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Author (up) Aveskamp, M.M.; Verkley, G.J.M.; de Gruyter, J.; Murace, M.A.; Perello, A.; Woudenberg, J.H.C.; Groenewald, J.Z.; Crous, P.W. file  url
  Title DNA phylogeny reveals polyphyly of Phoma section Peyronellaea and multiple taxonomic novelties Type Journal Article
  Year 2009 Publication Mycologia Abbreviated Journal Mycologia  
  Volume 101 Issue 3 Pages 363-382  
  Keywords Actins/analysis/genetics; Ascomycota/*classification/cytology/genetics; Biodiversity; DNA, Fungal/*analysis/genetics; DNA, Ribosomal Spacer/analysis/genetics; Genetic Speciation; Genetic Variation; Molecular Sequence Data; *Phylogeny; Polymerase Chain Reaction; Sequence Alignment; Sequence Analysis, DNA; Species Specificity; Tubulin/analysis/genetics  
  Abstract Species of the anamorph genus Phoma are commonly isolated from a wide range of ecological niches. They are notoriously difficult to identify due to the paucity of morphological features and the plasticity of these when cultivated on agar media. Species linked to Phoma section Peyronellaea are typified by the production of dictyochlamydospores and thus have additional characters to use in taxon delineation. However, the taxonomy of this section is still not fully understood. Furthermore the production of such chlamydospores also is known in some other sections of Phoma. DNA sequences were generated from three loci, namely ITS, actin, and 3-tubulin, to clarify the phylogeny of Phoma taxa that produce dictyochlamydospores. Results were unable to support section Peyronellaea as a taxonomic entity. Dictyochlamydospore formation appears to be a feature that developed, or was lost, many times during the evolution of Phoma. Furthermore, based on the multigene analyses, five new Phoma species could be delineated while a further five required taxonomic revision to be consistent with the genetic variation observed.  
  Call Number Serial 1999  
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Author (up) Chen, C.-H.; Tu, C.-C.; Kuo, H.-Y.; Zeng, R.-F.; Yu, C.-S.; Lu, H.H.-S.; Liou, M.-L. file  url
  Title Dynamic change of surface microbiota with different environmental cleaning methods between two wards in a hospital Type Journal Article
  Year 2017 Publication Applied Microbiology and Biotechnology Abbreviated Journal Appl Microbiol Biotechnol  
  Volume 101 Issue 2 Pages 771-781  
  Keywords Bacteria/*classification/genetics/*isolation & purification; Cluster Analysis; DNA, Bacterial/chemistry/genetics; DNA, Ribosomal/chemistry/genetics; Disinfection/*methods; *Environmental Microbiology; *Hospitals; Housekeeping, Hospital/*methods; Humans; Intensive Care Units; Metagenomics; Phylogeny; RNA, Ribosomal, 16S/genetics; Sequence Analysis, DNA; Taiwan; 16S rRNA metagenomics; Acinetobacter; Environmental cleaning methods; Healthcare-associated infection; Medical intensive care unit; Respiratory care centre  
  Abstract Terminal disinfection and daily cleaning have been performed in hospitals in Taiwan for many years to reduce the risks of healthcare-associated infections. However, the effectiveness of these cleaning approaches and dynamic changes of surface microbiota upon cleaning remain unclear. Here, we report the surface changes of bacterial communities with terminal disinfection and daily cleaning in a medical intensive care unit (MICU) and only terminal disinfection in a respiratory care center (RCC) using 16s ribosomal RNA (rRNA) metagenomics. A total of 36 samples, including 9 samples per sampling time, from each ward were analysed. The clinical isolates were recorded during the sampling time. A large amount of microbial diversity was detected, and human skin microbiota (HSM) was predominant in both wards. In addition, the colonization rate of the HSM in the MICU was higher than that in the RCC, especially for Moraxellaceae. A higher alpha-diversity (p = 0.005519) and a lower UniFrac distance was shown in the RCC due to the lack of daily cleaning. Moreover, a significantly higher abundance among Acinetobacter sp., Streptococcus sp. and Pseudomonas sp. was shown in the RCC compared to the MICU using the paired t test. We concluded that cleaning changes might contribute to the difference in diversity between two wards.  
  Call Number Serial 2098  
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Author (up) Coleman, C.; Copetti, D.; Cipriani, G.; Hoffmann, S.; Kozma, P.; Kovacs, L.; Morgante, M.; Testolin, R.; Di Gaspero, G. file  url
doi  openurl
  Title The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines Type Journal Article
  Year 2009 Publication BMC Genetics Abbreviated Journal BMC Genet  
  Volume 10 Issue Pages 89  
  Keywords *Evolution, Molecular; Genetic Markers; Genome, Plant; Multigene Family; Phenotype; Phylogeny; Plant Diseases/*genetics/microbiology; Plant Proteins/*genetics; Segmental Duplications, Genomic; Vitis/*genetics  
  Abstract BACKGROUND: Grape powdery mildew is caused by the North American native pathogen Erysiphe necator. Eurasian Vitis vinifera varieties were all believed to be susceptible. REN1 is the first resistance gene naturally found in cultivated plants of Vitis vinifera. RESULTS: REN1 is present in 'Kishmish vatkana' and 'Dzhandzhal kara', two grapevines documented in Central Asia since the 1920's. These cultivars have a second-degree relationship (half sibs, grandparent-grandchild, or avuncular), and share by descent the chromosome on which the resistance allele REN1 is located. The REN1 interval was restricted to 1.4 cM using 38 SSR markers distributed across the locus and the segregation of the resistance phenotype in two progenies of collectively 461 offspring, derived from either resistant parent. The boundary markers delimit a 1.4-Mbp sequence in the PN40024 reference genome, which contains 27 genes with known functions, 2 full-length coiled-coil NBS-LRR genes, and 9 NBS-LRR pseudogenes. In the REN1 locus of PN40024, NBS genes have proliferated through a mixture of segmental duplications, tandem gene duplications, and intragenic recombination between paralogues, indicating that the REN1 locus has been inherently prone to producing genetic variation. Three SSR markers co-segregate with REN1, the outer ones confining the 908-kb array of NBS-LRR genes. Kinship and clustering analyses based on genetic distances with susceptible cultivars representative of Central Asian Vitis vinifera indicated that 'Kishmish vatkana' and 'Dzhandzhal kara' fit well into local germplasm. 'Kishmish vatkana' also has a parent-offspring relationship with the seedless table grape 'Sultanina'. In addition, the distant genetic relatedness to rootstocks, some of which are derived from North American species resistant to powdery mildew and have been used worldwide to guard against phylloxera since the late 1800's, argues against REN1 being infused into Vitis vinifera from a recent interspecific hybridisation. CONCLUSION: The REN1 gene resides in an NBS-LRR gene cluster tightly delimited by two flanking SSR markers, which can assist in the selection of this DNA block in breeding between Vitis vinifera cultivars. The REN1 locus has multiple layers of structural complexity compared with its two closely related paralogous NBS clusters, which are located some 5 Mbp upstream and 4 Mbp downstream of the REN1 interval on the same chromosome.  
  Call Number Serial 193  
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Author (up) Gajer, P.; Brotman, R.M.; Bai, G.; Sakamoto, J.; Schutte, U.M.E.; Zhong, X.; Koenig, S.S.K.; Fu, L.; Ma, Z.S.; Zhou, X.; Abdo, Z.; Forney, L.J.; Ravel, J. file  url
  Title Temporal dynamics of the human vaginal microbiota Type Journal Article
  Year 2012 Publication Science Translational Medicine Abbreviated Journal Sci Transl Med  
  Volume 4 Issue 132 Pages 132ra52  
  Keywords Bacteria/classification/genetics; Female; Humans; Magnetic Resonance Spectroscopy; Metabolome; Metabolomics; Metagenome/genetics/*physiology; Models, Biological; Phylogeny; Time Factors; Vagina/*microbiology; Microbiome  
  Abstract Elucidating the factors that impinge on the stability of bacterial communities in the vagina may help in predicting the risk of diseases that affect women's health. Here, we describe the temporal dynamics of the composition of vaginal bacterial communities in 32 reproductive-age women over a 16-week period. The analysis revealed the dynamics of five major classes of bacterial communities and showed that some communities change markedly over short time periods, whereas others are relatively stable. Modeling community stability using new quantitative measures indicates that deviation from stability correlates with time in the menstrual cycle, bacterial community composition, and sexual activity. The women studied are healthy; thus, it appears that neither variation in community composition per se nor higher levels of observed diversity (co-dominance) are necessarily indicative of dysbiosis.  
  Call Number Serial 2175  
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Author (up) Gray, R.D.; Atkinson, Q.D. file  url
doi  openurl
  Title Language-tree divergence times support the Anatolian theory of Indo-European origin Type Journal Article
  Year 2003 Publication Nature Abbreviated Journal Nature  
  Volume 426 Issue 6965 Pages 435-439  
  Keywords Agriculture/history; Algorithms; Archaeology/methods; Bayes Theorem; *Emigration and Immigration; Europe/ethnology; History, Ancient; Humans; India/ethnology; *Language; Linguistics; Markov Chains; Middle East/ethnology; Models, Biological; Monte Carlo Method; *Phylogeny; Time Factors  
  Abstract Languages, like genes, provide vital clues about human history. The origin of the Indo-European language family is “the most intensively studied, yet still most recalcitrant, problem of historical linguistics”. Numerous genetic studies of Indo-European origins have also produced inconclusive results. Here we analyse linguistic data using computational methods derived from evolutionary biology. We test two theories of Indo-European origin: the 'Kurgan expansion' and the 'Anatolian farming' hypotheses. The Kurgan theory centres on possible archaeological evidence for an expansion into Europe and the Near East by Kurgan horsemen beginning in the sixth millennium BP. In contrast, the Anatolian theory claims that Indo-European languages expanded with the spread of agriculture from Anatolia around 8,000-9,500 years bp. In striking agreement with the Anatolian hypothesis, our analysis of a matrix of 87 languages with 2,449 lexical items produced an estimated age range for the initial Indo-European divergence of between 7,800 and 9,800 years bp. These results were robust to changes in coding procedures, calibration points, rooting of the trees and priors in the bayesian analysis.  
  Call Number Serial 500  
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Author (up) Haslbeck, M.; Franzmann, T.; Weinfurtner, D.; Buchner, J. file  url
  Title Some like it hot: the structure and function of small heat-shock proteins Type Journal Article
  Year 2005 Publication Nature Structural & Molecular Biology Abbreviated Journal Nat Struct Mol Biol  
  Volume 12 Issue 10 Pages 842-846  
  Keywords Heat-Shock Proteins, Small/*chemistry/classification/*metabolism; Phylogeny; Protein Conformation; Protein Folding  
  Abstract Small heat-shock proteins (sHsps) are a widespread and diverse class of molecular chaperones. Recent evidence suggests that they maintain protein homeostasis by binding proteins in non-native conformations, thereby preventing substrate aggregation. Some members of the sHsp family are inactive or only partially active under physiological conditions, and transition toward the active state is induced by specific triggers, such as elevated temperature. Release of substrate proteins bound to sHsps requires cooperation with ATP-dependent chaperones, suggesting that sHsps create a reservoir of non-native proteins for subsequent refolding.  
  Call Number Serial 2181  
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Author (up) Kampfer, P.; Albrecht, A.; Buczolits, S.; Busse, H.-J. file  url
doi  openurl
  Title Psychrobacter faecalis sp. nov., a new species from a bioaerosol originating from pigeon faeces Type Journal Article
  Year 2002 Publication Systematic and Applied Microbiology Abbreviated Journal Syst Appl Microbiol  
  Volume 25 Issue 1 Pages 31-36  
  Keywords Aerosols; *Air Microbiology; Air Pollution; Animals; Columbidae/*microbiology; Fatty Acids/analysis; Feces/*microbiology; Gammaproteobacteria/genetics/*isolation & purification; Molecular Sequence Data; Phenotype; Phylogeny; RNA, Ribosomal, 16S/analysis/classification; Sequence Alignment  
  Abstract The taxonomy of strain Iso-46T isolated from a bioaerosol generated by cleaning of a pigeon faeces contaminated room was investigated in a polyphasic approach. The beige pigmented Gram-negative, oxidase-negative organism contained a quinone system with mainly ubiquinone Q-8, and the polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, beside some hitherto uncharacterized phospholipids. Major polyamines were spermidine and putrescine and also small amounts of cadaverine. The analysis of the fatty acids revealed 3-OH 12:0 and 3-OH 14:0 (within summed feature 3) as hydroxylated fatty acids. These chemotaxonomic characteristics suggest that the strain belongs to the gamma-subclass of the Proteobacteria namely into the genus Psychrobacter. Analysis of the 16S rRNA gene supported the allocation into the genus Psychrobacter, but showing similarities to all described species of this genus lower than 97%. Iso-46T was able to grow on MacConkey agar and other high nutrient containing media within a temperature range of 4 degrees C to 36 degrees C. On the basis of nutritional and further physiological features, a clear differentiation from all other Psychrobacter species was possible. For these reasons it is proposed to create a new species with the name Psychrobacter faecalis sp. nov.  
  Call Number Serial 435  
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Author (up) Koch, A.M.; Kuhn, G.; Fontanillas, P.; Fumagalli, L.; Goudet, J.; Sanders, I.R. file  url
  Title High genetic variability and low local diversity in a population of arbuscular mycorrhizal fungi Type Journal Article
  Year 2004 Publication Proceedings of the National Academy of Sciences of the United States of America Abbreviated Journal Proc Natl Acad Sci U S A  
  Volume 101 Issue 8 Pages 2369-2374  
  Keywords Analysis of Variance; Evolution, Molecular; *Genetic Variation; Mycorrhizae/classification/*genetics/growth & development/isolation & purification; Phenotype; *Phylogeny; Trees/microbiology  
  Abstract Arbuscular mycorrhizal fungi (AMF) are ecologically important root symbionts of most terrestrial plants. Ecological studies of AMF have concentrated on differences between species; largely assuming little variability within AMF species. Although AMF are clonal, they have evolved to contain a surprisingly high within-species genetic variability, and genetically different nuclei can coexist within individual spores. These traits could potentially lead to within-population genetic variation, causing differences in physiology and symbiotic function in AMF populations, a consequence that has been largely neglected. We found highly significant genetic and phenotypic variation among isolates of a population of Glomus intraradices but relatively low total observed genetic diversity. Because we maintained the isolated population in a constant environment, phenotypic variation can be considered as variation in quantitative genetic traits. In view of the large genetic differences among isolates by randomly sampling two individual spores, <50% of the total observed population genetic diversity is represented. Adding an isolate from a distant population did not increase total observed genetic diversity. Genetic variation exceeded variation in quantitative genetic traits, indicating that selection acted on the population to retain similar traits, which might be because of the multigenomic nature of AMF, where considerable genetic redundancy could buffer the effects of changes in the genetic content of phenotypic traits. These results have direct implications for ecological research and for studying AMF genes, improving commercial AMF inoculum, and understanding evolutionary mechanisms in multigenomic organisms.  
  Call Number Serial 930  
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Author (up) Naxerova, K.; Jain, R.K. file  url
  Title Using tumour phylogenetics to identify the roots of metastasis in humans Type Journal Article
  Year 2015 Publication Nature Reviews. Clinical Oncology Abbreviated Journal Nat Rev Clin Oncol  
  Volume 12 Issue 5 Pages 258-272  
  Keywords Disease Progression; Epigenomics; Genetic Predisposition to Disease; Genome-Wide Association Study; Humans; Microsatellite Repeats; Models, Biological; Neoplasm Metastasis/genetics/*pathology; Neoplasms/genetics; Neoplastic Cells, Circulating/pathology; Phylogeny; Polymorphism, Single Nucleotide  
  Abstract In cancer, much uncertainty remains regarding the origins of metastatic disease. Models of metastatic progression offer competing views on when dissemination occurs (at an early or late stage of tumour development), whether metastases at different sites arise independently and directly from the primary tumour or give rise to each other, and whether dynamic cell exchange occurs between synchronously growing lesions. Although it is probable that many routes can lead to the establishment of systemic disease, clinical observations suggest that distinct modes of metastasis might prevail in different tumour types. Gaining a more-comprehensive understanding of the evolutionary processes that underlie metastasis is not only relevant from a basic biological perspective, but also has profound clinical implications. The 'tree of life' of metastatic cancer contains answers to many outstanding questions about the development of systemic disease, but has only been reconstructed in a limited number of patients. Here we review available data on the phylogenetic relationships between primary solid tumours and their metastases, and examine to what degree they support different models of metastatic progression. We provide a description of experimental methods for lineage tracing in human cancer, ranging from broad DNA-sequencing approaches to more-targeted techniques, and discuss their respective benefits and caveats. Finally, we propose future research questions in the area of cancer phylogenetics.  
  Call Number Serial 1928  
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Author (up) Pellerin, A.; Lacelle, D.; Fortin, D.; Clark, I.D.; Lauriol, B. file  url
doi  openurl
  Title Microbial diversity in endostromatolites (cf. Fissure Calcretes) and in the surrounding permafrost landscape, Haughton impact structure region, Devon Island, Canada Type Journal Article
  Year 2009 Publication Astrobiology Abbreviated Journal Astrobiology  
  Volume 9 Issue 9 Pages 807-822  
  Keywords Actinobacteria/genetics; Arctic Regions; Bacteria/classification/isolation & purification; *Biodiversity; Calcium Carbonate/*chemistry; Canada; Clone Cells; Desert Climate; Exobiology; Geography; *Ice; Microscopy, Electron, Scanning; Phylogeny; Proteobacteria/genetics; Soil Microbiology  
  Abstract In recent years, endostromatolites, which consist of finely laminated calcite columns that grow orthogonally within millimeter- to centimeter-thick fissures in limestone bedrock outcrops, have been discovered in dolomitic outcrops in the Haughton impact structure region, Devon Island, Canada. The growth mechanism of the endostromatolites is believed to be very slow and possibly intertwined with biotic and abiotic processes. Therefore, to discern how endostromatolites form in this polar desert environment, the composition of the microbial community of endostromatolites was determined by means of molecular phylogenetic analysis and compared to the microbial communities found in the surrounding soils. The microbial community present within endostromatolites can be inferred to be (given the predominant metabolic traits of related organisms) mostly aerobic and chemoheterotrophic, and belongs in large part to the phylum Actinobacteria and the subphylum Alphaproteobacteria. The identification of these bacteria suggests that the conditions within the fissure were mostly oxidizing during the growth of endostromatolite. The DNA sequences also indicate that a number of bacteria that closely resemble Rubrobacter radiotolerans are abundant in the endostromatolites as well as other Actinobacteria and Alphaproteobacteria. Some of these taxa have been associated with calcite precipitation, which suggests that the endostromatolites might in fact be microbially mediated. Bacterial communities from nearby permanently frozen soils were more diverse and harbored all the phyla found in the endostromatolites with additional taxa. This study on the microbial communities preserved in potentially microbially mediated secondary minerals in the Arctic could help in the search for evidence of life-forms near the edge of habitability on other planetary bodies.  
  Call Number Serial 221  
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