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Suh S.-O.,10801 University Blvd | Maslov D.A.,University of California at Riverside | Molestina R.E.,10801 University Blvd | Zhou J.J.,10801 University Blvd
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology | Year: 2012

Two strains of a basidiomycetous yeast were derived from an insect trypanosomatid culture isolated from the intestine of a plant bug, Collaria oleosa (Heteroptera: Miridae), collected in Costa Rica. The yeast did not form ballistoconidia but reproduced only by budding. Teliospores were not observed in individual and crossed cultures of each strain. Morphological and other taxonomic characteristics of the yeast were similar to those of the species in the polyphyletic genus Rhodotorula. However, molecular phylogeny inferred from the internal transcribed spacers and D1/D2 region of the large subunit rRNA gene showed that the strains represent a new species placed among the smut fungi in the family Ustilentylomataceae, which includes Aurantiosporium subnitens, Fulvisporium restifaciens, Ustilentyloma fluitans, and Rhodotorula hordea. Given the well distinguished phylogenetic position of this novel species within the Ustilentylomataceae, we propose Microbotryozyma collariae gen. nov., sp. nov. to accommodate the yeast isolated from C. oleosa, with strain American Type Culture Collection MYA-4666 T (= PRA303-1S = CBS 12537) designated as the type strain. © 2012 Springer Science+Business Media B.V.

Suh S.-O.,10801 University Blvd | Gujjari P.,10801 University Blvd | Beres C.,bioMerieux | Beck B.,10801 University Blvd | Zhou J.,10801 University Blvd
International Journal of Systematic and Evolutionary Microbiology | Year: 2013

Twenty-three yeast strains traditionally identified as Zygosaccharomyces bailii were studied in order to clarify their taxonomy and phylogenetic relationships. The molecular phylogeny from rRNA gene sequences showed that these yeasts were well divided into three major groups, and two of the groups could be clearly distinguished from the type strain of Z. bailii at the species level. Therefore, we propose Zygosaccharomyces parabailii sp. nov. (type strain ATCC 56075T = NBRC 1047T = NCYC 128T = CBS 12809T) and Zygosaccharomyces pseudobailii sp. nov. (type strain ATCC 56074T = NBRC 0488T = CBS 2856T) to accommodate the yeasts belonging to the two groups. By conventional physiological tests, Z. bailii and the two novel species are not clearly distinguished from one another, as variations exist more frequently between individual strains and are not species-specific. However, the conclusions from rRNA gene sequence analyses are well supported by genome fingerprinting patterns as well as other protein-coding gene sequence comparisons. © 2013 IUMS.

Kerrigan L.,10801 University Blvd | Nims R.W.,RMC Pharmaceutical Solutions Inc.
Regenerative Medicine | Year: 2011

Authentication of human tissues, cell lines and primary cell cultures (including stem cell preparations) used as therapeutic modalities is often performed using phenotyping and technologies capable of assessing identity to the species level (e.g., isoenzyme analysis and/or karyotyping). This authentication paradigm alone cannot provide assurance that the correct human cell preparation is administered, so careful labeling and tracking of cells from the donor, during manufacture and as part of the final product are also employed. Precise, accurate identification of human cells to the individual donor level could, however, significantly reduce the risks of exposing human subjects to misidentified cells. The availability of a standardized method for achieving this will provide a way to improve the safety profile of human cell-based products by providing assurance that a given lot of cells originated from the intended donor and were not inadvertently mixed or replaced with cells from other donors. In support of this goal, an international team of scientists has prepared a consensus standard on authentication of human cells using short tandem repeat profiling. Associated with the standard itself will be the establishment and maintenance of a public database of short tandem repeat profiles for commonly used cell lines. © 2011 Future Medicine Ltd.

Houseknecht J.L.,10801 University Blvd | Suh S.-O.,10801 University Blvd | Zhou J.J.,10801 University Blvd
Fungal Biology | Year: 2012

Living stock cultures with constant phenotypes and genotypes are required for a wide range of research and industrial applications; however, long-term, stable preservation of fastidious Phytophthora strains has been challenging. In this study, we systematically evaluated different cryopreservation treatments to identify and clarify freezing, thawing, and other conditions appropriate for long-term maintenance. Optimal preservation conditions were largely strain-specific, with robust strains remaining fully viable and the fastidious yielding lower recovery under all test conditions. Nevertheless, several procedures were shown to be generally applicable for effective cryopreservation of most Phytophthora organisms. Fastidious strains retained higher viability following the -1 °C min-1 freezing protocol (Mr Frosty's) than either of two widely used programmed freezing procedures. Revival was higher when frozen mycelium plugs were thawed at 37 °C for 2 min or 25 °C for 5 min, while lower viability was apparent for fastidious strains thawed at 55 °C for 1.5 min. Among 15 cryoprotective solutions assessed, 5 % dimethyl sulfoxide produced the highest viability for all fastidious strains. The effect of prefreeze and postfreeze treatments on revival was mild, if any, and strain-dependent. This study has generated reliable, practical, long-term preservation solutions applicable to a majority of Phytophthora species. It also has revealed a need for in-depth physiological and morphological investigations to further enhance the preservation methods for fastidious strains. © 2012 The British Mycological Society.

Suh S.-O.,10801 University Blvd | Zhou J.J.,10801 University Blvd
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology | Year: 2011

Three ascosporogenous yeast strains were isolated from the gut of the passalid beetle, Odontotaenius disjunctus, inhabiting on rotten oak trees. DNA sequence comparison and other taxonomic characteristics identified the strains as a novel species in the genus Kazachstania. The name Kazachstania intestinalis sp. nov. (type strain EH085 T = ATCC MYA-4658 T = CBS 11839 T) is proposed for the strains. The yeast is homothallic, producing persistent asci with 1-4 spheroidal ascospores. Molecular phylogeny from ribosomal RNA gene sequences placed this novel species on the basal lineage of a clade including Kazachstania lodderae, Kazachstania exigua, Kazachstania martiniae, and other related Kazachstania spp., but none of those species was a close sister to K. intestinalis. © 2011 Springer Science+Business Media B.V.

Gujjari P.,10801 University Blvd | Suh S.-O.,10801 University Blvd | Lee C.-F.,National Hsinchu University of Education | Zhou J.J.,10801 University Blvd
International Journal of Systematic and Evolutionary Microbiology | Year: 2011

Four arthroconidium-producing yeasts were isolated from the gut of wood-inhabiting tenebrionid and passalid beetles. The rRNA genes of these yeast strains were sequenced, compared and analysed. The sequence results and other taxonomic characterizations placed two of the strains into Trichosporon porosum, and the remaining strains, EH024 T and EH026 which were isolated from Xylopinus saperdioides (Coleoptera: Tenebrionidae), into a novel species of the genus Trichosporon in the Porosum clade. Strain EN6S23 was independently isolated from forest soil in Taiwan and was identified as the same novel species based on identical sequences in the internal transcribed spacers (ITS) and the D1/D2 region of the LSU rRNA gene and similar physiological characteristics to those of strains EH024 T and EH026. The three strains can assimilate cellulose and xylan as sole carbon source, and are clearly distinguished from their closest taxon, T. porosum, by 14 nt differences in the ITS and D1/D2 region. These strains did not reproduce sexually under the laboratory conditions tested. The novel species is proposed as Trichosporon xylopini sp. nov. (type strain EH024 T =ATCC MYA-4670 T =CBS 11841 T). © 2011 IUMS.

Suh S.-O.,10801 University Blvd | Houseknecht J.L.,10801 University Blvd | Gujjari P.,10801 University Blvd | Zhou J.J.,10801 University Blvd
International Journal of Systematic and Evolutionary Microbiology | Year: 2013

During a survey of yeasts associated with wood-ingesting insects, 69 strains in the Scheffersomyces clade and related taxa were isolated from passalid and tenebrionid beetles and the decayed wood inhabited by them. The majority of these yeasts was found to be capable of fermenting xylose, and was recognized as Scheffersomyces stipitis or its close relative Scheffersomyces illinoinensis, which are known to be associated with wood-decaying beetles and rotten wood. Yeasts in 'Scheffersomyces' (5Candida) ergatensis and 'Scheffersomyces' (5Candida) coipomoensis were also frequently isolated. The remaining six strains were identified as representing four novel species in the genera Scheffersomyces and Candida based on multilocus sequence analyses of nuclear rRNA genes and four protein-coding genes, as well as other taxonomic characteristics. Two xylose-fermenting species, Scheffersomyces parashehatae f.a., sp. nov. (type strain ATCC MYA-4653T5CBS 12535T5EH045T; MycoBank MB805440) and Scheffersomyces xylosifermentans f.a., sp. nov. (type strain ATCC MYA-4859T5CBS 12540T5MY10-052T; MycoBank MB805441), formed a clade with Scheffersomyces shehatae and related Scheffersomyces species. Interestingly, S. xylosifermentans can survive at 40 °C, which is a rare property among xylose-fermenting yeasts. Candida broadrunensis sp. nov. (type strain ATCC MYA-4650T5CBS 11838T5EH019T; MycoBank MB805442) is a sister taxon of C. ergatensis, while Candida manassasensis sp. nov. (type strain ATCC MYA-4652T5CBS 12534T5EH030T; MycoBank MB805443) is closely related to Candida palmioleophila in the Candida glaebosa clade. The multilocus DNA sequence comparisons in this study suggest that the genus Scheffersomyces needs to be circumscribed to the species near S. stipitis (type species) and S. shehatae that can be characterized by the ability to ferment xylose. © 2013 IUMS.

Suh S.-O.,10801 University Blvd | Zhou J.J.,10801 University Blvd
FEMS Yeast Research | Year: 2010

Ogataea (Hansenula) polymorpha and related yeasts were studied to clarify their taxonomy and phylogenetic relationships. The molecular analyses based on ribosomal DNA sequences revealed that (1) ATCC 14755, type strain of Pichia angusta, is phylogenetically distinguished from the majority of O. polymorpha strains including ATCC 34438T (=NRRL Y-5445T=CBS 4732 T), type of the species; (2) Ogataea thermophila is conspecific to O. polymorpha; and (3) two of the strains, ATCC 26012 and ATCC 58401, are a novel Candida species closely related to O. polymorpha. The conclusions were also supported by physiological characteristics and other taxonomic features of these strains. Therefore, we propose here two novel species, Ogataea angusta comb. nov. (ATCC 14755T=CBS 7073T=NRRL Y-2214T) and Candida parapolymorpha sp. nov. (ATCC 26012T=NRRL Y-7560 T), and conclude that O. thermophila is a synonym of O. polymorpha. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Houseknecht J.L.,10801 University Blvd | Hart E.L.,10801 University Blvd | Suh S.-O.,10801 University Blvd | Zhou J.J.,10801 University Blvd
International Journal of Systematic and Evolutionary Microbiology | Year: 2011

During a survey of yeasts associated with wood-ingesting insects, six strains of the Sugiyamaella clade were isolated from the gut of passalid and tenebrionid beetles and the decayed wood inhabited by them. Phylogeny based on rRNA gene sequences placed these yeasts as members of Sugiyamaella smithiae, Sugiyamaella americana, Candida lignohabitans and a novel species closely related to Su. americana. The only strain of the novel species, EH008 T, could be unquestionably distinguished from its relatives by DNA sequences and other taxonomic characteristics. Ascospore production was not observed under the laboratory conditions tested. Therefore, this novel species is proposed as Candida bullrunensis sp. nov. (type strain EH008 T=ATCC MYA-4660 T=CBS 11840 T). © 2011 IUMS.

Nims R.W.,RMC Pharmaceutical Solutions Inc | Sykes G.,10801 University Blvd | Cottrill K.,10801 University Blvd | Ikonomi P.,10801 University Blvd
In Vitro Cellular and Developmental Biology - Animal | Year: 2010

The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line's species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification. © 2010 The Author(s).

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