measurements for monitoring changes in jump height. Foot length can explain the substantially higher jump height observed with motion capture.

Characterization of Newly Bred Cordyceps militaris Strains for Higher Production of Cordycepin through HPLC and URP-PCR Analysis.

PubMed

Lee, Hyun-Hee; Kang, Naru; Park, Inmyoung; Park, Jungwook; Kim, Inyoung; Kim, Jieun; Kim, Namgyu; Lee, Jae-Yun; Seo, Young-Su

2017-07-28

Cordyceps militaris , a member of Ascomycota, a mushroom referred to as caterpillar Dongchung-ha-cho, is commercially valuable because of its high content of bioactive substances, including cordycepin, and its potential for artificial cultivation. Cordycepin (3'-deoxyadenosine) is highly associated with the pharmacological effects of C. militaris . C. militaris is heterothallic in that two mating-type loci, idiomorph MAT1-1 and MAT1-2 , exist discretely in two different spores. In this study, nine C. militaris strains were mated with each other to prepare newly bred strains that produced a larger amount of cordycepin than the parent strains. Nine strains of C. militaris were identified by comparing the internal transcribed spacer sequence, and a total of 12 single spores were isolated from the nine strains of C. militaris . After the MAT idiomorph was confirmed by PCR, 36 mating combinations were performed with six single spores with MAT1-1 and the others with MAT1-2 . Eight mating combinations were successfully mated, producing stroma with perithecia. Cordycepin content analysis of all strains by high-performance liquid chromatography revealed that the KASP4-bred strain produced the maximum cordycepin among all strains, regardless of the medium and stroma parts. Finally, universal rice primer-PCR was performed to demonstrate that the bred strains were genetically different from the parental strains and new C. militaris strains. These results may be related to the recombination of genes during mating. The newly produced strains can be used to meet the industrial demand for cordycepin. In addition, breeding through mating suggests the possibility of producing numerous cordycepin-producing C. militaris strains.

Trimethylamine and Organic Matter Additions Reverse Substrate Limitation Effects on the δ13C Values of Methane Produced in Hypersaline Microbial Mats

PubMed Central

Nicholson, Brooke E.; Beaudoin, Claire S.; Detweiler, Angela M.; Bebout, Brad M.

2014-01-01

Methane production has been observed in a number of hypersaline environments, and it is generally thought that this methane is produced through the use of noncompetitive substrates, such as the methylamines, dimethylsulfide and methanol. Stable isotope measurements of the produced methane have also suggested that the methanogens are operating under conditions of substrate limitation. Here, substrate limitation in gypsum-hosted endoevaporite and soft-mat hypersaline environments was investigated by the addition of trimethylamine, a noncompetitive substrate for methanogenesis, and dried microbial mat, a source of natural organic matter. The δ13C values of the methane produced after amendments were compared to those in unamended control vials. At all hypersaline sites investigated, the δ13C values of the methane produced in the amended vials were statistically lower (by 10 to 71‰) than the unamended controls, supporting the hypothesis of substrate limitation at these sites. When substrates were added to the incubation vials, the methanogens within the vials fractionated carbon isotopes to a greater degree, resulting in the production of more 13C-depleted methane. Trimethylamine-amended samples produced lower methane δ13C values than the mat-amended samples. This difference in the δ13C values between the two types of amendments could be due to differences in isotope fractionation associated with the dominant methane production pathway (or substrate used) within the vials, with trimethylamine being the main substrate used in the trimethylamine-amended vials. It is hypothesized that increased natural organic matter in the mat-amended vials would increase fermentation rates, leading to higher H2 concentrations and increased CO2/H2 methanogenesis. PMID:25239903

Attachment of nanoparticulate drug-release systems on poly(ε-caprolactone) nanofibers via a graftpolymer as interlayer.

PubMed

de Cassan, Dominik; Sydow, Steffen; Schmidt, Nadeschda; Behrens, Peter; Roger, Yvonne; Hoffmann, Andrea; Hoheisel, Anna Lena; Glasmacher, Birgit; Hänsch, Robert; Menzel, Henning

2018-03-01

Electrospun poly(ε-caprolactone) (PCL) fiber mats are modified using a chitosan grafted with PCL (CS-g-PCL), to improve the biological performance and to enable further modifications. The graft copolymer is immobilized by the crystallization of the PCL grafts on the PCL fiber surface as binding mechanism. In this way, the surface of the fibers is covered with chitosan bearing cationic amino groups, which allow adsorption of oppositely charged nanoparticulate drug-delivery systems. The modification of the fiber mats and the attachment of the drug delivery systems are easy and scalable dip processes. The process is also versatile; it is possible to attach different polymeric and inorganic nanoparticulate drug-release systems of cationic or anionic nature. The modifications are verified using scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). As proof of principle, the release of ciprofloxacin from silica nanoparticles attached to the modified fiber mats is shown; however, the method is also suited for other biologically active substances including growth factors. The initial cellular attachment and proliferation as well as vitality of the cells is improved by the modification with CS-g-PCL and is further influenced by the type of the drug delivery system attached. Hence, this method can be used to transfer PCL fiber mats into bioactive implants for in-situ tissue engineering applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of disease-resistant marker-free tomato by R/RS site-specific recombination.

PubMed

Khan, Raham Sher; Nakamura, Ikuo; Mii, Masahiro

2011-06-01

The selection marker genes, imparting antibiotic or herbicide resistance, in the final transgenics have been criticized by the public and considered a hindrance in their commercialization. Multi-auto-transformation (MAT) vector system has been one of the strategies to produce marker-free transgenic plants without using selective chemicals and plant growth regulators (PGRs). In the study reported here, isopentenyltransferase (ipt) gene was used as a selection marker and wasabi defensin (WD) gene, isolated from Wasabia japonica as a target gene. WD was cloned from the binary vector, pEKH-WD to an ipt-type MAT vector, pMAT21 by gateway cloning and transferred to Agrobacterium tumefaciens strain EHA105. Infected cotyledons of tomato cv. Reiyo were cultured on PGR- and antibiotic-free MS medium. Adventitious shoots were developed by the explants infected with the pMAT21/wasabi defensin. The same PGR- and antibiotic-free MS medium was used in subcultures of the adventitious shoot lines (ASLs) to produce ipt and normal shoots. Approximately, 6 months after infection morphologically normal shoots were produced. Molecular analyses of the developed shoots confirmed the integration of gene of interest (WD) and excision of the selection marker (ipt). Expression of WD was confirmed by Northern blot and Western blot analyses. The marker-free transgenic plants exhibited enhanced resistance against Botrytis cinerea (gray mold), Alternaria solani (early blight), Fusarium oxysporum (Fusarium wilt) and Erysiphe lycopersici (powdery mildew).

The Secrets of Effective Floor Care.

ERIC Educational Resources Information Center

Michels, Ed

2002-01-01

Discusses the importance of staff training and a maintenance program to the care of hard floors. Describes four key features to look for in a computer-based training program and types of floor pads and matting used to keep flooring clean. (EV)

MATCON MODIFIED ASPHALT COVER CONTAINMENT SYSTEM DEMONSTRATION

EPA Science Inventory

In order to make improvements to conventional paving asphalt to make it more suitable for containment applications, Wilder Construction Co. of Everett, WA offers MatCon, a polymer modified asphalt system comprised of proprietary binder, when coupled with a selected aggregate type...

MAT2B promotes adipogenesis by modulating SAMe levels and activating AKT/ERK pathway during porcine intramuscular preadipocyte differentiation

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

Zhao, Cunzhen; Chen, Xiaochang; Wu, Wenjing

Intramuscular fat (IMF) has been demonstrated as one of the crucial factors of livestock meat quality. The MAT2B protein with MAT2α catalyzes the formation of methyl donor S- adenosylmethionine (SAMe) to mediate cell metabolism including proliferation and apoptosis. However, the regulatory effect of MAT2B on IMF deposition is still unclear. In this study, the effect of MAT2B on adipogenesis and its potential mechanism during porcine intramuscular preadipocyte differentiation was studied. The results showed that overexpression of MAT2B promoted adipogenesis and significantly up-regulated the mRNA and protein levels of adipogenic marker genes including FASN, PPARγ and aP2, consistently, knockdown of MAT2Bmore » inhibited lipid accumulation and down-regulated the mRNA and protein levels of the above genes. Furthermore, flow cytometry and EdU-labeling assay indicated that MAT2B regulate adipogenesis was partly due to influence intracellular SAMe levels and further affect cell clonal expansion. Also, increased expression of MAT2B activated the phosphorylations of AKT and ERK1/2, whereas knockdown of MAT2B blocked AKT signaling and repressed the phosphorylation of ERK1/2. Moreover, the inhibitory effect of LY294002 (a specific PI3K inhibitor) on the activities of AKT and ERK1/2 was partially recovered by overexpression of MAT2B in porcine intramuscular adipocytes. Finally, Co-IP experiments showed that MAT2B can directly interact with AKT. Taken together, our findings suggested that MAT2B acted as a positive regulator through modifying SAMe levels as well as activating AKT/ERK signaling pathway to promote porcine intramuscular adipocyte differentiation. - Highlights: • MAT2B up-regulates the expression of adipogenic marker genes and promotes porcine intramuscular preadipocyte differentiation. • MAT2B influences intracellular SAMe levels and further affects cell clonal expansion. • MAT2B interacts with AKT and activates AKT/ERK signaling pathway.« less

Vegetative Incompatibility and the Mating-Type Locus in the Cellular Slime Mold DICTYOSTELIUM DISCOIDEUM

PubMed Central

Robson, Gillian E.; Williams, Keith L.

1979-01-01

The genetic basis of vegetative incompatibility in the cellular slime mold, Dictyostelium discoideum, is elucidated. Vegetatively compatible haploid strains from parasexual diploids at a frequency of between 10-6 and 10-5, whereas "escaped" diploids are formed between vegetatively incompatible strains at a frequency of ∼10-8. There is probably only a single vegetative incompatibility site, which appears to be located at, or closely linked to, the mating-type locus. The nature of the vegetative incompatibility is deduced from parasexual diploid formation between wild isolates and tester strains of each mating type, examination of the frequency of formation of "escaped" diploids formed between vegetatively incompatible strains, and examination of the mating type and vegetative incompatibility of haploid segregants obtained from "escaped" diploids. PMID:17248984

Enhanced antibacterial nanocomposite mats by coaxial electrospinning of polycaprolactone fibers loaded with Zn-based nanoparticles.

PubMed

Prado-Prone, Gina; Silva-Bermudez, Phaedra; Almaguer-Flores, Argelia; García-Macedo, Jorge A; García, Victor I; Rodil, Sandra E; Ibarra, Clemente; Velasquillo, Cristina

2018-04-16

ZnO and Zn acetate nanoparticles were embedded in polycaprolactone coaxial-fibers and uniaxial-fibers matrices to develop potential antibacterial nanocomposite wound dressings (mats). Morphology, composition, wettability, crystallinity and fiber structure of mats were characterized. Antibacterial properties of mats were tested against E. coli and S. aureus by turbidity and MTT assays. The effect of UVA illumination (prior to bacteria inoculation) on mats' antibacterial activity was also studied. Results showed that a coaxial-fibers design maintained nanoparticles distributed in the outer-shell of fibers and, in general, enhanced the antibacterial effect of the mats, in comparison to conventional uniaxial-fibers mats. Results indicated that mats simultaneously inhibited planktonic and biofilm bacterial growth by, probably, two main antibacterial mechanisms; 1) release of Zn 2+ ions (mainly from Zn acetate nanoparticles) and 2) photocatalytic oxidative processes exerted by ZnO nanoparticles. Antibacterial properties of mats were significantly improved by coaxial-fibers design and exposure to UVA-light prior to bacteria inoculation. Copyright © 2018 Elsevier Inc. All rights reserved.

Sub-typing of extended-spectrum-β-lactamase-producing isolates from a nosocomial outbreak: application of a 10-loci generic Escherichia coli multi-locus variable number tandem repeat analysis.

PubMed

Karami, Nahid; Helldal, Lisa; Welinder-Olsson, Christina; Ahrén, Christina; Moore, Edward R B

2013-01-01

Extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) were isolated from infants hospitalized in a neonatal, post-surgery ward during a four-month-long nosocomial outbreak and six-month follow-up period. A multi-locus variable number tandem repeat analysis (MLVA), using 10 loci (GECM-10), for 'generic' (i.e., non-STEC) E. coli was applied for sub-species-level (i.e., sub-typing) delineation and characterization of the bacterial isolates. Ten distinct GECM-10 types were detected among 50 isolates, correlating with the types defined by pulsed-field gel electrophoresis (PFGE), which is recognized to be the 'gold-standard' method for clinical epidemiological analyses. Multi-locus sequence typing (MLST), multiplex PCR genotyping of bla CTX-M, bla TEM, bla OXA and bla SHV genes and antibiotic resistance profiling, as well as a PCR assay specific for detecting isolates of the pandemic O25b-ST131 strain, further characterized the outbreak isolates. Two clusters of isolates with distinct GECM-10 types (G06-04 and G07-02), corresponding to two major PFGE types and the MLST-based sequence types (STs) 131 and 1444, respectively, were confirmed to be responsible for the outbreak. The application of GECM-10 sub-typing provided reliable, rapid and cost-effective epidemiological characterizations of the ESBL-producing isolates from a nosocomial outbreak that correlated with and may be used to replace the laborious PFGE protocol for analyzing generic E. coli.

Mapping recessive ophthalmic diseases: linkage of the locus for Usher syndrome type II to a DNA marker on chromosome 1q.

PubMed

Lewis, R A; Otterud, B; Stauffer, D; Lalouel, J M; Leppert, M

1990-06-01

Usher syndrome is a heterogeneous group of autosomal recessive disorders that combines variably severe congenital neurosensory hearing impairment with progressive night-blindness and visual loss similar to that in retinitis pigmentosa. Usher syndrome type I is distinguished by profound congenital (preverbal) deafness and retinal disease with onset in the first decade of life. Usher syndrome type II is characterized by partial hearing impairment and retinal dystrophy that occurs in late adolescence or early adulthood. The chromosomal assignment and the regional localization of the genetic mutation(s) causing the Usher syndromes are unknown. We analyzed a panel of polymorphic genomic markers for linkage to the disease gene among six families with Usher syndrome type I and 22 families with Usher syndrome type II. Significant linkage was established between Usher syndrome type II and the DNA marker locus THH33 (D1S81), which maps to chromosome 1q. The most likely location of the disease gene is at a map distance of 9 cM from THH33 (lod score 6.5). The same marker failed to show linkage in families segregating an allele for Usher syndrome type I. These data confirm the provisional assignment of the locus for Usher syndrome type II to the distal end of chromosome 1q and demonstrate that the clinical heterogeneity between Usher types I and II is caused by mutational events at different genetic loci. Regional localization has the potential to improve carrier detection and to provide antenatal diagnosis in families at risk for the disease.

Evaluating the association of common APOA2 variants with type 2 diabetes

PubMed Central

Duesing, Konsta; Charpentier, Guillaume; Marre, Michel; Tichet, Jean; Hercberg, Serge; Balkau, Beverley; Froguel, Philippe; Gibson, Fernando

2009-01-01

Background APOA2 is a positional and biological candidate gene for type 2 diabetes at the chromosome 1q21-q24 susceptibility locus. The aim of this study was to examine if HapMap phase II tag SNPs in APOA2 are associated with type 2 diabetes and quantitative traits in French Caucasian subjects. Methods We genotyped the three HapMap phase II tagging SNPs (rs6413453, rs5085 and rs5082) required to capture the common variation spanning the APOA2 locus in our type 2 diabetes case-control cohort comprising 3,093 French Caucasian subjects. The association between these variants and quantitative traits was also examined in the normoglycaemic adults of the control cohort. In addition, meta-analysis of publicly available whole genome association data was performed. Results None of the APOA2 tag SNPs were associated with type 2 diabetes in the French Caucasian case-control cohort (rs6413453, P = 0.619; rs5085, P = 0.245; rs5082, P = 0.591). However, rs5082 was marginally associated with total cholesterol levels (P = 0.026) and waist-to-hip ratio (P = 0.029). The meta-analysis of data from 12,387 subjects confirmed our finding that common variation at the APOA2 locus is not associated with type 2 diabetes. Conclusion The available data does not support a role for common variants in APOA2 on type 2 diabetes susceptibility or related quantitative traits in Northern Europeans. PMID:19216768

Evaluating the association of common APOA2 variants with type 2 diabetes.

PubMed

Duesing, Konsta; Charpentier, Guillaume; Marre, Michel; Tichet, Jean; Hercberg, Serge; Balkau, Beverley; Froguel, Philippe; Gibson, Fernando

2009-02-13

APOA2 is a positional and biological candidate gene for type 2 diabetes at the chromosome 1q21-q24 susceptibility locus. The aim of this study was to examine if HapMap phase II tag SNPs in APOA2 are associated with type 2 diabetes and quantitative traits in French Caucasian subjects. We genotyped the three HapMap phase II tagging SNPs (rs6413453, rs5085 and rs5082) required to capture the common variation spanning the APOA2 locus in our type 2 diabetes case-control cohort comprising 3,093 French Caucasian subjects. The association between these variants and quantitative traits was also examined in the normoglycaemic adults of the control cohort. In addition, meta-analysis of publicly available whole genome association data was performed. None of the APOA2 tag SNPs were associated with type 2 diabetes in the French Caucasian case-control cohort (rs6413453, P = 0.619; rs5085, P = 0.245; rs5082, P = 0.591). However, rs5082 was marginally associated with total cholesterol levels (P = 0.026) and waist-to-hip ratio (P = 0.029). The meta-analysis of data from 12,387 subjects confirmed our finding that common variation at the APOA2 locus is not associated with type 2 diabetes. The available data does not support a role for common variants in APOA2 on type 2 diabetes susceptibility or related quantitative traits in Northern Europeans.

Deletion of 7q31.1 supports involvement of FOXP2 in language impairment: clinical report and review.

PubMed

Lennon, P A; Cooper, M L; Peiffer, D A; Gunderson, K L; Patel, A; Peters, Sarika; Cheung, S W; Bacino, C A

2007-04-15

We report on a young male with moderate mental retardation, dysmorphic features, and language delay who is deleted for 7q31.1-7q31.31. His full karyotype is 46,XY,der(7)del(7)(q31.1q31.31)ins(10;7)(q24.3;q31.1q31.31)mat. This child had language impairment, including developmental verbal dyspraxia, but did not meet criteria for autism according to standardized ADOS testing. Our patient's deletion, which is the smallest reported deletion including FOXP2, adds to the body of evidence that supports the role of FOXP2 in speech and language impairment, but not in autism. A reported association between autism and deletions of WNT2, a gene also deleted in our patient, is likewise not supported by our case. Previously, fine mapping with microsatellites markers within in a large three-generation family, in which half the members had severe specific language impairment, aided the localization of the SPCH1 locus to 7q31 within markers D7S2459 (107.1 Mb) and D7S643 (120.5 Mb). Additionally, chromosome rearrangement of 7q31 and mutational analyses have supported the growing evidence that FOXP2, a gene within the SPCH1 region, is involved with speech and language development. It is unclear however whether the AUTS1 (autistic spectrum 1) locus, highly linked to 7q31, overlaps with the SPCH1 and FOXP2. Copyright 2007 Wiley-Liss, Inc.

Machado Joseph disease maps to the same region of chromosome 14 as the spinocerebellar ataxia type 3 locus.

PubMed Central

Twist, E C; Casaubon, L K; Ruttledge, M H; Rao, V S; Macleod, P M; Radvany, J; Zhao, Z; Rosenberg, R N; Farrer, L A; Rouleau, G A

1995-01-01

Machado Joseph disease (MJD) is an autosomal dominantly inherited neuro-degenerative disorder primarily affecting the motor system. It can be divided into three phenotypes based on the variable combination of a range of clinical symptoms including pyramidal and extra-pyramidal features, cerebellar deficits, and distal muscle atrophy. MJD is thought to be caused by mutation of a single gene which has recently been mapped, using genetic linkage analysis, to a 29 cM region on chromosome 14q24.3-q32 in five Japanese families. A second disorder, spinocerebellar ataxia type 3 (SCA3), which has clinical symptoms similar to MJD, has also been linked to the same region of chromosome 14q in two French families. In order to narrow down the region of chromosome 14 which contains the MJD locus and to determine if this region overlaps with the predisposing locus for SCA3, we have performed genetic linkage analysis in seven MJD families, six of Portuguese/Azorean origin and one of Brazilian origin, using nine microsatellite markers mapped to 14q24.3-q32. Our results localise the MJD locus in these families to an 11 cM interval flanked by the markers D14S68 and AFM343vf1. In addition we show that this 11 cM interval maps within the 15 cM interval containing the SCA3 locus, suggesting that these diseases are allelic. PMID:7897622

Identification of a functional capsule locus in Streptococcus mitis.

PubMed

Rukke, H V; Hegna, I K; Petersen, F C

2012-04-01

The polysaccharide capsule of Streptococcus pneumoniae is a hallmark for virulence in humans. In its close relative Streptococcus mitis, a common human commensal, analysis of the sequenced genomes of six strains revealed the presence of a putative capsule locus in four of them. We constructed an isogenic S. mitis mutant from the type strain that lacked the 19 open reading frames in the capsule locus (Δcps mutant), using a deletion strategy similar to previous capsule functional studies in S. pneumoniae. Transmission electron microscopy and atomic force microscopy revealed a capsule-like structure in the S. mitis type strain that was absent or reduced in the Δcps mutant. Since S. mitis are predominant oral colonizers of tooth surfaces, we addressed the relevance of the capsule locus for the S. mitis overall surface properties, autoaggregation and biofilm formation. The capsule deletion resulted in a mutant with approximately two-fold increase in hydrophobicity. Binding to the Stains-all cationic dye was reduced by 40%, suggesting a reduction in the overall negative surface charge of the mutant. The mutant exhibited also increased autoaggregation in coaggregation buffer, and up to six-fold increase in biofilm levels. The results suggested that the capsule locus is associated with production of a capsule-like structure in S. mitis and indicated that the S. mitis capsule-like structure may confer surface attributes similar to those associated with the capsule in S. pneumoniae. © 2011 John Wiley & Sons A/S.

Single locus typing of MHC class I and class II B loci in a population of red jungle fowl.

PubMed

Worley, K; Gillingham, M; Jensen, P; Kennedy, L J; Pizzari, T; Kaufman, J; Richardson, D S

2008-05-01

In species with duplicated major histocompatibility complex (MHC) genes, estimates of genetic variation often rely on multilocus measures of diversity. It is possible that such measures might not always detect more detailed patterns of selection at individual loci. Here, we describe a method that allows us to investigate classical MHC diversity in red jungle fowl (Gallus gallus), the wild ancestor of the domestic chicken, using a single locus approach. This is possible due to the well-characterised gene organisation of the 'minimal essential' MHC (BF/BL region) of the domestic chicken, which comprises two differentially expressed duplicated class I (BF) and two class II B (BLB) genes. Using a combination of reference strand-mediated conformation analysis, cloning and sequencing, we identify nine BF and ten BLB alleles in a captive population of jungle fowl. We show that six BF and five BLB alleles are from the more highly expressed locus of each gene, BF2 and BLB2, respectively. An excess of non-synonymous substitutions across the jungle fowl BF/BL region suggests that diversifying selection has acted on this population. Importantly, single locus screening reveals that the strength of selection is greatest on the highly expressed BF2 locus. This is the first time that a population of red jungle fowl has been typed at the MHC region, laying the basis for further research into the underlying processes acting to maintain MHC diversity in this and other species.

Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

NASA Astrophysics Data System (ADS)

Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

2014-12-01

Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

Accuracy of a vertical jump contact mat for determining jump height and flight time.

PubMed

Whitmer, Tyler D; Fry, Andrew C; Forsythe, Charles M; Andre, Matthew J; Lane, Michael T; Hudy, Andrea; Honnold, Darric E

2015-04-01

Several devices are available to measure vertical jump (VJ) height based on flight time, VJ reach height, or ground reaction forces. The purpose of this study was to determine the accuracy of a VJ mat for measuring flight time and VJ height compared with a VJ tester or a force plate. Seventeen men and 18 women (X ± SD; age = 20.9 ± 0.7 years, height = 176.1 ± 0.9 cm, weight = 72.6 ± 13.5 kg) served as subjects. Subjects performed counter-movement vertical jumps while standing on both a force plate (1,000 Hz) and a VJ mat. A Vertec VJ tester was used to measure jump reach. Compared with the force plate, the VJ mat reported greater VJ height (VJ mat = 0.50 ± 0.12 m, force plate = 0.34 ± 0.10 m) and flight time (VJ mat = 0.629 ± 0.078 seconds, force plate = 0.524 ± 0.077 seconds). Comparison of VJ heights from the VJ mat and the Vertec revealed no significant differences (Vertec = 0.48 ± 0.11 m). Regression analyses indicated strong relationships between testing methods and suggested that high VJ performances may be underestimated with the VJ mat. This particular VJ mat compared favorably with the Vertec but not the force plate. It seems that the different flight times derived from the VJ mat may permit the VJ mat to be in closer agreement with VJ heights from the Vertec. Also, the VJ mat may not be an appropriate tool for assessing high VJ performances (i.e., ≥0.70 m; ≈28 inches). Practitioners and researchers using similar VJ mats may not obtain accurate flight times and may underestimate high performers.

Framboidal iron oxide: Chondrite-like material from the black mat, Murray Springs, Arizona

NASA Astrophysics Data System (ADS)

Fayek, Mostafa; Anovitz, Lawrence M.; Allard, Lawrence F.; Hull, Sharon

2012-02-01

At the end of the Pleistocene a Younger Dryas "black mat" was deposited on top of the Pleistocene sediments in many parts of North America. A study of the magnetic fraction (~ 10,900 ± 50 B.P.) from the basal section of the black mat at Murray Springs, AZ revealed the presence of amorphous iron oxide framboids in a glassy iron-silica matrix. These framboids are very similar in appearance and chemistry to those reported from several types of carbonaceous chondrites. The glass contains iron, silicon, oxygen, vanadium and minor titanium, while the framboidal particles contain calcium as well. The major element chemistry of both the spherules and the glass matrix are consistent with the chemistry of material associated with meteorite impact sites and meteorites. Electron microscopy confirms that the glassy material is indeed amorphous, and also shows that what appear to be individual oxide particles are amorphous as well. The latter appears consistent with their overall morphology that, while euhedral, typically shows significant fracture. Based on these data, we argue that these particles are the product of a hypervelocity impact.

The New Rga Locus Encodes a Negative Regulator of Gibberellin Response in Arabidopsis Thaliana

PubMed Central

Silverstone, A. L.; Mak, PYA.; Martinez, E. C.; Sun, T.

1997-01-01

We have identified a new locus involved in gibberellin (GA) signal transduction by screening for suppressors of the Arabidopsis thaliana GA biosynthetic mutant ga1-3. The locus is named RGA for repressor of ga1-3. Based on the recessive phenotype of the digenic rga/ga1-3 mutant, the wild-type gene product of RGA is probably a negative regulator of GA responses. Our screen for suppressors of ga1-3 identified 17 mutant alleles of RGA as well as 10 new mutant alleles at the previously identified SPY locus. The digenic (double homozygous) rga/ga1-3 mutants are able to partially repress several defects of ga1-3 including stem growth, leaf abaxial trichome initiation, flowering time, and apical dominance. The phenotype of the trigenic mutant (triple homozygous) rga/spy/ga1-3 shows that rga and spy have additive effects regulating flowering time, abaxial leaf trichome initiation and apical dominance. This trigenic mutant is similar to wild type with respect to each of these developmental events. Because rga/spy/ga1-3 is almost insensitive to GA for hypocotyl growth and its bolting stem is taller than the wild-type plant, the combined effects of the rga and spy mutations appear to allow GA-independent stem growth. Our studies indicate that RGA lies on a separate branch of the GA signal transduction pathway from SPY, which leads us to propose a modified model of the GA response pathway. PMID:9215910

New Locus for Skin Intrinsic Fluorescence in Type 1 Diabetes Also Associated With Blood and Skin Glycated Proteins

PubMed Central

Roshandel, Delnaz; Klein, Ronald; Klein, Barbara E.K.; Wolffenbuttel, Bruce H.R.; van der Klauw, Melanie M.; van Vliet-Ostaptchouk, Jana V.; Atzmon, Gil; Ben-Avraham, Danny; Crandall, Jill P.; Barzilai, Nir; Bull, Shelley B.; Canty, Angelo J.; Hosseini, S. Mohsen; Hiraki, Linda T.; Maynard, John; Sell, David R.; Monnier, Vincent M.; Cleary, Patricia A.; Braffett, Barbara H.

2016-01-01

Skin fluorescence (SF) noninvasively measures advanced glycation end products (AGEs) in the skin and is a risk indicator for diabetes complications. N-acetyltransferase 2 (NAT2) is the only known locus influencing SF. We aimed to identify additional genetic loci influencing SF in type 1 diabetes (T1D) through a meta-analysis of genome-wide association studies (N = 1,359) including Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) and Wisconsin Epidemiologic Study of Diabetic Retinopathy (WESDR). A locus on chromosome 1, rs7533564 (P = 1.9 × 10−9), was associated with skin intrinsic fluorescence measured by SCOUT DS (excitation 375 nm, emission 435–655 nm), which remained significant after adjustment for time-weighted HbA1c (P = 1.7 × 10−8). rs7533564 was associated with mean HbA1c in meta-analysis (P = 0.0225), mean glycated albumin (P = 0.0029), and glyoxal hydroimidazolones (P = 0.049), an AGE measured in skin biopsy collagen, in DCCT. rs7533564 was not associated with diabetes complications in DCCT/EDIC or with SF in subjects without diabetes (nondiabetic [ND]) (N = 8,721). In conclusion, we identified a new locus associated with SF in T1D subjects that did not show similar effect in ND subjects, suggesting a diabetes-specific effect. This association needs to be investigated in type 2 diabetes. PMID:27207532

Genome-wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21.

PubMed

Tabassum, Rubina; Chauhan, Ganesh; Dwivedi, Om Prakash; Mahajan, Anubha; Jaiswal, Alok; Kaur, Ismeet; Bandesh, Khushdeep; Singh, Tejbir; Mathai, Benan John; Pandey, Yogesh; Chidambaram, Manickam; Sharma, Amitabh; Chavali, Sreenivas; Sengupta, Shantanu; Ramakrishnan, Lakshmi; Venkatesh, Pradeep; Aggarwal, Sanjay K; Ghosh, Saurabh; Prabhakaran, Dorairaj; Srinath, Reddy K; Saxena, Madhukar; Banerjee, Monisha; Mathur, Sandeep; Bhansali, Anil; Shah, Viral N; Madhu, Sri Venkata; Marwaha, Raman K; Basu, Analabha; Scaria, Vinod; McCarthy, Mark I; Venkatesan, Radha; Mohan, Viswanathan; Tandon, Nikhil; Bharadwaj, Dwaipayan

2013-03-01

Indians undergoing socioeconomic and lifestyle transitions will be maximally affected by epidemic of type 2 diabetes (T2D). We conducted a two-stage genome-wide association study of T2D in 12,535 Indians, a less explored but high-risk group. We identified a new type 2 diabetes-associated locus at 2q21, with the lead signal being rs6723108 (odds ratio 1.31; P = 3.32 × 10⁻⁹). Imputation analysis refined the signal to rs998451 (odds ratio 1.56; P = 6.3 × 10⁻¹²) within TMEM163 that encodes a probable vesicular transporter in nerve terminals. TMEM163 variants also showed association with decreased fasting plasma insulin and homeostatic model assessment of insulin resistance, indicating a plausible effect through impaired insulin secretion. The 2q21 region also harbors RAB3GAP1 and ACMSD; those are involved in neurologic disorders. Forty-nine of 56 previously reported signals showed consistency in direction with similar effect sizes in Indians and previous studies, and 25 of them were also associated (P < 0.05). Known loci and the newly identified 2q21 locus altogether explained 7.65% variance in the risk of T2D in Indians. Our study suggests that common susceptibility variants for T2D are largely the same across populations, but also reveals a population-specific locus and provides further insights into genetic architecture and etiology of T2D.

Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat

NASA Astrophysics Data System (ADS)

Canfield, Donald E.; Des Marais, David J.

1993-08-01

Complete budgets for carbon and oxygen have been constructed for cyanobacterial mats dominated by Microcoleus chthonoplastes from the evaporating ponds of a salt works located in Guerrero Negro, Baja California Sur, Mexico. Included in the budget are measured rates of O 2 production, sulfate reduction, and elemental exchange across the mat/brine interface, day and night, at various temperatures and times of the year. We infer from this data the various sinks for O 2, as well as the sources of carbon for primary production. To summarize, although seasonal variability exists, a major percentage of the O 2 produced during the day did not diffuse out of the mat but was used within the mat to oxidize both organic carbon and the sulfide produced by sulfate reduction. At night, most of the O 2 that diffused into the mat was used to oxidize sulfide, with O 2 respiration of minor importance. During the day, the internal mat processes of sulfate reduction and O 2 respiration generated as much or more inorganic carbon (DIC) for primary production as diffusion into the mat. Also, oxygenic photosynthesis was the most important process of carbon fixation, although anoxygenic photosynthesis may have been important at low light levels during some times of the year. At night, the DIC lost from the mat was mostly from sulfate reduction. Elemental fluxes across the mat/brine interface indicated that carbon with an oxidation state of greater than zero was taken up by the mat during the day and liberated from the mat at night. Overall, carbon with an average oxidation state of near zero accumulated in the mat. Both carbon fixation and carbon oxidation rates varied with temperature by a similar amount. These mats are thus closely coupled systems where rapid rates of photosynthesis both require and fuel rapid rates of heterotrophic carbon oxidation.

Bone marrow fat accumulation accelerated by high fat diet is suppressed by exercise

PubMed Central

Styner, Maya; Thompson, William R.; Galior, Kornelia; Uzer, Gunes; Wu, Xin; Kadari, Sanjay; Case, Natasha; Xie, Zhihui; Sen, Buer; Romaine, Andrew; Pagnotti, Gabriel M.; Rubin, Clinton T.; Styner, Martin A.; Horowitz, Mark C.; Rubin, Janet

2014-01-01

Marrow adipose tissue (MAT), associated with skeletal fragility and hematologic insufficiency, remains poorly understood and difficult to quantify. We tested the response of MAT to high fat diet (HFD) and exercise using a novel volumetric analysis, and compared it to measures of bone quantity. We hypothesized that HFD would increase MAT and diminish bone quantity, while exercise would slow MAT acquisition and promote bone formation. Eight week-old female C57BL/6 mice were fed a regular (RD) or HFD, and exercise groups were provided voluntary access to running wheels (RD-E, HFD-E). Femoral MAT was assessed by μCT (lipid binder osmium) using a semi-automated approach employing rigid co-alignment, regional bone masks and was normalized for total femoral volume (TV) of the bone compartment. MAT was 2.6-fold higher in HFD relative to RD mice. Exercise suppressed MAT in RD-E mice by more than half compared with RD. Running similarly inhibited MAT acquisition in HFD mice. Exercise significantly increased bone quantity in both diet groups. Thus, HFD caused significant accumulation of MAT; importantly running exercise limited MAT acquisition while promoting bone formation during both diets. That MAT is exquisitely responsive to diet and exercise, and its regulation by exercise appears to be inversely proportional to effects on exercise induced bone formation, is relevant for an aging and sedentary population. PMID:24709686

Alignment of Irregular Grains by Mechanical Torques

NASA Astrophysics Data System (ADS)

Hoang, Thiem; Cho, Jungyeon; Lazarian, A.

2018-01-01

We study the alignment of irregular dust grains by mechanical torques due to the drift of grains through the ambient gas. We first calculate mechanical alignment torques (MATs) resulting from specular reflection of gas atoms for seven irregular shapes: one shape of mirror symmetry, three highly irregular shapes (HIS), and three weakly irregular shapes (WIS). We find that the grain with mirror symmetry experiences negligible MATs due to its mirror-symmetry geometry. Three HIS can produce strong MATs, which exhibit some generic properties as radiative torques (RATs), while three WIS produce less efficient MATs. We then study grain alignment by MATs for the different angles between the drift velocity and the ambient magnetic field, for paramagnetic and superparamagnetic grains assuming efficient internal relaxation. We find that for HIS grains, MATs can align subsonically drifting grains in the same way as RATs, with low-J and high-J attractors. For supersonic drift, MATs can align grains with low-J and high-J attractors, analogous to RAT alignment by anisotropic radiation. We also show that the joint action of MATs and magnetic torques in grains with iron inclusions can lead to perfect MAT alignment. Our results point out the potential importance of MAT alignment for HIS grains predicted by the analytical model of Lazarian & Hoang, although more theoretical and observational studies are required due to uncertainty in the shape of interstellar grains. We outline astrophysical environments where MAT alignment is potentially important.

Lipophilic pigments from cyanobacterial (blue-green algal) and diatom mats in Hamelin Pool, Shark Bay, Western Australia

NASA Technical Reports Server (NTRS)

Palmisano, A. C.; Summons, R. E.; Cronin, S. E.; Des Marais, D. J.

1989-01-01

Lipophilic pigments were examined in microbial mat communities dominated by cyanobacteria in the intertidal zone and by diatoms in the subtidal and sublittoral zones of Hamelin Pool, Shark Bay, Western Australia. These microbial mats have evolutionary significance because of their similarity to lithfied stromatolites from the Proterozoic and Early Paleozoic eras. Fucoxanthin, diatoxanthin, diadinoxanthin, beta-carotene, and chlorophylls a and c characterized the diatom mats, whereas cyanobacterial mats contained myxoxanthophyll, zeaxanthin, echinenone, beta-carotene, chlorophyll a and, in some cases, sheath pigment. The presence of bacteriochlorophyll a within the mats suggest a close association of photosynthetic bacteria with diatoms and cyanobacteria. The high carotenoids : chlorophyll a ratios (0.84-2.44 wt/wt) in the diatom mats suggest that carotenoids served a photoprotective function in this high light environment. By contrast, cyanobacterial sheath pigment may have largely supplanted the photoprotective role of carotenoids in the intertidal mats.

Material Model Evaluation of a Composite Honeycomb Energy Absorber

NASA Technical Reports Server (NTRS)

Jackson, Karen E.; Annett, Martin S.; Fasanella, Edwin L.; Polanco, Michael A.

2012-01-01

A study was conducted to evaluate four different material models in predicting the dynamic crushing response of solid-element-based models of a composite honeycomb energy absorber, designated the Deployable Energy Absorber (DEA). Dynamic crush tests of three DEA components were simulated using the nonlinear, explicit transient dynamic code, LS-DYNA . In addition, a full-scale crash test of an MD-500 helicopter, retrofitted with DEA blocks, was simulated. The four material models used to represent the DEA included: *MAT_CRUSHABLE_FOAM (Mat 63), *MAT_HONEYCOMB (Mat 26), *MAT_SIMPLIFIED_RUBBER/FOAM (Mat 181), and *MAT_TRANSVERSELY_ANISOTROPIC_CRUSHABLE_FOAM (Mat 142). Test-analysis calibration metrics included simple percentage error comparisons of initial peak acceleration, sustained crush stress, and peak compaction acceleration of the DEA components. In addition, the Roadside Safety Verification and Validation Program (RSVVP) was used to assess similarities and differences between the experimental and analytical curves for the full-scale crash test.

Lignin-based active anode materials synthesized from low-cost renewable resources

DOEpatents

Rios, Orlando; Tenhaeff, Wyatt Evan; Daniel, Claus; Dudney, Nancy Johnston; Johs, Alexander; Nunnery, Grady Alexander; Baker, Frederick Stanley

2016-06-07

A method of making an anode includes the steps of providing fibers from a carbonaceous precursor, the carbon fibers having a glass transition temperature T.sub.g. In one aspect the carbonaceous precursor is lignin. The carbonaceous fibers are placed into a layered fiber mat. The fiber mat is fused by heating the fiber mat in the presence of oxygen to above the T.sub.g but no more than 20% above the T.sub.g to fuse fibers together at fiber to fiber contact points and without melting the bulk fiber mat to create a fused fiber mat through oxidative stabilization. The fused fiber mat is carbonized by heating the fused fiber mat to at least 650.degree. C. under an inert atmosphere to create a carbonized fused fiber mat. A battery anode formed from carbonaceous precursor fibers is also disclosed.

Simple Strategy to Prevent Severe Head Trauma in Judo —Biomechanical Analysis—

PubMed Central

Murayama, Haruo; Hitosugi, Masahito; Motozawa, Yasuki; Ogino, Masahiro; Koyama, Katsuhiro

2013-01-01

To determine whether the use of an under-mat has an effect on impact forces to the head in Judo, a Judo expert threw an anthropomorphic test device using the Osoto-gari and Ouchi-gari techniques onto a tatami (judo mat) with and without an under-mat. Head acceleration was measured and the head injury criterion (HIC) values with or without under-mat were compared. The use of an under-mat significantly decreased (p = 0.021) the HIC values from 1174.7 ± 246.7 (without under-mat) to 539.3 ± 43.5 in Ouchi-gari and from 330.0 ± 78.3 (without under-mat) to 156.1 ± 30.4 in Osoto-gari. The use of an under-mat simply reduces impact forces to the head in Judo. Rule changes are not necessary and the enjoyment and health benefits of Judo are maintained. PMID:24067767

Simple strategy to prevent severe head trauma in Judo.

PubMed

Murayama, Haruo; Hitosugi, Masahito; Motozawa, Yasuki; Ogino, Masahiro; Koyama, Katsuhiro

2013-01-01

To determine whether the use of an under-mat has an effect on impact forces to the head in Judo, a Judo expert threw an anthropomorphic test device using the Osoto-gari and Ouchi-gari techniques onto a tatami (judo mat) with and without an under-mat. Head acceleration was measured and the head injury criterion (HIC) values with or without under-mat were compared. The use of an under-mat significantly decreased (p = 0.021) the HIC values from 1174.7 ± 246.7 (without under-mat) to 539.3 ± 43.5 in Ouchi-gari and from 330.0 ± 78.3 (without under-mat) to 156.1 ± 30.4 in Osoto-gari. The use of an under-mat simply reduces impact forces to the head in Judo. Rule changes are not necessary and the enjoyment and health benefits of Judo are maintained.

Rising Mean Annual Temperature Increases Carbon Flux and Alters Partitioning, but Does Not Change Ecosystem Carbon Storage in Hawaiian Tropical Montane Wet Forest

NASA Astrophysics Data System (ADS)

Litton, C. M.; Giardina, C. P.; Selmants, P.

2014-12-01

Terrestrial ecosystem carbon (C) storage exceeds that in the atmosphere by a factor of four, and represents a dynamic balance among C input, allocation, and loss. This balance is likely being altered by climate change, but the response of terrestrial C cycling to warming remains poorly quantified, particularly in tropical forests which play a disproportionately large role in the global C cycle. Over the past five years, we have quantified above- and belowground C pools and fluxes in nine permanent plots spanning a 5.2°C mean annual temperature (MAT) gradient (13-18.2°C) in Hawaiian tropical montane wet forest. This elevation gradient is unique in that substrate type and age, soil type, soil water balance, canopy vegetation, and disturbance history are constant, allowing us to isolate the impact of long-term, whole ecosystem warming on C input, allocation, loss and storage. Across the gradient, soil respiration, litterfall, litter decomposition, total belowground C flux, aboveground net primary productivity, and estimates of gross primary production (GPP) all increase linearly and positively with MAT. Carbon partitioning is dynamic, shifting from below- to aboveground with warming, likely in response to a warming-induced increase in the cycling and availability of soil nutrients. In contrast to observed patterns in C flux, live biomass C, soil C, and total ecosystem C pools remained remarkably constant with MAT. There was also no difference in soil bacterial taxon richness, phylogenetic diversity, or community composition with MAT. Taken together these results indicate that in tropical montane wet forests, increased temperatures in the absence of water limitation or disturbance will accelerate C cycling, will not alter ecosystem C storage, and will shift the products of photosynthesis from below- to aboveground. These results agree with an increasing number of studies, and collectively provide a unique insight into anticipated warming-induced changes in tropical forest C cycling.

High fat diet attenuates hyperglycemia, body composition changes, and bone loss in male streptozotocin-induced type 1 diabetic mice.

PubMed

Carvalho, Adriana Lelis; DeMambro, Victoria E; Guntur, Anyonya R; Le, Phuong; Nagano, Kenichi; Baron, Roland; de Paula, Francisco José Albuquerque; Motyl, Katherine J

2018-02-01

There is a growing and alarming prevalence of obesity and the metabolic syndrome in type I diabetic patients (T1DM), particularly in adolescence. In general, low bone mass, higher fracture risk, and increased marrow adipose tissue (MAT) are features of diabetic osteopathy in insulin-deficient subjects. On the other hand, type 2 diabetes (T2DM) is associated with normal or high bone mass, a greater risk of peripheral fractures, and no change in MAT. Therefore, we sought to determine the effect of weight gain on bone turnover in insulin-deficient mice. We evaluated the impact of a 6-week high-fat (HFD) rich in medium chain fatty acids or low-fat diet (LFD) on bone mass and MAT in a streptozotocin (STZ)-induced model using male C57BL/6J mice at 8 weeks of age. Dietary intervention was initiated after diabetes confirmation. At the endpoint, lower non-fasting glucose levels were observed in diabetic mice fed with high fat diet compared to diabetic mice fed the low fat diet (STZ-LFD). Compared to euglycemic controls, the STZ-LFD had marked polydipsia and polyphagia, as well as reduced lean mass, fat mass, and bone parameters. Interestingly, STZ-HFD mice had higher bone mass, namely less cortical bone loss and more trabecular bone than STZ-LFD. Thus, we found that a HFD, rich in medium chain fatty acids, protects against bone loss in a T1DM mouse model. Whether this may also translate to T1DM patients who are overweight or obese in respect to maintenance of bone mass remains to be determined through longitudinal studies. © 2017 Wiley Periodicals, Inc.

Use of palm-mat geotextiles for rainsplash erosion control

NASA Astrophysics Data System (ADS)

Bhattacharyya, R.; Fullen, M. A.; Davies, K.; Booth, C. A.

2010-07-01

Soil detachment by raindrop action (rainsplash erosion) is a very important subprocess of erosion by water. It is a particular problem in the UK as most soils are sandy or loamy sand in texture and lands have gentle to medium slope. However, few studies report potential rainsplash erosion control options under field conditions. Hence, the utilization of palm-mat geotextiles as a rainsplash erosion control technique was investigated at Hilton, east Shropshire, U.K. (52°33'5.7″ N, 2°19'18.3″ W). Geotextile-mats constructed from Borassus aethiopum (Borassus palm of West Africa) and Mauritia flexuosa (Buriti palm of South America) leaves are termed Borassus mats and Buriti mats, respectively. Two-year field experiments were conducted at Hilton to study the effects of emplacing Borassus and Buriti mats on rainsplash erosion of a loamy sand soil. Two sets (12 plots each) of experiments were established to study the effects of these mats on splash height and splash erosion. Splash height needs to be known to assess the transport mechanism of major soil fraction and its constituents on sloping land by rainsplash. In both sets, six randomly-selected plots were covered with mats, and the rest were bare. Results (during 22/01/2007‒23/01/2009; total precipitation = 1731.5 mm) show that Borassus mat-covered plots had ˜ 89% ( P < 0.001) less total splash erosion (2.97 kg m - 2 ) than bare plots (27.02 kg m - 2 ). Comparatively, mean splash height from Borassus mat-covered plots (0.12 m) was significantly ( P < 0.001) less than the bare plots, by ˜ 54%. However, Buriti mat-cover on bare plots had no significant ( P > 0.05) effect in rainsplash erosion control during that period, although plots with Buriti mats significantly ( P < 0.05) decreased splash height (by ˜ 18%) compared with bare plots (0.26 m). Buriti mats, probably due to their ˜ 43, 62 and 50% lower cover percentage (44%), mass per unit area (413 g - 2 ) and thickness (10 mm), respectively, compared with Borassus mats, were not effective in rainsplash erosion control. Both mats did not significantly ( P > 0.05) improve selected soil properties (i.e., soil organic matter, particle size distribution, aggregate stability and total soil carbon) as soil organic matter (SOM) input from mat-decomposition was much less than total SOM content. However, the changes in fine and medium sand contents (after 2 years) in the Borassus covered plots were significantly ( P < 0.05; n = 6) related to the total rainsplash erosion during 2007‒2009. Emplacement of Borassus and Buriti mats on bare soils did not decrease SOM contents after 2 years, indicating that improvements in some soil properties might occur over longer durations. After ˜ 10 months, Buriti mats lost ˜ 70% of their initial weight ( P < 0.001) and their initial cover percentage ( C, %) decreased drastically ( P < 0.05); whereas, Borassus mats maintained similar C to the initial condition, although mass per unit area decreased by ˜ 20% ( P < 0.05). Moreover, the functional longevity of Borassus mats was ˜ 2 years against only 1 year for Buriti mats. Hence, use of Borassus mats is highly effective for rainsplash erosion control in the UK.

Evaluation of polyacrylonitrile electrospun nano-fibrous mats as leukocyte removal filter media.

PubMed

Pourbaghi, Raha; Zarrebini, Mohammad; Semnani, Dariush; Pourazar, Abbasali; Akbari, Nahid; Shamsfar, Reihaneh

2018-07-01

Removal of leukocytes from blood products is the most effective means for elimination of undesirable side effects and prevention of possible reactions in recipients. Micro-fibrous mats are currently used for removal of leukocytes from blood. In this study, samples of electrospun nano-fibrous mats were produced. The performance of the produced electrospun nano-fibrous mats as means of leukocytes removal from fresh whole blood was both evaluated and compared with that of commercially available micro-fibrous mats. In order to produce the samples, polyacrylonitrile (PAN) nano-fibrous mats were made under different electrospinning conditions. Mean fiber diameter, pore characterization and surface roughness of the PAN nano-fibrous mats were determined using image processing technique. In order to evaluate the surface tension of the fabricated mats, water contact angle was measured. The leukocyte removal performance, erythrocytes recovery percent and hemolysis rate of the nano-fibrous mats were compared. The effectiveness of nano-fibrous mats in removing leukocyte was established using both scanning electron microscope and optical microscope. Results showed that for given weight, the fabricated nano-fibrous mats were not only more efficient but also more cost-effective than their commercial counterparts. Results confirmed that changes in mean fiber diameter, the number of layer and weight of each layer in the absence of any chemical reaction or physical surface modification, the fabricated nano-fibrous mats were able to remove 5-log of leukocytes. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1759-1769, 2018. © 2017 Wiley Periodicals, Inc.

Graft extrusion in both the coronal and sagittal planes is greater after medial compared with lateral meniscus allograft transplantation but is unrelated to early clinical outcomes.

PubMed

Lee, Dae-Hee; Lee, Chang-Rack; Jeon, Jin-Ho; Kim, Kyung-Ah; Bin, Seong-Il

2015-01-01

Graft extrusion after meniscus allograft transplantation (MAT) may be affected by horn fixation, which differs between medial and lateral MAT. Few studies have compared graft extrusion, especially sagittal extrusion, after medial and lateral MAT. In patients undergoing medial and lateral MAT, graft extrusion is likely similar and not correlated with postoperative Lysholm scores. Cohort study; Level of evidence, 2. Meniscus graft extrusion in the coronal and sagittal planes was compared in 51 knees undergoing medial MAT and 84 undergoing lateral MAT. Distances from the anterior and posterior articular cartilage margins to the anterior (anterior cartilage meniscus distance [ACMD]) and posterior (posterior cartilage meniscus distance [PCMD]) horns, respectively, were assessed on immediate postoperative magnetic resonance imaging and compared in patients undergoing medial and lateral MAT. Correlations between coronal and sagittal graft extrusion and between extrusion and the Lysholm score were compared in the 2 groups. In the coronal plane, mean absolute (4.3 vs 2.7 mm, respectively; P<.001) and relative (39% vs 21%, respectively; P<.001) graft extrusions were significantly greater for medial than lateral MAT. In the sagittal plane, mean absolute and relative ACMD and PCMD values were significantly greater for medial than lateral MAT (P<.001 each). For both medial and lateral MAT, mean absolute and relative ACMDs were significantly larger than PCMDs (P<.001 each). Graft extrusion>3 mm in the coronal plane was significantly more frequent in the medial (78%) than in the lateral (35%) MAT group. In the sagittal plane, the frequencies of ACMDs (72% vs 39%, respectively) and PCMDs (23% vs 4%, respectively) >3 mm were also significantly greater in the medial than in the lateral MAT group. Coronal and sagittal extrusions were not correlated with postoperative Lysholm scores for both medial and lateral MAT. The amount and incidence of graft extrusion were greater after medial than lateral MAT in both the coronal and sagittal planes. In the sagittal plane, graft extrusion was greater and more frequent on the anterior than the posterior horn in both medial and lateral MAT. However, graft extrusion was not correlated with early clinical outcomes after both medial and lateral MAT. © 2014 The Author(s).

Development of AFLP and RAPD markers linked to a locus associated with twisted growth in corkscrew willow (Salix matsudana 'Tortuosa').

PubMed

Lin, Juan; Gunter, Lee E; Harding, Scott A; Kopp, Richard F; McCord, Rachel P; Tsai, Chung-Jui; Tuskan, Gerald A; Smart, Lawrence B

2007-11-01

Salix matsudana Koidz. cultivar 'Tortuosa' (corkscrew willow) is characterized by extensive stem bending and curling of leaves. To investigate the genetic basis of this trait, controlled crosses were made between a corkscrew female (S. matsudana 'Tortuosa') and a straight-stemmed, wild-type male (Salix alba L. Clone 99010). Seventy-seven seedlings from this family (ID 99270) were grown in the field for phenotypic observation. Among the progeny, 39 had straight stems and leaves and 38 had bent stems and curled leaves, suggesting that a dominant allele at a single locus controls this phenotype. As a first step in characterizing the locus, we searched for amplified fragment length polymorphism (AFLP) and randomly amplified polymorphic DNA (RAPD) markers linked to the tortuosa allele using bulked segregant analysis. Samples of DNA from 10 corkscrew individuals were combined to produce a corkscrew pool, and DNA from 10 straight progeny was combined to make a wild-type pool. Sixty-four AFLP primer combinations and 640 RAPD primers were screened to identify marker bands amplified from the corkscrew parent and progeny pool, but not from the wild-type parent or progeny pool. An AFLP marker and a RAPD marker linked to and flanking the tortuosa locus were placed on a preliminary linkage map constructed based on segregation among the 77 progeny. Sectioning and analysis of shoot tips revealed that the corkscrew phenotype is associated with vascular cell collapse, smaller cell size in regions near the cambium and less developed phloem fibers than in wild-type progeny. Identification of a gene associated with this trait could lead to greater understanding of the control of normal stem development in woody plants.

Electrospun polyvinylpyrrolidone (PVP)/green tea extract composite nanofiber mats and their antioxidant activities

NASA Astrophysics Data System (ADS)

Pusporini, Pusporini; Edikresnha, Dhewa; Sriyanti, Ida; Suciati, Tri; Miftahul Munir, Muhammad; Khairurrijal, Khairurrijal

2018-05-01

Electrospinning was employed to make PVP (polyvinylpyrrolidone)/GTE (green tea extract) composite nanofiber mats. The electrospun PVP nanofiber mat as well as the PVP/GTE nanofiber mats were uniform. The average fiber diameter of PVP/GTE composite nanofiber mat decreased with increasing the GTE weight fraction (or decreasing the PVP weight fraction) in the PVP/GTE solution because the PVP/GTE solution concentration decreased. Then, the broad FTIR peak representing the stretching vibrations of O–H in hydroxyl groups of phenols and the stretching of N–H in amine groups of the GTE paste shifted to higher wavenumbers in the PVP/GTE composite nanofiber mats. These peak shifts implied that PVP and catechins of GTE in the PVP/GTE composite nanofiber mats had intermolecular interactions via hydrogen bonds between carbonyl groups of PVP and hydroxyl groups of catechins in GTE. Lastly, the antioxidant activity of the PVP/GTE composite nanofiber mat increased with reducing the average fiber diameter because the amount of catechins in the composite nanofiber mat increased with the increase of surface area due to the reduction of the average fiber diameter.

Aerobic sulfate reduction in microbial mats

NASA Technical Reports Server (NTRS)

Canfield, Donald E.; Des Marais, David J.

1991-01-01

Measurements of bacterial sulfate reduction and dissolved oxygen (O2) in hypersaline bacterial mats from Baja California, Mexico, revealed that sulfate reduction occurred consistently within the well-oxygenated photosynthetic zone of the mats. This evidence that dissimilatory sulfate reduction can occur in the presence of O2 challenges the conventional view that sulfate reduction is a strictly anaerobic process. At constant temperature, the rates of sulfate reduction in oxygenated mats during daytime were similar to rates in anoxic mats at night: thus, during a 24-hour cycle, variations in light and O2 have little effect on rates of sulfate reduction in these mats.

Sensitometric and archival evaluation of Kodak RA films in dental automatic processing.

PubMed

Thunthy, K H; Yeadon, W R; Winberg, R

1994-04-01

The Kodak Rapid Access System is an extension of the T-grain technology (T-Mat film). Unlike the T-Mat film, the T-Mat/Rapid Access film is forehardened by the addition of more hardener to the film emulsion. It can thus be processed rapidly in a Kodak Rapid Access medical processor in only 45 seconds dry-to-dry cycle by using the Kodak X-Omat RA/30 developer that does not contain a hardener. The absence of the hardener, glutaraldehyde, in the developer also makes this solution environmentally safer. In medical radiography, the T-Mat film has been replaced by the T-Mat/Rapid Access film. However, in dental extraoral radiography the T-Mat film is still being used because the processing solutions and the comparatively low temperatures of dental automatic processors are different from those used in medical radiography. This report shows that, for panoramic and other dental extraoral radiography, T-Mat films can be replaced by T-Mat/RA films by processing them in conventional Kodak X-Omat RP solutions using a dental automatic processing cycle. The differences in the sensitometric properties of the T-Mat and T-Mat/rapid Access films were negligible and therefore clinically insignificant. All films tested well for archival quality.

Time budgets of lactating dairy cattle in commercial freestall herds.

PubMed

Gomez, A; Cook, N B

2010-12-01

The aim of this study was to examine the time budgets of 205 lactating dairy cows housed in 16 freestall barns in Wisconsin and to determine the relationships between components of the time budget and herd- and cow-level fixed effects using mixed models. Using continuous video surveillance, time lying in the stall, time standing in the stall, time standing in the alleys (including drinking), time feeding, and time milking (time out of the pen for milking and transit) during a 24-h period were measured for each cow. In addition, the number of lying bouts and the mean duration of each lying bout per 24-h period were determined. Time milking varied between cows from 0.5 to 6.0 h/d, with a mean ± standard deviation of 2.7 ± 1.1h/d. Time milking was influenced significantly by pen stocking density, and time milking negatively affected time feeding, time lying, and time in the alley, but not time standing in the stall. Locomotion score, either directly or through an interaction with stall base type (a rubber crumb-filled mattress, MAT, or sand bedding, SAND), influenced pen activity. Lame cows spent less time feeding, less time in the alleys, and more time standing in the stalls in MAT herds, but not in SAND herds. The effect of lameness on lying time is complex and dependent on the time available for rest and differences in resting behavior observed between cows in MAT and SAND herds. In MAT herds, rest was characterized by a larger number of lying bouts of shorter duration than in SAND herds (mean = 14.4; confidence interval, CI: 12.4 to 16.5 vs. mean = 10.2; CI: 8.2 to 12.2 bouts per d, and mean = 1.0; CI: 0.9 to 1.1 vs. mean = 1.3, CI: 1.2 to 1.4h bout duration for MAT and SAND herds, respectively). Lameness was associated with an increase in time standing in the stall and a reduction in the mean (CI) number of lying bouts per day from 13.2 (CI: 12.3 to 14.1) bouts/d for nonlame cows to 10.9 (CI: 9.30 to 12.8) bouts/d for moderately lame cows, and an overall reduction in lying time in MAT herds compared with SAND herds (11.5; CI: 10.0 to 13.0 vs. 12.7; CI: 11.0 to 14.3h/d, respectively). These results show that time out of the pen milking, stall base type, and lameness significantly affect time budgets of cows housed in freestall facilities. Copyright © 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Transient Neonatal Diabetes Mellitus: A Challenge and Opportunity for Specialized Nursing Care.

PubMed

Zammit, Martha Anne; Agius, Stefanie Marie; Calleja-Agius, Jean

2017-07-01

Transient neonatal diabetes mellitus (TNDM) is a rare disorder, with a reported incidence of approximately 1 in 450,000 live births. It is characterized by insulin-requiring hyperglycemia in the neonatal period. The disease improves by early childhood, but the patient may relapse in later life. Diagnosis is made after genetic testing following presentation with hyperglycemia not conforming to Type 1 or Type 2 diabetes. Management is based on insulin and possible sulfonylurea administration. Three genetically distinct subtypes of TNDM are recognized. Type 1 TNDM is due to overexpression of genes at the 6q24 locus, whereas the 11p15 locus is involved in Type 2 and 3 TNDM. In this article the clinical presentation, management, and genetics of TNDM are discussed, particularly emphasizing the role of the neonatal nurse.

The gene for autosomal dominant cerebellar ataxia with pigmentary macular dystrophy maps to chromosome 3p12-p21.1.

PubMed

Benomar, A; Krols, L; Stevanin, G; Cancel, G; LeGuern, E; David, G; Ouhabi, H; Martin, J J; Dürr, A; Zaim, A

1995-05-01

Autosomal dominant cerebellar ataxia with pigmentary macular dystrophy (ADCA type II) is a rare neurodegenerative disorder with marked anticipation. We have mapped the ADCA type II locus to chromosome 3 by linkage analysis in a genome-wide search and found no evidence for genetic heterogeneity among four families of different geographic origins. Haplotype reconstruction initially restricted the locus to the 33 cM interval flanked by D3S1300 and D3S1276 located at 3p12-p21.1. Combined multipoint analysis, using the Zmax-1 method, further reduced the candidate interval to an 8 cM region around D3S1285. Our results show that ADCA type II is a genetically homogenous disorder, independent of the heterogeneous group of type I cerebellar ataxias.

Distribution of the messenger RNA for the small conductance calcium-activated potassium channel SK3 in the adult rat brain and correlation with immunoreactivity.

PubMed

Tacconi, S; Carletti, R; Bunnemann, B; Plumpton, C; Merlo Pich, E; Terstappen, G C

2001-01-01

Small conductance calcium-activated potassium channels are voltage independent potassium channels which modulate the firing patterns of neurons by activating the slow component of the afterhyperpolarization. The genes encoding a family of small conductance calcium-activated potassium channels have been cloned and up to now three known members have been described and named small conductance calcium-activated potassium channel type 1, small conductance calcium-activated potassium channel type 2 and small conductance calcium-activated potassium channel type 3; the distribution of their messenger RNA in the rat CNS has already been performed but only in a limited detail. The present study represents the first detailed analysis of small conductance calcium-activated potassium channel type 3 mRNA distribution in the adult rat brain and resulted in a strong to moderate expression of signal in medial habenular nucleus, substantia nigra compact part, suprachiasmatic nucleus, ventral tegmental area, lateral septum, dorsal raphe and locus coeruleus. Immunohistological experiments were also performed and confirmed the presence of small conductance calcium-activated potassium channel type 3 protein in medial habenular nucleus, locus coeruleus and dorsal raphe. Given the importance of dorsal raphe, locus coeruleus and substantia nigra/ventral tegmental area for serotonergic, noradrenergic and dopaminergic transmission respectively, our results pose the morphological basis for further studies on the action of small conductance calcium-activated potassium channel type 3 in serotonergic, noradrenergic and dopaminergic transmission.

Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a Subset of 237 Donors in the South African Bone Marrow Registry

PubMed Central

Ingram, Charlotte; Schlaphoff, Terry; Borrill, Veronica; Christoffels, Alan

2018-01-01

Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR). Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC) format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A∗02:02g (0.096), B∗07:02g (0.082), C∗07:02g (0.180), DQB1∗06:02 (0.157), and DRB1∗15:01 (0.072). The most common haplotype was A∗03:01g~B∗07:02g~C∗07:02g~DQB1∗06:02~DRB1∗15:01 (0.067), which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies. PMID:29850621

The vegetative compatibility group to which the US biocontrol agent Aspergillus flavus AF36 belongs is also endemic to Mexico.

PubMed

Ortega-Beltran, A; Grubisha, L C; Callicott, K A; Cotty, P J

2016-04-01

To assess frequencies of the Aspergillus flavus atoxigenic vegetative compatibility group (VCG) YV36, to which the biocontrol agent AF36 belongs, in maize-growing regions of Mexico. Over 3500 A. flavus isolates recovered from maize agroecosystems in four states of Mexico during 2005 through 2008 were subjected to vegetative compatibility analyses based on nitrate nonutilizing mutants. Results revealed that 59 (1·6%) isolates belong to VCG YV36. All 59 isolates had the MAT1-2 idiomorph at the mating-type locus and the single nucleotide polymorphism in the polyketide synthase gene that confers atoxigenicity. Additional degradation of the aflatoxin gene cluster was detected in three isolates. Microsatellite loci analyses revealed low levels of genetic diversity and no linkage disequilibrium within VCG YV36. The VCG to which the biocontrol agent AF36 belongs, YV36, is also native to Mexico. The North American Free Trade Agreement should facilitate adoption of AF36 for use by Mexico in aflatoxin prevention programs. An USEPA registered biocontrol agent effective at preventing aflatoxin contamination of crops in the US, is also native to Mexico. This should facilitate the path to registration of AF36 as the first biopesticide for aflatoxin mitigation of maize in Mexico. Economic and health benefits to the population of Mexico should result once aflatoxin mitigation programs based on AF36 applications are implemented. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Nomenclatural Benchmarking: The roles of digital typification and telemicroscopy

USDA-ARS?s Scientific Manuscript database

The process of nomenclatural benchmarking is the examination of type specimens of all available names to ascertain which currently accepted species the specimen bearing the name falls within. We propose a strategy for addressing four challenges for nomenclatural benchmarking. First, there is the mat...

Spatially-resolved carbon flow through a hypersaline phototrophic microbial mat

NASA Astrophysics Data System (ADS)

Moran, J.; Lindemann, S. R.; Cory, A. B.; Courtney, S.; Cole, J. K.; Fredrickson, J.

2013-12-01

Hot Lake is a hypersaline, meromictic lake located in an endorheic basin in north-central Washington. Low annual rainfall and high evaporation rates contribute to the lake's high salinity. The predominant dissolved salt is magnesium sulfate, of which monimolimnion waters may seasonally exceed 2 M concentrations. Induced by its high salinity and meromictic nature, Hot Lake displays an inverse thermal gradient with deep horizons seasonally exceeding 50 °C. Despite extreme conditions, dense benthic microbial mats composed of cyanobacteria, anoxygenic photoheterotrophs, and bacterial heterotroph populations develop in the lake. These mats can exceed 1 cm in thickness and display vertical stratification in color due to bacterial pigmentation. Typical mat stratification includes an orange surface layer underlain by green and purple layers at increasing depth. Carbonates, including aragonite and magnesite, are observed within the mat and their formation is likely induced or influenced by microbial metabolic activities and associated pH excursions. We are exploring the role Hot Lake's microbial mats play in carbon cycling. Cyanobacteria are the dominant CO2-fixing organisms in the mat and we seek to understand the spatial and metabolic controls on how the carbon initially fixed by mat cyanobacteria is transferred to associated heterotrophic populations spread throughout the mat strata. Secondly, we seek to understand the overall net carbon balance of the mat through a growing season. We are using a stable isotope probing approach for assessing carbon uptake and migration through representative mat samples. We performed a series of ex situ incubations of freshly harvested mat samples in lake water amended with 13C-labeled bicarbonate or substrates commonly consumed by heterotrophs (including acetate and glucose) and using multiple stable isotope techniques to track label uptake, residence time, remineralization, and location within the mat. In addition to bulk isotope analysis (via elemental analysis IRMS and gas bench IRMS) we are employing laser ablation IRMS (LA-IRMS) to provide a spatially-resolved accounting of label uptake through the mat cross section. This technique permits isotope analysis at the 50 μm scale, and can provide multiple isotope analyses within each mat strata. By coupling LA-IRMS analysis with laminar sectioning of the mat and amplicon sequencing of the rrnA gene, we seek to establish linkages between phylogeny and function over the course of a diel cycle with highlighted emphasis on evidence of carbon transfer between mat laminae and the phylotypes that inhabit them. We are also using a series of carbon accumulation microcosms to quantify net carbon fixation over the seasonal cycle. These microcosms are deployed at multiple depths to provide an accounting of carbon cycling under the specific geochemical conditions experienced at variable depth. Coupling the data from these individual microcosms to our bathymetric survey of Hot Lake permits us to estimate total mat carbon fixation, and therefore to begin to assess the impact of the mat on the greater lake carbon cycle.

Fusarium verticillioides from finger millet in Uganda.

PubMed

Saleh, Amgad A; Esele, J P; Logrieco, Antonio; Ritieni, Alberto; Leslie, John F

2012-01-01

Finger millet (Eleusine coracana) is a subsistence crop grown in Sub-Saharan Africa and the Indian Sub-continent. Fusarium species occurring on this crop have not been reported. Approximately 13% of the Fusarium isolates recovered from finger millet growing at three different locations in eastern Uganda belong to Fusarium verticillioides, and could produce up to 18,600 µg/g of total fumonisins when cultured under laboratory conditions. These strains are all genetically unique, based on AFLP analyses, and form fertile perithecia when crossed with the standard mating type tester strains for this species. All but one of the strains is female-fertile and mating-type segregates 13:20 Mat-1:Mat-2. Three new sequences of the gene encoding translation elongation factor 1-α were found within the population. These results indicate a potential health risk for infants who consume finger millet gruel as a weaning food, and are consistent with the hypothesis that F. verticillioides originated in Africa and not in the Americas, despite its widespread association with maize grown almost anywhere worldwide.

European Forest Cover During the Past 12,000 Years: A Palynological Reconstruction Based on Modern Analogs and Remote Sensing

PubMed Central

Zanon, Marco; Davis, Basil A. S.; Marquer, Laurent; Brewer, Simon; Kaplan, Jed O.

2018-01-01

Characterization of land cover change in the past is fundamental to understand the evolution and present state of the Earth system, the amount of carbon and nutrient stocks in terrestrial ecosystems, and the role played by land-atmosphere interactions in influencing climate. The estimation of land cover changes using palynology is a mature field, as thousands of sites in Europe have been investigated over the last century. Nonetheless, a quantitative land cover reconstruction at a continental scale has been largely missing. Here, we present a series of maps detailing the evolution of European forest cover during last 12,000 years. Our reconstructions are based on the Modern Analog Technique (MAT): a calibration dataset is built by coupling modern pollen samples with the corresponding satellite-based forest-cover data. Fossil reconstructions are then performed by assigning to every fossil sample the average forest cover of its closest modern analogs. The occurrence of fossil pollen assemblages with no counterparts in modern vegetation represents a known limit of analog-based methods. To lessen the influence of no-analog situations, pollen taxa were converted into plant functional types prior to running the MAT algorithm. We then interpolate site-specific reconstructions for each timeslice using a four-dimensional gridding procedure to create continuous gridded maps at a continental scale. The performance of the MAT is compared against methodologically independent forest-cover reconstructions produced using the REVEALS method. MAT and REVEALS estimates are most of the time in good agreement at a trend level, yet MAT regularly underestimates the occurrence of densely forested situations, requiring the application of a bias correction procedure. The calibrated MAT-based maps draw a coherent picture of the establishment of forests in Europe in the Early Holocene with the greatest forest-cover fractions reconstructed between ∼8,500 and 6,000 calibrated years BP. This forest maximum is followed by a general decline in all parts of the continent, likely as a result of anthropogenic deforestation. The continuous spatial and temporal nature of our reconstruction, its continental coverage, and gridded format make it suitable for climate, hydrological, and biogeochemical modeling, among other uses. PMID:29568303

European Forest Cover During the Past 12,000 Years: A Palynological Reconstruction Based on Modern Analogs and Remote Sensing.

PubMed

Zanon, Marco; Davis, Basil A S; Marquer, Laurent; Brewer, Simon; Kaplan, Jed O

2018-01-01

Characterization of land cover change in the past is fundamental to understand the evolution and present state of the Earth system, the amount of carbon and nutrient stocks in terrestrial ecosystems, and the role played by land-atmosphere interactions in influencing climate. The estimation of land cover changes using palynology is a mature field, as thousands of sites in Europe have been investigated over the last century. Nonetheless, a quantitative land cover reconstruction at a continental scale has been largely missing. Here, we present a series of maps detailing the evolution of European forest cover during last 12,000 years. Our reconstructions are based on the Modern Analog Technique (MAT): a calibration dataset is built by coupling modern pollen samples with the corresponding satellite-based forest-cover data. Fossil reconstructions are then performed by assigning to every fossil sample the average forest cover of its closest modern analogs. The occurrence of fossil pollen assemblages with no counterparts in modern vegetation represents a known limit of analog-based methods. To lessen the influence of no-analog situations, pollen taxa were converted into plant functional types prior to running the MAT algorithm. We then interpolate site-specific reconstructions for each timeslice using a four-dimensional gridding procedure to create continuous gridded maps at a continental scale. The performance of the MAT is compared against methodologically independent forest-cover reconstructions produced using the REVEALS method. MAT and REVEALS estimates are most of the time in good agreement at a trend level, yet MAT regularly underestimates the occurrence of densely forested situations, requiring the application of a bias correction procedure. The calibrated MAT-based maps draw a coherent picture of the establishment of forests in Europe in the Early Holocene with the greatest forest-cover fractions reconstructed between ∼8,500 and 6,000 calibrated years BP. This forest maximum is followed by a general decline in all parts of the continent, likely as a result of anthropogenic deforestation. The continuous spatial and temporal nature of our reconstruction, its continental coverage, and gridded format make it suitable for climate, hydrological, and biogeochemical modeling, among other uses.

Maté: a risk factor for oral and oropharyngeal cancer.

PubMed

Goldenberg, David

2002-10-01

Maté is a tea-like beverage consumed mainly in Argentina, Uruguay, Paraguay, southern Brazil and to a lesser degree in other areas of the world such as Germany, Syria, Lebanon and Northern Israel. It is brewed from the dried leaves and stemlets of the perennial tree Ilex paraguarensis ("yerba mate") a species that belongs to the Aquifoliaceae family. Maté consumption has been associated with an increased rate of oral and oropharyngeal cancers. The purpose of this study is to review the literature and discuss the role of Maté consumption in the development of oral and oropharyngeal cancer and the potential carcinogenic mechanisms. A review of the relevant literature linking Maté consumption with oral and oropharyngeal cancer and the carcinogenicity of Maté was performed. The search was performed using Medline, library catalogues, OCLC first search and ISI web of science databases. Case control studies on Maté drinking populations and, in vivo and in vitro studies on the carcinogenicity of Maté were reviewed. The populations reviewed in many of these studies also used alcohol and tobacco products confounding the influence of Maté as an independent risk factor. There is evidence in the literature that Maté consumption is in itself carcinogenic and plays a role in the development of cancers of the oral cavity and oropharynx. Although the exact mechanism of carcinogenesis is still unknown, available information suggests that Maté drinking should be considered one of the risk factors for oral and oropharyngeal cancer.

Comparative protein modeling of methionine S-adenosyltransferase (MAT) enzyme from Mycobacterium tuberculosis: a potential target for antituberculosis drug discovery.

PubMed

Khedkar, Santosh A; Malde, Alpeshkumar K; Coutinho, Evans C

2005-01-01

Mycobacterium tuberculosis (Mtb) is a successful pathogen that overcomes the numerous challenges presented by the immune system of the host. In the last 40 years few anti-TB drugs have been developed, while the drug-resistance problem is increasing; there is thus a pressing need to develop new anti-TB drugs active against both the acute and chronic growth phases of the mycobacterium. Methionine S-adenosyltransferase (MAT) is an enzyme involved in the synthesis of S-adenosylmethionine (SAM), a methyl donor essential for mycolipid biosynthesis. As an anti-TB drug target, Mtb-MAT has been well validated. A homology model of MAT has been constructed using the X-ray structures of E. coli MAT (PDB code: 1MXA) and rat MAT (PDB code: 1QM4) as templates, by comparative protein modeling principles. The resulting model has the correct stereochemistry as gauged from the Ramachandran plot and good three-dimensional (3D) structure compatibility as assessed by the Profiles-3D score. The structurally and functionally important residues (active site) of Mtb-MAT have been identified using the E. coli and rat MAT crystal structures and the reported point mutation data. The homology model conserves the topological and active site features of the MAT family of proteins. The differences in the molecular electrostatic potentials (MEP) of Mtb and human MAT provide evidences that selective and specific Mtb-MAT inhibitors can be designed using the homology model, by the structure-based drug design approaches.

The mutY gene: a mutator locus in Escherichia coli that generates G.C----T.A transversions.

PubMed Central

Nghiem, Y; Cabrera, M; Cupples, C G; Miller, J H

1988-01-01

We have used a strain with an altered lacZ gene, which reverts to wild type via only certain transversions, to detect transversion-specific mutators in Escherichia coli. Detection relied on a papillation technique that uses a combination of beta-galactosides to reveal blue Lac+ papillae. One class of mutators is specific for the G.C----T.A transversion as determined by the reversion pattern of a set of lacZ mutations and by the distribution of forward nonsense mutations in the lacI gene. The locus responsible for the mutator phenotype is designated mutY and maps near 64 min on the genetic map of E. coli. The mutY locus may act in a similar but reciprocal fashion to the previously characterized mutT locus, which results in A.T----C.G transversions. Images PMID:3128795

Microbial and Functional Gene Diversity in the Thrombolitic Mats of Highborne Cay, Bahamas

NASA Astrophysics Data System (ADS)

Foster, J. S.; Mobberley, J. M.

2010-04-01

In this study we examine the metagenome of modern thrombolitic mats. Our results indicate that thrombolitic mats are far more diverse than previously assumed; and gene analysis is now elucidating the molecular pathways needed for thrombolitic mat development.

Polymeric materials from renewable resources

NASA Astrophysics Data System (ADS)

Frollini, Elisabete; Rodrigues, Bruno V. M.; da Silva, Cristina G.; Castro, Daniele O.; Ramires, Elaine C.; de Oliveira, Fernando; Santos, Rachel P. O.

2016-05-01

The goals of our studies have been the use of renewable raw materials in the preparation of polymeric materials with diversified properties. In this context, lignosulfonate, which is produced in large scale around the world, but not widely used in the production of polymeric materials, was used to replace phenol and polyols in the preparation of phenolic- (Ligno-PH) and polyurethane-type (Ligno-PU) polymers, respectively. These polymers were used to prepare composites reinforced with sisal lignocellulosic fibers. The use of lignosulfonate in the formulation of both types of polymers was beneficial, because in general composites with improved properties, specially impact strength, were obtained. Composites were also prepared from the so called "biopolyethylene" (HDPE), curaua lignocellulosic fiber, and castor oil (CO). All composites HDBPE/CO/Fiber exhibited higher impact strength, when compared to those of the corresponding HDBPE/Fiber. These results, combined with others (eg SEM images of the fractured surfaces) indicated that, in addition to acting as a plasticizer, this oil may have acted as a compatibilizer of the hydrophilic fiber with the hydrophobic polymer. The set of results indicated that (i) mats with nano (diameter ≤ 100nm) and/or ultrafine (submicron scale) fibers were produced, (ii) hybrid fibers were produced (bio-based mats composites), (iii) cellulosic pulp (CP) and/or lignin (Lig) can be combined with PET matrices to control properties such as stiffness and hydrophilicity of the respective mats. Materials with diversified properties were prepared from high content of renewable raw materials, thus fulfilling the proposed targets.

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data.

PubMed

Shen, Shihao; Park, Juw Won; Lu, Zhi-xiang; Lin, Lan; Henry, Michael D; Wu, Ying Nian; Zhou, Qing; Xing, Yi

2014-12-23

Ultra-deep RNA sequencing (RNA-Seq) has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of transcript splicing (MATS), a statistical method for detecting differential alternative splicing between two RNA-Seq samples. Here we describe a new statistical model and computer program, replicate MATS (rMATS), designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates. In addition to the analysis of unpaired replicates, rMATS also includes a model specifically designed for paired replicates between sample groups. The hypothesis-testing framework of rMATS is flexible and can assess the statistical significance over any user-defined magnitude of splicing change. The performance of rMATS is evaluated by the analysis of simulated and real RNA-Seq data. rMATS outperformed two existing methods for replicate RNA-Seq data in all simulation settings, and RT-PCR yielded a high validation rate (94%) in an RNA-Seq dataset of prostate cancer cell lines. Our data also provide guiding principles for designing RNA-Seq studies of alternative splicing. We demonstrate that it is essential to incorporate biological replicates in the study design. Of note, pooling RNAs or merging RNA-Seq data from multiple replicates is not an effective approach to account for variability, and the result is particularly sensitive to outliers. The rMATS source code is freely available at rnaseq-mats.sourceforge.net/. As the popularity of RNA-Seq continues to grow, we expect rMATS will be useful for studies of alternative splicing in diverse RNA-Seq projects.

Development of electrospun beaded fibers from Thai silk fibroin and gelatin for controlled release application.

PubMed

Somvipart, Siraporn; Kanokpanont, Sorada; Rangkupan, Rattapol; Ratanavaraporn, Juthamas; Damrongsakkul, Siriporn

2013-04-01

Thai silk fibroin and gelatin are attractive biomaterials for tissue engineering and controlled release applications due to their biocompatibility, biodegradability, and bioactive properties. The development of electrospun fiber mats from silk fibroin and gelatin were reported previously. However, burst drug release from such fiber mats remained the problem. In this study, the formation of beads on the fibers aiming to be used for the sustained release of drug was of our interest. The beaded fiber mats were fabricated using electrospinning technique by controlling the solution concentration, weight blending ratio of Thai silk fibroin/gelatin blend, and applied voltage. It was found that the optimal conditions including the solution concentration and the weight blending ratio of Thai silk fibroin/gelatin at 8-10% (w/v) and 70/30, respectively, with the applied voltage at 18 kV provided the fibers with homogeneous formation of beads. Then, the beaded fiber mats obtained were crosslinked by the reaction of carbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS). Methylene blue as a model active compound was loaded on the fiber mats. The release test of methylene blue from the beaded fiber mats was carried out in comparison to that of the smooth fiber mats without beads. It was found that the beaded fiber mats could prolong the release of methylene blue, comparing to the smooth fiber mats without beads. This was possibly due to the beaded fiber mats that would absorb and retain higher amount of methylene blue than the fiber mats without beads. Thai silk fibroin/gelatin beaded fiber mats were established as an effective carrier for the controlled release applications. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of post-fracture non-weight-bearing immobilization on muscle atrophy, intramuscular and intermuscular adipose tissues in the thigh and calf.

PubMed

Yoshiko, Akito; Yamauchi, Koun; Kato, Takayuki; Ishida, Koji; Koike, Teruhiko; Oshida, Yoshiharu; Akima, Hiroshi

2018-06-09

Disuse and/or a non-weight-bearing condition changes muscle composition, with decreased skeletal muscle tissue and increased fat within (intramuscular adipose tissue, IntraMAT) and between (intermuscular adipose tissue, InterMAT) given muscles. Excessive adipose tissue contributes to dysfunctional and metabolically impaired muscle. How these adipose tissues change during orthopedic treatment (e.g., cast immobilization, daily use of crutches) is not well documented. This study aimed to quantify changes in IntraMAT, InterMAT, and thigh and calf muscle tissue during orthopedic treatment. We studied 8 patients with fifth metatarsal bone or fibular fractures. The ankle joint involved underwent plaster casting for approximately 4 weeks, with crutches used during that time. Axial T1-weighted MRI at the mid-thigh and a 30% proximal site at the calf were obtained to measure IntraMAT and InterMAT cross-sectional areas (CSAs) and skeletal muscle tissue CSA before treatment and 4 weeks afterward. Thigh and calf muscle tissue CSAs were significantly decreased from before to after treatment: thigh, 85.8 ± 7.6 to 77.1 ± 7.3 cm 2 ; calf, 53.3 ± 5.5 to 48.9 ± 5.0 cm 2 (p < 0.05). None of the IntraMAT or InterMAT changes was statistically significant. There was a relation between the percentage change of thigh IntraMAT CSA and muscle tissue CSA (r s  = -0.86, p < 0.01). The 4 weeks of treatment primarily induced skeletal muscle atrophy with less of an effect on IntraMAT or InterMAT. There is a risk of increasing IntraMAT relatively by decreasing skeletal muscle tissue size during orthopedic treatment.

B-Scan Based Acoustic Source Reconstruction for Magnetoacoustic Tomography with Magnetic Induction (MAT-MI)

PubMed Central

Mariappan, Leo; Li, Xu; He, Bin

2011-01-01

We present in this study an acoustic source reconstruction method using focused transducer with B mode imaging for magnetoacoustic tomography with magnetic induction (MAT-MI). MAT-MI is an imaging modality proposed for non-invasive conductivity imaging with high spatial resolution. In MAT-MI acoustic sources are generated in a conductive object by placing it in a static and a time-varying magnetic field. The acoustic waves from these sources propagate in all directions and are collected with transducers placed around the object. The collected signal is then usedto reconstruct the acoustic source distribution and to further estimate the electrical conductivity distribution of the object. A flat piston transducer acting as a point receiver has been used in previous MAT-MI systems to collect acoustic signals. In the present study we propose to use B mode scan scheme with a focused transducer that gives a signal gain in its focus region and improves the MAT-MI signal quality. A simulation protocol that can take into account different transducer designs and scan schemes for MAT-MI imaging is developed and used in our evaluation of different MAT-MI system designs. It is shown in our computer simulations that, as compared to the previous approach, the MAT-MI system using B-scan with a focused transducer allows MAT-MI imaging at a closer distance and has improved system sensitivity. In addition, the B scan imaging technique allows reconstruction of the MAT-MI acoustic sources with a discrete number of scanning locations which greatly increases the applicability of the MAT-MI approach especially when a continuous acoustic window is not available in real clinical applications. We have also conducted phantom experiments to evaluate the proposed method and the reconstructed image shows a good agreement with the target phantom. PMID:21097372

Microbial Diversity and Lipid Abundance in Microbial Mats from a Sulfidic, Saline, Warm Spring in Utah, USA

NASA Astrophysics Data System (ADS)

Gong, J.; Edwardson, C.; Mackey, T. J.; Dzaugis, M.; Ibarra, Y.; Course 2012, G.; Frantz, C. M.; Osburn, M. R.; Hirst, M.; Williamson, C.; Hanselmann, K.; Caporaso, J.; Sessions, A. L.; Spear, J. R.

2012-12-01

The microbial diversity of Stinking Springs, a sulfidic, saline, warm spring northeast of the Great Salt Lake was investigated. The measured pH, temperature, salinity, and sulfide concentration along the flow path ranged from 6.64-7.77, 40-28° C, 2.9-2.2%, and 250 μM to negligible, respectively. Five sites were selected along the flow path and within each site microbial mats were dissected into depth profiles based on the color and texture of the mat layers. Genomic DNA was extracted from each layer, and the 16S rRNA gene was amplified and sequenced on the Roche 454 Titanium platform. Fatty acids were also extracted from the mat layers and analyzed by liquid chromatography and mass spectrometry. The mats at Stinking Springs were classified into roughly two morphologies with respect to their spatial distribution: loose, sometimes floating mats proximal to the spring source; and thicker, well-laminated mats distal to the spring source. Loosely-laminated mats were found in turbulent stream flow environments, whereas well-laminated mats were common in less turbulent sheet flows. Phototrophs, sulfur oxidizers, sulfate reducers, methanogens, other bacteria and archaea were identified by 16S rRNA gene sequences. Diatoms, identified by microscopy and lipid analysis were found to increase in abundance with distance from the source. Methanogens were generally more abundant in deeper mat laminae. Photoheterotrophs were found in all mat layers. Microbial diversity increased significantly with depth at most sites. In addition, two distinct microbial streamers were identified and characterized at the two fast flowing sites. These two streamer varieties were dominated by either cyanobacteria or flavobacteria. Overall, our genomic and lipid analysis suggest that the physical and chemical environment is more predictive of the community composition than mat morphology. Site Map

The Oncogene PDRG1 Is an Interaction Target of Methionine Adenosyltransferases

PubMed Central

Garrido, Francisco; Reytor, Edel; Portillo, Francisco; Pajares, María A.

2016-01-01

Methionine adenosyltransferases MAT I and MAT III (encoded by Mat1a) catalyze S-adenosylmethionine synthesis in normal liver. Major hepatic diseases concur with reduced levels of this essential methyl donor, which are primarily due to an expression switch from Mat1a towards Mat2a. Additional changes in the association state and even in subcellular localization of these isoenzymes are also detected. All these alterations result in a reduced content of the moderate (MAT I) and high Vmax (MAT III) isoenzymes, whereas the low Vmax (MAT II) isoenzyme increases and nuclear accumulation of MAT I is observed. These changes derive in a reduced availability of cytoplasmic S-adenosylmethionine, together with an effort to meet its needs in the nucleus of damaged cells, rendering enhanced levels of certain epigenetic modifications. In this context, the putative role of protein-protein interactions in the control of S-adenosylmethionine synthesis has been scarcely studied. Using yeast two hybrid and a rat liver library we identified PDRG1 as an interaction target for MATα1 (catalytic subunit of MAT I and MAT III), further confirmation being obtained by immunoprecipitation and pull-down assays. Nuclear MATα interacts physically and functionally with the PDRG1 oncogene, resulting in reduced DNA methylation levels. Increased Pdrg1 expression is detected in acute liver injury and hepatoma cells, together with decreased Mat1a expression and nuclear accumulation of MATα1. Silencing of Pdrg1 expression in hepatoma cells alters their steady-state expression profile on microarrays, downregulating genes associated with tumor progression according to GO pathway analysis. Altogether, the results unveil the role of PDRG1 in the control of the nuclear methylation status through methionine adenosyltransferase binding and its putative collaboration in the progression of hepatic diseases. PMID:27548429

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

Aplin, H.M.; Hirst, K.L.; Crosby, A.H.

Dentinogenesis imperfecta type II (DGI1) is an autosomal dominant disorder of dentin formation, which has been mapped to human chromosome 4q12-q21. The region most likely to contain the DGI1 locus is a 3.2-cM region surrounding the osteopontin (SPP1) locus. Recently, a novel dentin-specific acidic phosphoprotein (dmp1) has been cloned in the rat and mapped to mouse chromosome 5q21. In the current investigation, we have isolated a cosmid containing the human DMP1 gene. The isolation of a short tandem repeat polymorphism at this locus has allowed us to map the DMP1 locus to human chromosome 4q21 and demonstrate that it ismore » tightly linked to DGI1 in two families (Z{sub max} = 11.01, {theta} = 0.001). The creation of a yeast artificial chromosome contig around SPP1 has further allowed us to demonstrate that DMP1 is located within 150 kb of the bone sialoprotein and 490 kb of the SPP1 loci, respectively. DMP1 is therefore a strong candidate for the DGI1 locus. 12 refs., 2 figs., 1 tab.« less

USH1K, a novel locus for type I Usher syndrome, maps to chromosome 10p11.21-q21.1.

PubMed

Jaworek, Thomas J; Bhatti, Rashid; Latief, Noreen; Khan, Shaheen N; Riazuddin, Saima; Ahmed, Zubair M

2012-10-01

We ascertained two large Pakistani consanguineous families (PKDF231 and PKDF608) segregating profound hearing loss, vestibular dysfunction, and retinitis pigmentosa; the defining features of Usher syndrome type 1 (USH1). To date, seven USH1 loci have been reported. Here, we map a novel locus, USH1K, on chromosome 10p11.21-q21.1. In family PKDF231, we performed a genome-wide linkage screen and found a region of homozygosity shared among the affected individuals at chromosome 10p11.21-q21.1. Meiotic recombination events in family PKDF231 define a critical interval of 11.74 cM (20.20 Mb) bounded by markers D10S1780 (63.83 cM) and D10S546 (75.57 cM). Affected individuals of family PKDF608 were also homozygous for chromosome 10p11.21-q21.1-linked STR markers. Of the 85 genes within the linkage interval, PCDH15, GJD4, FZD4, RET and LRRC18 were sequenced in both families, but no potential pathogenic mutation was identified. The USH1K locus overlaps the non-syndromic deafness locus DFNB33 raising the possibility that the two disorders may be caused by allelic mutations.

T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus.

PubMed

Houtman, Miranda; Shchetynsky, Klementy; Chemin, Karine; Hensvold, Aase Haj; Ramsköld, Daniel; Tandre, Karolina; Eloranta, Maija-Leena; Rönnblom, Lars; Uebe, Steffen; Catrina, Anca Irinel; Malmström, Vivianne; Padyukov, Leonid

2018-06-01

Non-coding SNPs in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) locus have been linked with several autoimmune diseases, including rheumatoid arthritis, type I diabetes, and inflammatory bowel disease. However, the functional consequences of these SNPs are poorly characterized. Herein, we show in blood cells that SNPs in the PTPN2 locus are highly correlated with DNA methylation levels at four CpG sites downstream of PTPN2 and expression levels of the long non-coding RNA (lncRNA) LINC01882 downstream of these CpG sites. We observed that LINC01882 is mainly expressed in T cells and that anti-CD3/CD28 activated naïve CD4 + T cells downregulate the expression of LINC01882. RNA sequencing analysis of LINC01882 knockdown in Jurkat T cells, using a combination of antisense oligonucleotides and RNA interference, revealed the upregulation of the transcription factor ZEB1 and kinase MAP2K4, both involved in IL-2 regulation. Overall, our data suggests the involvement of LINC01882 in T cell activation and hints towards an auxiliary role of these non-coding SNPs in autoimmunity associated with the PTPN2 locus. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Allelic association at the D14S43 locus in early onset Alzheimer`s disease

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

Brice, A.; Tardieu, S.; Campion, D.

1995-04-24

The D14S43 marker is closely linked to the major gene for early onset autosomal dominant Alzheimer`s disease on chromosome 14. Allelic frequencies at the D14S43 locus were compared in 113 familial and isolated cases of early onset Alzheimer`s disease (<60 years of age at onset) (EOAD) and 109 unaffected individuals of the same geographic origin. Allele 7 was significantly (P = 0.033) more frequent in type 1 EOAD patients (13.2%), defined by the presence of at least another first degree relative with EOAD, than in controls (4.1%). Since an autosomal dominant gene is probably responsible for type 1 patients, allelicmore » association may reflect linkage disequilibrium at the D14S43 locus. This would mean that some patients share a common ancestral mutation. However, since multiple tests were carried out, this result must be interpreted with caution, and needs confirmation in an independent sample. 16 refs., 2 tabs.« less

Solution blowing of chitosan/PVA hydrogel nanofiber mats.

PubMed

Liu, Ruifang; Xu, Xianlin; Zhuang, Xupin; Cheng, Bowen

2014-01-30

Both nanofiber mats and hydrogel have their own advantages in wound healing. In this study, a novel hydrogel nanofiber mats were fabricated via solution blowing of chitosan and PVA solution, with various content of ethylene glycol diglycidyl ether (EGDE) as cross-linker. SEM observation showed that the fibers were several hundred nanometers in diameter with smooth surface and distributed randomly forming three-dimensional mats. The structure of the chitosan/PVA nanofibers was examined by FTIR and XPS, and the results showed that the cross-linking reaction occurred between EGDE and the hydroxyl groups. The mats could quickly hydrate in an aqueous environment to form hydrogel. Their value of equilibrate water absorption varied from 680 to 459% various content of EGDE. The nanofiber mats showed good bactericidal activity against Escherichia coli. The chitosan/PVA hydrogel nanofiber mats showed the combination advantages of nanofibrous mats and hydrogel dressing, and were suggested as potential application in wound healing. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microbial Species Richness and Metabolic Activities in Hypersaline Microbial Mats: Insight into Biosignature Formation Through Lithification

NASA Astrophysics Data System (ADS)

Baumgartner, Laura K.; Dupraz, Christophe; Buckley, Daniel H.; Spear, John R.; Pace, Norman R.; Visscher, Pieter T.

2009-11-01

Microbial mats in the hypersaline lake of Salt Pan, Eleuthera, Bahamas, display a gradient of lithification along a transect from the center to the shore of the lake. These mats exist under similar geochemical conditions, with light quantity and quality as the sole major environmental difference. Therefore, we hypothesized that the microbial community may be driving the differences in lithification and, by extension, mineral biosignature formation. The lithifying and non-lithifying mat communities were compared (via 16S rRNA gene sequencing, 485 and 464 sequences, respectively) over both temporal and spatial scales. Seven bacterial groups dominated in all the microbial mat libraries: bacteriodetes, alphaproteobacteria, deltaproetobacteria, chloroflexi, spirochaetes, cyanobacteria, and planctomycetes. The mat communities were all significantly different over space, time, and lithification state. Species richness is significantly higher in the non-lithifying mats, potentially due to differences in mat structure and activity. This increased richness may impact lithification and, hence, biosignature production.

Maternal uniparental disomy 14 syndrome demonstrates prader-willi syndrome-like phenotype.

PubMed

Hosoki, Kana; Kagami, Masayo; Tanaka, Touju; Kubota, Masaya; Kurosawa, Kenji; Kato, Mitsuhiro; Uetake, Kimiaki; Tohyama, Jun; Ogata, Tsutomu; Saitoh, Shinji

2009-12-01

To delineate the significance of maternal uniparental disomy 14 (upd(14)mat) and related disorders in patients with a Prader-Willi syndrome (PWS)-like phenotype. We examined 78 patients with PWS-like phenotype who lacked molecular defects for PWS. The MEG3 methylation test followed by microsatellite polymorphism analysis of chromosome 14 was performed to detect upd(14)mat or other related abnormalities affecting the 14q32.2-imprinted region. We identified 4 patients with upd(14)mat and 1 patient with an epimutation in the 14q32.2 imprinted region. Of the 4 patients with upd(14)mat, 3 had full upd(14)mat and 1 was mosaic. Upd(14)mat and epimutation of 14q32.2 represent clinically discernible phenotypes and should be designated "upd(14)mat syndrome." This syndrome demonstrates a PWS-like phenotype particularly during infancy. The MEG3 methylation test can detect upd(14)mat syndrome defects and should therefore be performed for all undiagnosed infants with hypotonia.

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats.

PubMed

Aubé, Johanne; Senin, Pavel; Pringault, Olivier; Bonin, Patricia; Deflandre, Bruno; Bouchez, Olivier; Bru, Noëlle; Biritxinaga-Etchart, Edurne; Klopp, Christophe; Guyoneaud, Rémy; Goñi-Urriza, Marisol

2016-10-15

Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Use of rbcL and trnL-F as a Two-Locus DNA Barcode for Identification of NW-European Ferns: An Ecological Perspective

PubMed Central

de Groot, G. Arjen; During, Heinjo J.; Maas, Jan W.; Schneider, Harald; Vogel, Johannes C.; Erkens, Roy H. J.

2011-01-01

Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes—while playing an essential role in fern colonization and reproduction—generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNA-identifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distance-based analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a whole range of questions previously unaddressed in fern gametophyte ecology. PMID:21298108

Distribution and Composition of Thiotrophic Mats in the Hypoxic Zone of the Black Sea (150–170 m Water Depth, Crimea Margin)

PubMed Central

Jessen, Gerdhard L.; Lichtschlag, Anna; Struck, Ulrich; Boetius, Antje

2016-01-01

At the Black Sea chemocline, oxygen- and sulfide-rich waters meet and form a niche for thiotrophic pelagic bacteria. Here we investigated an area of the Northwestern Black Sea off Crimea close to the shelf break, where the chemocline reaches the seafloor at around 150–170 m water depth, to assess whether thiotrophic bacteria are favored in this zone. Seafloor video transects were carried out with the submersible JAGO covering 20 km2 on the region between 110 and 200 m depth. Around the chemocline we observed irregular seafloor depressions, covered with whitish mats of large filamentous bacteria. These comprised 25–55% of the seafloor, forming a belt of 3 km width around the chemocline. Cores from the mats obtained with JAGO showed higher accumulations of organic matter under the mats compared to mat-free sediments. The mat-forming bacteria were related to Beggiatoa-like large filamentous sulfur bacteria based on 16S rRNA sequences from the mat, and visual characteristics. The microbial community under the mats was significantly different from the surrounding sediments and enriched with taxa affiliated with polymer degrading, fermenting and sulfate reducing microorganisms. Under the mats, higher organic matter accumulation, as well as higher remineralization and radiotracer-based sulfate reduction rates were measured compared to outside the mat. Mat-covered and mat-free sediments showed similar degradability of the bulk organic matter pool, suggesting that the higher sulfide fluxes and subsequent development of the thiotrophic mats in the patches are consequences of the accumulation of organic matter rather than its qualitative composition. Our observations suggest that the key factors for the distribution of thiotrophic mat-forming communities near to the Crimean shelf break are hypoxic conditions that (i) repress grazers, (ii) enhance the accumulation and degradation of labile organic matter by sulfate-reducers, and (iii) favor thiotrophic filamentous bacteria which are adapted to exploit steep gradients in oxygen and sulfide availability; in addition to a specific seafloor topography which may relate to internal waves at the shelf break. PMID:27446049

Tracking the Effect of Algal Mats on Coral Bleaching Using Remote Sensing

NASA Astrophysics Data System (ADS)

El-Askary, H. M.; Johnson, S. H.; Idris, N.; Qurban, M. A. B.

2014-12-01

Benthic habitats rely on relatively stable environmental conditions for survival. The introduction of algal mats into an ecosystem can have a notable effect on the livelihood of organisms such as coral reefs by causing changes in the biogeochemistry of the surrounding water. Increasing levels of acidity and new competition for sunlight caused by congregations of cyanobacteria essentially starve coral reefs of natural resources. These changes are particularly prevalent in waters near quickly developing population centers, such as the ecologically diverse Arabian Gulf. While ground-truthing studies to determine the extensiveness of coral death proves useful on a microcosmic level, new ventures in remote sensing research allow scientists to utilize satellite data to track these changes on a broader scale. Satellite images acquired from Landsat 5, 1987, Landsat 7, 2000, and Landsat 8, 2013 along with higher resolution IKONOS data are digitally analyzed in order to create spectral libraries for relevant benthic types, which in turn can be used to perform supervised classifications and change detection analyses over a larger area. The supervised classifications performed over the three scenes show five significant marine-related classes, namely coral, mangroves, macro-algae, and seagrass, in different degrees of abundance, yet here we focus only on the algal mats impact on corals bleaching. The change detection analysis is introduced to study see the degree of algal mats impact on coral bleaching over the course of time with possible connection to the local meteorology and current climate scenarios.

Survey of Lake Ontario bottom sediment off Rochester, New York, to define the extent of jettisoned World War II material and its potential for sediment contamination

USGS Publications Warehouse

Kennedy, Gregory; Kappel, William M.

2000-01-01

Military-type mat??riel was recovered from the bottom of Lake Ontario near Rochester, N.Y., during bottom-trawl, fish-stock surveys at depths of 75 to 180 feet each year from 1978 through 1996. The recovered mat??riel included many shell-detonator nose cones (2 inches in diameter by about 3.5 inches long); several electronic components; one corroded box of detonators; a corrugated container of mercury-filled capsules; and corroded batteries. Most of the recovered mat??riel has been identified as defective components of shell detonators (proximity-fuze assemblies) that were jettisoned in the lake to protect them from discovery during World War II. Side-scan SONAR, metal-detector, and ROV (remotely-operated-vehicle) surveys found no evidence of any large piles of mat??riel containing potentially hazardous, toxic, or polluting materials within the 17-square-mile study site. Many scattered magnetic anomalies were detected in this area, but chemical analysis of bottom sediment and of zebra- and quagga-mussel (Dreissena spp.) tissue indicate that the concentrations of mercury and other heavy metals are within the previously documented ranges for Lake Ontario sediment. The failure of ROV videos and of SCUBA-diver surveys and probes of the lake bottom to locate any debris indicates that most, if not all, of the debris is scattered and buried under a layer of fine-grained sediment and, possibly, mussels.

Why Does a Method That Fails Continue To Be Used: The Answer

PubMed Central

Templeton, Alan R.

2009-01-01

It has been claimed that hundreds of researchers use nested clade phylogeographic analysis (NCPA) based on what the method promises rather than requiring objective validation of the method. The supposed failure of NCPA is based upon the argument that validating it by using positive controls ignored type I error, and that computer simulations have shown a high type I error. The first argument is factually incorrect: the previously published validation analysis fully accounted for both type I and type II errors. The simulations that indicate a 75% type I error rate have serious flaws and only evaluate outdated versions of NCPA. These outdated type I error rates fall precipitously when the 2003 version of single locus NCPA is used or when the 2002 multi-locus version of NCPA is used. It is shown that the treewise type I errors in single-locus NCPA can be corrected to the desired nominal level by a simple statistical procedure, and that multilocus NCPA reconstructs a simulated scenario used to discredit NCPA with 100% accuracy. Hence, NCPA is a not a failed method at all, but rather has been validated both by actual data and by simulated data in a manner that satisfies the published criteria given by its critics. The critics have come to different conclusions because they have focused on the pre-2002 versions of NCPA and have failed to take into account the extensive developments in NCPA since 2002. Hence, researchers can choose to use NCPA based upon objective critical validation that shows that NCPA delivers what it promises. PMID:19335340

Forensic botany II, DNA barcode for land plants: Which markers after the international agreement?

PubMed

Ferri, G; Corradini, B; Ferrari, F; Santunione, A L; Palazzoli, F; Alu', M

2015-03-01

The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for forensic botany. Based on obtained results, we recommend the adoption of a two-locus combination with rbcL+trnH-psbA plastid markers, which currently best satisfies forensic needs for botanical species identification. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

MatLab Programming for Engineers Having No Formal Programming Knowledge

NASA Technical Reports Server (NTRS)

Shaykhian, Linda H.; Shaykhian, Gholam Ali

2007-01-01

MatLab is one of the most widely used very high level programming languages for Scientific and engineering computations. It is very user-friendly and needs practically no formal programming knowledge. Presented here are MatLab programming aspects and not just the MatLab commands for scientists and engineers who do not have formal programming training and also have no significant time to spare for learning programming to solve their real world problems. Specifically provided are programs for visualization. Also, stated are the current limitations of the MatLab, which possibly can be taken care of by Mathworks Inc. in a future version to make MatLab more versatile.

Polyelectrolyte-Functionalized Nanofiber Mats Control the Collection and Inactivation of Escherichia coli

PubMed Central

Rieger, Katrina A.; Porter, Michael; Schiffman, Jessica D.

2016-01-01

Quantifying the effect that nanofiber mat chemistry and hydrophilicity have on microorganism collection and inactivation is critical in biomedical applications. In this study, the collection and inactivation of Escherichia coli K12 was examined using cellulose nanofiber mats that were surface-functionalized using three polyelectrolytes: poly (acrylic acid) (PAA), chitosan (CS), and polydiallyldimethylammonium chloride (pDADMAC). The polyelectrolyte functionalized nanofiber mats retained the cylindrical morphology and average fiber diameter (~0.84 µm) of the underlying cellulose nanofibers. X-ray photoelectron spectroscopy (XPS) and contact angle measurements confirmed the presence of polycations or polyanions on the surface of the nanofiber mats. Both the control cellulose and pDADMAC-functionalized nanofiber mats exhibited a high collection of E. coli K12, which suggests that mat hydrophilicity may play a larger role than surface charge on cell collection. While the minimum concentration of polycations needed to inhibit E. coli K12 was 800 µg/mL for both CS and pDADMAC, once immobilized, pDADMAC-functionalized nanofiber mats exhibited a higher inactivation of E. coli K12, (~97%). Here, we demonstrate that the collection and inactivation of microorganisms by electrospun cellulose nanofiber mats can be tailored through a facile polyelectrolyte functionalization process. PMID:28773422

Structure and Genetic Content of the Megaplasmids of Neurotoxigenic Clostridium butyricum Type E Strains from Italy

PubMed Central

Iacobino, Angelo; Scalfaro, Concetta; Franciosa, Giovanna

2013-01-01

We determined the genetic maps of the megaplasmids of six neutoroxigenic Clostridium butyricum type E strains from Italy using molecular and bioinformatics techniques. The megaplasmids are circular, not linear as we had previously proposed. The differently-sized megaplasmids share a genetic region that includes structural, metabolic and regulatory genes. In addition, we found that a 168 kb genetic region is present only in the larger megaplasmids of two tested strains, whereas it is absent from the smaller megaplasmids of the four remaining strains. The genetic region unique to the larger megaplasmids contains, among other features, a locus for clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated (cas) genes, i.e. a bacterial adaptive immune system providing sequence-specific protection from invading genetic elements. Some CRISPR spacer sequences of the neurotoxigenic C. butyricum type E strains showed homology to prophage, phage and plasmid sequences from closely related clostridia species or from distant species, all sharing the intestinal habitat, suggesting that the CRISPR locus might be involved in the microorganism adaptation to the human or animal intestinal environment. Besides, we report here that each of four distinct CRISPR spacers partially matched DNA sequences of different prophages and phages, at identical nucleotide locations. This suggests that, at least in neurotoxigenic C. butyricum type E, the CRISPR locus is potentially able to recognize the same conserved DNA sequence of different invading genetic elements, besides targeting sequences unique to previously encountered invading DNA, as currently predicted for a CRISPR locus. Thus, the results of this study introduce the possibility that CRISPR loci can provide resistance to a wider range of invading DNA elements than previously appreciated. Whether it is more advantageous for the peculiar neurotoxigenic C. butyricum type E strains to maintain or to lose the CRISPR-cas system remains an open question. PMID:23967192

Method for production of carbon nanofiber mat or carbon paper

DOEpatents

Naskar, Amit K.

2015-08-04

Method for the preparation of a non-woven mat or paper made of carbon fibers, the method comprising carbonizing a non-woven mat or paper preform (precursor) comprised of a plurality of bonded sulfonated polyolefin fibers to produce said non-woven mat or paper made of carbon fibers. The preforms and resulting non-woven mat or paper made of carbon fiber, as well as articles and devices containing them, and methods for their use, are also described.

Genetic mapping and predictive testing for multiple endocrine neoplasia type 1 (MEN1)

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

Pandit, S.D.; Read, C.; Liu, L.

1994-09-01

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder with an estimated prevalance of 20-200 per million persons. It is characterized by the combined occurence of tumors involving two or more endocrine glands, namely the parathyroid glands, the endocrine pancreas and the anterior pituitary. This disorder affects virtually all age groups with an average range of 20-60 years. Linkage analysis mapped the MEN1 locus to 11q13 near the human muscle glycogen phosphorylase (PYGM) locus. Additional genetic mapping and deletion analysis studies have refined the region containing the MEN1 locus to a 3 cM interval flanked by markers PYGMmore » and D11S146/D11S97, a physical distance of approximately 1.5 Mb. We have identified 8 large families segregating MEN1 (71 affected from a population of 389 individuals). A high resolution reference map for the 11q13 region has been constructed using four new microsatellite markers, the CEPH reference (40 family) pedigree resource, and the CRI-MAP program package. Subsequent analyses using the LINKAGE program package and 8 MEN 1 families placed the MEN1 locus within the context of the microsatellite map. This map was used to develop a linkage-based predictive test. These markers have also been used to further refine the interval containing the MEN1 locus from the study of chromosome deletions (loss of heterozygosity, LOH studies) in paired sets of tumor and germline DNA from 87 MEN 1 affected individuals.« less

CRISPR: A Useful Genetic Feature to Follow Vaginal Carriage of Group B Streptococcus

PubMed Central

Beauruelle, Clémence; Pastuszka, Adeline; Horvath, Philippe; Perrotin, Franck; Mereghetti, Laurent; Lanotte, Philippe

2017-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) and Cas (CRISPR-associated proteins) play a critical role in adaptive immunity against mobile genetic elements, especially phages, through their ability to acquire novel spacer sequences. Polarized spacer acquisition results in spacer polymorphism and temporal organization of CRISPR loci, making them attractive epidemiological markers. Group B Streptococcus (GBS), a genital commensal for 10 to 30% of healthy women and a major neonatal pathogen, possesses a ubiquitous and functional CRISPR1 locus. Our aim was to assess the CRISPR1 locus as an epidemiological marker to follow vaginal carriage of GBS in women. This study also allowed us to observe the evolution of the CRISPR1 locus in response to probable phage infection occurring in vivo. We followed carriage of GBS among 100 women over an 11-year period, with a median duration of approximately 2 years. The CRISPR1 locus was highly conserved over time. The isolates that show the same CRISPR1 genotype were collected from 83% of women. There was an agreement between CRISPR genotyping and other typing methods [MLVA (multilocus variable number of tandem repeat Analysis) and MLST (multilocus sequence typing)] for 94% of the cases. The CRISPR1 locus of the isolates from 18 women showed modifications, four of which acquired polarized spacer, highlighting the in vivo functionality of the system. The novel spacer of one isolate had sequence similarity with phage, suggesting that phage infection occurred during carriage. These findings improve our understanding of CRISPR-Cas evolution in GBS and provide a glimpse of host-phage dynamics in vivo. PMID:29075246

Maximizing Hard Floor Maintenance.

ERIC Educational Resources Information Center

Steger, Michael

2000-01-01

Explains the maintenance options available for hardwood flooring that can help ensure long life cycles and provide inviting spaces. Developing a maintenance system, knowing the type of traffic that the floor must endure, using entrance matting, and adhering to manufacturers guidelines are discussed. Daily, monthly or quarterly, and long-term…

Developing guidelines for elementary flow nomenclature

EPA Science Inventory

In general, a flow in life cycle inventory data refers to an input or output to a process. Flows may be of two broad types: elementary flows or intermediate (known as “technosphere”) flows according to ISO 14044 (ISO 14044 2006). Elementary flows may be defined as mat...

Phylogenetic Analysis of Nuclear-Encoded RNA Maturases

PubMed Central

Malik, Sunita; Upadhyaya, KC; Khurana, SM Paul

2017-01-01

Posttranscriptional processes, such as splicing, play a crucial role in gene expression and are prevalent not only in nuclear genes but also in plant mitochondria where splicing of group II introns is catalyzed by a class of proteins termed maturases. In plant mitochondria, there are 22 mitochondrial group II introns. matR, nMAT1, nMAT2, nMAT3, and nMAT4 proteins have been shown to be required for efficient splicing of several group II introns in Arabidopsis thaliana. Nuclear maturases (nMATs) are necessary for splicing of mitochondrial genes, leading to normal oxidative phosphorylation. Sequence analysis through phylogenetic tree (including bootstrapping) revealed high homology with maturase sequences of A thaliana and other plants. This study shows the phylogenetic relationship of nMAT proteins between A thaliana and other nonredundant plant species taken from BLASTP analysis. PMID:28607538

Validity Study of a Jump Mat Compared to the Reference Standard Force Plate.

PubMed

Rogan, Slavko; Radlinger, Lorenz; Imhasly, Caroline; Kneubuehler, Andrea; Hilfiker, Roger

2015-12-01

In the field of vertical jump diagnostics, force plates (FP) are the reference standard. Recently, despite a lack of evidence, jump mats have been used increasingly. Important factors in favor of jumping mats are their low cost and portability. This validity study compared the Haynl-Elektronik jump mat (HE jump mat) with the reference standard force plate. Ten healthy volunteers participated and each participant completed three series of five drop jumps (DJ). The parameters ground contact time (GCT) and vertical jump height (VJH) from the HE jump mat and the FP were used to evaluate the concurrent validity. The following statistical calculations were performed: Pearson's correlation (r), Bland-Altman plots (standard and for adjusted trend), and regression equations. The Bland-Altman plots suggest that the HE jump mat measures shorter contact times and higher jump heights than the FP. The trend-adjusted Bland-Altman plot shows higher mean differences and wider wing-spreads of confidence limits during longer GCT. During the VJH the mean differences and the wing-spreads of the confidence limits throughout the range present as relatively constant. The following regression equations were created, as close as possible to the true value: GCT = 5.920385 + 1.072293 × [value HE jump mat] and VJH = -1.73777 + 1.011156 × [value HE jump mat]. The HE jump mat can be recommended in relation to the validity of constraints. In this study, only a part of the quality criteria were examined. For the final recommendation it is advised to examine the HE jump mat on the other quality criteria (test-retest reliability, sensitivity change).

Diversity and stratification of archaea in a hypersaline microbial mat.

PubMed

Robertson, Charles E; Spear, John R; Harris, J Kirk; Pace, Norman R

2009-04-01

The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.

Earth's Earliest Ecosystems in the C: The Use of Microbial Mats to Demonstrate General Principles of Scientific Inquiry and Microbial Ecology

NASA Technical Reports Server (NTRS)

Bebout, Brad M.; Bucaria, Robin

2006-01-01

Microbial mats are living examples of the most ancient biological communities on Earth. As Earth's earliest ecosystems, they are centrally important to understanding the history of life on our planet and are useful models for the search for life elsewhere. As relatively compact (but complete) ecosystems, microbial mats are also extremely useful for educational activities. Mats may be used to demonstrate a wide variety of concepts in general and microbial ecology, including the biogeochemical cycling of elements, photosynthesis and respiration, and the origin of the Earth's present oxygen containing atmosphere. Microbial mats can be found in a number of common environments accessible to teachers, and laboratory microbial mats can be constructed using materials purchased from biological supply houses. With funding from NASA's Exobiology program, we have developed curriculum and web-based activities centered on the use of microbial mats as tools for demonstrating general principles in ecology, and the scientific process. Our web site (http://microbes.arc.nasa.gov) includes reference materials, lesson plans, and a "Web Lab", featuring living mats maintained in a mini-aquarium. The site also provides information as to how research on microbial mats supports NASA's goals, and various NASA missions. A photo gallery contains images of mats, microscopic views of the organisms that form them, and our own research activities. An animated educational video on the web site uses computer graphic and video microscopy to take students on a journey into a microbial mat. These activities are targeted to a middle school audience and are aligned with the National Science Standards.

Colonization of oak wilt fungal mats by Ophiostoma piceae during spring in Minnesota

Treesearch

Jennifer Juzwik; Jason M. Meyer

1997-01-01

The colonization of Ceratocystis fagacearum fungal mats of different ages by Ophiostoma piceae on Quercus spp. was determined in three east-central Minnesota locations during the spring of 1995. The extent of the mat area colonized by O. piceae generally increased with mat age. Subsamples per...

Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) Users' Workshop Presentations

NASA Technical Reports Server (NTRS)

Litt, Jonathan S. (Compiler)

2018-01-01

NASA Glenn Research Center hosted a Users' Workshop on the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) on August 21, 2017. The objective of this workshop was to update the user community on the latest features of T-MATS, and to provide a forum to present work performed using T-MATS. Presentations highlighted creative applications and the development of new features and libraries, and emphasized the flexibility and simulation power of T-MATS.

The response of vegetation dynamics of the different alpine grassland types to temperature and precipitation on the Tibetan Plateau.

PubMed

Sun, Jian; Qin, Xiaojing; Yang, Jun

2016-01-01

The spatiotemporal variability of the Normalized Difference Vegetation Index (NDVI) of three vegetation types (alpine steppe, alpine meadow, and alpine desert steppe) across the Tibetan Plateau was analyzed from 1982 to 2013. In addition, the annual mean temperature (MAT) and annual mean precipitation (MAP) trends were quantified to define the spatiotemporal climate patterns. Meanwhile, the relationships between climate factors and NDVI were analyzed in order to understand the impact of climate change on vegetation dynamics. The results indicate that the maximum of NDVI increased by 0.3 and 0.2 % per 10 years in the entire regions of alpine steppe and alpine meadow, respectively. However, no significant change in the NDVI of the alpine desert steppe has been observed since 1982. A negative relationship between NDVI and MAT was found in all these alpine grassland types, while MAP positively impacted the vegetation dynamics of all grasslands. Also, the effects of temperature and precipitation on different vegetation types differed, and the correlation coefficient for MAP and NDVI in alpine meadow is larger than that for other vegetation types. We also explored the percentages of precipitation and temperature influence on NDVI variation, using redundancy analysis at the observation point scale. The results show that precipitation is a primary limiting factor for alpine vegetation dynamic, rather than temperature. Most importantly, the results can serve as a tool for grassland ecosystem management.

Effects of tacky mat contamination on bond degradation for Chemlok/liner and NBR/liner bonds

NASA Technical Reports Server (NTRS)

Padilla, A. M.

1989-01-01

Tacky mats are placed by the rubber lay-up areas for the solid rocket motor segments. These mats dust off the shoes prior to entering the platform where the lay-up work is performed. The possibility exists that a tacky mat could be touched with gloved hands prior to handling the uncured nitride butadiene rubber (NBR). Tests were run to determine if NBR were accidentally touched would there be any degradation of the liner/NBR bond. The tacky mats were judged solely on the basis of bond degradation caused by either direct or indirect contamination. Test results all indicate that there was no notable NBR/Chemlok or liner/NBR bond degradation on samples that came into contact with the tacky mat material. Testing procedures are described. The tacky mat adhesive composition does not contain fluorocarbons or release agents that would affect bonding.

Comparative functional ultrastructure of two hypersaline submerged cyanobacterial mats - Guerrero Negro, Baja California Sur, Mexico, and Solar Lake, Sinai, Egypt

NASA Technical Reports Server (NTRS)

D'Amelio, Elisa D'antoni; Des Marais, David J.; Cohen, Jehuda

1989-01-01

The ultrastructure of the submerged microbial mat from the Solar Lake (SL), Egypt, was compared to that of samples from the Guerrero Negro (GN), Mexico, salt pans. The locations and distributions of the main organisms were determined light microscopy, and the corresponding ultrathin sections were examined under TEM; chemical microprofile analyses were carried out on the day of sampling for microscopic studies. Both communities were found to be dominated by Microleus chthonoplastes, although several morphological species found in the GN mat were absent from the SL mat, including the Tropica nigra and the 'big' Microleus chthonoplastes component. The chemical microprofiles of oxygen, sulfide, pH, and the oxygenic photosynthesis in the two mats were virtually identical. In both mats, the photic zone was restricted to the upper 800 microns of the mat, and oxygenic photosynthesis was detected down to 600 microns.

Micropatterned stretchable circuit and strain sensor fabricated by lithography on an electrospun nanofiber mat.

PubMed

Park, Minwoo; Im, Jungkyun; Park, Jongjin; Jeong, Unyong

2013-09-11

This paper describes a novel approach for composite nanofiber mats and its application to fabricate a strain sensor. Electrospun poly(4-vinylpyridine) (P4VP) nanofiber mats are micropatterned by a lithographic approach that includes selective oxidation of the nanofibers and removal of unreacted fibers. The P4VP/HAuCl4 complex is converted to P4VP/Au composites by chemical reduction. We investigate the electrical resistivity of the composite mats according to the number of complexation-and-reduction cycles, the thickness of the fiber mats, and the annealing temperatures which control the percolation of the Au nanoparticles in the fiber mats. Nozzle printing of a polymeric solution on the patterned nanofiber mats simply produces an array of strain-sensitive and strain-invariant units. The patterns demonstrate high strain-sensing performance without any mechanical and electrical failure over 200 bending cycles in the strain range of ε<0.17.

49 CFR 393.122 - What are the rules for securing paper rolls?

Code of Federal Regulations, 2014 CFR

2014-10-01

... prevented by filling the void, blocking, bracing, tiedowns or friction mats. The paper rolls may also be... vehicle, exceeds the diameter of the paper rolls, rearward movement must be prevented by friction mats... less than 1.75 times its diameter, and it is restrained against forward movement by friction mat(s...

Users guide for ERB 7 MAT (including the first year quality control)

NASA Technical Reports Server (NTRS)

Groveman, B.

1984-01-01

In the first section of this report background information for the use of the ERB-7 Master Archival Tapes (MAT) is provided. The second section gives details regarding the scientific validity and quality of the MAT. The MAT data analyzed covers the period from November 16, 1978 to October 31, 1979.

Fabricating poly(1,8-octanediol citrate) elastomer based fibrous mats via electrospinning for soft tissue engineering scaffold.

PubMed

Zhu, Lei; Zhang, Yuanzheng; Ji, Yali

2017-06-01

Poly(1,8-octanediol citrate) (POC) is a recently developed biodegradable crosslinked elastomer that possesses good cytocompatibility and matchable mechanical properties to soft tissues. However, the thermosetting characteristic reveals a big challenge to manufacture its porous scaffold. Herein, POC elastomer was electrospun into fiber mat using poly(L-lactic acid) (PLLA) as a spinnable carrier. The obtained POC/PLLA fiber mats were characterized by scanning electron microscopy (SEM), dynamic mechanical analysis (DMA), uniaxial tensile test, static-water-contact-angle, thermal analysis, in vitro degradation and biocompatibility test. It was found that the fibrous structure could be formed so long as the POC pre-polymer's content was no more than 50 wt%. The presence of elastic POC component not only strengthened the fiber mats but also toughened the fiber mats. The hydrophilicity of 50/50 fiber mat significantly improved. In vitro degradation rate of POC based fiber mats was much faster than that of pure PLLA. Cyto- and histo-compatibility tests confirmed that the POC/PLLA fiber mats had good biocompatibility for potential applications in soft tissue engineering.

Mycorrhization of pecan (Carya illinoinensis) with black truffles: Tuber melanosporum and Tuber brumale.

PubMed

Marozzi, Giorgio; Sánchez, Sergio; Benucci, Gian Maria Niccolò; Bonito, Gregory; Falini, Leonardo Baciarelli; Albertini, Emidio; Donnini, Domizia

2017-04-01

Pecan, Carya illinoinensis, is an economically important nut producing tree that can establish ectomycorrhizal symbiosis with a high diversity of fungi. In the southern USA, truffles (Tuber spp.) sometimes fruit prolifically in cultivated pecan orchards and regularly associate with pecan roots as ectomycorrhizae (ECMs). It has been demonstrated that some valuable European truffle species (e.g., Tuber borchii and Tuber aestivum) can form ECMs with pecan seedlings in nursery conditions. Thus, pecan may represent an attractive alternative host to forest trees for truffle growers given the potential for co-cropping truffles and pecans. To further explore the capacity of pecan to host truffle symbionts, pecan seedlings were inoculated with species of black truffles that are economically important in Europe, T. melanosporum and T. brumale. Ectomycorrhizae were characterized molecularly and their morphology was described in detail. Mycorrhization rates on pecan roots were assessed over a 2-year period. Tuber melanosporum and T. brumale produced well-formed ECMs with a level of root colonization in the first year of 37.3 and 34.5%, respectively. After 24 months, the level of mycorrhization increased for T. brumale (49.4%) and decreased for T. melanosporum (10.5%) inversely to that of non-target ECM greenhouse contaminants (e.g., Sphaerosporella brunnea, Trichophaea woolhopeia, Pulvinula constellatio). To assess whether mating types segregated in T. melanosporum as been reported for other host species, we amplified the mating-type locus from single T. melanosporum ECM belonging to different seedlings over a 2-year period. The two mating idiomorphs were nearly equally represented along the 2-year time span: MAT 1-1-1 decreased from 59.4% in the first year to 48.5% in the second year after inoculation. Data reported in this study add to knowledge on the mycorrhization of pecan trees with commercial truffles and has application to truffle and nut co-cropping systems.

Sporangiospore size dimorphism is linked to virulence of Mucor circinelloides.

PubMed

Li, Charles H; Cervantes, Maria; Springer, Deborah J; Boekhout, Teun; Ruiz-Vazquez, Rosa M; Torres-Martinez, Santiago R; Heitman, Joseph; Lee, Soo Chan

2011-06-01

Mucor circinelloides is a zygomycete fungus and an emerging opportunistic pathogen in immunocompromised patients, especially transplant recipients and in some cases otherwise healthy individuals. We have discovered a novel example of size dimorphism linked to virulence. M. circinelloides is a heterothallic fungus: (+) sex allele encodes SexP and (-) sex allele SexM, both of which are HMG domain protein sex determinants. M. circinelloides f. lusitanicus (Mcl) (-) mating type isolates produce larger asexual sporangiospores that are more virulent in the wax moth host compared to (+) isolates that produce smaller less virulent sporangiospores. The larger sporangiospores germinate inside and lyse macrophages, whereas the smaller sporangiospores do not. sexMΔ mutants are sterile and still produce larger virulent sporangiospores, suggesting that either the sex locus is not involved in virulence/spore size or the sexP allele plays an inhibitory role. Phylogenetic analysis supports that at least three extant subspecies populate the M. circinelloides complex in nature: Mcl, M. circinelloides f. griseocyanus, and M. circinelloides f. circinelloides (Mcc). Mcc was found to be more prevalent among clinical Mucor isolates, and more virulent than Mcl in a diabetic murine model in contrast to the wax moth host. The M. circinelloides sex locus encodes an HMG domain protein (SexP for plus and SexM for minus mating types) flanked by genes encoding triose phosphate transporter (TPT) and RNA helicase homologs. The borders of the sex locus between the three subspecies differ: the Mcg sex locus includes the promoters of both the TPT and the RNA helicase genes, whereas the Mcl and Mcc sex locus includes only the TPT gene promoter. Mating between subspecies was restricted compared to mating within subspecies. These findings demonstrate that spore size dimorphism is linked to virulence of M. circinelloides species and that plasticity of the sex locus and adaptations in pathogenicity have occurred during speciation of the M. circinelloides complex.

Sporangiospore Size Dimorphism Is Linked to Virulence of Mucor circinelloides

PubMed Central

Li, Charles H.; Cervantes, Maria; Springer, Deborah J.; Boekhout, Teun; Ruiz-Vazquez, Rosa M.; Torres-Martinez, Santiago R.; Heitman, Joseph; Lee, Soo Chan

2011-01-01

Mucor circinelloides is a zygomycete fungus and an emerging opportunistic pathogen in immunocompromised patients, especially transplant recipients and in some cases otherwise healthy individuals. We have discovered a novel example of size dimorphism linked to virulence. M. circinelloides is a heterothallic fungus: (+) sex allele encodes SexP and (−) sex allele SexM, both of which are HMG domain protein sex determinants. M. circinelloides f. lusitanicus (Mcl) (−) mating type isolates produce larger asexual sporangiospores that are more virulent in the wax moth host compared to (+) isolates that produce smaller less virulent sporangiospores. The larger sporangiospores germinate inside and lyse macrophages, whereas the smaller sporangiospores do not. sexMΔ mutants are sterile and still produce larger virulent sporangiospores, suggesting that either the sex locus is not involved in virulence/spore size or the sexP allele plays an inhibitory role. Phylogenetic analysis supports that at least three extant subspecies populate the M. circinelloides complex in nature: Mcl, M. circinelloides f. griseocyanus, and M. circinelloides f. circinelloides (Mcc). Mcc was found to be more prevalent among clinical Mucor isolates, and more virulent than Mcl in a diabetic murine model in contrast to the wax moth host. The M. circinelloides sex locus encodes an HMG domain protein (SexP for plus and SexM for minus mating types) flanked by genes encoding triose phosphate transporter (TPT) and RNA helicase homologs. The borders of the sex locus between the three subspecies differ: the Mcg sex locus includes the promoters of both the TPT and the RNA helicase genes, whereas the Mcl and Mcc sex locus includes only the TPT gene promoter. Mating between subspecies was restricted compared to mating within subspecies. These findings demonstrate that spore size dimorphism is linked to virulence of M. circinelloides species and that plasticity of the sex locus and adaptations in pathogenicity have occurred during speciation of the M. circinelloides complex. PMID:21698218

Mechanisms of anaphylaxis in human low-affinity IgG receptor locus knock-in mice.

PubMed

Gillis, Caitlin M; Jönsson, Friederike; Mancardi, David A; Tu, Naxin; Beutier, Héloïse; Van Rooijen, Nico; Macdonald, Lynn E; Murphy, Andrew J; Bruhns, Pierre

2017-04-01

Anaphylaxis can proceed through distinct IgE- or IgG-dependent pathways, which have been investigated in various mouse models. We developed a novel mouse strain in which the human low-affinity IgG receptor locus, comprising both activating (hFcγRIIA, hFcγRIIIA, and hFcγRIIIB) and inhibitory (hFcγRIIB) hFcγR genes, has been inserted into the equivalent murine locus, corresponding to a locus swap. We sought to determine the capabilities of hFcγRs to induce systemic anaphylaxis and identify the cell types and mediators involved. hFcγR expression on mouse and human cells was compared to validate the model. Passive systemic anaphylaxis was induced by injection of heat-aggregated human intravenous immunoglobulin and active systemic anaphylaxis after immunization and challenge. Anaphylaxis severity was evaluated based on hypothermia and mortality. The contribution of receptors, mediators, or cell types was assessed based on receptor blockade or depletion. The human-to-mouse low-affinity FcγR locus swap engendered hFcγRIIA/IIB/IIIA/IIIB expression in mice comparable with that seen in human subjects. Knock-in mice were susceptible to passive and active anaphylaxis, accompanied by downregulation of both activating and inhibitory hFcγR expression on specific myeloid cells. The contribution of hFcγRIIA was predominant. Depletion of neutrophils protected against hypothermia and mortality. Basophils contributed to a lesser extent. Anaphylaxis was inhibited by platelet-activating factor receptor or histamine receptor 1 blockade. Low-affinity FcγR locus-switched mice represent an unprecedented model of cognate hFcγR expression. Importantly, IgG-related anaphylaxis proceeds within a native context of activating and inhibitory hFcγRs, indicating that, despite robust hFcγRIIB expression, activating signals can dominate to initiate a severe anaphylactic reaction. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Influence of layer-by-layer assembled electrospun poly (L-lactic acid) nanofiber mats on the bioactivity of endothelial cells

NASA Astrophysics Data System (ADS)

Wu, Keke; Zhang, Xiazhi; Yang, Wufeng; Liu, Xiaoyan; Jiao, Yanpeng; Zhou, Changren

2016-12-01

Electrospun poly(L-lactic acid) (PLLA) nanofiber mats were successfully modified by deposition of multilayers with chitosan (CS), heparin (Hep) and graphene oxide (GO) through electrostatic layer-by-layer (LBL) self-assembly method. In this study, the surface properties of PLLA nanofiber mats before and after modification were investigated via scanning electron microscope (SEM), atomic force microscopy (AFM), attenuated total reflectance fourier transformation infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS) and water contact angle measurement. In addition, the cytocompatibility of the modified PLLA nanofiber mats were investigated by testing endothelial cells compatibility, including cell attachment, cell proliferation and cell cycle. The results revealed that the surfaces of modified PLLA nanofiber mats become much rougher, stifiness and the hydrophilicity of the LBL modified PLLA nanofiber mats were improved compared to original PLLA one. Moreover, the modified PLLA nanofiber mats had promoted the endothelial cells viability attachment significantly. Besides, we studied the PLLA nanofiber mats on the expression of necrosis factor (TNF-α), interleukine-1β (IL-1β), monocyte chemoattractant protein-1 (MCP-1) and vascular cell adhesion molecule-1 (VCAM-1) in endothelial cells. The results showed that modified PLLA nanofiber mats had inhibited the inflammatory response to some extent.

Magnetoacoustic tomography with magnetic induction (MAT-MI)

NASA Astrophysics Data System (ADS)

Xu, Yuan; He, Bin

2005-11-01

We report our theoretical and experimental investigations on a new imaging modality, magnetoacoustic tomography with magnetic induction (MAT-MI). In MAT-MI, the sample is located in a static magnetic field and a time-varying (µs) magnetic field. The time-varying magnetic field induces an eddy current in the sample. Consequently, the sample will emit ultrasonic waves by the Lorentz force. The ultrasonic signals are collected around the object to reconstruct images related to the electrical impedance distribution in the sample. MAT-MI combines the good contrast of electrical impedance tomography with the good spatial resolution of sonography. MAT-MI has two unique features due to the solenoid nature of the induced electrical field. Firstly, MAT-MI could provide an explicit or simple quantitative reconstruction algorithm for the electrical impedance distribution. Secondly, it promises to eliminate the shielding effects of other imaging modalities in which the current is applied directly with electrodes. In the theoretical part, we provide formulae for both the forward and inverse problems of MAT-MI and estimate the signal amplitude in biological tissues. In the experimental part, the experimental setup and methods are introduced and the signals and the image of a metal object by means of MAT-MI are presented. The promising pilot experimental results suggest the feasibility of the proposed MAT-MI approach.

Interaction of gelatin with polyenes modulates antifungal activity and biocompatibility of electrospun fiber mats

PubMed Central

Lakshminarayanan, Rajamani; Sridhar, Radhakrishnan; Loh, Xian Jun; Nandhakumar, Muruganantham; Barathi, Veluchamy Amutha; Kalaipriya, Madhaiyan; Kwan, Jia Lin; Liu, Shou Ping; Beuerman, Roger Wilmer; Ramakrishna, Seeram

2014-01-01

Topical application of antifungals does not have predictable or well-controlled release characteristics and requires reapplication to achieve therapeutic local concentration in a reasonable time period. In this article, the efficacy of five different US Food and Drug Administration-approved antifungal-loaded (amphotericin B, natamycin, terbinafine, fluconazole, and itraconazole) electrospun gelatin fiber mats were compared. Morphological studies show that incorporation of polyenes resulted in a two-fold increase in fiber diameter and the mats inhibit the growth of yeasts and filamentous fungal pathogens. Terbinafine-loaded mats were effective against three filamentous fungal species. Among the two azole antifungals compared, the itraconazole-loaded mat was potent against Aspergillus strains. However, activity loss was observed for fluconazole-loaded mats against all of the test organisms. The polyene-loaded mats displayed rapid candidacidal activities as well. Biophysical and rheological measurements indicate strong interactions between polyene antifungals and gelatin matrix. As a result, the polyenes stabilized the triple helical conformation of gelatin and the presence of gelatin decreased the hemolytic activity of polyenes. The polyene-loaded fiber mats were noncytotoxic to primary human corneal and sclera fibroblasts. The reduction of toxicity with complete retention of activity of the polyene antifungal-loaded gelatin fiber mats can provide new opportunities in the management of superficial skin infections. PMID:24920895

The green alga, Cladophora, promotes Escherichia coli growth and contamination of recreational waters in Lake Michigan.

PubMed

Vanden Heuvel, Amy; McDermott, Colleen; Pillsbury, Robert; Sandrin, Todd; Kinzelman, Julie; Ferguson, John; Sadowsky, Michael; Byappanahalli, Muruleedhara; Whitman, Richard; Kleinheinz, Gregory T

2010-01-01

A linkage between Cladophora mats and exceedances of recreational water quality criteria has been suggested, but not directly studied. This study investigates the spatial and temporal association between Escherichia coli concentrations within and near Cladophora mats at two northwestern Lake Michigan beaches in Door County, Wisconsin. Escherichia coli concentrations in water underlying mats were significantly greater than surrounding water (p < 0.001). Below mat E. coli increased as the stranded mats persisted at the beach swash zone. Water adjacent to Cladophora mats had lower E. coli concentrations, but surpassed EPA swimming criteria the majority of sampling days. A significant positive association was found between E. coli concentrations attached to Cladophora and in underlying water (p < 0.001). The attached E. coli likely acted as a reservoir for populating water underlying the mat. Fecal bacterial pathogens, however, could not be detected by microbiological culture methods either attached to mat biomass or in underlying water. Removal of Cladophora mats from beach areas may improve aesthetic and microbial water quality at affected beaches. These associations and potential natural growth of E. coli in bathing waters call into question the efficacy of using E. coli as a recreational water quality indicator of fecal contaminations.

Evaluation of porous pavements used in Oregon : volume II : appendices.

DOT National Transportation Integrated Search

1994-12-01

Porous pavements or open graded asphalt mixtures have been in use in Oregon since the late 1960s. The use of this pavement type has increased over the years because the pores in the mat provide a better way for water to drain from the surface. This g...

Do erosion control and snakes mesh?

Treesearch

Christopher Barton; Karen Kinkead

2005-01-01

In the battle to curb soil erosion and sedimentation, numberous techniques and products for controlling erosion and sedimentation have been developed and are being implemented. Rolled erosion control products, such as a temporary erosion control blankets and permanent turf reinforcement mats, represent one type of erosion control product that has been used extensively...

Evaluation of porous pavements used in Oregon : volume I.

DOT National Transportation Integrated Search

1994-12-01

Porous pavements or open graded asphalt mixtures have been in use in Oregon since the late 1960s. The use of this pavement type has increased over the years because the pores in the mat provide a better way for water to drain from the surface. This g...

Long Term Manipulations of Intact Microbial Mat Communities in a Greenhouse Collaboratory: Simulating Earth's Present and Past Field Environments

NASA Technical Reports Server (NTRS)

Bebout, Brad; DesMarais, David J.; Discipulo, Mykell; Embaye, Tsegereda; Garcia-Pichel, Ferran; Hogan, Mary; Jahnke, Linda L.; Keller, Richard M.; Miller, Scott R.; Prufert-Bebout, Leslie E.;

Long-Term Manipulations of Intact Microbial Mat Communities in a Greenhouse Collaboratory: Simulating Earth's Present and Past Field Environments

NASA Astrophysics Data System (ADS)

Bebout, Brad M.; Carpenter, Steven P.; Des Marais, David J.; Discipulo, Mykell; Embaye, Tsegereda; Garcia-Pichel, Ferran; Hoehler, Tori M.; Hogan, Mary; Jahnke, Linda L.; Keller, Richard M.; Miller, Scott R.; Prufert-Bebout, Leslie E.; Raleigh, Chris; Rothrock, Michael; Turk, Kendra

2002-12-01

Photosynthetic microbial mat communities were obtained from marine hypersaline saltern ponds, maintained in a greenhouse facility, and examined for the effects of salinity variations. Because these microbial mats are considered to be useful analogs of ancient marine communities, they offer insights about evolutionary events during the >3 billion year time interval wherein mats co-evolved with Earth's lithosphere and atmosphere. Although photosynthetic mats can be highly dynamic and exhibit extremely high activity, the mats in the present study have been maintained for >1 year with relatively minor changes. The major groups of microorganisms, as assayed using microscopic, genetic, and biomarker methodologies, are essentially the same as those in the original field samples. Field and greenhouse mats were similar with respect to rates of exchange of oxygen and dissolved inorganic carbon across the mat-water interface, both during the day and at night. Field and greenhouse mats exhibited similar rates of efflux of methane and hydrogen. Manipulations of salinity in the water overlying the mats produced changes in the community that strongly resemble those observed in the field. A collaboratory testbed and an array of automated features are being developed to support remote scientific experimentation with the assistance of intelligent software agents. This facility will permit teams of investigators the opportunity to explore ancient environmental conditions that are rare or absent today but that might have influenced the early evolution of these photosynthetic ecosystems.

Waardenberg syndrome (WS) type I is caused by defects at multiple loci, one of which is near ALPP on chromosome 2: First report of the WS consortium

PubMed Central

Farrer, Lindsay A.; Grundfast, Kenneth M.; Amos, Jean; Arnos, Kathleen S.; Asher, James H.; Beighton, Peter; Diehl, Scott R.; Fex, Jörgen; Foy, Carole; Friedman, Thomas B.; Greenberg, Jacquie; Hoth, Christopher; Marazita, Mary; Milunsky, Aubrey; Morell, Robert; Nance, Walter; Newton, Valerie; Ramesar, Rajkumar; Agustin, Theresa B. San; Skare, James; Stevens, Cathy A.; Wagner, Ronald G.; Wilcox, Edward R.; Winship, Ingrid; Read, Andrew P.

1992-01-01

Previous studies have localized the gene for Waardenburg syndrome (WS) type I to the distal portion of chromosome 2q, near the ALPP locus. We pooled linkage data obtained from 41 WS type I and 3 WS type II families which were typed for six polymorphic loci on chromosome 2q in order to refine the location of the WS locus (WS1) and evaluate the extent of genetic heterogeneity. In the course of this work, we developed diagnostic criteria for genetic and phenotypic studies. Our findings, based on two-locus and multilocus analysis using a linkage map established from reference pedigrees, suggest that there are two or more mutations causing WS, one of which (i.e., WS1) is located on chromosome 2q, between the ALPP and FN1 loci, at distances of 7.8 cM and 11.2 cM for each marker, respectively. The results also indicate that WS1 is responsible for the illness in approximately 45% of all families in this sample. However, the odds favoring this position over a location between ALPP and SAG are only 2:1 when alternate assumptions about the proportion of linked families are considered. We conclude that a more saturated map of this region of chromosome 2q, including highly polymorphic markers, will be needed to accurately distinguish linked families and, ultimately, isolate the mutant gene. PMID:1349198

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat.

PubMed

Babauta, Jerome T; Atci, Erhan; Ha, Phuc T; Lindemann, Stephen R; Ewing, Timothy; Call, Douglas R; Fredrickson, James K; Beyenal, Haluk

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

PubMed Central

Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.; Lindemann, Stephen R.; Ewing, Timothy; Call, Douglas R.; Fredrickson, James K.; Beyenal, Haluk

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1–V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community. PMID:24478768

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

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

Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell wasmore » light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode- associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.« less

Fabrication of a novel scaffold of clotrimazole-microemulsion-containing nanofibers using an electrospinning process for oral candidiasis applications.

PubMed

Tonglairoum, Prasopchai; Ngawhirunpat, Tanasait; Rojanarata, Theerasak; Kaomongkolgit, Ruchadaporn; Opanasopit, Praneet

2015-02-01

Clotrimazole (CZ)-loaded microemulsion-containing nanofiber mats were developed as an alternative for oral candidiasis applications. The microemulsion was composed of oleic acid (O), Tween 80 (T80), and a co-surfactant such as benzyl alcohol (BzOH), ethyl alcohol (EtOH) or isopropyl alcohol (IPA). The nanofiber mats were obtained by electrospinning a blended solution of a CZ-loaded microemulsion and a mixed polymer solution of 2% (w/v) chitosan (CS) and 10% (w/v) polyvinyl alcohol (PVA) at a weight ratio of 30:70. The nanofiber mats were characterized using various analytical techniques. The entrapment efficiency, drug release, antifungal activity and cytotoxicity were investigated. The average diameter of the nanofiber mats was in the range of 105.91-125.56 nm. The differential scanning calorimetry (DSC) and powder X-ray diffractometry (PXRD) results revealed the amorphous state of the CZ-loaded microemulsions incorporated into the nanofiber mats. The entrapment efficiency of CZ in the mats was approximately 72.58-98.10%, depended on the microemulsion formulation. The release experiment demonstrated different CZ release characteristics from nanofiber mats prepared using different CZ-loaded microemulsions. The extent of drug release from the fiber mats at 4h was approximately 64.81-74.15%. The release kinetics appeared to follow Higuchi's model. In comparison with CZ lozenges (10mg), the nanofiber mats exhibited more rapid killing activity. Moreover, the nanofiber mats demonstrated desirable mucoadhesive properties and were safe for 2h. Therefore, the nanofiber mats have the potential to be promising candidates for oral candidiasis applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Chlorophyll and carotenoid pigments in solar saltern microbial mats

NASA Astrophysics Data System (ADS)

Villanueva, Joan; Grimalt, Joan O.; de Wit, Rutger; Keely, Brendan J.; Maxwell, James R.

1994-11-01

The distributions of carotenoids, chlorophylls, and their degradation products have been studied in two microbial mat systems developed in the calcite and calcite/gypsum evaporite domains of a solar saltern system. Phormidium valderianum and Microcoleus chthonoplastes are the dominant cyanobacterial species, respectively, and large amounts of Chloroflexus-like bacteria occur in the carbonate/gypsum mat. In both systems, the major pigments are chlorophyll a, zeaxanthin, β-carotene and myxoxanthophyll, which originate from these mat-building cyanobacteria. This common feature contrasts with differences in other pigments that are specific for each mat community. Thus, chlorophyll c and fucoxanthin, reflecting diatom inputs, are only found in the calcite mat, whereas the calcite/gypsum mat contains high concentrations of bacteriochlorophylls c produced by the multicellular green filamentous bacteria. In both cases, the depth concentration profiles (0-30 and 0-40 mm) show a relatively good preservation of the cyanobacterial carotenoids, zeaxanthin, β-carotene, myxoxanthophyll, and echinenone. This contrasts with the extensive biodegradation of cyanobacterial remains observed microscopically. Fucoxanthin in the calcite mat is also transformed at a faster rate than the cyanobacterial carotenoids. Chlorophyll a, the major pigment in both mats, exhibits different transformation pathways. In the calcite/gypsum mat, it is transformed via C-13 2 carbomethoxy defunctionalization prior to loss of the phytyl chain, leading to the formation of pyrophaeophytin a and, subsequently, pyrophaeophorbide a. On the other hand, the occurrence of the enzyme chlorophyllase, attributed to diatoms in the calcite mat, gives rise to extensive phytyl hydrolysis, with the formation of chlorophyllide a, pyrophaeophorbide a and, in minor proportion, phaeophorbide a. Studies of the sources of the photosynthetic pigments and of their transformation pathways in such simplified ecosystems provide a basis for the understanding of the distribution patterns of these compounds in more complex aquatic environments.

Spatial patterns of cyanobacterial mat growth on sand ripples

NASA Astrophysics Data System (ADS)

Mariotti, G.; Klepac-Ceraj, V.; Perron, J. T.; Bosak, T.

2016-02-01

Photosynthetic microbial mats produce organic matter, cycle nutrients, bind pollutants and stabilize sediment in sandy marine environments. Here, we investigate the influence of bedforms and wave motion on the growth rate, composition and spatial variability of microbial mats by growing cyanobacterial mats on a rippled bed of carbonate sand in a wave tank. The tank was forced with an oscillatory flow with velocities below the threshold for sediment motion yet able to induce a porewater flow within the sediment. Different spatial patterns developed in mats depending on the initial biochemistry of the water medium. When growing in a medium rich in nitrogen, phosphorous and micronutrients, mats grew faster on ripple troughs than on ripple crests. After two months, mats covered the bed surface uniformly, and the microbial communities on the crests and in the troughs had similar compositions. Differences in bed shear stress and nutrient availability between crests and troughs were not able to explain the faster growth in the troughs. We hypothesize that this growth pattern is due to a "strainer" effect, i.e. the suspended bacteria from the inoculum were preferentially delivered to troughs by the wave-induced porewater flow. In the experiments initiated in a medium previously used up by a microbial mat and thus depleted in nutrients, mats grew preferentially on the ripple crests. This spatial pattern persisted for nearly two years, and the microbial composition on troughs and crests was different. We attribute this pattern to the upwelling of porewater in the crests, which increased the delivery of nutrients from sediment to the cyanobacteria on the bed surface. Thus, the macroscopic patterns formed by photosynthetic microbial mats on sand ripples may be used to infer whether mats are nutrient-limited and whether they are recently colonized or older than a month.

UAV, DGPS, and Laser Transit Mapping of Microbial Mat Ecosystems on Little Ambergris Cay, B.W.I.

NASA Astrophysics Data System (ADS)

Stein, N.; Quinn, D. P.; Grotzinger, J. P.; Fischer, W. W.; Knoll, A. H.; Cantine, M.; Gomes, M. L.; Grotzinger, H. M.; Lingappa, U.; Metcalfe, K.; O'Reilly, S. S.; Orzechowski, E. A.; Riedman, L. A.; Strauss, J. V.; Trower, L.

2016-12-01

Little Ambergris Cay is a 6 km long, 1.6 km wide uninhabited island on the Caicos platform in the Turks and Caicos. Little Ambergris provides an analog for the study of microbial mat development in the sedimentary record. Recent field mapping during July of 2016 used UAV- and satellite-based images, differential GPS (DGPS), and total station theodolite (TST) measurements to characterize sedimentology and biofacies across the entirety of Little Ambergris Cay. Nine facies were identified in-situ during DGPS island transects including oolitic grainstone bedrock, sand flats, cutbank and mat-filled channels, hardground-lined bays with EPS-rich mat particles, mangroves, EPS mats, polygonal mats, and mats with blistered surface texture. These facies were mapped onto a 15 cm/pixel visible light orthomosaic of the island generated from more than 1500 nadir images taken by a UAV at 350 m standoff distance. A corresponding stereogrammetric digital elevation map was generated from drone images and 910 DGPS measurements acquired during several island transects. More than 1000 TST measurements provide additional facies elevation constraints, control points for satellite-based water depth calculations, and means to cross-calibrate and reconstruct the topographic profile of bedrock exposed at the beach. Additionally, the thickness of the underlying Holocene sediment fill was estimated over several island transects using a depth probe. Sub-cm resolution drone-based orthophotos of microbial mats were used to quantify polygonal mat size and textures. The mapping results highlight that sedimentary and bio-facies (including mat morphology and fabrics) correlate strongly with elevation. Notably, mat morphology was observed to be highly sensitive to cm-scale variations in topography and water depth. The productivity metric NDVI was computed for mat and vegetation facies using nadir images from a UAV-mounted two-band red-NIR camera. In combination with in situ facies mapping, these measurements provided ground truth for reduction of multispectral Landsat and Worldview-2 satellite images to evaluate mat distribution and diversity across a range of spatial and spectral facies variations.

Characterizing Microbial Mat Morphology with Structure from Motion Techniques in Ice-Covered Lake Joyce, McMurdo Dry Valleys, Antarctica

NASA Astrophysics Data System (ADS)

Mackey, T. J.; Leidman, S. Z.; Allen, B.; Hawes, I.; Lawrence, J.; Jungblut, A. D.; Krusor, M.; Coleman, L.; Sumner, D. Y.

2015-12-01

Structure from Motion (SFM) techniques can provide quantitative morphological documentation of otherwise inaccessible benthic ecosystems such as microbial mats in Lake Joyce, a perennially ice-covered lake of the Antarctic McMurdo Dry Valleys (MDV). Microbial mats are a key ecosystem of MDV lakes, and diverse mat morphologies like pinnacles emerge from interactions among microbial behavior, mineralization, and environmental conditions. Environmental gradients can be isolated to test mat growth models, but assessment of mat morphology along these gradients is complicated by their inaccessibility: the Lake Joyce ice cover is 4-5 m thick, water depths containing diverse pinnacle morphologies are 9-14 m, and relevant mat features are cm-scale. In order to map mat pinnacle morphology in different sedimentary settings, we deployed drop cameras (SeaViewer and GoPro) through 29 GPS referenced drill holes clustered into six stations along a transect spanning 880 m. Once under the ice cover, a boom containing a second GoPro camera was unfurled and rotated to collect oblique images of the benthic mats within dm of the mat-water interface. This setup allowed imaging from all sides over a ~1.5 m diameter area of the lake bottom. Underwater lens parameters were determined for each camera in Agisoft Lens; images were reconstructed and oriented in space with the SFM software Agisoft Photoscan, using the drop camera axis of rotation as up. The reconstructions were compared to downward facing images to assess accuracy, and similar images of an object with known geometry provided a test for expected error in reconstructions. Downward facing images identify decreasing pinnacle abundance in higher sedimentation settings, and quantitative measurements of 3D reconstructions in KeckCAVES LidarViewer supplement these mat morphological facies with measurements of pinnacle height and orientation. Reconstructions also help isolate confounding variables for mat facies trends with measurements of lake bottom slope and underlying relief that could influence pinnacle growth. Comparison of 3D reconstructions to downward-facing drop camera images demonstrate that SFM is a powerful tool for documenting diverse mat morphologies across environmental gradients in ice-covered lakes.

Outcomes of Osteochondral Allograft Transplantation With and Without Concomitant Meniscus Allograft Transplantation: A Comparative Matched Group Analysis.

PubMed

Frank, Rachel M; Lee, Simon; Cotter, Eric J; Hannon, Charles P; Leroux, Timothy; Cole, Brian J

2018-03-01

Osteochondral allograft transplantation (OCA) is often performed with concomitant meniscus allograft transplantation (MAT) as a strategy for knee joint preservation, although to date, the effect of concomitant MAT on outcomes and failure rates after OCA has not been assessed. To determine clinical outcomes for patients undergoing OCA with MAT as compared with a matched cohort of patients undergoing isolated OCA. Control study; Level of evidence, 3. Patients who underwent OCA of the medial or lateral femoral condyle without concomitant MAT by a single surgeon were compared with a matched group of patients who underwent OCA with concomitant MAT (ipsilateral compartment). The patients were matched per age, sex, body mass index, and number of previous ipsilateral knee operations ±1. Patient-reported outcomes, complications, reoperations, and survival rates were compared between groups. One hundred patients undergoing OCA (50 isolated, 50 with MAT) with a mean ± SD follow-up of 4.9 ± 2.7 years (minimum, 2 years) were included (age, 31.7 ± 9.8 years; 52% male). Significantly more patients underwent OCA to the medial femoral condyle (n = 59) than the lateral femoral condyle (n = 41, P < .0001). Patients underwent 2.7 ± 1.7 operations on the ipsilateral knee before OCA. There were no significant differences between the groups regarding reoperation rate (n = 18 for OCA with MAT, n = 17 for OCA without MAT, P = .834), time to reoperation (2.2 ± 2.4 years for OCA with MAT, 3.4 ± 2.7 years for OCA without MAT, P = .149), or failure rates (n = 7 [14%] for OCA with MAT, n = 7 [14%] for OCA without MAT, P > .999). There were no significant differences in patient-reported clinical outcome scores between the groups at final follow-up. There was no significant difference in failure rates between patients undergoing medial femoral condyle OCA (n = 12, 15.3%) and lateral femoral condyle OCA (n = 5, 12.2%, P = .665). These results imply that with appropriate surgical indications to address meniscus deficiency in patients otherwise indicated for OCA and despite the added surgical time and complexity of concomitant MAT, outcomes are favorable, with an 86% OCA graft survivorship at 5 years. This information can be used to counsel patients undergoing OCA with concomitant MAT as part of a knee joint preservation strategy.

Identifying the interacting roles of stressors in driving the global loss of canopy-forming to mat-forming algae in marine ecosystems.

PubMed

Strain, Elisabeth M A; Thomson, Russell J; Micheli, Fiorenza; Mancuso, Francesco P; Airoldi, Laura

2014-11-01

Identifying the type and strength of interactions between local anthropogenic and other stressors can help to set achievable management targets for degraded marine ecosystems and support their resilience by identifying local actions. We undertook a meta-analysis, using data from 118 studies to test the hypothesis that ongoing global declines in the dominant habitat along temperate rocky coastlines, forests of canopy-forming algae and/or their replacement by mat-forming algae are driven by the nonadditive interactions between local anthropogenic stressors that can be addressed through management actions (fishing, heavy metal pollution, nutrient enrichment and high sediment loads) and other stressors (presence of competitors or grazers, removal of canopy algae, limiting or excessive light, low or high salinity, increasing temperature, high wave exposure and high UV or CO2 ), not as easily amenable to management actions. In general, the cumulative effects of local anthropogenic and other stressors had negative effects on the growth and survival of canopy-forming algae. Conversely, the growth or survival of mat-forming algae was either unaffected or significantly enhanced by the same pairs of stressors. Contrary to our predictions, the majority of interactions between stressors were additive. There were however synergistic interactions between nutrient enrichment and heavy metals, the presence of competitors, low light and increasing temperature, leading to amplified negative effects on canopy-forming algae. There were also synergistic interactions between nutrient enrichment and increasing CO2 and temperature leading to amplified positive effects on mat-forming algae. Our review of the current literature shows that management of nutrient levels, rather than fishing, heavy metal pollution or high sediment loads, would provide the greatest opportunity for preventing the shift from canopy to mat-forming algae, particularly in enclosed bays or estuaries because of the higher prevalence of synergistic interactions between nutrient enrichment with other local and global stressors, and as such it should be prioritized. © 2014 John Wiley & Sons Ltd.

A Rare Glimpse of Paleoarchean Life: Geobiology of an Exceptionally Preserved Microbial Mat Facies from the 3.4 Ga Strelley Pool Formation, Western Australia.

PubMed

Duda, Jan-Peter; Van Kranendonk, Martin J; Thiel, Volker; Ionescu, Danny; Strauss, Harald; Schäfer, Nadine; Reitner, Joachim

2016-01-01

Paleoarchean rocks from the Pilbara Craton of Western Australia provide a variety of clues to the existence of early life on Earth, such as stromatolites, putative microfossils and geochemical signatures of microbial activity. However, some of these features have also been explained by non-biological processes. Further lines of evidence are therefore required to convincingly argue for the presence of microbial life. Here we describe a new type of microbial mat facies from the 3.4 Ga Strelley Pool Formation, which directly overlies well known stromatolitic carbonates from the same formation. This microbial mat facies consists of laminated, very fine-grained black cherts with discontinuous white quartz layers and lenses, and contains small domical stromatolites and wind-blown crescentic ripples. Light- and cathodoluminescence microscopy, Raman spectroscopy, and time of flight-secondary ion mass spectrometry (ToF-SIMS) reveal a spatial association of carbonates, organic material, and highly abundant framboidal pyrite within the black cherts. Nano secondary ion mass spectrometry (NanoSIMS) confirmed the presence of distinct spheroidal carbonate bodies up to several tens of μm that are surrounded by organic material and pyrite. These aggregates are interpreted as biogenic. Comparison with Phanerozoic analogues indicates that the facies represents microbial mats formed in a shallow marine environment. Carbonate precipitation and silicification by hydrothermal fluids occurred during sedimentation and earliest diagenesis. The deciphered environment, as well as the δ13C signature of bulk organic matter (-35.3‰), are in accord with the presence of photoautotrophs. At the same time, highly abundant framboidal pyrite exhibits a sulfur isotopic signature (δ34S = +3.05‰; Δ33S = 0.268‰; and Δ36S = -0.282‰) that is consistent with microbial sulfate reduction. Taken together, our results strongly support a microbial mat origin of the black chert facies, thus providing another line of evidence for life in the 3.4 Ga Strelley Pool Formation.

Dolomite Formation within Microbial Mats in the Sabkha of Abu Dhabi (UAE) and Associated Microsedimentary Structures

NASA Astrophysics Data System (ADS)

Bontognali, T. R.; Vasconcelos, C.; McKenzie, J. A.

2008-12-01

The link between microbial activity and dolomite formation has been evaluated in the coastal sabkha of Abu Dhabi (UAE). This modern dolomite-forming environment is frequently cited as the type analogue for the interpretation of many ancient evaporitic sequences. The investigation of sabkha sediments along a transect from intertidal to supratidal zones revealed a close association between microbial mats and dolomite. Authigenic dolomite occurs within surface and buried microbial mats, which are comprised of exopolymeric substances (EPS). Dolomite forms as a direct consequence of mineral nucleation and growth within microbially produced EPS. The cation-binding effect of the EPS molecules influences the composition of the precipitate. The early stage of this process is characterized by the complexation of an amorphous Mg-Si precipitate, which promotes dolomite development. Mineral formation within EPS appears to be enhanced by evaporation with consequent supersaturation of the pore waters with respect to dolomite. Partial EPS degradation during diagenesis may also provide an additional source of cations. However, the specific mineral-template property of EPS, rather than an increase in cation concentrations, is the key factor for dolomite formation in the studied area of the sabkha. Indeed, within the modern microbial mat located at the surface, dolomite precipitates from pore waters whose composition is very close to seawater. In the supratidal zone, pore water analysis and stable isotope values did not reveal any linkage between dolomite formation and microbial excretion and/or consumption of metabolites along the sediment profiles. This is in contrast with current models, in which dolomite formation is mainly linked to microbial increase of pH and alkalinity or consumption of dissolved SO4 in pore-waters. The EPS of the microbial mats is characterized by an alveolar microfabric, which can be mineralized during early diagenesis, preserving fossil imprints of the original biofilm. Recognition of this biostructure, combined with the atypical Mg-Si phase, may be used to interpret ancient microbial dolomite throughout the geological record.

A Rare Glimpse of Paleoarchean Life: Geobiology of an Exceptionally Preserved Microbial Mat Facies from the 3.4 Ga Strelley Pool Formation, Western Australia

PubMed Central

Duda, Jan-Peter; Van Kranendonk, Martin J.; Thiel, Volker; Ionescu, Danny; Strauss, Harald; Schäfer, Nadine; Reitner, Joachim

2016-01-01

Paleoarchean rocks from the Pilbara Craton of Western Australia provide a variety of clues to the existence of early life on Earth, such as stromatolites, putative microfossils and geochemical signatures of microbial activity. However, some of these features have also been explained by non-biological processes. Further lines of evidence are therefore required to convincingly argue for the presence of microbial life. Here we describe a new type of microbial mat facies from the 3.4 Ga Strelley Pool Formation, which directly overlies well known stromatolitic carbonates from the same formation. This microbial mat facies consists of laminated, very fine-grained black cherts with discontinuous white quartz layers and lenses, and contains small domical stromatolites and wind-blown crescentic ripples. Light- and cathodoluminescence microscopy, Raman spectroscopy, and time of flight—secondary ion mass spectrometry (ToF-SIMS) reveal a spatial association of carbonates, organic material, and highly abundant framboidal pyrite within the black cherts. Nano secondary ion mass spectrometry (NanoSIMS) confirmed the presence of distinct spheroidal carbonate bodies up to several tens of μm that are surrounded by organic material and pyrite. These aggregates are interpreted as biogenic. Comparison with Phanerozoic analogues indicates that the facies represents microbial mats formed in a shallow marine environment. Carbonate precipitation and silicification by hydrothermal fluids occurred during sedimentation and earliest diagenesis. The deciphered environment, as well as the δ13C signature of bulk organic matter (-35.3‰), are in accord with the presence of photoautotrophs. At the same time, highly abundant framboidal pyrite exhibits a sulfur isotopic signature (δ34S = +3.05‰; Δ33S = 0.268‰; and Δ36S = -0.282‰) that is consistent with microbial sulfate reduction. Taken together, our results strongly support a microbial mat origin of the black chert facies, thus providing another line of evidence for life in the 3.4 Ga Strelley Pool Formation. PMID:26807732

Evaluating Spatial Heterogeneity and Environmental Variability Inferred from Branched Glycerol Dialkyl Glycerol Tetraethers (GDGTs) Distribution in Soils from Valles Caldera, New Mexic

NASA Astrophysics Data System (ADS)

Contreras Quintana, S. H.; Werne, J. P.; Brown, E. T.; Halbur, J.; Sinninghe Damsté, , J.; Schouten, S.; Correa-Metrio, A.; Fawcett, P. J.

2014-12-01

Branched glycerol dialkyl glycerol tetraethers (GDGTs) are recently discovered bacterial membrane lipids, ubiquitously present in peat bogs and soils, as well as in rivers, lakes and lake sediments. Their distribution appears to be controlled mainly by soil pH and annual mean air temperature (MAT) and they have been increasingly used as paleoclimate proxies in sedimentary records. In order to validate their application as paleoclimate proxies, it is essential evaluate the influence of small scale environmental variability on their distribution. Initial application of the original soil-based branched GDGT distribution proxy to lacustrine sediments from Valles Caldera, New Mexico (NM) was promising, producing a viable temperature record spanning two glacial/interglacial cycles. In this study, we assess the influence of analytical and spatial soil heterogeneity on the concentration and distribution of 9 branched GDGTs in soils from Valles Caldera, and show how this variability is propagated to MAT and pH estimates using multiple soil-based branched GDGT transfer functions. Our results show that significant differences in the abundance and distribution of branched GDGTs in soil can be observed even within a small area such as Valles Caldera. Although the original MBT-CBT calibration appears to give robust MAT estimates and the newest calibration provides pH estimates in better agreement with modern local soils in Valles Caldera, the environmental heterogeneity (e.g. vegetation type and soil moisture) appears to affect the precision of MAT and pH estimates. Furthermore, the heterogeneity of soils leads to significant variability among samples taken even from within a square meter. While such soil heterogeneity is not unknown (and is typically controlled for by combining multiple samples), this study quantifies heterogeneity relative to branched GDGT-based proxies for the first time, indicating that care must be taken with samples from heterogeneous soils in MAT and pH reconstructions.

Population structure of Fusarium fujikuroi from California rice and water grass.

PubMed

Carter, L L A; Leslie, J F; Webster, R K

2008-09-01

The recent observance of Fusarium fujikuroi, the causal agent of Bakanae disease of rice, in California provides a unique opportunity to assess the population diversity of an introduced pathogen in a new environment. We collected 172 isolates of this pathogen between 2000 and 2003 from California rice and two from water grass (Echinochloa spp.). Pathogenicity of F. fujikuroi was demonstrated on early water grass (E. oryzoides) and barnyard grass (E. crus-galli) indicating that weed control should be part of Bakanae management programs. Both mating types and six unique amplified fragment length polymorphism haplotypes corresponding to six identified vegetative compatibility groups were detected. The two most frequently isolated haplotypes encompassed 94% of the collected isolates, suggesting that clonal reproduction dominates. Coefficients of similarity between the unique haplotypes ranged from 0.94 to 0.98, and indicate that there is very little genotypic variation in the F. fujikuroi population in California. The near fixation of the MAT-1 idiomorph (observed ratio 170 MAT-1:4 MAT-2), is consistent with a hypothesis of predominant or exclusive asexual reproduction. The low level of introduced genotypic diversity, in conjunction with the asexual reproductive strategy of this population will slow evolutionary processes, including adaptation to the California environment.

Controls on development and diversity of Early Archean stromatolites

PubMed Central

Allwood, Abigail C.; Grotzinger, John P.; Knoll, Andrew H.; Burch, Ian W.; Anderson, Mark S.; Coleman, Max L.; Kanik, Isik

2009-01-01

The ≈3,450-million-year-old Strelley Pool Formation in Western Australia contains a reef-like assembly of laminated sedimentary accretion structures (stromatolites) that have macroscale characteristics suggestive of biological influence. However, direct microscale evidence of biology—namely, organic microbial remains or biosedimentary fabrics—has to date eluded discovery in the extensively-recrystallized rocks. Recently-identified outcrops with relatively good textural preservation record microscale evidence of primary sedimentary processes, including some that indicate probable microbial mat formation. Furthermore, we find relict fabrics and organic layers that covary with stromatolite morphology, linking morphologic diversity to changes in sedimentation, seafloor mineral precipitation, and inferred microbial mat development. Thus, the most direct and compelling signatures of life in the Strelley Pool Formation are those observed at the microscopic scale. By examining spatiotemporal changes in microscale characteristics it is possible not only to recognize the presence of probable microbial mats during stromatolite development, but also to infer aspects of the biological inputs to stromatolite morphogenesis. The persistence of an inferred biological signal through changing environmental circumstances and stromatolite types indicates that benthic microbial populations adapted to shifting environmental conditions in early oceans. PMID:19515817

Identification of the sex genes in an early diverged fungus.

PubMed

Idnurm, Alexander; Walton, Felicia J; Floyd, Anna; Heitman, Joseph

2008-01-10

Sex determination in fungi is controlled by a small, specialized region of the genome in contrast to the large sex-specific chromosomes of animals and some plants. Different gene combinations reside at these mating-type (MAT) loci and confer sexual identity; invariably they encode homeodomain, alpha-box, or high mobility group (HMG)-domain transcription factors. So far, MAT loci have been characterized from a single monophyletic clade of fungi, the Dikarya (the ascomycetes and basidiomycetes), and the ancestral state and evolutionary history of these loci have remained a mystery. Mating in the basal members of the kingdom has been less well studied, and even their precise taxonomic inter-relationships are still obscure. Here we apply bioinformatic and genetic mapping to identify the sex-determining (sex) region in Phycomyces blakesleeanus (Zygomycota), which represents an early branch within the fungi. Each sex allele contains a single gene that encodes an HMG-domain protein, implicating the HMG-domain proteins as an earlier form of fungal MAT loci. Additionally, one allele also contains a copy of a unique, chromosome-specific repetitive element, suggesting a generalized mechanism for the earliest steps in the evolution of sex determination and sex chromosome structure in eukaryotes.

Design, construction and long life endurance testing of cathode assemblies for use in microwave high-power transmitting tubes

NASA Technical Reports Server (NTRS)

Batra, R.; Marino, D.

1986-01-01

The cathode life test program sponsored by NASA Lewis Research Center at Watkins-Johnson Company has been in continuous operation since 1972. Its primary objective has been to evaluate the long life capability of barium dispenser cathodes to produce emission current densities of 2 A sq. cm. or more in an operational environment simulating that of a highpower microwave tube. The life test vehicles were equipped with convergent flow electron guns, drift space tubes with solenoid magnets for electron beam confinement and water-cooled depressed collectors. A variety of cathode types has been tested, including GE Tungstate, Litton Impregnated, Philips Type B and M, Semicon types S and M, and Spectra-Mat Type M. Recent emphasis has been on monitoring the performance of Philips Type M cathodes at 2 A sq. cm. and Sprectra-Mat and Semicon Type M cathodes at 4 A sq. cm. These cathodes have been operated at a constant current of 616 mA and a cathode anode voltage on the order of 10 kV. Cathode temperatures were maintained at 1010 C true as measured from black body holes in the backs of the cathodes. This report presents results of the cathode life test program from July l982 through April l986. The results include hours of operation and performance data in the form of normalized emission current density versus temperature curves (Miram plots).

Ectomycorrhizal mats alter forest soil biogeochemistry

Treesearch

Laurel A. Kluber; Kathryn M. Tinnesand; Bruce A. Caldwell; Susie M. Dunham; Rockie R. Yarwood; Peter J. Bottomley; David D. Myrold

2010-01-01

Dense hyphal mats formed by ectomycorrhizal (EcM) fungi are prominent features in Douglas-fir forest ecosystems, and have been estimated to cover up to 40% of the soil surface in some forest stands. Two morphotypes of EcM mats have been previously described: rhizomorphic mats, which have thick hyphal rhizomorphs and are found primarily in the organic horizon, and...

Elevated mutation rate during meiosis in Saccharomyces cerevisiae.

PubMed

Rattray, Alison; Santoyo, Gustavo; Shafer, Brenda; Strathern, Jeffrey N

2015-01-01

Mutations accumulate during all stages of growth, but only germ line mutations contribute to evolution. While meiosis contributes to evolution by reassortment of parental alleles, we show here that the process itself is inherently mutagenic. We have previously shown that the DNA synthesis associated with repair of a double-strand break is about 1000-fold less accurate than S-phase synthesis. Since the process of meiosis involves many programmed DSBs, we reasoned that this repair might also be mutagenic. Indeed, in the early 1960's Magni and Von Borstel observed elevated reversion of recessive alleles during meiosis, and found that the revertants were more likely to be associated with a crossover than non-revertants, a process that they called "the meiotic effect." Here we use a forward mutation reporter (CAN1 HIS3) placed at either a meiotic recombination coldspot or hotspot near the MAT locus on Chromosome III. We find that the increased mutation rate at CAN1 (6 to 21 -fold) correlates with the underlying recombination rate at the locus. Importantly, we show that the elevated mutation rate is fully dependent upon Spo11, the protein that introduces the meiosis specific DSBs. To examine associated recombination we selected for random spores with or without a mutation in CAN1. We find that the mutations isolated this way show an increased association with recombination (crossovers, loss of crossover interference and/or increased gene conversion tracts). Polζ appears to contribute about half of the mutations induced during meiosis, but is not the only source of mutations for the meiotic effect. We see no difference in either the spectrum or distribution of mutations between mitosis and meiosis. The correlation of hotspots with elevated mutagenesis provides a mechanism for organisms to control evolution rates in a gene specific manner.

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

PubMed Central

Cruaud, Corinne; Bousquet, Jean; Frascaria-Lacoste, Nathalie

2012-01-01

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed. PMID:22479532

Identification of processed Chinese medicinal materials using DNA mini-barcoding.

PubMed

Song, Ming; Dong, Gang-Qiang; Zhang, Ya-Qin; Liu, Xia; Sun, Wei

2017-07-01

Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and identification of processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA mini-barcoding, based on the sequencing of a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In the present study, six DNA barcode loci including ITS2, psbA-trnH, rbcL, matK, trnL (UAA) intron and its P6 loop, were employed for the authentication of 45 processed samples belonging to 15 species. We evaluated the amplification efficiency of each locus. We also examined the identification accuracy of the potential mini-barcode locus, of trnL (UAA) intron P6 loop. Our results showed that the five primary barcode loci were successfully amplified in only 8.89%-20% of the processed samples, while the amplification rates of the trnL (UAA) intron P6 loop were higher, at 75.56% successful amplification. We compared the mini-barcode sequences with Genbank using the Blast program. The analysis showed that 45.23% samples could be identified to genus level, while only one sample could be identified to the species level. We conclude that trnL (UAA) p6 loop is a candidate mini-barcode that has shown its potential and may become a universal mini-barcode as complementary barcode for authenticity testing and will play an important role in medicinal materials control. Copyright © 2017 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

A multi-locus plastid phylogenetic analysis of the pantropical genus Diospyros (Ebenaceae), with an emphasis on the radiation and biogeographic origins of the New Caledonian endemic species.

PubMed

Duangjai, Sutee; Samuel, Rosabelle; Munzinger, Jérôme; Forest, Félix; Wallnöfer, Bruno; Barfuss, Michael H J; Fischer, Gunter; Chase, Mark W

2009-09-01

We aimed to clarify phylogenetic relationships within the pantropical genus Diospyros (Ebenaceae sensulato), and ascertain biogeographical patterns in the New Caledonian endemic species. We used DNA sequences from eight plastid regions (rbcL, atpB, matK, ndhF, trnK intron, trnL intron, trnL-trnF spacer, and trnS-trnG spacer) and included 149 accessions representing 119 Diospyros species in our analysis. Results from this study confirmed the monophyly of Diospyros with good support and provided a clearer picture of the relationships within the genus than in previous studies. Evidence from phylogenetic analyses suggests that Diospyros colonized New Caledonia multiple times. The four lineages of Diospyros in New Caledonia also differ in their degree of diversification. The molecular data indicate that one lineage is paleoendemic and derived from an ancient Australian species. The other three lineages are more closely related to several Southeast Asian species; two of them are neoendemics, and one has radiated rapidly and recently.

[POLYMORPHISM OF ALFA-AMYLASE AND CONJUGATION IN COMMON WHEAT ENZYME TYPES WITH QUANTITATIVE TRAITS OF PLANTS].

PubMed

Netsvetaev, V P; Bondarenko, L S; Motorina, I P

2015-01-01

Using polymorphism of alpha-amylase in the winter common wheat studied inheritance isoenzymes and its conjugation enzyme types with germinating grain on the "vine", grain productivity, plant height and time of ear formation. It is shown that the polymorphism isoenzyme of alpha-amylase wheat is limited by the presence of different loci whose products are similar in electrophoretic parameters. In this regard, one component of the enzyme can be controlling at one or two or three genes. Identification of a locus controlling alpha-amylase isoenzyme in the fast moving part of the electrophoretogram, designated as α-Amy-B7. Determine the distance of the locus to factor α-Amy-B6.

Pressure distribution on mattresses.

PubMed

Nicol, K; Rusteberg, D

1993-12-01

Measurements of pressure distribution are usually performed on a hard base, such as those in gait analysis or tire research; measurements on soft surfaces are avoided because of technical problems. A sensor mat was developed which consists of 512 pressure sensors, glued to arbitrary locations of a fabric. The mat can be bent to spherical and saddle shapes so that it can be utilised on soft and flexible surfaces like chairs and beds. Performance of eight hospital mattresses concerning decubitus prophylactics and support in supine and side position was studied in four subjects representing extreme body build. It was found that one particular mattress served well for three subjects, whereas no mattress was suitable for the high and heavy type. It was concluded that measurement of pressure distribution is a valuable tool for designing and selecting.

Rolled-out collectors

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

Shurcliff, W.A.

1979-04-01

SolaRoll is a solar collector material composed of extruded strips of black ethylene propylene diene monomer (EPDM) that is suitable for water or air type collectors. SolaRoll is provided in rolls and consists of an absorber mat with tubes and fins and a framing strip comprising all the parts of the collector frame. The rolls are bent in a counterflow pattern to cover the entire collector area and the mat is fastened with a thermosetting mastic adhesive. The heat transfer fluid is plain water as freezing does not injure the EPDM. Installation of the glazing in the framing strip ismore » described. EPDM has the disadvantage of low thermal conductivity but its use does not require antifreeze or a heat exchanger. Design options and suitable applications of SolaRoll systems are discussed.« less

Model Identification and FE Simulations: Effect of Different Yield Loci and Hardening Laws in Sheet Forming

NASA Astrophysics Data System (ADS)

Flores, P.; Duchêne, L.; Lelotte, T.; Bouffioux, C.; El Houdaigui, F.; Van Bael, A.; He, S.; Duflou, J.; Habraken, A. M.

2005-08-01

The bi-axial experimental equipment developed by Flores enables to perform Baushinger shear tests and successive or simultaneous simple shear tests and plane-strain tests. Such experiments and classical tensile tests investigate the material behavior in order to identify the yield locus and the hardening models. With tests performed on two steel grades, the methods applied to identify classical yield surfaces such as Hill or Hosford ones as well as isotropic Swift type hardening or kinematic Armstrong-Frederick hardening models are explained. Comparison with the Taylor-Bishop-Hill yield locus is also provided. The effect of both yield locus and hardening model choice will be presented for two applications: Single Point Incremental Forming (SPIF) and a cup deep drawing.

Genetic mapping reveals that sinefungin resistance in Toxoplasma gondii is controlled by a putative amino acid transporter locus that can be used as a negative selectable marker.

PubMed

Behnke, Michael S; Khan, Asis; Sibley, L David

2015-02-01

Quantitative trait locus (QTL) mapping studies have been integral in identifying and understanding virulence mechanisms in the parasite Toxoplasma gondii. In this study, we interrogated a different phenotype by mapping sinefungin (SNF) resistance in the genetic cross between type 2 ME49-FUDR(r) and type 10 VAND-SNF(r). The genetic map of this cross was generated by whole-genome sequencing of the progeny and subsequent identification of single nucleotide polymorphisms (SNPs) inherited from the parents. Based on this high-density genetic map, we were able to pinpoint the sinefungin resistance phenotype to one significant locus on chromosome IX. Within this locus, a single nonsynonymous SNP (nsSNP) resulting in an early stop codon in the TGVAND_290860 gene was identified, occurring only in the sinefungin-resistant progeny. Using CRISPR/CAS9, we were able to confirm that targeted disruption of TGVAND_290860 renders parasites sinefungin resistant. Because disruption of the SNR1 gene confers resistance, we also show that it can be used as a negative selectable marker to insert either a positive drug selection cassette or a heterologous reporter. These data demonstrate the power of combining classical genetic mapping, whole-genome sequencing, and CRISPR-mediated gene disruption for combined forward and reverse genetic strategies in T. gondii. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Characterization and structural analysis of wild type and a non-abscission mutant at the development funiculus (Def) locus in Pisum sativum L.

PubMed

Ayeh, Kwadwo Owusu; Lee, YeonKyeong; Ambrose, Mike J; Hvoslef-Eide, Anne Kathrine

2009-06-23

In pea seeds (Pisum sativum L.), the Def locus defines an abscission event where the seed separates from the funicle through the intervening hilum region at maturity. A spontaneous mutation at this locus results in the seed failing to abscise from the funicle as occurs in wild type peas. In this work, structural differences between wild type peas that developed a distinct abscission zone (AZ) between the funicle and the seed coat and non-abscission def mutant were characterized. A clear abscission event was observed in wild type pea seeds that were associated with a distinct double palisade layers at the junction between the seed coat and funicle. Generally, mature seeds fully developed an AZ, which was not present in young wild type seeds. The AZ was formed exactly below the counter palisade layer. In contrast, the palisade layers at the junction of the seed coat and funicle were completely absent in the def mutant pea seeds and the cells in this region were seen to be extensions of surrounding parenchymatous cells. The Def wild type developed a distinct AZ associated with palisade layer and counterpalisade layer at the junction of the seed coat and funicle while the def mutant pea seed showed non-abscission and an absence of the double palisade layers in the same region. We conclude that the presence of the double palisade layer in the hilum of the wild type pea seeds plays an important structural role in AZ formation by delimiting the specific region between the seed coat and the funicle and may play a structural role in the AZ formation and subsequent detachment of the seed from the funicle.

Unique Footprint in the scl1.3 Locus Affects Adhesion and Biofilm Formation of the Invasive M3-Type Group A Streptococcus.

PubMed

Bachert, Beth A; Choi, Soo J; LaSala, Paul R; Harper, Tiffany I; McNitt, Dudley H; Boehm, Dylan T; Caswell, Clayton C; Ciborowski, Pawel; Keene, Douglas R; Flores, Anthony R; Musser, James M; Squeglia, Flavia; Marasco, Daniela; Berisio, Rita; Lukomski, Slawomir

2016-01-01

The streptococcal collagen-like proteins 1 and 2 (Scl1 and Scl2) are major surface adhesins that are ubiquitous among group A Streptococcus (GAS). Invasive M3-type strains, however, have evolved two unique conserved features in the scl1 locus: (i) an IS1548 element insertion in the scl1 promoter region and (ii) a nonsense mutation within the scl1 coding sequence. The scl1 transcript is drastically reduced in M3-type GAS, contrasting with a high transcription level of scl1 allele in invasive M1-type GAS. This leads to a lack of Scl1 expression in M3 strains. In contrast, while scl2 transcription and Scl2 production are elevated in M3 strains, M1 GAS lack Scl2 surface expression. M3-type strains were shown to have reduced biofilm formation on inanimate surfaces coated with cellular fibronectin and laminin, and in human skin equivalents. Repair of the nonsense mutation and restoration of Scl1 expression on M3-GAS cells, restores biofilm formation on cellular fibronectin and laminin coatings. Inactivation of scl1 in biofilm-capable M28 and M41 strains results in larger skin lesions in a mouse model, indicating that lack of Scl1 adhesin promotes bacterial spread over localized infection. These studies suggest the uniquely evolved scl1 locus in the M3-type strains, which prevents surface expression of the major Scl1 adhesin, contributed to the emergence of the invasive M3-type strains. Furthermore these studies provide insight into the molecular mechanisms mediating colonization, biofilm formation, and pathogenesis of group A streptococci.