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1

Evaluation of YeastIdent and Uni-Yeast-Tek yeast identification systems.  

PubMed Central

The accuracy of the new API YeastIdent system and the Flow Laboratories Uni-Yeast-Tek identification kit with an expanded data base was evaluated in comparison to the API 20C yeast identification system by three laboratories. A total of 489 test isolates were used, biased toward yeasts commonly encountered in clinical specimens. Isolates not in a system's data base were not counted in the evaluation of that system. For isolates in their data base, YeastIdent was 55% accurate and Uni-Yeast-Tek was 40% accurate. By the manufacturer's criteria of reliable identification without additional tests, both systems failed to identify many common and uncommon species. The limited number of substrates and difficulties in assessing results obtained with 11 of the API YeastIdent substrates and apparent errors in the expanded Uni-Yeast-Tek data base appeared to be major factors limiting the accuracy of these systems.

Salkin, I F; Land, G A; Hurd, N J; Goldson, P R; McGinnis, M R

1987-01-01

2

Evaluation of the Quantum II yeast identification system.  

PubMed Central

We compared three methods for identifying clinical yeast isolates: Abbott Quantum II, API 20C, and a modified BBL Minitek system. The API 20C and modified Minitek systems agreed on the identification of 243 of 245 yeasts (99.2%). The Quantum II system correctly identified 197 (80.4%), incorrectly identified 19 (7.8%), and did not identify 29 (11.8%) of the yeasts. Most of the misidentifications with the Quantum II occurred because assimilation or biochemical results were false-positive. Sixteen different species of yeasts and 16 different Quantum II substrates contributed to the discrepancies. On retesting with the Quantum II, 31% of the discrepant strains were correctly identified, while the remaining 69% were incorrectly identified or were not identified. Erroneous biochemical and assimilation results were also noted with yeasts that were correctly identified by the Quantum II system.

Kiehn, T E; Edwards, F F; Tom, D; Lieberman, G; Bernard, E M; Armstrong, D

1985-01-01

3

Update and evaluation of the AutoMicrobic yeast identification system.  

PubMed Central

The AutoMicrobic system (AMS) Yeast Biochemical Card (Vitek Systems Inc., Hazelwood, Mo.) is a system which has been designed for rapid and automated reporting of yeast identification in the clinical laboratory. Recent improvements have been implemented in the AMS data base to expand and enhance its yeast identification capabilities. These improvements include the addition of seven biotypes, changes in data analysis scheme, and construction of the taxonomic keys. The updated system was compared with the API 20C (Analytab Products, Plainview, N.Y.) yeast identification system and a rapid conventional method, using 1,106 clinical and stock yeast isolates. With these improvements, the AMS Yeast Biochemical Card had a correlation of 98.8% with the API 20C system and 93.4% with the rapid conventional method and significantly increased its capability of identifying Cryptococcus neoformans (98%). The most difficult organisms for the system to identify in 22 to 24 h were Cryptococcus terreus (58%) and Cryptococcus uniguttulatus (73%). The updated AMS not only provided more rapid results which were comparable to the other two systems but gave a substantial savings in set-up and reporting time as well.

Land, G; Stotler, R; Land, K; Staneck, J

1984-01-01

4

Efficacy of API 20C and ID 32C Systems for Identification of Common and Rare Clinical Yeast Isolates  

PubMed Central

The abilities of the API 20C and ID 32C yeast identification systems to identify 123 common and 120 rare clinical yeast isolates were compared. API 20C facilitated correct identification of 97% common and 88% rare isolates while ID 32C facilitated correct identification of 92% common and 85% rare isolates.

Ramani, Rama; Gromadzki, Sally; Pincus, David H.; Salkin, Ira F.; Chaturvedi, Vishnu

1998-01-01

5

Comparison of Enzymatic Method Rapid Yeast Plus System with RFLP-PCR for Identification of Isolated Yeast from Vulvovaginal Candidiasis  

PubMed Central

Objective(s) To compare two identification methods, i.e., restriction fragment length polymorphism (RFLP)-PCR analysis and enzymatic method Rapid TM Yeast Plus System to identify different species causing vulvovaginal candidiasis (VVC). Materials and Methods Vaginal discharges of women who had attended the gynecology outpatient clinic of Mobini Hospital in Sabzevar, Iran were collected using cotton swabs and were cultured on Sabouraud dextrose agar. Isolated yeasts were identified by germ-tube testing and Rapid TM Yeast Plus System (Remel USA). For molecular identification, the isolated DNA was amplified with ITS1 and ITS4 universal primers and PCR products digested with the enzyme Hpa?? followed by agarose gel electrophoresis. Epidemiological and clinical features of women with respect to identified species were also evaluated. Results Out of 231 subjects enrolled, 62 VVC cases were detected. The isolated species were identified as follows: Candida albicans, 24 (38.7%), C. glabrata, 15 (24.2%), C. kefyr, 13 (21.0%) C. krusei, 9 (14.5%), and Saccharomyces cerevisiae, 1 (1.6%) by RFLP-PCR method; whereas findings by Rapid TM Yeast Plus System were C. albicans, 24 (38.7%), C. glabrata, 5 (8%), C. kefyr, 11 (17.7%) C. krusei, 2 (3.2%), S. cerevisiae, 9 (14.5%), and C. tropicalis, 6 (9.6%) as well as other nonpathogenic yeasts, 4 (6.9%). Conclusion Statistical comparison showed that there is no significant difference in identification of C. albicans by the two methods; although, in this study, it was not true about other species of yeasts. A correlation between clinical and laboratory findings is important as it enables us to administer an appropriate treatment on time.

Hossein, Moallaei; Mirhendi, Seied Hossein; Brandao, Joao; Mirdashti, Reza; Rosado, Laura

2011-01-01

6

Species level identification and antifungal susceptibility of yeasts isolated from various clinical specimens and evaluation of Integral System Yeasts Plus.  

PubMed

It is essential to use easy, standard, cost-effective and accurate methods for identification and susceptibility testing of yeasts in routine practice. This study aimed to establish the species distribution and antifungal susceptibility of yeast isolates and also to evaluate the performance of the colorimetric and commercially available Integral System Yeasts Plus (ISYP). Yeast isolates (n=116) were identified by conventional methods and ISYP. Antifungal susceptibility testing was performed by the microdilution method according to the standards of CLSI M27-A3 and ISYP. Candida albicans (50%) was the most common species isolated, followed by C. parapsilosis (25%) (mostly in blood samples). According to the CLSI M27-S3 criteria, resistance rates for amphotericin B, flucytosine, fluconazole, itraconazole, and voriconazole were 0%, 0%, 4.6%, 4.5% and 1.8%, respectively. Resistance for miconazole (MIC >1 mg/L) was found as 17.9%. Sixty-two (53.4%) of the isolates which were analyzed by ISYP showed disagreement with those identified by the conventional methods and API ID 32C identification kit or a specific identification code could not be assigned by ISYP. The performance of ISYP could be indicated as low for all antifungal drugs tested according to the ROC analysis (AUC: 0.28-0.56). As the current version of ISYP displays a poor performance, it is recommended to use the other commercial systems whose results are approved as reliable and in agreement with those of the reference methods in identification and susceptibility testing of yeasts. PMID:22842602

Bicmen, Can; Doluca, Mine; Gulat, Sinem; Gunduz, Ayriz T; Tuksavul, Fevziye

2012-06-30

7

Comparative evaluation of three commercial identification systems using common and rare bloodstream yeast isolates.  

PubMed

The commercial yeast identification systems API ID32C, Auxacolor, and Vitek were evaluated using 251 molecularly identified bloodstream isolates and 2 reference strains, representing a total of 35 species (6 common and 29 rare). Correct identification rates were higher for common species (Auxacolor, 95%; API ID32C, 94%; Vitek, 92%) than for rare species (Auxacolor, 43%; API ID32C, 56%; Vitek, 64%). All systems performed equally among the former, and Vitek performed best among the latter. PMID:21543578

Meletiadis, Joseph; Arabatzis, Michael; Bompola, Maria; Tsiveriotis, Konstantinos; Hini, Stavroula; Petinaki, Efthymia; Velegraki, Aristea; Zerva, Loukia

2011-05-04

8

Evaluation of the modified API 20C system for identification of clinically important yeasts.  

PubMed Central

The modified API 20C system (Analytab Products, Inc.) containing 19 carbohydrate assimilation tests was used to identify stock cultures of clinical isolates and routine clinical isolates from the Mayo Clinic mycology laboratory. The system provided correct identifications for 96% of the 505 organisms tested. The API 20C represents a commercial system useful for the identification of yeasts from clinical specimens. Although reliable, it is not a complete system and must be used in conjunction with microscopic morphological features for definitive identification. Since the system requires 72 h for identification, it is not designed for the rapid presumptive identification of such organisms as Cryptococcus neoformans; other biochemical tests must be used for this purpose.

Buesching, W J; Kurek, K; Roberts, G D

1979-01-01

9

Comparison of the Rapid Yeast Plus Panel with the API20C Yeast System for Identification of Clinically Significant Isolates of Candida Species  

PubMed Central

The RapID Yeast Plus system (Innovative Diagnostic Systems, Norcross, Ga.) is a qualitative micromethod employing conventional tests and single-substrate chromogenic tests and having a 4-h incubation period. This system was compared with the API20C (bioMerieux Vitek, Hazelwood, Mo.) system, a 24- to 72-h carbohydrate assimilation method. One hundred thirty-three clinical yeast isolates, including 57 of Candida albicans, 26 of Candida tropicalis, 23 of Candida glabrata, and 27 of other yeasts, were tested by both methods. When discrepancies occurred, isolates were further tested by the Automated Yeast Biochemical Card (bioMerieux Vitek). Germ tube production and microscopic morphology were used as needed to definitively identify yeast isolates. The RapID Yeast Plus system correctly identified 125 yeast isolates, with an overall accuracy of 94% (125 of 133). Excellent correlation was found in the recognition of the three yeasts most commonly isolated from human sources. The test was 99% (105 of 106 isolates) accurate with C. albicans, C. tropicalis, and C. glabrata. The RapID Yeast Plus system compares favorably with the API20C system and provides a simple, accurate alternative to conventional assimilation methods for the rapid identification of the most commonly encountered isolates of Candida species.

Heelan, Judith S.; Sotomayor, Edgar; Coon, Kimberly; D'Arezzo, Julia B.

1998-01-01

10

YeastIdent-Food\\/ProleFood, a new system for the identification of food yeasts based on physiological and biochemical tests  

Microsoft Academic Search

A new kit for the identification of yeasts in foods called YeastIdent-Food\\/ProleFood has been developed. The kit comprises a set of 24 physiological and biochemical tests and computer software (ProleFood) for personal or Macintosh computers that analyses the data obtained from physiological and biochemical tests. Validation of the system in the laboratory revealed that it is very efficient at identifying

E. Velázquez; J. M. Cruz-Sánchez; T. Rivas-Palá; J. L. Zurdo-Piñeiro; P. F. Mateos; E. Monte; E. Mart??nez-Molina; A. Chordi

2001-01-01

11

Evaluation of the API 20C yeast identification system for the differentiation of some dematiaceous fungi.  

PubMed Central

Ninety-seven isolates of Cladosporium spp., Exophiala spp., Fonsecaea spp., Lecythophora hoffmannii, Phaeoannellomyces werneckii, Phialophora spp., Wangiella dermatitidis, and Xylohypha bantiana were used to evaluate the API 20C Yeast Identification System for the differentiation of dematiaceous fungi. Using the API 20C system, we were able to distinguish most species of Phialophora and Cladosporium and to separate L. hoffmannii from the species of Phialophora tested; X. bantiana from C. carrionii, C. resinae, and C. sphaerospermum; and W. dermatitidis from Exophiala jeanselmei and Exophiala spinifera. Ninety-two (60.1%) of 153 possible species-pair combinations were separated.

Espinel-Ingroff, A; McGinnis, M R; Pincus, D H; Goldson, P R; Kerkering, T M

1989-01-01

12

Comparative Evaluation of BD Phoenix and Vitek 2 Systems for Species Identification of Common and Uncommon Pathogenic Yeasts.  

PubMed

The BD Phoenix system was evaluated for species-level identification of yeasts (250 clinical isolates) and compared with the Vitek 2 system, using ribosomal internal transcribed spacer (ITS) sequence analysis as the gold standard. Considering only the species included in each system's database, 96.3% (236/245) and 91.4% (224/245) of the isolates were correctly identified by BD Phoenix and Vitek 2, respectively. PMID:23966500

Posteraro, Brunella; Ruggeri, Alberto; De Carolis, Elena; Torelli, Riccardo; Vella, Antonietta; De Maio, Flavio; Ricciardi, Walter; Posteraro, Patrizia; Sanguinetti, Maurizio

2013-08-21

13

[Identification of the proteins interacting with neuroprotective peptide humanin in a yeast two-hybrid system].  

PubMed

Humanine is a human neuroprotective peptide with a wide action spectrum. To analyze molecular mechanisms of humanin functioning, a search for proteins interacting with this peptide was conducted using yeast two-hybrid system. Screening of human fetal brain cDNA library identified seven proteins with different functions that specifically interacted with humanin. PMID:16583711

Maksimov, V V; Arman, I P; Tarantul, V Z

2006-02-01

14

Identification of the proteins interacting with neuroprotective peptide humanin in a yeast two-hybrid system  

Microsoft Academic Search

Humanine is a human neuroprotective peptide with a wide action spectrum. To analyze molecular mechanisms of humanin functioning,\\u000a a search for proteins interacting with this peptide was conducted using yeast two-hybrid system. Screening of human fetal\\u000a brain cDNA library identified seven proteins with different functions that specifically interacted with humanin.

V. V. Maximov; I. P. Arman; V. Z. Tarantul

2006-01-01

15

A modified yeast one-hybrid system for genome-wide identification of transcription factor binding sites.  

PubMed

The yeast one-hybrid system is a powerful genetic method to identify DNA-protein interactions, but there is a major limitation inherent to the system. Namely, frequency of false positives generated by yeast endogenous transcription factors has been thought to be higher than that of true positives by orders of magnitude. However, our modification efficiently can eliminate the false positives. When compared to the other methods for the analysis of DNA-protein interactions on a genome-wide scale, a modified yeast one-hybrid system offers several advantages including low initial and running cost, large-scale output, and easy handling. PMID:23436358

Yanai, Kazuyuki

2013-01-01

16

Rapid methods for identification of yeasts.  

PubMed Central

Opportunistic infections by yeasts have been implicated as one of the major causes of complications in the compromised patient. Rapid recognition and identification of these yeasts is essential for patient management, but conventional liquid medium methods for completing identification tests are cumbersome and time consuming. Rapid tests have been devised based on modifications of methods commonly used in bacteriology. These rapid methods included tests for carbohydrate and nitrate assimilation, fermentation, and urease production. These were compared with several current methods for accuracy of results, for time to final identification, and for economy of time and reagents. In addition, the usual tests for pseudogerm tube formation, for production of hyphae or pseudohyphae, and for growth temperatures were included. The rapid tests achieved 96% or better accuracy compared with expected results, and 46 species of yeasts were identified in 1 to 2 days compared with the 10 to 14 days required by conventional liquid culture methods. Images

Huppert, M; Harper, G; Sun, S H; Delanerolle, V

1975-01-01

17

Yeast killer systems.  

PubMed Central

The killer phenomenon in yeasts has been revealed to be a multicentric model for molecular biologists, virologists, phytopathologists, epidemiologists, industrial and medical microbiologists, mycologists, and pharmacologists. The surprisingly widespread occurrence of the killer phenomenon among taxonomically unrelated microorganisms, including prokaryotic and eukaryotic pathogens, has engendered a new interest in its biological significance as well as its theoretical and practical applications. The search for therapeutic opportunities by using yeast killer systems has conceptually opened new avenues for the prevention and control of life-threatening fungal diseases through the idiotypic network that is apparently exploited by the immune system in the course of natural infections. In this review, the biology, ecology, epidemiology, therapeutics, serology, and idiotypy of yeast killer systems are discussed.

Magliani, W; Conti, S; Gerloni, M; Bertolotti, D; Polonelli, L

1997-01-01

18

Identification of novel protein-protein interactions of Yersinia pestis type III secretion system by yeast two hybrid system.  

PubMed

Type III secretion system (T3SS) of the plague bacterium Y. pestis encodes a syringe-like structure consisting of more than 20 proteins, which can inject virulence effectors into host cells to modulate the cellular functions. Here in this report, interactions among the possible components in T3SS of Yersinia pestis were identified using yeast mating technique. A total of 57 genes, including all the pCD1-encoded genes except those involved in plasmid replication and partition, pseudogenes, and the putative transposase genes, were subjected to yeast mating analysis. 21 pairs of interaction proteins were identified, among which 9 pairs had been previously reported and 12 novel pairs were identified in this study. Six of them were tested by GST pull down assay, and interaction pairs of YscG-SycD, YscG-TyeA, YscI-YscF, and YopN-YpCD1.09c were successfully validated, suggesting that these interactions might play potential roles in function of Yersinia T3SS. Several potential new interactions among T3SS components could help to understand the assembly and regulation of Yersinia T3SS. PMID:23349800

Yang, Huiying; Tan, Yafang; Zhang, Tingting; Tang, Liujun; Wang, Jian; Ke, Yuehua; Guo, Zhaobiao; Yang, Xiaoming; Yang, Ruifu; Du, Zongmin

2013-01-22

19

Evaluation of the MicroScan Rapid Yeast Identification panel.  

PubMed Central

The MicroScan Rapid Yeast Identification (RYI) panel is a 4-h microdilution system for identification of clinical yeastlike isolates. Its accuracy was evaluated by using 357 isolates encompassing 11 genera and 30 species. The RYI panel identifications were compared with those obtained by the API 20C system assisted with morphological characterization on cornmeal-Tween 80 agar. The panels were read both visually and with the AutoScan-4, a computer-controlled microplate reader. Both the RYI panel and the API 20C system correctly identified 78% of the strains within 4 and 72 h, respectively, with no additional tests. Supplementary tests recommended by the manufacturers made it possible to identify up to 96.6% (AutoScan-4) and 98.9% (API 20C) of the strains. The accuracy of the RYI panel was 99.5% with common strains and 92.1% with less common strains. The RYI panel misidentified 10 or 12 strains and failed to identify 2 or 3 strains, depending on whether it was read with the AutoScan-4 or visually. Errors occurred with one strain of Torulopsis glabrata and the less common yeasts T. candida, Candida lusitaniae, C. lambica, C. rugosa, C. stellatoidea, Cryptococcus albidus, C. laurentii, and C. uniguttulatus. Overall, the RYI panel appears to be a reliable system for identification of the more common clinical yeast isolates.

St Germain, G; Beauchesne, D

1991-01-01

20

Yeast identification in floral nectar of Mimulus aurantiacus (Invited)  

Microsoft Academic Search

Nectar is such a sugar-rich resource that serves as a natural habitat in which microbes thrive. As a result, yeasts arrive to nectar on the bodies of pollinators such as hummingbirds and bees. Yeasts use the sugar in nectar for their own needs when introduced. This research focuses on the identification of different types of yeast that are found in

C. Kyauk; M. Belisle; T. Fukami

2009-01-01

21

Identification of amelotin- and ODAM-interacting enamel matrix proteins using the yeast two-hybrid system.  

PubMed

The formation of dental enamel is a prototype of functional tissue development through biomineralization. Amelotin (AMTN) is a recently discovered secreted enamel protein predominantly expressed during the maturation stage of enamel formation. It accumulates in a basal lamina-like structure at the interface between ameloblasts and enamel mineral and it co-localizes with another recently described enamel protein, odontogenic ameloblast-associated protein (ODAM). The purpose of this study was to determine whether AMTN and ODAM bind to each other and/or to other well-established enamel matrix proteins. The coding sequences of all enamel proteins were cloned into appropriate vectors of the GAL4-based Matchmaker Gold Yeast Two-Hybrid System. The growth of yeast cells on selective media and color induction were used as indicators for reporter gene expression through protein-protein interactions in combinations of prey and bait constructs. We found that AMTN interacts with itself and with ODAM, but not with amelogenin (AMEL), ameloblastin (AMBN), or enamelin (ENAM). Using ODAM as bait, the interaction with AMTN was confirmed. Furthermore, ODAM was found to bind to itself and to AMBN, as well as weakly to AMEL but not to ENAM. We propose a model where the distinct expression of AMTN and ODAM and their interaction are involved in defining the enamel microstructure at the enamel surface. PMID:22243260

Holcroft, James; Ganss, Bernhard

2011-12-01

22

Yeast metabolic state identification using micro-fiber optics spectroscopy  

NASA Astrophysics Data System (ADS)

Saccharomyces cerevisiae morphology is known to be dependent on the cell physiological state and environmental conditions. On their environment, wild yeasts tend to form complex colonies architectures, such as stress response and pseudohyphal filaments morphologies, far away from the ones found inside bioreactors, where the regular cell cycle is observed under controlled conditions (e.g. budding and flocculating colonies). In this work we explore the feasibility of using micro-fiber optics spectroscopy to classify Saccharomyces cerevisiae S288C colony structures in YPD media, under different growth conditions, such as: i) no alcohol; ii) 1 % (v/v) Ethanol; iii) 1 % (v/v) 1-butanol; iv) 1 % (v/v) Isopropanol; v) 1 % (v/v) Tert-Amyl alcohol (2 Methyl-2-butanol); vi) 0,2 % (v/v) 2-Furaldehyde; vii) 5 % (w/v) 5 (Hydroxymethyl)-furfural; and viii) 1 % (w/v) (-)-Adenosine3', 5'cyclic monophosphate. The microscopy system includes a hyperspectral camera apparatus and a micro fiber (sustained by micro manipulator) optics system for spectroscopy. Results show that micro fiber optics system spectroscopy has the potential for yeasts metabolic state identification once the spectral signatures of colonies differs from each others. This technique associated with others physico-chemical information can benefit the creation of an information system capable of providing extremely detailed information about yeast metabolic state that will aid both scientists and engineers to study and develop new biotechnological products.

Silva, J. S.; Castro, C. C.; Vicente, A. A.; Tafulo, P.; Jorge, P. A. S.; Martins, R. C.

2011-05-01

23

Molecular identification of yeasts associated with traditional Egyptian dairy products.  

PubMed

This study aimed to examine the diversity and ecology of yeasts associated with traditional Egyptian dairy products employing molecular techniques in yeast identification. A total of 120 samples of fresh and stored Domiati cheese, kariesh cheese, and "Matared" cream were collected from local markets and examined. Forty yeast isolates were cultured from these samples and identified using the restriction-fragment length polymorphism (RFLPs) of 5.8S-ITS rDNA region and sequencing of the domains D1 and D2 of the 26S rRNA gene. Yeasts were identified as Issatchenkia orientalis (13 isolates), Candida albicans (4 isolates), Clavispora lusitaniae (Candida lusitaniae) (9 isolates), Kodamaea ohmeri (Pichia ohmeri) (1 isolate), Kluyveromyces marxianus (6 isolates), and Candida catenulata (7 isolates). With the exception of C. lusitaniae, the D1/D2 26S rRNA gene sequences were 100% identical for the yeast isolates within the same species. Phylogenetic reconstruction of C. lusitaniae isolates grouped them into 3 distinguished clusters. Kariesh cheese was found to be the most diverse in its yeast floras and contained the highest total yeast count compared with other examined dairy products. This was linked to the acidic pH and lower salt content of this cheese, which favor the growth and survival of yeasts in foodstuffs. Stored Domiati cheese also contained diverse yeast species involving isolates of the pathogenic yeast C. albicans. This raises the possibility of dairy products being vehicles of transmission of pathogenic yeasts. PMID:19895478

El-Sharoud, W M; Belloch, C; Peris, D; Querol, A

2009-09-01

24

Identification of yeast strains isolated from a two-phase decanter system olive oil waste and investigation of their ability for its fermentation.  

PubMed

A dynamic fed-batch microcosm system is described which permits assessment of the progressive growth of yeasts through olive oil waste. We report on its application to measure the effects of the growth of yeast strains upon the chemical composition of "alpeorujo", the waste of a two-phase decanter system used for the extraction of olive oil. Six phenotypically distinct groups of yeasts were isolated. Three selected isolates were identified as being most closely related to Saccharomyces sp., Candida boidinii and Geotrichum candidum using biochemical tests and partial 18S rDNA gene sequence analysis. This is the first report of yeast growth on "alpeorujo" by the use of a fed-batch microcosm system, resulting in the change of the initial chemical composition of "alpeorujo" and in the decrease of the toxic substances such as phenols. PMID:15062826

Giannoutsou, E P; Meintanis, C; Karagouni, A D

2004-07-01

25

Performance of CHROMAGAR candida and BIGGY agar for identification of yeast species  

Microsoft Academic Search

BACKGROUND: The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species. METHODS: A total number of 270 yeast strains including 169 Candida albicans, 33 C.

Mine Yücesoy; Serhat Marol

2003-01-01

26

Multicenter Evaluation of the New VITEK 2 Advanced Colorimetric Yeast Identification Card?  

PubMed Central

The performance of the new VITEK 2 Advanced Colorimetry yeast identification (YST) card for use with the VITEK 2 system (bioMérieux, Inc., Hazelwood, MO) was compared to that of the API 20C AUX (API) system (bioMérieux SA, Marcy-l'Etoile, France) in a multicenter evaluation. A total of 12 quality control, 64 challenge, and 623 clinical yeast isolates were used in the study. Comparisons of species identification, platform reliability, and substrate reproducibility were made between YST and API, with API considered the reference standard. Quality control testing to assess system and substrate reproducibility matched expected results ?95% of the time. The YST card correctly identified 100% of the challenge strains, which covered the species range of the manufacturer's performance claims. Using clinical isolates, the YST card correctly identified 98.5%, with 1.0% of isolates incorrectly identified and 0.5% unidentified. Among clinical isolates, the YST card generated fewer low-discrimination results (18.9%) than did API (30.0%). The time to identification with YST was 18 h, compared to 48 to 72 h with API. The colorimetric YST card used with the VITEK 2 provides a highly automated, objective yeast identification method with excellent performance and reproducibility. We found this system useful for timely and accurate identification of significant yeast species in the clinical microbiology laboratory.

Hata, D. Jane; Hall, Leslie; Fothergill, Annette W.; Larone, Davise H.; Wengenack, Nancy L.

2007-01-01

27

Evaluation of the new API 20C strip for yeast identification against a conventional method.  

PubMed Central

The new API 20C yeast identification system together with appropriate microscopic morphology determinations achieved a 97% correlation with a rapid conventional method. Whereas a group composed of Candida, Torulopsis, Saccharomyces, and Rhodotorula was identified with ease (98% overall correlation), a second group, containing Cryptococcus, Trichosporon, and Geotrichum species, appeared to give the system the most difficulty (90% correlation). Within this group particular difficulty was encountered in identifying varieties of Cryptococcus albidus, C. terreus, C. laurentii, Trichosporon beigelli, and Geotrichum spp. as to species. The API 20C system should be incubated the full 72 h prescribed by the manufacturer. However, when used in conjunction with appropriate morphological tests, presumptive identifications of some Candida and Torulopsis species may be made at 24 to 48 h. To facilitate identifications of the more difficult group of yeasts, ancillary tests for determining nitrate reductase, urease, and phenol oxidase activities should be considered as additions to the strip. Incorporating the phenol oxidase test would be especially important for identification of Cryptococcus neoformans, a yeast which should be identified as quickly and as accurately as possible. The API 20C system with computer assistance has proved to be an easy-to-inoculate, versatile, and fairly rapid method of yeast identification, giving results comparable to those obtained by conventional methodologies.

Land, G A; Harrison, B A; Hulme, K L; Cooper, B H; Byrd, J C

1979-01-01

28

Identification of a Novel System for Boron Transport: Atr1 Is a Main Boron Exporter in Yeast? †  

PubMed Central

Boron is a micronutrient in plants and animals, but its specific roles in cellular processes are not known. To understand boron transport and functions, we screened a yeast genomic DNA library for genes that confer resistance to the element in Saccharomyces cerevisiae. Thirty boron-resistant transformants were isolated, and they all contained the ATR1 (YML116w) gene. Atr1 is a multidrug resistance transport protein belonging to the major facilitator superfamily. C-terminal green fluorescent protein-tagged Atr1 localized to the cell membrane and vacuole, and ATR1 gene expression was upregulated by boron and several stress conditions. We found that atr1? mutants were highly sensitive to boron treatment, whereas cells overexpressing ATR1 were boron resistant. In addition, atr1? cells accumulated boron, whereas ATR1-overexpressing cells had low intracellular levels of the element. Furthermore, atr1? cells showed stronger boron-dependent phenotypes than mutants deficient in genes previously reported to be implicated in boron metabolism. ATR1 is widely distributed in bacteria, archaea, and lower eukaryotes. Our data suggest that Atr1 functions as a boron efflux pump and is required for boron tolerance.

Kaya, Alaattin; Karakaya, Huseyin C.; Fomenko, Dmitri E.; Gladyshev, Vadim N.; Koc, Ahmet

2009-01-01

29

Application of fatty acid profiles in the identification of yeasts.  

PubMed

In order to develop a rapid yeast identification technique using fatty acid profiles, an extensive survey has been conducted in our laboratory on the long-chain fatty acid composition (CLFAC) of yeasts representing the endomycetous and basidiomycetous yeast domain. It was accomplished by cultivating the yeast strains under standardized conditions in a synthetic liquid medium. When stationary phase was reached the cells of each culture were freeze-dried and the CLFAC was examined by gas chromatography. It was found that the fatty acid profile obtained for each strain was reproducible. However, as work progressed, it became clear that variation exists within species and that the relative percentages of some strains from different species may overlap. Identification of species could therefore not be achieved in all attempts, even when the resolution of the fatty acid analyses was enhanced by using capillary columns, useful for the detection of minor fatty acids. When used in isolation, CLFAC analyses is therefore not a generally applicable identification technique for yeast species. However, the technique was found to be a valuable chemotaxanomical tool to distinguish between strains of certain species, species of certain genera and species from particular environments. The technique currently finds application in the South African food and beverage industry as a quick, cheap and easy way to distinguish between strains of Saccharomyces cerevisiae. It is also used by an industry which produces bioprotein from Geotrichum candidum, to determine fungal contaminants in a quality control process. PMID:8357755

Botha, A; Kock, J L

1993-06-25

30

Comparison between the Biflex III-Biotyper and the Axima-SARAMIS Systems for Yeast Identification by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry  

PubMed Central

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is emerging in laboratories as a new diagnostic tool for microorganism identification. We prospectively compared the performances of the Biflex III-Biotyper (Bruker Daltonics) and the Axima (Shimadzu)-SARAMIS (AnagnosTec) systems for the identification of 312 yeasts isolated from clinical specimens (249 Candida spp., including 19 C. albicans and 230 non-albicans species and 63 isolates belonging to different species of the genera Saccharomyces [20 isolates], Rhodotorula [8 isolates], Cryptococcus [8 isolates], Trichosporon [7 isolates], Pichia [7 isolates], Geotrichum [12 isolates], and Sporopachydermia cereana [1 isolate]). Species were identified by using routine conventional phenotypical methods and internal transcribed spacer (ITS) sequencing in case of discrepancy. We used expanded thresholds for species identification (log score of ?1.7 with 3 identical consecutive propositions and no discrepancy between the duplicates for the Bruker Daltonics system and similitude of ?40% with 5 successive identical propositions and no discrepancy between the duplicates for the Shimadzu system). Of the 312 isolates, 272 (87.2%) and 258 (82.7%) were successfully identified by the Bruker Daltonics and Shimadzu systems, respectively. All isolates were successfully identified within the most frequent and clinically relevant Candida species by the two systems. Nonvalid results corresponded mainly to species not or poorly represented in the databases. Major misidentifications were observed for 2 isolates (0.6%) by the Bruker Daltonics system and 4 isolates (1.3%) by the Shimadzu system. In conclusion, the performances of the Bruker Daltonics and the Shimadzu systems for yeast identification were good and comparable under routine clinical conditions, despite their differences in sample preparation, database content, and spectrum analysis.

Lohmann, Caroline; Sabou, Marcela; Moussaoui, Wardi; Prevost, Gilles; Delarbre, Jean-Marie; Candolfi, Ermanno; Gravet, Alain

2013-01-01

31

Comparison between the Biflex III-Biotyper and the Axima-SARAMIS systems for yeast identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry.  

PubMed

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is emerging in laboratories as a new diagnostic tool for microorganism identification. We prospectively compared the performances of the Biflex III-Biotyper (Bruker Daltonics) and the Axima (Shimadzu)-SARAMIS (AnagnosTec) systems for the identification of 312 yeasts isolated from clinical specimens (249 Candida spp., including 19 C. albicans and 230 non-albicans species and 63 isolates belonging to different species of the genera Saccharomyces [20 isolates], Rhodotorula [8 isolates], Cryptococcus [8 isolates], Trichosporon [7 isolates], Pichia [7 isolates], Geotrichum [12 isolates], and Sporopachydermia cereana [1 isolate]). Species were identified by using routine conventional phenotypical methods and internal transcribed spacer (ITS) sequencing in case of discrepancy. We used expanded thresholds for species identification (log score of ?1.7 with 3 identical consecutive propositions and no discrepancy between the duplicates for the Bruker Daltonics system and similitude of ?40% with 5 successive identical propositions and no discrepancy between the duplicates for the Shimadzu system). Of the 312 isolates, 272 (87.2%) and 258 (82.7%) were successfully identified by the Bruker Daltonics and Shimadzu systems, respectively. All isolates were successfully identified within the most frequent and clinically relevant Candida species by the two systems. Nonvalid results corresponded mainly to species not or poorly represented in the databases. Major misidentifications were observed for 2 isolates (0.6%) by the Bruker Daltonics system and 4 isolates (1.3%) by the Shimadzu system. In conclusion, the performances of the Bruker Daltonics and the Shimadzu systems for yeast identification were good and comparable under routine clinical conditions, despite their differences in sample preparation, database content, and spectrum analysis. PMID:23390281

Lohmann, Caroline; Sabou, Marcela; Moussaoui, Wardi; Prévost, Gilles; Delarbre, Jean-Marie; Candolfi, Ermanno; Gravet, Alain; Letscher-Bru, Valérie

2013-02-06

32

Identification and analysis of Escherichia coli proteins that interact with the histidine kinase NtrB in a yeast two-hybrid system  

Microsoft Academic Search

In this work we used the yeast two-hybrid (Y2H) system to deepen our understanding of protein-protein interactions that are involved in the nitrogen regulatory network in Escherichia coli. Three different genes, encoding GlnB, GlnK and AspA, respectively, were found among 64 positive clones identified from E. coli Sau3AI Y2H libraries using the nitrogen regulator NtrB as bait. Structural and functional

P. Salinas; A. Contreras

2003-01-01

33

Transformation systems of non-Saccharomyces yeasts.  

PubMed

This review describes the transformation systems including vectors, replicons, genetic markers, transformation methods, vector stability, and copy numbers of 13 genera and 31 species of non-Saccharomyces yeasts. Schizosaccharomyces pombe was the first non-Saccharomyces yeast studied for transformation and genetics. The replicons of non-Saccharomyces yeast vectors are from native plasmids, chromosomal DNA, and mitochondrial DNA of Saccharomyces cerevisiae, non-Saccharomyces yeasts, protozoan, plant, and animal. Vectors such as YAC, YCp, YEp, YIp, and YRp were developed for non-Saccharomyces yeasts. Forty-two types of genes from bacteria, yeasts, fungi, and plant were used as genetic markers that could be classified into biosynthetic, dominant, and colored groups to construct non-Saccharomyces yeasts vectors. The LEU2 gene and G418 resistance gene are the two most popular markers used in the yeast transformation. All known transformation methods such as spheroplast-mediating method, alkaline ion treatment method, electroporation, trans-kingdom conjugation, and biolistics have been developed successfully for non-Saccharomyces yeasts, among which the first three are most widely used. The highest copy number detected from non-Saccharomyces yeasts is 60 copies in Kluyveromyces lactis. No general rule is known to illustrate the transformation efficiency, vector stability, and copy number, although factors such as vector composition, host strain, transformation method, and selective pressure might influence them. PMID:11599715

Wang, T T; Choi, Y J; Lee, B H

2001-01-01

34

Efficient Identification of Clinically Relevant Candida Yeast Species by Use of an Assay Combining Panfungal Loop-Mediated Isothermal DNA Amplification with Hybridization to Species-Specific Oligonucleotide Probes  

Microsoft Academic Search

The occurrence of invasive mycoses has progressively increased in recent years. Yeasts of the genus Candida remain the leading etiologic agents of those infections. Early identification of opportunistic yeasts may contribute significantly to improved disease management and the selection of appropriate antifungal therapy. We developed a rapid and reliable molecular identification system for clinically relevant yeasts that makes use of

Joao Inacio; Orfeu Flores; Isabel Spencer-Martins

35

Yeast identification in floral nectar of Mimulus aurantiacus (Invited)  

NASA Astrophysics Data System (ADS)

Nectar is such a sugar-rich resource that serves as a natural habitat in which microbes thrive. As a result, yeasts arrive to nectar on the bodies of pollinators such as hummingbirds and bees. Yeasts use the sugar in nectar for their own needs when introduced. This research focuses on the identification of different types of yeast that are found in the nectar of Mimulus aurantiacus (commonly known as sticky monkey-flower). Unopened Mimulus aurantiacus flower buds were tagged at Jasper Ridge and bagged three days later. Floral nectar was then extracted and plated on potato dextrose agar. Colonies on the plates were isolated and DNA was extracted from each sample using QIAGEN DNeasy Plant Mini Kit. The DNA was amplified through PCR and ran through gel electrophoresis. The PCR product was used to clone the nectar samples into an E.coli vector. Finally, a phylogenetic tree was created by BLAST searching sequences in GenBank using the Internal Transcribed Space (ITS) locus. It was found that 18 of the 50 identified species were Candida magnifica, 14 was Candida rancensis, 6 were Crytococcus albidus and there were 3 or less of the following: Starmella bombicola, Candida floricola, Aureobasidium pullulans, Pichia kluyvera, Metschnikowa cibodaserisis, Rhodotorua colostri, and Malassezia globosa. The low diversity of the yeast could have been due to several factors: time of collection, demographics of Jasper Ridge, low variety of pollinators, and sugar concentration of the nectar. The results of this study serve as a necessary first step for a recently started research project on ecological interactions between plants, pollinators, and nectar-living yeast. More generally, this research studies the use of the nectar-living yeast community as a natural microcosm for addressing basic questions about the role of dispersal and competitive and facilitative interactions in ecological succession.

Kyauk, C.; Belisle, M.; Fukami, T.

2009-12-01

36

Identification and analysis of yeast nucleosomal histone acetyltransferase complexes.  

PubMed

Many studies have linked acetylation of lysine residues on the amino-terminal tails of the core histones to transcriptional activity of cellular chromatin. New insights into this field were gained on the identification of the first nuclear, type A histone acetyltransferase (HAT). The yeast transcriptional adaptor protein Gcn5 was identified as a nuclear HAT and thus provided a direct link between pathways of transcriptional activation and histone acetylation. However, while recombinant Gcn5 can efficiently acetylate free histone H3 and, to a lesser extent, H4 it is unable to acetylate nucleosomal histones. It is therefore very likely that additional proteins are required for Gcn5-mediated acetylation of chromosomal histones. We have recently shown that Gcn5 is the catalytic subunit of two high-molecular-weight histone acetyltransferase complexes in yeast. In addition to the Gcn5-containing ADA and SAGA HAT complexes we have identified two other HAT complexes in yeast. These are called NuA3 and NuA4 for their predominant specificity to acetylate histones H3 and H4, respectively. Here we describe the identification and characterization of four native nuclear high-molecular-weight HAT complexes in Saccharomyces cerevisiae. These purified HATs can be used in a variety of functional assays to further address questions of how acetylation has an impact on transcriptional regulation. PMID:9740719

Eberharter, A; John, S; Grant, P A; Utley, R T; Workman, J L

1998-08-01

37

Identification and Characterization of Yeast Isolates from Pharmaceutical Waste Water  

Microsoft Academic Search

Summary In order to develop an efficient an system for waste water pretreatment, the isolation of indigenous population of microorganisms from pharmaceutical waste water was done. We obtained pure cultures of 16 yeast isolates that differed slightly in colony morphology. Ten out of 16 isolates efficiently reduced COD in pharmaceutical waste water. Initial physiological characterization failed to match the 10

Marjeta Recek; Peter Raspor

2002-01-01

38

Comparison of cultural methods for the identification and molecular investigation of yeasts from sourdoughs for Italian sweet baked products  

Microsoft Academic Search

Twenty-five yeast strains isolated from sourdough samples for Panettone, Pandoro and Cornetto brioche manufactured by eight different bakeries in northern Italy were characterised. Classification was performed by the simplified identification method (SIM), Kurtzman and Fell’s identification protocol, the API system from bioMérieux (France) and the MicroLogTM system from Biolog (USA). Genetic diversity was investigated by randomly amplified polymorphic DNA fingerprinting

Roberto Foschino; Silvia Gallina; Christian Andrighetto; Lia Rossetti; Antonietta Galli

2004-01-01

39

Yeast as a model system for identification of metabolic targets of a ‘glucosamine complex’ used as a therapeutic agent of osteoarthritis  

Microsoft Academic Search

This manuscript describes the effect of a glucosamine complex and its different constituents on the metabolism of yeast cells. Indeed, the yeast model biosystem offers important advantages in the understanding of basic cellular and molecular processes. For example, the possibility to differentiate aerobic and anaerobic metabolism allows the measurement of glycolysis and mitochondria importance in the control of energetic metabolism

Monique Dillemans; Thierry Appelboom; Laurence Van Nedervelde

2008-01-01

40

Comparative Performance of the RapID Yeast Plus System and the API 20C AUX Clinical Yeast System  

PubMed Central

The performance of the RapID Yeast Plus System (Innovative Diagnostic Systems, Norcross, Ga.), a 4-h micropanel using single-substrate enzymatic test reactions, was compared with that of the API 20C AUX Clinical Yeast System (bioMerieux Vitek, Hazelwood, Mo.), a 48- to 72-h carbohydrate assimilation panel. Two hundred twenty-five yeasts, yeast-like fungi, and algae, comprising 28 species and including 30 isolates of Cryptococcus neoformans, an important pathogen not tested in appreciable numbers in other comparisons, were tested by both methods. On initial testing, 196 (87.1%) and 215 (95.6%) isolates were correctly identified by the RapID and API systems, respectively. Upon repeat testing, the number of correctly identified isolates increased to 220 (97.8%) for the RapID system and 223 (99.1%) for the API system. Reducing the turbidity of the test inoculum to that of a no. 3 McFarland turbidity standard, which is below that recommended by the manufacturer, resulted in the correct identification of most of the isolates initially misidentified by the RapID system, including 10 of 30 C. neoformans isolates. Concordance between the RapID and API results after repeat testing was 97.3%.

Smith, Michael B.; Dunklee, Daisy; Vu, Hangna; Woods, Gail L.

1999-01-01

41

Actin-dependent mitochondrial motility in mitotic yeast and cell-free systems: identification of a motor activity on the mitochondrial surface  

Microsoft Academic Search

Using fluorescent membrane potential sens- ing dyes to stain budding yeast, mitochondria are re- solved as tubular organeUes aligned in radial arrays that converge at the bud neck. Time-lapse fluorescence mi- croscopy reveals region-specific, directed mitochon- drial movement during polarized yeast cell growth and mitotic cell division. Mitochondria in the central region of the mother cell move linearly towards the

Viviana R. Simon; Theresa C. Swayne; Liza A. Port

1995-01-01

42

Locally isolated yeasts from Malaysia: identification, phylogenetic study and characterization.  

PubMed

Yeasts are a convenient platform for many applications. They have been widely used as the expression hosts. There is a need to have a new yeast expression system to contribute the molecular cloning demands. Eight yeast isolates were screened from various environment sources and identified through ribosomal DNA (rDNA) Internal Transcribed Spacer (ITS). Full sequence of the rDNA ITS region for each isolate was BLASTed and phylogenetic study was constructed by using MEGA4. Among the isolates, isolate WB from 'ragi' (used to ferment carbohydrates) could be identified as a new species in order Saccharomycetales according to rDNA ITS region, morphology and biochemical tests. Isolate SO (from spoiled orange), RT (rotten tomato) and RG (different type of 'ragi') were identified as Pichia sp. Isolates R1 and R2, S4 and S5 (from the surrounding of a guava tree) were identified as Issatchenkia sp. and Hanseniaspora sp., respectively. Geneticin, 50 µg/mL, was determined to be the antibiotic marker for all isolates excepted for isolates RT and SO which used 500 µg/mL and 100 µg/mL Zeocin, respectively. Intra-extracellular proteins were screened for lipolytic activity at 30°C and 70°C. Thermostable lipase activity was detected in isolates RT and R1 with 0.6 U/mg and 0.1 U/mg, respectively. In conclusion, a new yeast-vector system for isolate WB can be developed by using phleomycin or geneticin as the drugs resistance marker. Moreover, strains RT and R1 can be investigated as a novel source of a thermostable lipase. PMID:22577620

Oslan, Siti Nurbaya; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Raja Abd; Basri, Mahiran; Chor, Adam Leow Thean

2012-05-11

43

Detection and Identification of Wild Yeast Contaminants of the Industrial Fuel Ethanol Fermentation Process  

Microsoft Academic Search

Monitoring for wild yeast contaminants is an essential component of the management of the industrial fuel ethanol manufacturing\\u000a process. Here we describe the isolation and molecular identification of 24 yeast species present in bioethanol distilleries\\u000a in northeast Brazil that use sugar cane juice or cane molasses as feeding substrate. Most of the yeast species could be identified\\u000a readily from their

A. C. M. Basílio; P. R. L. de Araújo; J. O. F. de Morais; E. A. da Silva Filho; M. A. de Morais; D. A. Simões

2008-01-01

44

Identification and assessment of kefir yeast potential for sugar/ethanol-resistance  

PubMed Central

Biochemical and molecular analysis was used for identification of different kefir yeasts species from Brazil, Canada and the United States of America. The sugar/ethanol-resistant activity of the yeasts was evaluated. Saccharomyces cerevisiae and Kluyveromyces marxianus had the highest growth rates, suggesting biotechnological applications possible for these strains.

Miguel, M.G.C.P.; Cardoso, P.G.; Magalhaes-Guedes, K.T.; Schwan, R.F.

2013-01-01

45

Use of denaturing gradient gel electrophoresis for the identification of mixed oral yeasts in human saliva.  

PubMed

A PCR-denaturing gradient gel electrophoresis (DGGE) method was established for the simultaneous presumptive identification of multiple yeast species commonly present in the oral cavity. Published primer sets targeting different regions of the Saccharomyces cerevisiae 26-28S rRNA gene (denoted primer sets N and U) and the 18S rRNA gene (primer set E) were evaluated with ten Candida and four non-Candida yeast species, and twenty Candida albicans isolates. Optimized PCR-DGGE conditions using primer set N were applied to presumptively identify, by band matching, yeasts in the saliva of 25 individuals. Identities were confirmed by DNA sequencing and compared with those using CHROMagar Candida culture. All primer sets yielded detectable DGGE bands for all species tested. Primer set N yielded mainly single bands and could distinguish all species examined, including differentiating Candida dubliniensis from C. albicans. Primer set U was less discriminatory among species but yielded multiple bands that distinguished subspecies groups within C. albicans. Primer set E gave poor yeast discrimination. DGGE analysis identified yeasts in 17 of the 25 saliva samples. Six saliva samples contained two yeast species: three contained C. albicans and three C. dubliniensis. C. dubliniensis was present alone in one saliva sample (total prevalence 16?%). CHROMagar culture detected yeasts in 16 of the yeast-containing saliva samples and did not enable identification of 7 yeast species identified by DGGE. In conclusion, DGGE identification of oral yeast species with primer set N is a relatively fast and reliable method for the simultaneous presumptive identification of mixed yeasts in oral saliva samples. PMID:23065546

Weerasekera, Manjula M; Sissons, Chris H; Wong, Lisa; Anderson, Sally; Holmes, Ann R; Cannon, Richard D

2012-10-11

46

Author Identification Systems  

ERIC Educational Resources Information Center

|Many efforts are currently underway to disambiguate author names and assign unique identification numbers so that publications by a given scholar can be reliably grouped together. This paper reviews a number of operational and in-development services. Some systems like ResearcherId.Com depend on self-registration and self-identification of a…

Wagner, A. Ben

2009-01-01

47

Comparative evaluation of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry systems for identification of yeasts of medical importance.  

PubMed

We report the first comparative evaluation between the Bruker Biotyper MS (BMS) and the Vitek MS (VMS) for the identification of yeasts. The rate of correct identifications at the species level was comparable using the commercial databases (89.8% versus 84.3%; P = 0.712), but higher for BMS using an in-house-extended database (100% versus 84.3%; P = 0.245). Importantly, the rate of misidentification was significantly higher for VMS (1% versus 12.1%; P < 0.0001), including the rate of major errors (0% versus 4.5%; P = 0.0036). PMID:23678071

Mancini, Nicasio; De Carolis, Elena; Infurnari, Laura; Vella, Antonietta; Clementi, Nicola; Vaccaro, Luisa; Ruggeri, Alberto; Posteraro, Brunella; Burioni, Roberto; Clementi, Massimo; Sanguinetti, Maurizio

2013-05-15

48

Identification of Pathogenic Rare Yeast Species in Clinical Samples: Comparison between Phenotypical and Molecular Methods?  

PubMed Central

Species identification using both phenotypic and molecular methods and antifungal susceptibility tests was carried out with 60 uncommon clinical yeasts. Our data show that phenotypic methods were insufficient for correct identification (only 25%) and that most of the wrongly identified strains showed a resistant antifungal profile.

Cendejas-Bueno, Emilio; Gomez-Lopez, Alicia; Mellado, Emilia; Rodriguez-Tudela, Juan L.; Cuenca-Estrella, Manuel

2010-01-01

49

Performance of matrix-assisted laser desorption-time of flight mass spectrometry for identification of clinical yeast isolates.  

PubMed

Accurate and fast yeast identification is important when treating patients with invasive fungal disease as susceptibility to antifungal agents is highly species related. Matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF-MS) provides a powerful tool with a clear potential to improve current diagnostic practice. Two MALDI-TOF-MS-systems (BioTyper/Bruker and Saramis/AXIMA) were evaluated using: (i) A collection of 102 archived, well characterised yeast isolates representing 14 different species and (ii) Prospectively collected isolates obtained from clinical samples at two participating laboratories. Of the 102 archived isolates, 81 (79%) and 92 (90%) were correctly identified by Saramis/AXIMA and BioTyper/Bruker respectively. Saramis/AXIMA was unable to separate Candida albicans, C. africana and C. dubliniensis in 13 of 32 isolates. After manual interpretation of the mass spectra output, all 13 isolates were correctly identified, resulting in an overall identification performance of 92%. No misidentifications occurred with the two systems. Of the routine isolates one laboratory identified 99/99 (100%) and 90/99 (91%) to species level by Saramis/Axima and conventional identification, respectively, whereas the other laboratory identified 83/98 (85%) to species level by both BioTyper/Bruker and conventional identification. Both MALDI-TOF-MS systems are fast, have built-in databases that cover the majority of clinically relevant Candida species, and have an accuracy that outperforms our conventional identification systems. PMID:22924975

Rosenvinge, Flemming S; Dzajic, Esad; Knudsen, Elisa; Malig, Sanne; Andersen, Line B; Løvig, Annette; Arendrup, Maiken C; Jensen, Thøger G; Gahrn-Hansen, Bente; Kemp, Michael

2012-08-26

50

Yeasts and yeast-like fungi associated with tree bark: diversity and identification of yeasts producing extracellular endoxylanases.  

PubMed

A total of 239 yeast strains was isolated from 52 tree bark samples of the Medaram and Srisailam forest areas of Andhra Pradesh, India. Based on analysis of D1/D2 domain sequence of 26S rRNA gene, 114 strains were identified as ascomycetous; 107 strains were identified as basidiomycetous yeasts; and 18 strains were identified as yeast-like fungi. Among the ascomycetous yeasts, 51% were identified as members of the genus Pichia, and the remaining 49% included species belonging to the genera Clavispora, Debaryomyces, Kluyveromyces, Hanseniaspora, Issatchenkia, Lodderomyces, Kodamaea, Metschnikowia, and Torulaspora. The predominant genera in the basidiomycetous yeasts were Cryptococcus (48.6%), Rhodotorula (29%), and Rhodosporidium (12.1%). The yeast-like fungi were represented by Aureobasidium pullulans (6.7%) and Lecythophora hoffmanii (0.8%). Of the 239 yeast strains tested for Xylanase, only five strains of Aureobasidium sp. produced xylanase on xylan-agar medium. Matrix-assisted laser desorption ionization-time of flight analysis and N-terminal amino-acid sequence of the xylanase of isolate YS67 showed high similarity with endo-1-4-beta-xylanase (EC 3.2.1.8) of Aureobasidium pullulans var. melanigenum. PMID:18219522

Bhadra, Bhaskar; Rao, R Sreenivas; Singh, Pavan K; Sarkar, Partha K; Shivaji, Sisinthy

2008-01-25

51

Routine Identification of Yeasts with the Aid of Molybdate-Agar Medium  

PubMed Central

A large number of yeasts, including a variety of species other than Candida albicans, were isolated from clinical specimens. C. tropicalis and Torulopsis glabrata were each found one-third as frequently as C. albicans. A schema is presented which made possible, by simple procedures, the identification of the great majority of the isolated yeasts. Preliminary isolation and differentiation was aided by the use of molybdate-agar medium. The use of the schema by diagnostic bacteriological laboratories is discussed.

Bump, Charles M.; Kunz, Lawrence J.

1968-01-01

52

Detection of anabolic steroid abuse using a yeast transactivation system.  

PubMed

The classical analytical method for detection of anabolic steroid abuse is gas chromatography followed by mass spectrometry (GC/MS). However, even molecules with a chemical structure typical for this class of substances, are sometimes not identified in routine screening by GC/MS when their precise chemical structure is still unknown. A supplementary approach to identify anabolic steroid abuse could be a structure-independent identification of anabolic steroids based on their biological activity. To test the suitability of such a system, we have analyzed the yeast androgen receptor (AR) reporter gene system to identify anabolic steroids in human urine samples. Analysis of different anabolic steroids dissolved in buffer demonstrated that the yeast reporter gene system is able to detect a variety of different anabolic steroids and their metabolites with high specificity, including the so-called 'designer steroid' tetrahydrogestrinone. In contrast, other non-androgenic steroids, like glucocordicoids, progestins, mineralocordicoids and estrogens had a low potency to stimulate transactivation. To test whether the system would also allow the detection of androgens in urine, experiments with spiked urine samples were performed. The androgen reporter gene in yeast responds very sensitive to 5alpha-dihydrotestosterone (DHT), even at high urine concentrations. To examine whether the test system would also be able to detect anabolic steroids in the urine of anabolic steroid abusers, anonymous urine samples previously characterized by GCMS were analyzed with the reporter gene assay. Even when the concentration of the anabolic metabolites was comparatively low in some positive samples it was possible to identify the majority of positive samples by their biological activity. In conclusion, our results demonstrate that the yeast reporter gene system detects anabolic steroids and corresponding metabolites with high sensitivity even in urine of anabolic steroid abusing athletes. Therefore we believe that this system can be developed towards a powerful (pre) screening tool for the established doping tests. The system is easy to handle, robust, cost-efficient and needs no high-tech equipment. But most importantly, a biological test system does not require knowledge of the chemical structure of androgenic substances and therefore suitable to detect previously unidentified substances, especially those of the class of so-called designer steroids. PMID:18550137

Zierau, Oliver; Lehmann, Sylvi; Vollmer, Günter; Schänzer, Willhelm; Diel, Patrick

2008-05-04

53

Rapid and Reliable Identification of Food-Borne Yeasts by Fourier-Transform Infrared Spectroscopy  

PubMed Central

Computer-based Fourier-transform infrared spectroscopy (FT-IR) was used to identify food-borne, predominantly fermentative yeasts. Dried yeast suspensions provided the films suitable for FT-IR measurement. Informative windows in the spectrum were selected and combined to achieve optimal results. A reference spectrum library was assembled, based on 332 defined yeast strains from international yeast collections and our own isolates. All strains were identified with conventional methods using physiological and morphological characteristics. In order to assess identification quality, another 722 unknown yeast isolates not included in the reference spectrum library were identified both by classical methods and by comparison of their FT-IR spectra with those of the reference spectrum library. Ninety-seven and one-half percent of these isolates were identified correctly by FT-IR. Easy handling, rapid identification within 24 h when starting from a single colony, and a high differentiation capacity thus render FT-IR technology clearly superior to other routine methods for the identification of yeasts.

Kummerle, Michael; Scherer, Siegfried; Seiler, Herbert

1998-01-01

54

Use of molecular methods for the identification of yeast associated with table olives.  

PubMed

A molecular approach is used for the identification of yeast isolated from table olives. Our results validate those obtained in the past by the classical biochemical methodology. Yeast were isolated from both aerobically and anaerobically processed black table olives and also from canned seasoned green table olives. Molecular identification methodology used included restriction pattern analysis of both PCR-amplified 5.8S rRNA gene and internal transcribed spacers ITS(1) and ITS(2). For some species, sequence analysis of the 26S rRNA gene was necessary. These techniques allowed the identification of three yeast species (Issatchenkia occidentalis, Geotrichum candidum and Hanseniaspora guilliermondii) which had not been described previously in table olives. Saccharomyces cerevisiae and Candida boidinii were the most frequent species in green seasoned olives and processed black olives, respectively. The molecular study of total DNA variability among the S. cerevisiae strains isolated indicates a quite heterogeneous population, with at least four different restriction patterns. PMID:16943084

Arroyo-López, F N; Durán-Quintana, M C; Ruiz-Barba, J L; Querol, A; Garrido-Fernández, A

2006-04-18

55

Identification of CCR4 and other essential thyroid hormone receptor co-activators by modified yeast synthetic genetic array analysis  

PubMed Central

Identification of thyroid hormone receptor (TR) co-regulators has enhanced our understanding of thyroid hormone (TH) action. However, it is likely that many other co-regulators remained unidentified, and unbiased methods are required to discover these proteins. We have previously demonstrated that the yeast Saccharomyces cerevisiae is an excellent system in which to study TR action, and that defined TR signaling complexes in a eukaryotic background devoid of complicating influences of mammalian cell co-regulators can be constructed and analyzed for endogenous yeast genes, many of which are conserved in mammals. Here, a modified synthetic genetic array analysis was performed by crossing a yeast strain that expressed TR?1 and the co-activator GRIP1/SRC2 with 384 yeast strains bearing deletions of known genes. Eight genes essential for TH action were isolated, of which 4 are conserved in mammals. Examination of one, the yeast CCR4 and its human homolog CCR4/NOT6 (hCCR4), confirmed that (i) transfected CCR4 potentiates a TH response in cultured cells more efficiently than established TR co-activators and (ii) knockdown of CCR4 expression strongly inhibited a TH response (>80%). TH treatment promoted rapid and sustained hCCR4 recruitment to the TH-responsive deiodinase 1 promoter and TR co-localizes with hCCR4 in the nucleus and interacts with hCCR4 in 2-hybrid and pull-down assays. These findings indicate that a modified yeast synthetic genetic array strategy is a feasible method for unbiased identification of conserved genes essential for TR and other nuclear receptor hormone functions in mammals.

Govindan, Manjapra; Meng, Xianwang; Denis, Clyde L.; Webb, Paul; Baxter, John D.; Walfish, Paul G.

2009-01-01

56

A systems-level approach for metabolic engineering of yeast cell factories.  

PubMed

The generation of novel yeast cell factories for production of high-value industrial biotechnological products relies on three metabolic engineering principles: design, construction, and analysis. In the last two decades, strong efforts have been put on developing faster and more efficient strategies and/or technologies for each one of these principles. For design and construction, three major strategies are described in this review: (1) rational metabolic engineering; (2) inverse metabolic engineering; and (3) evolutionary strategies. Independent of the selected strategy, the process of designing yeast strains involves five decision points: (1) choice of product, (2) choice of chassis, (3) identification of target genes, (4) regulating the expression level of target genes, and (5) network balancing of the target genes. At the construction level, several molecular biology tools have been developed through the concept of synthetic biology and applied for the generation of novel, engineered yeast strains. For comprehensive and quantitative analysis of constructed strains, systems biology tools are commonly used and using a multi-omics approach. Key information about the biological system can be revealed, for example, identification of genetic regulatory mechanisms and competitive pathways, thereby assisting the in silico design of metabolic engineering strategies for improving strain performance. Examples on how systems and synthetic biology brought yeast metabolic engineering closer to industrial biotechnology are described in this review, and these examples should demonstrate the potential of a systems-level approach for fast and efficient generation of yeast cell factories. PMID:22188344

Kim, Il-Kwon; Roldão, António; Siewers, Verena; Nielsen, Jens

2012-01-10

57

Immobilized yeast cell systems for continuous fermentation applications  

Microsoft Academic Search

In several yeast-related industries, continuous fermentation systems offer important economical advantages in comparison with traditional systems. Fermentation rates are significantly improved, especially when continuous fermentation is combined with cell immobilization techniques to increase the yeast concentration in the fermentor. Hence the technique holds a great promise for the efficient production of fermented beverages, such as beer, wine and cider as

Pieter J. Verbelen; David P. De Schutter; Filip Delvaux; Kevin J. Verstrepen; Freddy R. Delvaux

2006-01-01

58

Yeast microflora isolated from brazilian cassava roots: taxonomical classification based on molecular identification.  

PubMed

A rapid molecular identification technique was applied on microbial microflora isolated from Brazilian cassava roots given a yeast profile presented in the samples analyzed. A total of 24 strain isolated from cassava were initially grouped and identified in five groups using restriction-fragment length polymorphism (RFLPs) of 5.8S-ITS rDNA region. Sequencing analysis of the domains D1 and D2 of the 26S rRNA gene or 5.8S rRNA-ITS region were used to identify different groups of yeasts. Representative colonies of yeasts of each group were isolated and identified as Debaromyces hansenii, Kodamaea ohmeri, Candida glabrata, C. haemulonii, and Pichia gullhermondii. It is hoped that these results will contribute toward selecting yeast from this microflora capable to degrade cassava starch in the near future. PMID:19924478

Ferreira, Nelson; Belloch, Carmela; Querol, Amparo; Manzanares, Paloma; Vallez, Salvador; Santos, Alberdan

2009-11-19

59

Identification of Medically Important Yeast Species by Sequence Analysis of the Internal Transcribed Spacer Regions  

PubMed Central

Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as Pichia, Rhodotorula, Trichosporon, and Saccharomyces spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (Rhodotorula glutinis BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods.

Leaw, Shiang Ning; Chang, Hsien Chang; Sun, Hsiao Fang; Barton, Richard; Bouchara, Jean-Philippe; Chang, Tsung Chain

2006-01-01

60

Yeast pyruvate carboxylase: identification of two genes encoding isoenzymes.  

PubMed

In Saccharomyces cerevisiae, pyruvate carboxylase [EC 6.4.1.1] has an important anaplerotic role in the production of oxaloacetate from pyruvate. We report here the existence of two pyruvate carboxylase isozymes, which are encoded by separate genes within the yeast genome. Null mutants were constructed by one step gene disruption of the characterised PYC gene in the yeast genome. The mutants were found to have 10-20% residual pyruvate carboxylase activity, which was attributable to a protein of identical size and immunogenically related to pyruvate carboxylase. Immunocytochemical labelling studies on ultrathin sections of embedded whole cells from the null mutants showed the isozyme to be located exclusively in the cytoplasm. We have mapped the genes encoding both enzymes and shown the previously characterised gene, designated PYC1, to be on chromosome VII whilst PYC2 is on chromosome II. PMID:2039506

Walker, M E; Val, D L; Rohde, M; Devenish, R J; Wallace, J C

1991-05-15

61

Isolation and identification of killer yeast from fermented vegetables  

Microsoft Academic Search

Nine samples of fermented vegetables (pak-sein, bamboo shoot, sator and cabbage) taken from Pattani and Narathiwat provinces, were examined. The fermented liquid from these samples had pH and NaCl concentration ranges between 3.3-3.9 and 2.4-8.2%, respectively. Eighty two yeast isolates were collected for the killer activity screening against five sensitive reference strains, Candida tropicalis TISTR 5045, Hansenula anomala TISTR 5113,

Sunee Waema; Jaruwan Maneesri; Payap Masniyom

2009-01-01

62

Systematic identification of yeast proteins extracted into model wine during aging on the yeast lees.  

PubMed

Total protein and protein-associated mannan concentrations were measured, and individual proteins were identified during extraction into model wines over 9 months of aging on the yeast lees following completion of fermentations by seven wine strains of Saccharomyces cerevisiae. In aged wines, protein-associated mannan increased about 6-fold (+/-66%), while total protein only increased 2-fold (+/-20%), which resulted in a significantly greater protein-associated mannan/total protein ratio for three strains. A total of 219 proteins were identified among all wine samples taken over the entire time course. Of the 17 "long-lived" proteins detected in all 9 month samples, 13 were cell wall mannoproteins, and four were glycolytic enzymes. Most cytosolic proteins were not detected after 6 months. Native mannosylated yeast invertase was assayed for binding to wine tannin and was found to have a 10-fold lower affinity than nonglycosylated bovine serum albumin. Enrichment of mannoproteins in the aged model wines implies greater solution stability than other yeast proteins and the possibility that their contributions to wine quality may persist long after bottling. PMID:20108898

Rowe, Jeffrey D; Harbertson, James F; Osborne, James P; Freitag, Michael; Lim, Juyun; Bakalinsky, Alan T

2010-02-24

63

Application of the yeast two-hybrid system in molecular gerontology  

Microsoft Academic Search

Most – if not all – proteins are bound to interact with other proteins to exert their function, and thus the identification\\u000a of the interaction partners of a protein is vital in proteomics. The yeast two-hybrid system is a popular and effective tool\\u000a for studyingprotein–protein interactions. Although the advantages of the system are manifold, it also has certain drawbacks\\u000a and

Charlotte Rohde Knudsen; Mandana Jadidi; Irene Friis; Francisco Mansilla

2002-01-01

64

[Presumptive identification of Candida spp. and other clinically important yeasts: usefulness of Brilliance Candida Agar].  

PubMed

Fungal infections caused by yeasts have increased during the last decades and invasive forms represent a serious problem for human health. Candida albicans is the species most frequently isolated from clinical samples. However, other emerging yeast pathogens are increasingly responsible for mycotic infections, and some of them are resistant to some antifungal drugs. Consequently, it is necessary to have methods that can provide a rapid presumptive identification at species level. Numerous chromogenic agar media have been shown to be of value as diagnostic tools. We have compared a chromogenic medium, Brilliance Candida Agar, with CHROMagar Candida, the chromogenic medium most used in our country. A multicentre study was conducted in 16 Hospitals belonging to the Mycology Net of Buenos Aires City Government. A total of 240 yeast isolates were included in this research. The new chromogenic agar showed results very similar to those obtained with CHROMagar Candida. PMID:20346288

Alfonso, Claudia; López, Mónica; Arechavala, Alicia; Perrone, María Del Carmen; Guelfand, Liliana; Bianchi, Mario

2010-03-24

65

CHROMagar Candida medium as a practical tool for the differentiation and presumptive identification of yeast species isolated from salads  

Microsoft Academic Search

CHROMagar Candida medium was used to study the diversity of yeast biota of salad samples, and to presumptively identify the isolates. This medium was originally developed for the selective isolation and presumptive identification of some clinically important yeast species such as Candida albicans, Candida tropicalis, Candida krusei, and Candida glabrata on the basis of differences in colour and surface of

Judit Tornai-Lehoczki; Gábor Péter; Dénes Dlauchy

2003-01-01

66

Identification of four alcohol oxidases from methylotrophic yeasts.  

PubMed

Three yeast strains capable of utilizing methanol as sole carbon and energy source were isolated. Two were classified as Candida boidinii, while the third belonged in the genus Pichia. From these three strains, four alcohol oxidases genes were identified and the sequences of the coding regions were determined: one from each Candida boidinii (aox0673 and aox0680) and two from Pichia sp. 159 (aoxA and aoxB). Methanol induces both alcohol oxidases in Pichia sp. 159: the levels of aoxA and aoxB mRNA reach about 100% and 300%, respectively, of that of his4 mRNA. aoxA, but not aoxB, is expressed at a low level in the presence of glucose. The newly described alcohol oxidases have proper dinucleotide binding sites and PTS1-like C-terminal tripeptides, identified as important elements for peroxisomal localization. PMID:16032762

Szamecz, Béla; Urbán, Gabriella; Rubiera, Roger; Kucsera, Judit; Dorgai, László

2005-06-01

67

System identification of nonlinear resonant systems  

Microsoft Academic Search

This dissertation addresses the problem of thermo-acoustic combustion instability modelling using nonlinear system identification. Specifically we are interested in the identification of closed loop limit cycling systems composed of a linear transfer function with a static nonlinearity in feedback. To begin we address the feasibility of the identification task, in terms of both data quality and dynamical capabilities of the

Wayne John Dunstan

2003-01-01

68

Identification of the Proteins of the Yeast U1 Small Nuclear Ribonucleoprotein Complex by Mass Spectrometry  

Microsoft Academic Search

Here we report the rapid identification of the proteins of the spliceosomal U1 small nuclear ribonucleoprotein (snRNP) from the yeast Saccharomyces cerevisiae by searching mass spectrometric data in genomic sequence databases. The U1 snRNP, containing a histidine-tagged 70K protein, was isolated from cell extracts by anti m3G-cap immunoaffinity and subsequent nickel nitrilotriacetic acid chromatography. A U1 snRNP fraction containing 20

Gitte Neubauer; Alexander Gottschalk; Patrizia Fabrizio; Bertrand Seraphin; Reinhard Luhrmann; Matthias Mann

1997-01-01

69

Fourier-Transform Infrared Microspectroscopy, a Novel and Rapid Tool for Identification of Yeasts  

PubMed Central

Fourier-transform infrared (FT-IR) microspectroscopy was used in this study to identify yeasts. Cells were grown to microcolonies of 70 to 250 ?m in diameter and transferred from the agar plate by replica stamping to an IR-transparent ZnSe carrier. IR spectra of the replicas on the carrier were recorded using an IR microscope coupled to an IR spectrometer, and identification was performed by comparison to reference spectra. The method was tested by using small model libraries comprising reference spectra of 45 strains from 9 genera and 13 species, recorded with both FT-IR microspectroscopy and FT-IR macrospectroscopy. The results show that identification by FT-IR microspectroscopy is equivalent to that achieved by FT-IR macrospectroscopy but the time-consuming isolation of the organisms prior to identification is not necessary. Therefore, this method also provides a rapid tool to analyze mixed populations. Furthermore, identification of 21 Debaryomyces hansenii and 9 Saccharomyces cerevisiae strains resulted in 92% correct identification at the strain level for S. cerevisiae and 91% for D. hansenii, which demonstrates that the resolution power of FT-IR microspectroscopy may also be used for yeast typing at the strain level.

Wenning, Mareike; Seiler, Herbert; Scherer, Siegfried

2002-01-01

70

Yeast Species Associated with Orange Juice: Evaluation of Different Identification Methods  

Microsoft Academic Search

Five different methods were used to identify yeast isolates from a variety of citrus juice sources. A total of 99 strains, including reference strains, were identified using a partial sequence of the 26S rRNA gene, restriction pattern analysis of the internal transcribed spacer region (5.8S-ITS), classical methodology, the RapID Yeast Plus system, and API 20C AUX. Twenty-three different species were

Covadonga R. Arias; Jacqueline K. Burns; Lorrie M. Friedrich; Renee M. Goodrich; Mickey E. Parish

2002-01-01

71

International Specialised Symposium on Yeasts: ISSY25. Systems Biology of Yeasts from Models to Applications. Held in Hanasaari, Espoo, Finland on June 18-21, 2006.  

National Technical Information Service (NTIS)

The 25th International Specialized Symposium on Yeasts, ISSY25, dedicated to 'Yeast systems biology - from models to applications' is a symposium in a series organized by the members of the International Commission on Yeasts (ICY), an IUMS organization. T...

A. Kuokka M. Penttila

2006-01-01

72

Polyphasic identification of yeasts isolated from bark of cork oak during the manufacturing process of cork stoppers.  

PubMed

A two-step protocol was used for the identification of 52 yeasts isolated from bark of cork oak at initial stages of the manufacturing process of cork stoppers. The first step in the identification was the separation of the isolates into groups by their physiological properties and RFLPs of the ITS-5.8S rRNA gene. The second step was the sequencing of the D1/D2 domains of the 26S rRNA gene of selected isolates representing the different groups. The results revealed a predominance of basidiomycetous yeasts (11 species), while only two species represented the ascomycetous yeasts. Among the basidiomycetous yeasts, members representing the species Rhodosporidium kratochvilovae and Rhodotorula nothofagi, that have been previously isolated from plant material, were the most abundant. Yeasts pertaining to the species Debaryomyces hansenii var. fabryii, Rhodotorula mucilaginosa and Trichosporon mucoides were isolated in small numbers. PMID:15093778

Villa-Carvajal, Mercedes; Coque, Juan José R; Alvarez-Rodríguez, María Luísa; Uruburu, Federico; Belloch, Carmela

2004-05-01

73

Derivation, identification and validation of a computational model of a novel synthetic regulatory network in yeast.  

PubMed

Systems biology aims at building computational models of biological pathways in order to study in silico their behaviour and to verify biological hypotheses. Modelling can become a new powerful method in molecular biology, if correctly used. Here we present step-by-step the derivation and identification of the dynamical model of a biological pathway using a novel synthetic network recently constructed in the yeast Saccharomyces cerevisiae for In-vivo Reverse-Engineering and Modelling Assessment. This network consists of five genes regulating each other transcription. Moreover, it includes one protein-protein interaction, and its genes can be switched on by addition of galactose to the medium. In order to describe the network dynamics, we adopted a deterministic modelling approach based on non-linear differential equations. We show how, through iteration between experiments and modelling, it is possible to derive a semi-quantitative prediction of network behaviour and to better understand the biology of the pathway of interest. PMID:20549211

Marucci, Lucia; Santini, Stefania; di Bernardo, Mario; di Bernardo, Diego

2010-06-12

74

Improved Taxiway Exit Identification System.  

National Technical Information Service (NTIS)

A prototype enhanced visual taxiway identification system, consisting of a segment of green lights imbedded within the conventional runway centerline lighting system, was developed and tested at the Federal Aviation Administration (FAA) Technical Center. ...

E. Katz T. Paprocki

1994-01-01

75

Non-targeted Identification of Prions and Amyloid-forming Proteins from Yeast and Mammalian Cells.  

PubMed

The formation of amyloid aggregates is implicated both as a primary cause of cellular degeneration in multiple human diseases and as a functional mechanism for providing extraordinary strength to large protein assemblies. The recent identification and characterization of several amyloid proteins from diverse organisms argues that the amyloid phenomenon is widespread in nature. Yet identifying new amyloid-forming proteins usually requires a priori knowledge of specific candidates. Amyloid fibers can resist heat, pressure, proteolysis, and denaturation by reagents such as urea or sodium dodecyl sulfate. Here we show that these properties can be exploited to identify naturally occurring amyloid-forming proteins directly from cell lysates. This proteomic-based approach utilizes a novel purification of amyloid aggregates followed by identification by mass spectrometry without the requirement for special genetic tools. We have validated this technique by blind identification of three amyloid-based yeast prions from laboratory and wild strains and disease-related polyglutamine proteins expressed in both yeast and mammalian cells. Furthermore, we found that polyglutamine aggregates specifically recruit some stress granule components, revealing a possible mechanism of toxicity. Therefore, core amyloid-forming proteins as well as strongly associated proteins can be identified directly from cells of diverse origin. PMID:23926098

Kryndushkin, Dmitry; Pripuzova, Natalia; Burnett, Barrington G; Shewmaker, Frank

2013-08-07

76

A powerful yeast-based screening assay for the identification of inhibitors of indoleamine 2,3-dioxygenase.  

PubMed

Activation of the enzyme indoleamine 2,3-dioxygenase 1 (IDO1) underlies the course of several human pathological conditions and, to date, no efficacious therapeutic IDO inhibitors are available. We proposed to develop a robust screening system based on the use of yeast cells to identify new lead compounds for the pharmacological inhibition of IDO-the BLOCKADE platform. Yeast combines the advantages of a relevant surrogate model for eukaryotic cell processes with the amenity to miniaturization and automation. We brought added value to the system by increasing the stringency of our assay, as the BLOCKADE strain was not deleted for any efflux pump, thus creating additional challenges for test compounds to be identified as hits. Screening of a library of 50 080 small molecules led to the identification of 101 potential IDO inhibitors, a low hit rate of 0.2%, reflecting the stringent assay conditions imposed. Most important, secondary pharmacology assays in mammalian cells confirmed activity for 76% of the hits, whereas hepatotoxicity testing indicated that 87% of them displayed a safe profile. The high predictivity rates obtained using the BLOCKADE platform clearly validate our system as a powerful tool for drug discovery. PMID:22791376

Cerejo, Marta; Andrade, Gonçalo; Roca, Christophe; Sousa, José; Rodrigues, Cátia; Pinheiro, Ricardo; Chatterjee, Sukalyan; Vieira, Helena; Calado, Patrícia

2012-07-12

77

Rapid Identification of Yeasts in Positive Blood Cultures by a Multiplex PCR Method  

PubMed Central

Yeasts are emerging as important etiological agents of nosocomial bloodstream infections. A multiplex PCR method was developed to rapidly identify clinically important yeasts that cause fungemia. The method amplified the internal transcribed spacer 1 (ITS1) region between the 18S and 5.8S rRNA genes and a specific DNA fragment within the ITS2 region of Candida albicans. With this method, C. albicans produced two amplicons, whereas other species produced only one. Through sequence analysis, the precise lengths of the PCR products were found to be as follows: C. glabrata (482 or 483 bp), C. guilliermondii (248 bp), C. parapsilosis (229 bp), C. albicans (218 or 219 and 110 bp), C. tropicalis (218 bp), Cryptococcus neoformans (201 bp), and C. krusei (182 bp). The PCR products could be effectively separated by disk polyacrylamide gel electrophoresis. The method was used to test 249 positive blood cultures (255 isolates), from which the following species (strain number) were isolated: C. albicans (128), C. tropicalis (51), C. glabrata (28), C. parapsilosis (23), C. neoformans (9), C. krusei (5), C. guilliermondii (3), and other, minor species (8). The test sensitivity of the method was 96.9% (247 of 255 isolates). The eight minor species were either misidentified (one strain) or not identified (seven strains). From the time at which a positive bottle was found, the multiplex PCR could be completed within 8 h; the present method is simpler than any previously reported molecular method for the identification of blood yeasts.

Chang, Hsein Chang; Leaw, Shiang Ning; Huang, Ay Huey; Wu, Tsu Lan; Chang, Tsung Chain

2001-01-01

78

An autonomous system for identifying and governing a cell's state in yeast  

NASA Astrophysics Data System (ADS)

We present an approach for an autonomous system that detects a particular state of interest in a living cell and can govern cell fate accordingly. Cell states could be better identified by the expression pattern of several genes than of a single one. Therefore, autonomous identification can be achieved by a system that measures the expression of these several genes and integrates their activities into a single output. We have constructed a system that diagnoses a unique state in yeast, in which two independent pathways, methionine anabolism and galactose catabolism, are active. Our design is based on modifications of the yeast two-hybrid system. We show that cells could autonomously report on their state, identify the state of interest, and inhibit their growth accordingly. The system's sensitivity is adjustable to detect states with limited dynamic range of inputs. The system's output depends only on the activity of input pathways, not on their identity; hence it is straightforward to diagnose any pair of inputs. A simple model is presented that accounts for the data and provides predictive power. We propose that such systems could handle real-life states-of-interest such as identification of aberrant versus normal growth.

Nissim, Lior; Beatus, Tsevi; Bar-Ziv, Roy

2007-09-01

79

Efficient Identification of Clinically Relevant Candida Yeast Species by Use of an Assay Combining Panfungal Loop-Mediated Isothermal DNA Amplification with Hybridization to Species-Specific Oligonucleotide Probes?  

PubMed Central

The occurrence of invasive mycoses has progressively increased in recent years. Yeasts of the genus Candida remain the leading etiologic agents of those infections. Early identification of opportunistic yeasts may contribute significantly to improved disease management and the selection of appropriate antifungal therapy. We developed a rapid and reliable molecular identification system for clinically relevant yeasts that makes use of nonspecific primers to amplify a region of the 26S rRNA gene, followed by reverse hybridization of the digoxigenin-labeled products to a panel of species-specific oligonucleotide probes arranged on a nylon membrane macroarray format. DNA amplification was achieved by the recently developed loop-mediated isothermal DNA amplification technology, a promising option for the development of improved laboratory diagnostic kits. The newly developed method was successful in distinguishing among the major clinically relevant yeasts associated with bloodstream infections by using simple, rapid, and cost-effective procedures and equipment.

Inacio, Joao; Flores, Orfeu; Spencer-Martins, Isabel

2008-01-01

80

Systems biology of lipid metabolism: From yeast to human  

Microsoft Academic Search

Lipid metabolism is highly relevant as it plays a central role in a number of human diseases. Due to the highly interactive structure of lipid metabolism and its regulation, it is necessary to apply a holistic approach, and systems biology is therefore well suited for integrated analysis of lipid metabolism. In this paper it is demonstrated that the yeast Saccharomyces

Jens Nielsen

2009-01-01

81

Identification and characterization of yeasts causing chalk mould defects on par-baked bread.  

PubMed

Pichia anomala, Hyphopichia burtonii and Saccharomycopsis fibuligera are spoilage yeasts causing chalk mould defects on par-baked breads packaged under modified atmosphere. The first objective of this study was to identify yeasts isolated from spoiled par-baked breads by means of a RAPD protocol and to determine the dominant spoilers amongst identified strains. The second objective was to determine the effects of water activity (a(w)) and pH value on the growth rates and lag phase durations of P. anomala, H. burtonii and S. fibuligera. 95% of the yeasts tested were identified as P. anomala and 5% as S. fibuligera, H. burtonii was not detected. In order to investigate the effect of a(w) and pH the growth of the three yeasts was tested within an a(w) range of 0.88-0.98 and a pH range of 2.8-8.0. P. anomala was able to grow from pH 2.8 to 8 without a clear optimum. S. fibuligera and H. burtonii showed a pH optimum for growth of 5. The optimum water activity for growth was different for the three strains and varied between 0.96 and 0.98. These growth data were further used to develop secondary models that describe the relationship between a(w) and the radial or colony growth rate (g, mm/d) or the lag phase duration (?, d). The identification of the spoilage organisms and a good understanding of the effects of a(w) and pH on the growth behavior is essential for future development of adequate conservation strategies against chalk mould defects. PMID:21569947

Deschuyffeleer, N; Audenaert, K; Samapundo, S; Ameye, S; Eeckhout, M; Devlieghere, F

2011-02-23

82

Mapping the interactions of dengue virus NS1 protein with human liver proteins using a yeast two-hybrid system: identification of C1q as an interacting partner.  

PubMed

Dengue constitutes a global health concern. The clinical manifestation of this disease varies from mild febrile illness to severe hemorrhage and/or fatal hypovolemic shock. Flavivirus nonstructural protein 1 (NS1) is a secreted glycoprotein that is displayed on the surface of infected cells but is absent in viral particles. NS1 accumulates at high levels in the plasma of dengue virus (DENV)-infected patients, and previous reports highlight its involvement in immune evasion, dengue severity, liver dysfunction and pathogenesis. In the present study, we performed a yeast two-hybrid screen to search for DENV2 NS1-interacting partners using a human liver cDNA library. We identified fifty genes, including human complement component 1 (C1q), which was confirmed by coimmunoprecipitation, ELISA and immunofluorescence assays, revealing for the first time the direct binding of this protein to NS1. Furthermore, the majority of the identified genes encode proteins that are secreted into the plasma of patients, and most of these proteins are classified as acute-phase proteins (APPs), such as plasminogen, haptoglobin, hemopexin, ?-2-HS-glycoprotein, retinol binding protein 4, transferrin, and C4. The results presented here confirm the direct interaction of DENV NS1 with a key protein of the complement system and suggest a role for this complement protein in the pathogenesis of DENV infection. PMID:23516407

Silva, Emiliana M; Conde, Jonas N; Allonso, Diego; Nogueira, Mauricio L; Mohana-Borges, Ronaldo

2013-03-14

83

Mapping the Interactions of Dengue Virus NS1 Protein with Human Liver Proteins Using a Yeast Two-Hybrid System: Identification of C1q as an Interacting Partner  

PubMed Central

Dengue constitutes a global health concern. The clinical manifestation of this disease varies from mild febrile illness to severe hemorrhage and/or fatal hypovolemic shock. Flavivirus nonstructural protein 1 (NS1) is a secreted glycoprotein that is displayed on the surface of infected cells but is absent in viral particles. NS1 accumulates at high levels in the plasma of dengue virus (DENV)-infected patients, and previous reports highlight its involvement in immune evasion, dengue severity, liver dysfunction and pathogenesis. In the present study, we performed a yeast two-hybrid screen to search for DENV2 NS1-interacting partners using a human liver cDNA library. We identified fifty genes, including human complement component 1 (C1q), which was confirmed by coimmunoprecipitation, ELISA and immunofluorescence assays, revealing for the first time the direct binding of this protein to NS1. Furthermore, the majority of the identified genes encode proteins that are secreted into the plasma of patients, and most of these proteins are classified as acute-phase proteins (APPs), such as plasminogen, haptoglobin, hemopexin, ?-2-HS-glycoprotein, retinol binding protein 4, transferrin, and C4. The results presented here confirm the direct interaction of DENV NS1 with a key protein of the complement system and suggest a role for this complement protein in the pathogenesis of DENV infection.

Allonso, Diego; Nogueira, Mauricio L.; Mohana-Borges, Ronaldo

2013-01-01

84

Evaluation of four pretreatment procedures for MALDI-TOF MS yeast identification in the routine clinical laboratory.  

PubMed

MALDI-TOF MS-based yeast identification requires a pretreatment step for which four are described in the literature, i.e., direct smear, fast formic acid and two complete formic acid/acetonitrile extractions. In this study we compared the impact of these procedures on the performance of MALDI-TOF MS-based yeast identification of samples from colonies grown on Sabouraud or chromogenic media. A total of 103 yeast isolates recovered from clinical samples were identified in parallel using the four pretreatment procedures. The proportions of both correct identifications (regardless of LogScore values) and of reliable identifications (i.e., correct identifications with a LogScore ?2, as recommended by the manufacturer) obtained with the four techniques were compared. Even if the proportion of correct identifications exceeded 85% independent of the pretreatment procedure, results obtained with complete formic acid/acetonitril extractions of colonies grown on Sabouraud media were significantly superior to those with smear and fast formic acid extraction procedures. If one considers only reliable identifications, then both smear and fast formic acid extraction procedures yielded lower (<40%) correct identification rates than the use of the two complete extraction procedures (>77%) of portions of colonies on both Sabouraud and chromogenic media. The data would indicate that the direct smear and fast formic acid procedures cannot be recommended due to the LogScore values which were continually below those recommended by the manufacturer for biological validation. Thus, complete extraction methods are better suited for MALDI-TOF MS-based yeast identification in the clinical laboratory setting although they are more labor-intensive. PMID:22978312

Cassagne, Carole; Cella, Anne-Laure; Suchon, Pierre; Normand, Anne-Cecile; Ranque, Stephane; Piarroux, Renaud

2012-09-16

85

Combat ID - Combat Identification System.  

National Technical Information Service (NTIS)

This paper will document the development of the Combat Identification (CombatID) System. The CombatID System was designed to create a platform agnostic payload that could be attached to any fielded Unmanned Ground Vehicle (UGV) to assist the Soldier in co...

G. Salgian H. Chiu R. Hadsell X. Zhou Z. Kira

2012-01-01

86

Systems Level Modeling of the Cell Cycle Using Budding Yeast  

PubMed Central

Proteins involved in the regulation of the cell cycle are highly conserved across all eukaryotes, and so a relatively simple eukaryote such as yeast can provide insight into a variety of cell cycle perturbations including those that occur in human cancer. To date, the budding yeast Saccharomyces cerevisiae has provided the largest amount of experimental and modeling data on the progression of the cell cycle, making it a logical choice for in-depth studies of this process. Moreover, the advent of methods for collection of high-throughput genome, transcriptome, and proteome data has provided a means to collect and precisely quantify simultaneous cell cycle gene transcript and protein levels, permitting modeling of the cell cycle on the systems level. With the appropriate mathematical framework and sufficient and accurate data on cell cycle components, it should be possible to create a model of the cell cycle that not only effectively describes its operation, but can also predict responses to perturbations such as variation in protein levels and responses to external stimuli including targeted inhibition by drugs. In this review, we summarize existing data on the yeast cell cycle, proteomics technologies for quantifying cell cycle proteins, and the mathematical frameworks that can integrate this data into representative and effective models. Systems level modeling of the cell cycle will require the integration of high-quality data with the appropriate mathematical framework, which can currently be attained through the combination of dynamic modeling based on proteomics data and using yeast as a model organism.

Ingalls, B.P.; Duncker, B.P.; Kim, D.R.; McConkey, B.J.

2007-01-01

87

System identification for multivariable control  

NASA Astrophysics Data System (ADS)

System identification methods and modern control theory are applied to industrial processes. These processes must often be controlled in order to meet certain requirements with respect to the product quality, safety, energy consumption, and environmental load. Modern control system design methods which take the occurring interaction phenomena and stochastic disturbances into account are used. An accurate dynamic mathematical model of the process, by theoretical modelling and/or by system identification is obtained. The computational aspects of two important types of identifications methods, i.e., stochastic realization and prediction error based parameter estimation are studied. The studied computational aspects are the robustness, the accuracy, and the computational costs of the methods. Theoretical analyses and applications to a multivariable pilot scale process, operating under closed loop conditions are investigated.

Vanzee, G. A.

1981-05-01

88

Direct Identification and Recognition of Yeast Species from Clinical Material by Using Albicans ID and CHROMagar Candida Plates  

Microsoft Academic Search

Two chromogenic media, Albicans ID and CHROMagar Candida agar plates, were compared with a reference medium, Sabouraud-chloramphenicol agar, and standard methods for the identification of yeast species. This study involved 951 clinical specimens. The detection rates for the two chromogenic media for polymicrobialspecimenswere20%higherthanthatfortheSabouraud-chloramphenicolagarplates.Therates of identification ofCandida albicansfor Albicans ID and CHROMagar Candida agar plates were, respectively, 37.0 and 6.0% after

CECILE BAUMGARTNER; ANNE-MARIE FREYDIERE; ANDYVES GILLE

1996-01-01

89

Auxin-inducible protein depletion system in fission yeast  

PubMed Central

Background Inducible inactivation of a protein is a powerful approach for analysis of its function within cells. Fission yeast is a useful model for studying the fundamental mechanisms such as chromosome maintenance and cell cycle. However, previously published strategies for protein-depletion are successful only for some proteins in some specific conditions and still do not achieve efficient depletion to cause acute phenotypes such as immediate cell cycle arrest. The aim of this work was to construct a useful and powerful protein-depletion system in Shizosaccaromyces pombe. Results We constructed an auxin-inducible degron (AID) system, which utilizes auxin-dependent poly-ubiquitination of Aux/IAA proteins by SCFTIR1 in plants, in fission yeast. Although expression of a plant F-box protein, TIR1, decreased Mcm4-aid, a component of the MCM complex essential for DNA replication tagged with Aux/IAA peptide, depletion did not result in an evident growth defect. We successfully improved degradation efficiency of Mcm4-aid by fusion of TIR1 with fission yeast Skp1, a conserved F-box-interacting component of SCF (improved-AID system; i-AID), and the cells showed severe defect in growth. The i-AID system induced degradation of Mcm4-aid in the chromatin-bound MCM complex as well as those in soluble fractions. The i-AID system in conjunction with transcription repression (off-AID system), we achieved more efficient depletion of other proteins including Pol1 and Cdc45, causing early S phase arrest. Conclusion Improvement of the AID system allowed us to construct conditional null mutants of S. pombe. We propose that the off-AID system is the powerful method for in vivo protein-depletion in fission yeast.

2011-01-01

90

Yeast forward and reverse 'n'-hybrid systems  

Microsoft Academic Search

Since its original description almost 10 years ago, the yeast two-hybrid system has been used extensively to identify protein-protein interactions from many different organisms. Simultaneously, a number of 'variations on a theme' based on the original concept have been described. In one set of variations, systems were developed to detect other macromolecular interactions: DNA-protein (one-hybrid), RNA-protein (RNA-based three-hybrid) and small

Marc Vidal; Pierre Legrain

1999-01-01

91

System Identification of Surface Ship Dynamics.  

National Technical Information Service (NTIS)

The feasibility of applying a Newtonian system identification technique to a nonlinear three degree of freedom system of equations describing the steering and maneuvering of a surface ship is investigated. The input to the system identification program is...

T. P. Sargent P. Kaplan

1970-01-01

92

Identification of hybrid systems  

Microsoft Academic Search

Hybrid or continuous\\/discrete systems have attracted increased scientific attention in recent years. In fact, most technical systems consist of physical (sub)systems which are governed by continuous dynamics, continuous or discrete-time controllers, and logical systems which react to and trigger events in the continuous parts. Hybrid systems also arise from modeling of physical phenomena alone, e.g. in evaporation and other processes

Ingo Hoffmann; Sebastian Engell

1998-01-01

93

Linking Genome and Proteome by Mass Spectrometry: Large-Scale Identification of Yeast Proteins from Two Dimensional Gels  

Microsoft Academic Search

The function of many of the uncharacterized open reading frames discovered by genomic sequencing can be determined at the level of expressed gene products, the proteome. However, identifying the cognate gene from minute amounts of protein has been one of the major problems in molecular biology. Using yeast as an example, we demonstrate here that mass spectrometric protein identification is

Andrej Shevchenko; Ole N. Jensen; Alexandre V. Podtelejnikov; Francis Sagliocco; Matthias Wilm; Ole Vorm; Peter Mortensen; Anna Shevchenko; Helian Boucherie; Matthias Mann

1996-01-01

94

An evaluation of the cost-effectiveness of using CHROMagar for yeast identification in a routine microbiology laboratory  

Microsoft Academic Search

CHROMagar, a chromogenic differential culture medium, is claimed to facilitate the isolation and presumptive identification of certain clinically important yeast species, e.g., Candida albicans. This study evaluated the cost-effectiveness and time advantage of using it in comparison with Sabouraud dextrose agar (SDA). Three possible pathways, each of which included the use of one or both media, were compared in a

S. AINSCOUGH; C. C. KIBBLER

1998-01-01

95

Secure implementation of identification systems  

Microsoft Academic Search

In this paper we demonstrate that widely known identification systems, such as the public-file-based Feige-Fiat-Shamir scheme, can be insecure if proper care is not taken with their implementation. We suggest possible solutions. On the other hand, identity-based versions of the Feige-Fiat-Shamir scheme are conceptually more complicated than necessary.

Samy Bengio; Gilles Brassard; Yvo G. Desmedt; Claude Goutier; Jean-Jacques Quisquater

1991-01-01

96

The Yeast Two-hybrid System and Its Pharmaceutical Significance  

Microsoft Academic Search

The detected phenotypes in many diseases are caused from dysfunction in protein-protein, protein-DNA and receptor-ligand interactions. Therefore, determination of these molecular interactions followed by designing or screening the compounds to target these interactions provides a significant challenge in drug development. This review aims to highlight the yeast two-hybrid system in determination of protein-protein interactions and its possible outcomes in pharmaceutical

Zeki Topcu; Katherine L. B. Borden

2000-01-01

97

Experience with the MicroSeq D2 Large-Subunit Ribosomal DNA Sequencing Kit for Identification of Commonly Encountered, Clinically Important Yeast Species  

PubMed Central

Experience with a MicroSeq D2 large-subunit (LSU) ribosomal DNA (rDNA) sequencing kit for identification of yeast species commonly encountered in the mycology laboratory at Mayo Clinic is described here. A total of 131 isolates of yeasts recovered from clinical specimens were included in the study. Phenotypic methods used for initial identification included germ tube formation, urease production, microscopic morphological features on cornmeal agar, and an API 20C AUX system; all isolates were sequenced using a MicroSeq D2 LSU rDNA sequencing kit. Nucleic acid sequencing identified 93.9% of the isolates to the correct genus and species. A total of 100 of the isolates (representing 19 species of Candida) were sequenced, and 98% gave results concordant with identifications made by the API 20C AUX system; distance scores ranged from 0 to 1.88%, with an average value of 0.23%. Candida dubliniensis was not included in the MicroSeq database and was identified as Candida albicans. A total of 32 isolates representing 9 other genera (including Cryptococcus, Filobasidium, Kloeckera, Malassezia, Pichia, Sporidiobolus, Rhodotorula, Zygosaccharomyces, and Trichosporon) were included, and 81.3% showed concordant results when phenotypic and sequencing results were compared. Most discrepancies were attributed to the lack of inclusion of the species in the MicroSeq or API 20C AUX database. The MicroSeq D2 LSU rDNA sequencing kit appears to be accurate and useful for the identification of yeasts that might be seen in a clinical laboratory.

Hall, Leslie; Wohlfiel, Sherri; Roberts, Glenn D.

2003-01-01

98

System identification in experimental data  

SciTech Connect

A technique to identify the state of a dynamical system is proposed. The technique is based upon an identification of all period-one orbits present in the system. These orbits can then be classified in a way that permits an organization into a hierarchical ordering. The scheme is applied to time-series data gathered from a carefully constructed damped driven pendulum. {copyright} {ital 1996 American Institute of Physics.}

Hammel, S.; Bo Hammer, P.W. [Nonlinear Dynamics and Wavelets Group, B44, Naval Surface Warfare Center, White Oak, Maryland 20903-5640 (United States)

1996-06-01

99

A yeast screen system for aromatase inhibitors and ligands for androgen receptor: yeast cells transformed with aromatase and androgen receptor.  

PubMed Central

Endocrine disruptors are hormone mimics that modify hormonal action in humans and animals. It is thought that some endocrine disruptors modify estrogen and androgen action in humans and animals by suppressing aromatase activity. Aromatase cytochrome P450 is the key enzyme that converts C19 androgens to aromatic C18 estrogenic steroids. We have developed a novel aromatase inhibitor screening method that allows us to identify antiaromatase activity of various environmental chemicals. The screen was developed by coexpressing the human aromatase and the mouse androgen receptor in yeast cells, which carry the androgen-responsive ss-galactosidase reporter plasmid. Functional expression of aromatase in yeast has been demonstrated using the [3H]-water release assay with intact cells as well as with yeast microsomes. The aromatase activity could be blocked by known aromatase inhibitors such as aminoglutethimide (AG). Yeast-produced androgen receptors were able to transactivate a yeast basal promoter linked to an androgen-responsive element in response to androgens. The resultant triple yeast transformant responded to the treatment of testosterone, androstenedione, or 5 alpha-dihydrotestosterone (5 alpha-DHT). In the absence of the aromatase inhibitor AG, transcriptional activation was observed only for the nonaromatizable androgen 5 alpha-DHT. However, the two aromatizable androgens (testosterone and androstenedione) induced the reporter activity in the presence of AG. Using this yeast-based assay, we confirmed that two flavones, chrysin and alpha-naphtholflavone, are inhibitors of aromatase. Thus, this yeast system allows us to develop a high-throughput screening method, without using radioactive substrate, to identify aromatase inhibitors as well as new ligands (nonaromatizable androgen mimics) for the androgen receptors. In addition, this screening method also allows us to distinguish nonandrogenic aromatase inhibitors from inhibitors with androgenic activity. This yeast screening method will be useful to screen environmental chemicals for their antiaromatase activity and for their interaction with androgen receptor. Images Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9

Mak, P; Cruz, F D; Chen, S

1999-01-01

100

Killer systems of the yeast Saccharomyces cerevisiae  

SciTech Connect

The killer systems of Saccharomyces cerevisiae are an unusual class of cytoplasmic symbionts of primitive eukaryotes. The genetic material of these symbionts is double-stranded RNA. They are characterized by the linearity of the genome, its fragmentation into a major and a minor fraction, which replicate separately, and their ability to control the synthesis of secretory mycocin proteins possessing a toxic action on closely related strains. The secretion of mycocins at the same time ensures acquiring of resistance to them. Strains containing killer symbionts are toxigenic and resistant to the action of their own toxin, but strains that are free of killer double-stranded RNAs are sensitive to the action of mycocins. The killer systems of S. cerevisiae have retained features relating them to viruses and are apparently the result of evolution of infectious viruses. The occurrences of such systems among monocellular eukaryotic organisms is an example of complication of the genome by means of its assembly from virus-like components. We discuss the unusual features of replication and the expression of killer systems and their utilization in the construction of vector molecules.

Nesterova, G.F.

1989-01-01

101

Identification of essential host factors affecting tombusvirus RNA replication based on the yeast Tet promoters Hughes Collection.  

PubMed

To identify essential host genes affecting replication of Tomato bushy stunt virus (TBSV), a small model plant virus, we screened 800 yeast genes present in the yeast Tet promoters Hughes Collection. In total, we have identified 30 new host genes whose down-regulation either increased or decreased the accumulation of a TBSV replicon RNA. The identified essential yeast genes are involved in RNA transcription/metabolism, protein metabolism/transport, or other cellular processes. Detailed analysis of the effects of some of the identified yeast genes revealed that they might affect RNA replication by altering (i) the amounts/functions of p33 and p92(pol) viral replication proteins, (ii) the standard 10 to 20:1 ratio between p33 and p92(pol) in the viral replicase, (iii) the activity of the tombusvirus replicase, and (iv) the ratio of plus- versus minus-stranded RNA replication products. Altogether, this and previous genetic screening of yeast (Panavas et al., Proc. Natl. Acad. Sci. USA 102:7326-7331, 2005) led to the identification of 126 host genes (out of approximately 5,600 genes that represent approximately 95% of all the known and predicted yeast genes) that affected the accumulation of tombusvirus RNA. PMID:16840320

Jiang, Yi; Serviene, Elena; Gal, Jozsef; Panavas, Tadas; Nagy, Peter D

2006-08-01

102

Identification of the orotidine-5'-monophosphate decarboxylase gene of the oleaginous yeast Rhodosporidium toruloides.  

PubMed

Oleaginous yeast Rhodosporidium toruloides is an excellent microbial lipid producer of great industrial potential, yet there is no effective genetic tool for rationally engineering this microorganism. To develop a marker recycling system, the orotidine-5'-monophosphate (OMP) decarboxylase gene of R. toruloides (RtURA3) was isolated using methods of degenerate polymerase chain reaction (PCR) together with rapid amplification of cDNA ends. The results showed that RtURA3 contains four extrons and three introns, and that the encoded polypeptide holds a sequence of 279 amino acid residues with significant homology to those of OMP decarboxylases from other yeasts. A shuttle vector pYES2/CT-RtURA3 was constructed via site-specific insertion of RtURA3 into the commercial vector pYES2/CT. Transformation of the shuttle vector into Saccharomyces cerevisiae BY4741, a URA3-deficient yeast strain, ensured the viability of the strain on synthetic dextrose agar plate without uracil, suggesting that the isolated RtURA3 was functionally equivalent to the URA3 gene from S. cerevisiae. PMID:18698583

Yang, Fan; Zhang, Sufang; Tang, Wei; Zhao, Zongbao K

2008-09-01

103

NADP Regulates the Yeast GAL Induction System  

SciTech Connect

Transcriptional regulation of the galactose-metabolizing genes in Saccharomyces cerevisiae depends on three core proteins: Gal4p, the transcriptional activator that binds to upstream activating DNA sequences (UASGAL); Gal80p, a repressor that binds to the carboxyl terminus of Gal4p and inhibits transcription; and Gal3p, a cytoplasmic transducer that, upon binding galactose and adenosine 5'-triphosphate, relieves Gal80p repression. The current model of induction relies on Gal3p sequestering Gal80p in the cytoplasm. However, the rapid induction of this system implies that there is a missing factor. Our structure of Gal80p in complex with a peptide from the carboxyl-terminal activation domain of Gal4p reveals the existence of a dinucleotide that mediates the interaction between the two. Biochemical and in vivo experiments suggests that nicotinamide adenine dinucleotide phosphate (NADP) plays a key role in the initial induction event.

Kumar,P.; Yao, Y.; Sternglanz, R.; Johnston, S.; Joshua-Tor, L.

2008-01-01

104

Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.  

PubMed Central

A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers.

Latouche, G N; Daniel, H M; Lee, O C; Mitchell, T G; Sorrell, T C; Meyer, W

1997-01-01

105

System identification of jet engines  

SciTech Connect

System identification plays an important role in advanced control systems for jet engines, in which controls are performed adaptively using data from the actual engine and the identified engine. An identification technique for jet engine using the Constant Gain Extended Kalman Filter (CGEKF) is described. The filter is constructed for a two-spool turbofan engine. The CGEKF filter developed here can recognize parameter change in engine components and estimate unmeasurable variables over whole flight conditions. These capabilities are useful for an advanced Full Authority Digital Electric Control (FADEC). Effects of measurement noise and bias, effects of operating point and unpredicted performance change are discussed. Some experimental results using the actual engine are shown to evaluate the effectiveness of CGEKF filter.

Sugiyama, N.

2000-01-01

106

Automated systems for identification of microorganisms.  

PubMed Central

Automated instruments for the identification of microorganisms were introduced into clinical microbiology laboratories in the 1970s. During the past two decades, the capabilities and performance characteristics of automated identification systems have steadily progressed and improved. This article explores the development of the various automated identification systems available in the United States and reviews their performance for identification of microorganisms. Observations regarding deficiencies and suggested improvements for these systems are provided.

Stager, C E; Davis, J R

1992-01-01

107

Identification of Yeasts Isolated from Varieties of Apples and Citrus Using PCR-Fragment Size Polymorphism and Sequencing of ITS1–5.8S-ITS2 region  

Microsoft Academic Search

Yeasts play a significant role in the nutrition industry, medicine, and biocontrol of plant pathogens. Certain isolates of yeasts act as antagonist agents in postharvest infections on fruits such as apples and citrus. The main goal of this study was identification of yeasts isolated from different types of Iranian apples and citrus using reliable molecular methods. For preliminary identification of

Mona Mokhtari; Hassan Reza Etebarian; Mohammad Razavi; Ali Heydari; Hossein Mirhendi

2012-01-01

108

Distribution and identification of red yeasts in deep-sea environments around the northwest Pacific Ocean  

Microsoft Academic Search

We isolated 99 yeast strains, including 40 red yeasts, from benthic animals and sediments collected from the deep-sea floor in various areas in the northwest Pacific Ocean. Comparing the yeast isolates from animals and sediments collected from shallow locations, the proportion of red yeasts differed considerably, comprising 81.5% and 10.6% of the isolates from animals and sediments, respectively. All of

Takahiko Nagahama; Makiko Hamamoto; Takashi Nakase; Hideto Takami; Koki Horikoshi

2001-01-01

109

Advances in Identification of Clinical Yeast Isolates by Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry  

PubMed Central

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based identification is being adopted by clinical laboratories for routine identification of microorganisms. To date, the majority of studies have focused on the performance and optimization of MALDI-TOF MS for the identification of bacterial isolates. We review recent literature describing the use of MALDI-TOF MS for the routine identification of a variety of yeasts and yeast-like isolates. Specific topics include the effect of optimized or streamlined extraction methods, modified scoring thresholds, expanded reference libraries, and the possibility of conducting antifungal susceptibility testing using MALDI-TOF MS.

Buchan, Blake W.

2013-01-01

110

Identification and typing of the yeast strains isolated from bili bili, a traditional sorghum beer of Chad  

Microsoft Academic Search

Seventy six yeast strains isolated form bili bili and others sample were identified and typed in purpose of selecting appropriate starter culture. Identification techniques included conventional phenetic method, PCR\\/RFLP of NTS2 rDNA region, partial sequencing of the D1\\/D2 region of 26S rDNA and karyotyping using contour clamped homogenous electric field (CHEF) technique. The Saccharomyces cereviseiae strains were also compared to

Mbailao MBAIGUINAM; Huu Vang NGUYEN; Claude GAILLARDIN; Jacques POURQUIE

2005-01-01

111

Systematic identification of yeast cell cycle transcription factors using multiple data sources  

PubMed Central

Background Eukaryotic cell cycle is a complex process and is precisely regulated at many levels. Many genes specific to the cell cycle are regulated transcriptionally and are expressed just before they are needed. To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs) that regulate the expression of cell cycle-regulated genes. Results We developed a method to identify cell cycle TFs in yeast by integrating current ChIP-chip, mutant, transcription factor binding site (TFBS), and cell cycle gene expression data. We identified 17 cell cycle TFs, 12 of which are known cell cycle TFs, while the remaining five (Ash1, Rlm1, Ste12, Stp1, Tec1) are putative novel cell cycle TFs. For each cell cycle TF, we assigned specific cell cycle phases in which the TF functions and identified the time lag for the TF to exert regulatory effects on its target genes. We also identified 178 novel cell cycle-regulated genes, among which 59 have unknown functions, but they may now be annotated as cell cycle-regulated genes. Most of our predictions are supported by previous experimental or computational studies. Furthermore, a high confidence TF-gene regulatory matrix is derived as a byproduct of our method. Each TF-gene regulatory relationship in this matrix is supported by at least three data sources: gene expression, TFBS, and ChIP-chip or/and mutant data. We show that our method performs better than four existing methods for identifying yeast cell cycle TFs. Finally, an application of our method to different cell cycle gene expression datasets suggests that our method is robust. Conclusion Our method is effective for identifying yeast cell cycle TFs and cell cycle-regulated genes. Many of our predictions are validated by the literature. Our study shows that integrating multiple data sources is a powerful approach to studying complex biological systems.

Wu, Wei-Sheng; Li, Wen-Hsiung

2008-01-01

112

Glyoxalase system in yeasts: structure, function, and physiology.  

PubMed

The glyoxalase system consists of glyoxalase I and glyoxalase II. Glyoxalase I catalyzes the conversion of methylglyoxal (CH(3)COCHO), a metabolite derived from glycolysis, with glutathione to S-D-lactoylglutathione, while glyoxalase II hydrolyses this glutathione thiolester to D-lactic acid and glutathione. Since methylglyoxal is toxic due to its high reactivity, the glyoxalase system is crucial to warrant the efficient metabolic flux of this reactive aldehyde. The budding yeast Saccharomyces cerevisiae has the sole gene (GLO1) encoding the structural gene for glyoxalase I. Meanwhile, this yeast has two isoforms of glyoxalase II encoded by GLO2 and GLO4. The expression of GLO1 is regulated by Hog1 mitogen-activated protein kinase and Msn2/Msn4 transcription factors under highly osmotic stress conditions. The physiological significance of GLO1 expression in response to osmotic stress is to combat the increase in the levels of methylglyoxal in cells during the production of glycerol as a compatible osmolyte. Deficiency in GLO1 in S. cerevisiae causes pleiotropic phenotypes in terms of stress response, because the steady state level of methylglyoxal increases in glo1? cells thereby constitutively activating Yap1 transcription factor. Yap1 is crucial for oxidative stress response, although methylglyoxal per se does not enhance the intracellular oxidation level in yeast, but it directly modifies cysteine residues of Yap1 that are critical for the nucleocytoplasmic localization of this b-ZIP transcription factor. Consequently, glyoxalase I can be defined as a negative regulator of Yap1 through modulating the intracellular methylglyoxal level. PMID:21310260

Inoue, Yoshiharu; Maeta, Kazuhiro; Nomura, Wataru

2011-02-15

113

Multiharmonic excitation for nonlinear system identification  

NASA Astrophysics Data System (ADS)

Parametric identification of nonlinear systems is done using a hybrid time/frequency-domain-based Fourier series identification method. A multiharmonic force excitation is proposed to overcome identification problems encountered with a single harmonic excitation for certain classes of nonlinear systems. A Duffing oscillator and a system with quadratic damping are considered in detail for illustration of the proposed identification scheme using multiharmonic excitation. It is demonstrated that for most situations a multiharmonic excitation leads to significantly better identification results than a single harmonic excitation-based method.

Narayanan, M. D.; Narayanan, S.; Padmanabhan, Chandramouli

2008-04-01

114

Subproteomics: identification of plasma membrane proteins from the yeast Saccharomyces cerevisiae.  

PubMed

As a consequence of their poor solubility during isoelectric focusing, integral membrane proteins are generally absent from two-dimensional gel proteome maps. In order to analyze the yeast plasma membrane proteome, a plasma membrane purification protocol was optimized in order to reduce contaminating membranes and cytosolic proteins. Specifically, the new fractionation scheme largely depleted the plasma membrane fraction of cytosolic proteins by deoxycholate stripping and ribosomal proteins by sucrose gradient flotation. The plasma membrane complement was resolved by two-dimensional electrophoresis using the cationic detergent cetyl trimethyl ammonium bromide in the first, and sodium dodecyl sulfate in the second dimension, and fifty spots were identified by matrix-assisted laser desorption/ionization-time of flight mass spectometry. In spite of the presence of still contaminating ribosomal proteins, major proteins corresponded to known plasma membrane residents, the ABC transporters Pdr5p and Snq2p, the P-type H(+)-ATPase Pma1p, the glucose transporter Hxt7p, the seven transmembrane-span Mrh1p, the low affinity Fe(++) transporter Fet4p, the twelve-span Ptr2p, and the plasma membrane anchored casein kinase Yck2p. The four transmembrane-span proteins Sur7p and Nce102p were also present in the isolated plasma membranes, as well as the unknown protein Ygr266wp that probably contains a single transmembrane span. Thus, combining subcellular fractionation with adapted two-dimensional electrophoresis resulted in the identification of intrinsic plasma membrane proteins. PMID:12469340

Navarre, Catherine; Degand, Hervé; Bennett, Keiryn L; Crawford, Janne S; Mørtz, Ejvind; Boutry, Marc

2002-12-01

115

Significance of molecular identification and antifungal susceptibility of clinically significant yeasts and moulds in a global antifungal surveillance programme.  

PubMed

The increasing diversity of opportunistic fungi causing serious invasive fungal infections (IFI) has been documented. Accurate identification (ID) is important in guiding therapy, determining prognosis for IFIs and in epidemiological surveys. We assessed the utility of PCR-based methods for the ID of yeasts and moulds that either were uncommon, failed conventional ID, or represented unusual biochemical or phenotypic profiles of common species. Among 1,790 viable fungal clinical isolates received during the SENTRY Program in 2010, 322 strains from 40 study sites had ID confirmed by molecular methods. Isolates were previously identified in participant institutions. Yeasts that were not confirmed by morphology on CHROMagar, growth at 45 °C (Candida albicans/dubliniensis), or assimilation of trehalose (C. glabrata) as well as non-Candida yeasts and all moulds were amplified and sequenced using primers amplifying one or more of the following genes: ITS, 28S, ?-tubulin (Aspergillus spp.), TEF (Fusarium spp.), IGS (Trichosporon spp.). The isolates selected for molecular ID included 149 isolates of Candida species, 77 of Aspergillus species, 73 non-Candida yeasts, and 23 other moulds (a total of 41 different species). Overall, the ID determined by the submitting site was confirmed for 189 isolates (58.7 %): Aspergillus spp. (64.1 % correct); Candida spp. (60.1 % correct); non-Candida yeasts (58.9 % correct); non-Aspergillus moulds (30.4 % correct). Species with high levels of concordance between conventional and molecular ID included A. fumigatus (95.0  %), C. lusitaniae (100 %), C. dubliniensis (92.3 %), C. kefyr (100 %), and C. neoformans (90.2 %). Only 50.0 % of isolates of C. albicans and 59.1 % of C. glabrata selected due to unusual phenotypic or biochemical features were found to be correctly identified by the submitting site. Molecular methods for the identification of fungal pathogens are an important adjunct to the conventional identification of many less common clinically relevant yeasts and moulds including species of Candida with unusual or erroneous phenotypic or biochemical profiles. Molecular confirmation of fungal identification is essential in epidemiological surveys such as SENTRY. PMID:22580756

Pfaller, Michael A; Woosley, Leah N; Messer, Shawn A; Jones, Ronald N; Castanheira, Mariana

2012-05-13

116

Yeast as a model system for mammalian seven-transmembrane segment receptors  

SciTech Connect

Investigators have used the budding yeast Saccharomyces cerevisiae as a model system in which to study the {beta}-adrenergic receptor, the T-cell receptor pathway, initiation of mammalian DNA replication, initiation of mammalian transcription, secretion, the CDC2 kinase system, cell cycle control, and aging, as well as the function of oncogenes. This list continues to growth with the discovery of an immunoglobulin heavy-chain binding homologue in yeast, an Rb binding protein homologue, and a possible yeast arrestin. Yeast is relatively easy to maintain, to grow, and to genetically manipulate. A single gene can be overexpressed, selectively mutated or deleted from its chromosomal location. In this way, the in vivo function of a gene can be studied. It has become reasonable to consider yeast as a model system for studying the seven transmembrane segments (7-TMS) receptor family. Currently, subtypes of the {beta}-adrenergic receptor are being studied in yeast. The receptor and its G{sub {alpha}}-G-protein, trigger the mating pheromone receptor pathway. This provides a powerful assay for determining receptor function. Studies expressing the muscarinic cholinergic receptor in yeast are underway. The yeast pheromone receptor belongs to this receptor family, sharing sequences and secondary structure homology. An effective strategy has been to identify a yeast pathway or process which is homologous to a mammalian system. The pathway is delineated in yeast, identifying other genetic components. Then yeast genes are used to screen for human homologues of these components. The putative human homologues are then expressed in yeast and in mammalian cells to determine function. When this type of {open_quotes}mixing and matching{close_quotes} works, yeast genetics can be a powerful tool. 115 refs.

Jeansonne, N.E. [East Carolina Univ. Medical School, Greenville, NC (United States)

1994-05-01

117

Modal identification of dynamic mechanical systems  

NASA Astrophysics Data System (ADS)

This paper reviews modal identification techniques which are now helping designers all over the world to improve the dynamic behavior of vibrating engineering systems. In this context the need to develop more accurate and faster parameter identification is ever increasing. A new dynamic stiffness matrix based identification method which is highly accurate, fast and system-dynamic-modification compatible is presented. The technique is applicable to all those multidegree-of-freedom systems where full receptance matrix can be experimentally measured.

Srivastava, R. K.; Kundra, T. K.

1992-07-01

118

Raman Spectroscopy and Chemometrics for Identification and Strain Discrimination of the Wine Spoilage Yeasts Saccharomyces cerevisiae, Zygosaccharomyces bailii, and Brettanomyces bruxellensis.  

PubMed

The yeasts Zygosaccharomyces bailii, Dekkera bruxellensis (anamorph, Brettanomyces bruxellensis), and Saccharomyces cerevisiae are the major spoilage agents of finished wine. A novel method using Raman spectroscopy in combination with a chemometric classification tool has been developed for the identification of these yeast species and for strain discrimination of these yeasts. Raman spectra were collected for six strains of each of the yeasts Z. bailii, B. bruxellensis, and S. cerevisiae. The yeasts were classified with high sensitivity at the species level: 93.8% for Z. bailii, 92.3% for B. bruxellensis, and 98.6% for S. cerevisiae. Furthermore, we have demonstrated that it is possible to discriminate between strains of these species. These yeasts were classified at the strain level with an overall accuracy of 81.8%. PMID:23913433

Rodriguez, Susan B; Thornton, Mark A; Thornton, Roy J

2013-08-02

119

A combined yeast/bacterial two-hybrid system (YBTH): development and evaluation  

PubMed Central

Summary Two-hybrid screening is a standard methodology to identify and characterize protein-protein interactions that has become an integral component of many proteomic investigations. The two-hybrid system was initially developed using yeast as a host organism. However, bacterial two-hybrid systems have also become common laboratory tools and are preferred in some circumstances, although yeast and bacterial two-hybrid systems have never been directly compared. We describe here the development of a unified yeast and bacterial two-hybrid (YBTH) system in which a single bait expression plasmid is used in both organismal milieus. We use a series of leucine zipper fusion proteins of known affinities to compare interaction detection using both systems. While both two-hybrid systems detected interactions within a comparable range of interaction affinities, each demonstrated unique advantages. The yeast system produced quantitative readout over a greater dynamic range than that observed with bacteria. However, the phenomenon of “auto-activation” by baits was less problematic in the bacterial system than in yeast. Both systems identified physiological interactors for a library screen with a cI-Ras test bait; however, non-identical interactors were obtained in yeast and bacterial screens. The ability to rapidly shift between yeast and bacterial systems provided by these new reagents should provide a marked advantage for two-hybrid investigations. In addition, the modified expression vectors should be useful for any application requiring facile expression of a protein of interest in both yeast and bacteria.

Serebriiskii, Ilya G.; Fang, Rui; Latypova, Ekaterina; Hopkins, Richard; Vinson, Charles; Joung, J. Keith; Golemis, Erica A.

2009-01-01

120

Identification of yeast population dynamics of spontaneous fermentation in Beijing wine region, China  

Microsoft Academic Search

The aim of this study was (i) to investigate changes occurring in the yeast population profile during spontaneous fermentation\\u000a of grape juice; (ii) to assess the proliferation of commercial yeast starter culture strains in vineyards; and (iii) to identify\\u000a indigenous wine strains for future development of starter strains that better reflect the yeast biodiversity of China’s grape-growing\\u000a regions. To achieve

Huihui Sun; Huiqin Ma; Meiling Hao; Isak S. Pretorius; Shangwu Chen

2009-01-01

121

Occurrence and Identification of Yeast Species in Fermented Liquid Feed for Piglets  

Microsoft Academic Search

The major objective of the present study was to investigate the occurrence and identity of yeast species in fermented liquid\\u000a feed (FLF) used for feeding piglets. In total, 40 different Danish farms were included in the analysis. The preparation and\\u000a composition of FLF was found to be very heterogeneous with high variations in both yeast counts and yeast species composition.

Klaus Gori; Marina Kryger Bjørklund; Nuria Canibe; Anni Øyan Pedersen; Lene Jespersen

2011-01-01

122

MALDI-TOF MS Andromas strategy for the routine identification of bacteria, mycobacteria, yeasts, Aspergillus spp. and positive blood cultures.  

PubMed

All organisms usually isolated in our laboratory are now routinely identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using the Andromas software. The aim of this study was to describe the use of this strategy in a routine clinical microbiology laboratory. The microorganisms identified included bacteria, mycobacteria, yeasts and Aspergillus spp. isolated on solid media or extracted directly from blood cultures. MALDI-TOF MS was performed on 2665 bacteria isolated on solid media, corresponding to all bacteria isolated during this period except Escherichia coli grown on chromogenic media. All acquisitions were performed without extraction. After a single acquisition, 93.1% of bacteria grown on solid media were correctly identified. When the first acquisition was not contributory, a second acquisition was performed either the same day or the next day. After two acquisitions, the rate of bacteria identified increased to 99.2%. The failures reported on 21 strains were due to an unknown profile attributed to new species (9) or an insufficient quality of the spectrum (12). MALDI-TOF MS has been applied to 162 positive blood cultures. The identification rate was 91.4%. All mycobacteria isolated during this period (22) were correctly identified by MALDI-TOF MS without any extraction. For 96.3% and 92.2% of yeasts and Aspergillus spp., respectively, the identification was obtained with a single acquisition. After a second acquisition, the overall identification rate was 98.8% for yeasts (160/162) and 98.4% (63/64) for Aspergillus spp. In conclusion, the MALDI-TOF MS strategy used in this work allows a rapid and efficient identification of all microorganisms isolated routinely. PMID:22044600

Bille, E; Dauphin, B; Leto, J; Bougnoux, M-E; Beretti, J-L; Lotz, A; Suarez, S; Meyer, J; Join-Lambert, O; Descamps, P; Grall, N; Mory, F; Dubreuil, L; Berche, P; Nassif, X; Ferroni, A

2011-11-01

123

Detection and identification of Brettanomyces/Dekkera sp. yeasts with a loop-mediated isothermal amplification method.  

PubMed

Primer sets for a loop-mediated isothermal amplification (LAMP) method were developed to specifically identify each of the four Brettanomyces/Dekkera species, Dekkera anomala, Dekkera bruxellensis, Dekkera custersiana and Brettanomyces naardenensis. Each primer set was designed with target sequences in the ITS region of the four species and could specifically amplify the target DNA of isolates from beer, wine and soft drinks. Furthermore, the primer sets differentiated strains of the target species from strains belonging to other species, even within the genus Brettanomyces/Dekkera. Moreover, the LAMP method with these primer sets could detect about 1 x 10(1) cfu/ml of Brettanomyces/Dekkera yeasts from suspensions in distilled water, wine and beer. This LAMP method with primer sets for the identification of Brettanomyces/Dekkera yeasts is advantageous in terms of specificity, sensitivity and ease of operation compared with standard PCR methods. PMID:17613376

Hayashi, Nobuyuki; Arai, Ritsuko; Tada, Setsuzo; Taguchi, Hiroshi; Ogawa, Yutaka

2007-02-04

124

Identification of yeast strains isolated from marcha in Sikkim, a microbial starter for amylolytic fermentation  

Microsoft Academic Search

Marcha or murcha is a traditional amylolytic starter used to produce sweet–sour alcoholic drinks, commonly called jaanr in the Himalayan regions of India, Nepal, Bhutan, and Tibet (China). The aim of this study was to examine the microflora of marcha collected from Sikkim in India, focusing on yeast flora and their roles. Twenty yeast strains were isolated from six samples

Naoko Tsuyoshi; Ryosuke Fudou; Shigeru Yamanaka; Michio Kozaki; Namrata Tamang; Saroj Thapa; Jyoti P. Tamang

2005-01-01

125

Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization  

Microsoft Academic Search

We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures synchronized by three independent methods: alpha factor arrest, elutriation, and arrest of a cdc15 temperature-sensitive mutant. Using periodicity and correlation algorithms, we identified 800 genes that meet an objective

Paul Spellman; Gavin Sherlock; M. Zhang; Vishwanath R. Iyer; Kirk Anders; Michael B. Eisen; Patrick O. Brown; David Botstein; Bruce Futcher

126

The Use of a Colloidal Silica Preparation in Media Used for Yeast Identification  

Microsoft Academic Search

SUMMARY Nutritional tests on yeasts which utilize myo-inositol as the sole carbon source or which have red pigment have been carried out on defined media solidified with silica gel (Ludox HS-40) in multicompartment polystyrene dishes. Yeasts of the above types isolated from soft fruits were tested together with 189 named strains representing 28 genera and 110 species and varieties. The

R. W. M. Buhagiar

1977-01-01

127

Identification and characterization of yeasts causing chalk mould defects on par-baked bread  

Microsoft Academic Search

Pichia anomala, Hyphopichia burtonii and Saccharomycopsis fibuligera are spoilage yeasts causing chalk mould defects on par-baked breads packaged under modified atmosphere. The first objective of this study was to identify yeasts isolated from spoiled par-baked breads by means of a RAPD protocol and to determine the dominant spoilers amongst identified strains. The second objective was to determine the effects of

N. Deschuyffeleer; K. Audenaert; S. Samapundo; S. Ameye; M. Eeckhout; F. Devlieghere

2011-01-01

128

Identification of Medically Important Candida and Non-Candida Yeast Species by an Oligonucleotide Array  

Microsoft Academic Search

The incidence of yeast infections has increased in the recent decades, with Candida albicans still being the most common cause of infections. However, infections caused by less common yeasts have been widely reported in recent years. Based on the internal transcribed spacer 1 (ITS 1) and ITS 2 sequences of the rRNA genes, an oligonucleotide array was developed to identify

Shiang Ning Leaw; Hsien Chang Chang; Richard Barton; Jean-Philippe Bouchara; Tsung Chain Chang

2007-01-01

129

Identification of mass disaster victims: the Swiss identification system.  

PubMed

A new, simple, and reliable forensic identification system has been described. It permits the rapid and positive identification of victims of catastrophies such as airplane accidents, battles, floods, and fires. An electronic microprocessing unit directs a mechanical engraver to encode up to 13 alphanumeric characters on a small gold disk 0.25 mm thick and 2.0 mm in diameter. The identification chip is sealed in a 0.8-mm deep cavity prepared with a specially designed diamond burr in the lingual enamel of a molar tooth. The sealant is a stained composite material shown experimentally to be leakage proof, fire resistant, and readily detectable in teeth exposed to high temperatures. At the identification center the gold disk can easily be recovered and the victim positively identified without recourse to time-consuming comparison of dental records. Minimal training is required for the forensic personnel. PMID:512601

Mühlemann, H R; Steiner, E; Brandestini, M

1979-01-01

130

Evaluation of Pyrosequencing® Technology for the Identification of Clinically Relevant Non-Dematiaceous Yeasts and Related Species  

PubMed Central

Pyrosequencing was used to identify 133 isolates of clinically relevant non-dematiaceous yeasts. These included 97 ATCC strains (42 type strains), 7 UAMH strains, and 29 clinical isolates. Isolates belonged to the following genera: Candida (18 species), Trichosporon (10), Cryptococcus (7), Malassezia (3), Rhodotorula (2), Geotrichum (1), Blastoschizomyces (1) and Kodamaea (1). Amplicons were obtained of a hypervariable ITS region and analyzed using Pyrosequencing technology. The data were evaluated by a BLAST search against the GenBank database and correlated with data obtained by conventional cycle sequencing of the ITS1-5.8S-ITS2 region. Cycle sequencing identified (78.9%) if the isolates to the species level. Pyrosequencing technology identified 69.1%. In 90.1% of all the strains tested, identification results of both sequencing methods were identical. Most Candida isolates can be identified to the species level by pyrosequencing. Trichosporon species and some Cryptococcus cannot be differentiated at the species level. Pyrosequencing can be used for the reliable identification of most commonly isolated non-dematiaceous yeasts, with a reduction of cost per identification compared to conventional sequencing.

Montero, C.I.; Shea, Y.R.; Jones, P.A.; Harrington, S.M.; Tooke, N.E; Witebsky, F.G; Murray, P.R.

2008-01-01

131

Identification of yeasts during alcoholic fermentation of tchapalo, a traditional sorghum beer from Côte d'Ivoire.  

PubMed

This study investigated the diversity and dynamics of yeasts involved in alcoholic fermentation of a traditional sorghum beer from Côte d'Ivoire, tchapalo. A total of 240 yeast strains were isolated from fermenting sorghum wort inoculated with dry yeast from two geographic regions of Côte d'Ivoire (Abidjan and Bondoukou). Initial molecular identification to the species level was carried out using RFLP of PCR-amplified internal transcribed spacers of rDNA (ITS1-5.8S-ITS2). Ten different profiles were obtained from the restriction of PCR products with the three endonucleases HaeIII, CfoI and HinfI. Sequence analysis of the D1/D2 domain of the 26S rDNA and the ACT1 gene allowed us to assign these groups to six different species: Saccharomyces cerevisiae-like, Candida tropicalis, Pichia kudriavzevii, Pichia kluyveri, Kodamaea ohmeri and Meyerozyma caribbica. The most frequent species associated with tchapalo fermentation was S. cerevisiae-like (87.36%), followed by C. tropicalis (5.45%) and M. caribbica (2.71%). S. cerevisiae-like strains were diploid heterozygotes and exhibited three to four nucleotides divergence from the type strain in the D1/D2 domain and several indels in the more discriminant sequence of the intron of the ACT1 gene. During the process, the yeast species isolated and their frequencies varied according to the geographic origin of the dry yeast. The occurrence of some species was sporadic and only two non-Saccharomyces species were found in the final product. PMID:21318423

N'guessan, Kouadio Florent; Brou, Kouakou; Jacques, Noémie; Casaregola, Serge; Dje, Koffi Marcellin

2011-02-12

132

Stochastic system identification in structural dynamics  

USGS Publications Warehouse

Recently, new identification methods have been developed by using the concept of optimal-recursive filtering and stochastic approximation. These methods, known as stochastic identification, are based on the statistical properties of the signal and noise, and do not require the assumptions of current methods. The criterion for stochastic system identification is that the difference between the recorded output and the output from the identified system (i.e., the residual of the identification) should be equal to white noise. In this paper, first a brief review of the theory is given. Then, an application of the method is presented by using ambient vibration data from a nine-story building.

Safak, Erdal

1988-01-01

133

Comprehensive Screening of Human Genes with Inhibitory Effects on Yeast Growth and Validation of a Yeast Cell-Based System for Screening Chemicals  

Microsoft Academic Search

To evaluate yeast as a high-throughput cell-based system for screening chemicals that may lead to drug development, 10,302 full-length human cDNAs (~50% of the total cDNAs) were introduced into yeast. Approximately 5.6% (583 clones) of the cDNAs repressed the growth of yeast. Notably, ~25% of the repressive cDNAs encoded uncharacterized proteins. Small chemicals can be readily surveyed by monitoring their

Masayuki Sekigawa; Tatsuki Kunoh; Shu-Ichi Wada; Yukio Mukai; Kazuhiko Ohshima; Shinji Ohta; Naoki Goshima; Ryuzo Sasaki; Tamio Mizukami

2010-01-01

134

Weizmann Institute Heavy-Ion Identification System.  

National Technical Information Service (NTIS)

A new versatile, and highly efficient heavy-ion identification system developed for experiments with the 14 UD Pelletron accelerator of the Weizmann Institute of Science is described. The system combines various types of low-pressure gaseous detectors and...

I. Tserruya A. Breskin R. Chechik E. Deuring S. Kaplanis

1981-01-01

135

The viral killer system in yeast: from molecular biology to application  

Microsoft Academic Search

Since the initial discovery of the yeast killer system almost 40 years ago, intensive studies have substantially strengthened our knowledge in many areas of biology and provided deeper insights into basic aspects of eukaryotic cell biology as well as into virus–host cell interactions and general yeast virology. Analysis of killer toxin structure, synthesis and secretion has fostered understanding of essential

Manfred J. Schmitt; Frank Breinig

2002-01-01

136

System identification for robust control design  

SciTech Connect

System identification for the purpose of robust control design involves estimating a nominal model of a physical system and the uncertainty bounds of that nominal model via the use of experimentally measured input/output data. Although many algorithms have been developed to identify nominal models, little effort has been directed towards identifying uncertainty bounds. Therefore, in this document, a discussion of both nominal model identification and bounded output multiplicative uncertainty identification will be presented. This document is divided into several sections. Background information relevant to system identification and control design will be presented. A derivation of eigensystem realization type algorithms will be presented. An algorithm will be developed for calculating the maximum singular value of output multiplicative uncertainty from measured data. An application will be given involving the identification of a complex system with aliased dynamics, feedback control, and exogenous noise disturbances. And, finally, a short discussion of results will be presented.

Dohner, J.L.

1995-04-01

137

Identification of respiratory chain gene mutations that shorten replicative life span in yeast.  

PubMed

Aging is the progressive accumulation of alterations in cells that elevates the risk of death. The mitochondrial theory of aging postulates that free radicals produced by the mitochondrial respiratory system contribute to the aging process. However, the roles of individual electron transfer chain (ETC) components in cellular aging have not been elucidated. In this study, we analyzed the replicative life span of 73 yeast deletion mutants lacking the genes of the mitochondrial electron transfer chain system, and found that nine of these mutants (?nde1, ?tcm62, ?rip1, ?cyt1, ?qrc8, ?pet117, ?cox11, ?atp11, ?fmc1) had significantly shorter life spans. These mutants had lower rates of respiration and were slightly sensitive to exogenous administration of hydrogen peroxide. However, only two of them, ?nde1 and ?fmc1, produced higher amounts of intrinsic superoxide radicals in the presence of glucose compared to that of wild type cells. Interestingly, there were no significant alterations in the mitochondrial membrane potentials of these mutants. We speculate that the shorter life spans of ETC mutants result from multiple mechanisms including the low respiration rate and low energy production rather than just a ROS-dependent path. PMID:22137892

Hacioglu, Elise; Demir, Ayse Banu; Koc, Ahmet

2011-11-25

138

Combining SELEX and the yeast three-hybrid system for in vivo selection and classification of RNA aptamers  

PubMed Central

Aptamers are small nucleic acid ligands that bind to their targets with specificity and high affinity. They are generated by a combinatorial technology, known as SELEX. This in vitro approach uses iterative cycles of enrichment and amplification to select binders from nucleic acid libraries of high complexity. Here we combine SELEX with the yeast three-hybrid system in order to select for RNA aptamers with in vivo binding activity. As a target molecule, we chose the RNA recognition motif-containing RNA-binding protein Rrm4 from the corn pathogen Ustilago maydis. Rrm4 is an ELAV-like protein containing three N-terminal RNA recognition motifs (RRMs). It has been implicated in microtubule-dependent RNA transport during pathogenic development. After 11 SELEX cycles, four aptamer classes were identified. These sequences were further screened for their in vivo binding activity applying the yeast three-hybrid system. Of the initial aptamer classes only members of two classes were capable of binding in vivo. Testing representatives of both classes against Rrm4 variants mutated in one of the three RRM domains revealed that these aptamers interacted with the third RRM. Thus, the yeast three-hybrid system is a useful extension to the SELEX protocol for the identification and characterization of aptamers with in vivo binding activity.

Konig, Julian; Julius, Christian; Baumann, Sebastian; Homann, Matthias; Goringer, H. Ulrich; Feldbrugge, Michael

2007-01-01

139

Yeasts and their possible beneficial and negative effects on the quality of dairy products  

Microsoft Academic Search

This review deals with yeasts and their potential use as starter cultures in dairy products as well as their role as spoilage organisms. The taxonomy of relevant yeasts is described, with emphasis on molecular techniques and simplified identification systems applicable to industry. Quantitative assessment of undesirable yeast contamination is discussed with regard to present requirements for quality assurance in dairies.

Mogens Jakobsen; Judy Narvhus

1996-01-01

140

Isolation and identification of yeast flora from genital tract in healthy female camels (Camelus dromedarius).  

PubMed

Yeasts are commensal organisms found in the skin, genital and gastrointestinal tracts, and other mucosal sites in mammalians. The purposes of this study were to identify yeast flora and to determine the number of colony forming units (CFUs) in genital tract of healthy female dromedary camels, establishing their connection in both mated and unmated conditions. The samples were taken from different parts of genital tract including vestibule, vagina, cervix, uterine body, and uterine horns of 50 camels using sterilized cotton swabs. They were cultured onto Sabouraud glucose agar containing chloramphenicol and incubated at 30 degrees C for 7-10 days. A total of 454 yeast colonies were obtained from genital tract. Yeast isolates belonged to 8 genera: Candida (73.1%), Trichosporon (10.1%), Geotrichum (7.5%), Kluyveromyces (3.5%), Rhodotorula (2.4%), Aureobasidium (1.4%), Cryptococcus (1.1%) and Prototheca (0.8%). Among different Candida species, C. zeylanoides was the most common isolated species, representing significant difference with other Candida species (P<0.05). The mean number of yeasts found in the vestibule (46%) was significantly higher than the results obtained from other parts (P<0.05). In addition, the mean value of CFUs from unmated females (71.1%) was significantly higher than mated females (P<0.05). The results showed that C. zeylanoides was a common component of healthy camel females' genital mycoflora and the number of yeasts varied between mated and unmated females. PMID:20036469

Shokri, Hojjatollah; Khosravi, Alireza; Sharifzadeh, Aghil; Tootian, Zahra

2009-12-29

141

Using Domain Knowledge in Evolutionary System Identification  

Microsoft Academic Search

Two example of Evolutionary System Identification are presented to highlight the importance of incorportaing Domain Knowledge: the discovery of an analytical indentation law in Structural Mechanics using constrained Genetic Pro- gramming, and the identification of the repartition of underground velocities in Seimsi Prospection. Critical issues for sucessful ESI are discussed in the light of these results.

Marc Schoenauer; Michèle Sebag

2006-01-01

142

Identification of inhibitors of yeast-to-hyphae transition in Candida albicans by a reporter screening assay.  

PubMed

Candida albicans is one of the most common opportunistic fungal pathogens, causing life-threatening disease in immunocompromised patients. As it is not primarily a pathogen, but can exist in a commensal state, we aimed at the identification of new anti-infective compounds which do not eradicate the fungus, but primarily disable a virulence determinant. The yeast–hyphae-dimorphism of C. albicans is considered a major contributor to fungal disease, as mutants locked into either yeast or hyphal state have been shown to be less virulent in the mouse-model. We devised a high-throughput screening procedure which allows us to find inhibitors of the induction of hyphae. Hyphae-formation was induced by nitrogen starvation at 37 °C and neutral pH in a reporter strain, which couples promoter activity of the hyphae-specific HWP1 to ?-galactosidase expression. In a pilot screening of 720 novel synthetic compounds, we identified substances which inhibited the outgrowth of germ tubes. They belonged to chemical classes not yet known for antimycotic properties, namely methyl aryl-oxazoline carboxylates, dihydrobenzo[d]isoxazolones and thiazolo[4,5-e]benzoisoxazoles. In conclusion we developed a novel screening assay, which addresses the morphological switch from the yeast form of C. albicans to its hyphal form and identified novel chemical structures with activity against C. albicans. PMID:23262131

Heintz-Buschart, Anna; Eickhoff, Holger; Hohn, Erwin; Bilitewski, Ursula

2012-12-20

143

Yeast two-hybrid system for studying protein-protein interactions--stage 2: Transforming and characterizing the library.  

PubMed

An important element in the characterization of the function of a protein is the identification of other proteins with which it interacts. A powerful genetic strategy for this purpose, termed the "yeast two-hybrid system," uses transcriptional reporters in yeast to indirectly reflect the interaction between two proteins. The term "two-hybrid" derives from the two classes of chimeric, or "hybrid," proteins used in each screen. The first, commonly referred to as the "bait," is a fusion of a protein of interest "x" with a DNA-binding domain (DBD-x). The second, sometimes called the "prey," is a fusion of a cDNA library "y" to a transcriptional activation domain (AD-y). Together, DBD-x and AD-y provide the basis of the detection system. The two-hybrid approach has gained wide popularity because of the relative ease and speed with which it can be used to identify novel protein-protein interactions and to analyze known interactions. The second stage of the method, described in this protocol, includes the transformation of yeast with a cDNA library, followed by library characterization. It can be performed in parallel with construction of a bait protein (stage 1). PMID:20439417

Serebriiskii, Ilya

2010-05-01

144

Secretory protein translocation in a yeast cell-free system can occur posttranslationally and requires ATP hydrolysis  

Microsoft Academic Search

We describe an in vitro system with all components derived from the yeast Saccharomyces cerevisiae that can translocate a yeast secretory pro- tein across microsomal membranes. In vitro tran- scribed prepro-a-factor mRNA served to program a membrane-deplete d yeast translation system. Translo- cation and core glycosylation of prepro-a-factor were observed when yeast microsomal membranes were added during or after translation.

M. Gerard Waters; Giinter Blobel

1986-01-01

145

Identification of Multi-Input Biological Systems  

Microsoft Academic Search

The Wiener theory of nonlinear system identification is extended to multi-input-output systems and experimentally applied. The experimental applicability of the method is discussed with regard to biological systems. It is shown that the method is well suited for the treatment of the idiosyncratic features of such systems: nonlinearities, short lifetimes of experimental preparations, and high noise content. A preliminary analysis

Panos Z. Marmarelis; Ken-Ichi Naka

1974-01-01

146

Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfural tolerance for ethanologenic yeast  

Technology Transfer Automated Retrieval System (TEKTRAN)

Composed of linear difference equations, a discrete dynamic system model was designed to reconstruct transcriptional regulations in gene regulatory networks in response to 5-hydroxymethylfurfural, a bioethanol conversion inhibitor for ethanologenic yeast Saccharomyces cerevisiae. The modeling aims ...

147

Methods for yeast characterization from industrial products  

Microsoft Academic Search

This work compared the efficiency of four methods for the identification of industrial yeast strains and the establishment of a pattern for yeast characterization to be used during industrial fermentation processes, allowing the detection of yeast contaminants. Five strains of yeast currently used in the Brazilian fuel alcohol industry (about 99% of the yeast used for this purpose), and yeast

Luiz H Gomes; Keila M. R Duarte; Juan L Argueso; Sergio Echeverrigaray; Flavio C. A Tavares

2000-01-01

148

Treatment of wastewater from a monosodium glutamate manufacturing plant using successive yeast and activated sludge systems  

Microsoft Academic Search

Successive systems using yeast and activated sludge (AS) were developed to treat monosodium glutamate manufacturing wastewater (MSGW). The yeast system allowed over 80% removal of chemical oxygen demand (COD) and a rise of pH from 2.5 to 6.5 on treating MSGW directly (COD 25,000mg\\/l and NH4+–N 19,000mg\\/l). Observation of the microbial community using a scanning electron microscope indicated that the

Qingxiang Yang; Min Yang; Shujun Zhang; Wenzhou Lv

2005-01-01

149

Oxidative stress and neurodegeneration: the yeast model system.  

PubMed

In this chapter we are treating yeast cells as a model for oxidative stress response and the consequences of oxidative stress which are one cause for a number of human diseases, including neurodegenerative diseases, which form the main part of this paper. All such model building depends on orthologous relations between highly conserved yeast and human genes, which are easily recognized by sequence comparisons, but much more difficult to prove functionally. Previously we have treated Friedreich's ataxia, while presently we are describing in detail the neuronal ceroid lipofuscinoses, among them Batten disease. A general overview is given how yeast can aid current research in three of the most devastating and at the same time quantitatively most important neurodegenerative diseases of old age: Alzheimer's, Huntington's, and Parkinson's disease. In the ensuing part of the chapter, we describe yeast as model for metabolic regulation and hence as a model for inborn errors of metabolism that are in some instances very faithfully mirrored by introducing the same point mutations into yeast cells which are known from patients. PMID:23747875

Breitenbach, Michael; Ralser, Markus; Perrone, Gabriel G; Iglseder, Bernhard; Rinnerthaler, Mark; Dawes, Ian W

2013-06-01

150

Systematic Identification of Pathways That Couple Cell Growth and Division in Yeast  

Microsoft Academic Search

Size homeostasis in budding yeast requires that cells grow to a critical size before commitment to division in the late prereplicative growth phase of the cell cycle, an event termed Start. We determined cell size distributions for the complete set of ~6000 Saccharomyces cerevisiae gene deletion strains and identified ~500 abnormally small (whi) or large (lge) mutants. Genetic analysis revealed

Paul Jorgensen; Joy L. Nishikawa; Bobby-Joe Breitkreutz; Mike Tyers

2002-01-01

151

Identification and characterization of mitochondrial translation products in various yeasts and in Prototheca zopfii  

Microsoft Academic Search

Mitochondrial genomes of different eucaryotes are not all alike. We have examined mitochondrial translation products in a number of yeasts (Candida krusei, Hansenula saturnus, Rhodotorula glutinis, Rhodotorula rubra, Torulopsis glabrata andSaccharomyces cerevisiae) and in Prototheca zopfii, a colorless alga, in order to determine whether certain proteins are invariably synthesized within mitochondria, how different these proteins are, and what additional proteins,

M. Winnann Ewing; Donald W. Deters

1985-01-01

152

Identification of New Genes that Regulate Telomerase and Telomere Length in Budding Yeast.  

National Technical Information Service (NTIS)

In budding yeast, Cdc13 has both an essential function in chromosome end protection as well as a non-essential role in telomere replication, by mediating recruitment of telomerase to the chromosome end. Using fusion protein techniques, we have determined ...

J. Otero

2003-01-01

153

Identification of yeasts and coryneform bacteria from the surface microflora of brick cheeses  

Microsoft Academic Search

Coryneform bacteria and yeasts of 21 brick cheeses from six German dairies, produced by using undefined ripening cultures, were identified. Arthrobacter nicotianae, Brevibacterium linens, Corynebacterium ammoniagenes, Corynebacterium variabilis and Rhodococcus fascians were found in significant numbers. Out of 148 coryneform isolates 36 could not be identified at the species level. With the exception of a large rennet cheese, the coryneform

Natalia Valdés-Stauber; Siegfried Scherer; Herbert Seiler

1997-01-01

154

Identification of Small Molecule Inhibitors of Pseudomonas aeruginosa Exoenzyme S Using a Yeast Phenotypic Screen  

Microsoft Academic Search

Pseudomonas aeruginosa is an opportunistic human pathogen that is a key factor in the mortality of cystic fibrosis patients, and infection represents an increased threat for human health worldwide. Because resistance of Pseudomonas aeruginosa to antibiotics is increasing, new inhibitors of pharmacologically validated targets of this bacterium are needed. Here we demonstrate that a cell-based yeast phenotypic assay, combined with

Anthony Arnoldo; Jasna Curak; Saranya Kittanakom; Igor Chevelev; Vincent T. Lee; Mehdi Sahebol-Amri; Becky Koscik; Lana Ljuma; Peter J. Roy; Antonio Bedalov; Guri Giaever; Corey Nislow; Rod A. Merrill; Stephen Lory; Igor Stagljar

2008-01-01

155

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data  

Microsoft Academic Search

Mounting evidence shows that many protein complexes are conserved in evolution. Here we use conservation to find complexes that are common to yeast S. Cerevisiae and bacteria H. pylori. Our analysis combines protein interaction data, that are available for each of the two species, and orthology information based on protein sequence comparison. We develop a detailed probabilistic model for protein

Roded Sharan; Trey Ideker; Brian P. Kelley; Ron Shamir; Richard M. Karp

2004-01-01

156

Identification of Protein N-Terminal Methyltransferases in Yeast and Humans†  

PubMed Central

Protein modification by methylation is important in cellular function. We show here that the Saccharomyces cerevisiae YBR261C/TAE1 gene encodes an N-terminal protein methyltransferase catalyzing the modification of two ribosomal protein substrates, Rpl12ab and Rps25a/Rps25b. The YBR261C/Tae1 protein is conserved across eukaryotes; all of these proteins share sequence similarity with known seven beta strand class I methyltransferases. Wild type yeast cytosol and mouse heart cytosol catalyze the methylation of a synthetic peptide (PPKQQLSKY) that contains the first eight amino acids of the processed N-terminus of Rps25a/Rps25b. However, no methylation of this peptide is seen in yeast cytosol from a ?YBR261C/tae1 deletion strain. Yeast YBR261C/TAE1 and the human ortholog METTL11A genes were expressed as fusion proteins in Escherichia coli and were shown to be capable of stoichiometrically dimethylating the N-terminus of the synthetic peptide. Furthermore, the YBR261C/Tae1 and METTL11A recombinant proteins methylate variants of the synthetic peptide containing N-terminal alanine and serine residues. However, methyltransferase activity is largely abolished when the proline residue in position 2 or the lysine residue in position 3 is substituted. Thus, the methyltransferases described here specifically recognize the N-terminal X-Pro-Lys sequence motif and we suggest designating the yeast enzyme Ntm1 and the human enzyme NTMT1. These enzymes may account for nearly all previously described eukaryotic protein N-terminal methylation reactions. A number of other yeast and humans proteins also share the recognition motif and may be similarly modified. We conclude that protein X-Pro-Lys N-terminal methylation reactions catalyzed by the enzymes described here may be widespread in nature.

Webb, Kristofor J.; Lipson, Rebecca S.; Al-Hadid, Qais; Whitelegge, Julian P.; Clarke, Steven G.

2010-01-01

157

Identification and Population Dynamics of Yeasts in Sourdough Fermentation Processes by PCR-Denaturing Gradient Gel Electrophoresis  

PubMed Central

Four sourdoughs (A to D) were produced under practical conditions, using a starter obtained from a mixture of three commercially available sourdough starters and baker's yeast. The doughs were continuously propagated until the composition of the microbiota remained stable. A fungi-specific PCR-denaturing gradient gel electrophoresis (DGGE) system was established to monitor the development of the yeast biota. The analysis of the starter mixture revealed the presence of Candida humilis, Debaryomyces hansenii, Saccharomyces cerevisiae, and Saccharomyces uvarum. In sourdough A (traditional process with rye flour), C. humilis dominated under the prevailing fermentation conditions. In rye flour sourdoughs B and C, fermented at 30 and 40°C, respectively, S. cerevisiae became predominant in sourdough B, whereas in sourdough C the yeast counts decreased within a few propagation steps below the detection limit. In sourdough D, which corresponded to sourdough C in temperature but was produced with rye bran, Candida krusei became dominant. Isolates identified as C. humilis and S. cerevisiae were shown by randomly amplified polymorphic DNA-PCR analysis to originate from the commercial starters and the baker's yeast, respectively. The yeast species isolated from the sourdoughs were also detected by PCR-DGGE. However, in the gel, additional bands were visible. Because sequencing of these PCR fragments from the gel failed, cloning experiments with 28S rRNA amplicons obtained from rye flour were performed, which revealed Cladosporium sp., Saccharomyces servazii, S. uvarum, an unculturable ascomycete, Dekkera bruxellensis, Epicoccum nigrum, and S. cerevisiae. The last four species were also detected in sourdoughs A, B, and C.

Meroth, Christiane B.; Hammes, Walter P.; Hertel, Christian

2003-01-01

158

Identification of Medically Important Yeasts Using PCR-Based Detection of DNA Sequence Polymorphisms in the Internal Transcribed Spacer 2 Region of the rRNA Genes  

PubMed Central

Identification of medically relevant yeasts can be time-consuming and inaccurate with current methods. We evaluated PCR-based detection of sequence polymorphisms in the internal transcribed spacer 2 (ITS2) region of the rRNA genes as a means of fungal identification. Clinical isolates (401), reference strains (6), and type strains (27), representing 34 species of yeasts were examined. The length of PCR-amplified ITS2 region DNA was determined with single-base precision in less than 30 min by using automated capillary electrophoresis. Unique, species-specific PCR products ranging from 237 to 429 bp were obtained from 92% of the clinical isolates. The remaining 8%, divided into groups with ITS2 regions which differed by ?2 bp in mean length, all contained species-specific DNA sequences easily distinguishable by restriction enzyme analysis. These data, and the specificity of length polymorphisms for identifying yeasts, were confirmed by DNA sequence analysis of the ITS2 region from 93 isolates. Phenotypic and ITS2-based identification was concordant for 427 of 434 yeast isolates examined using sequence identity of ?99%. Seven clinical isolates contained ITS2 sequences that did not agree with their phenotypic identification, and ITS2-based phylogenetic analyses indicate the possibility of new or clinically unusual species in the Rhodotorula and Candida genera. This work establishes an initial database, validated with over 400 clinical isolates, of ITS2 length and sequence polymorphisms for 34 species of yeasts. We conclude that size and restriction analysis of PCR-amplified ITS2 region DNA is a rapid and reliable method to identify clinically significant yeasts, including potentially new or emerging pathogenic species.

Chen, Y. C.; Eisner, J. D.; Kattar, M. M.; Rassoulian-Barrett, S. L.; LaFe, K.; Yarfitz, S. L.; Limaye, A. P.; Cookson, B. T.

2000-01-01

159

Routine identification of medical fungi by the new Vitek MS matrix-assisted laser desorption ionization-time of flight system with a new time-effective strategy.  

PubMed

We report here a clinical evaluation of the Vitek MS system for rapid fungal identification. A strategy that uses a single deposit without prior protein extraction was utilized to save time and money. Clinical isolates from the Toulouse University hospital were used to evaluate the performance of the Vitek MS compared to that of both routine laboratory techniques and Vitek2. The Vitek MS performed well in the identification of yeasts and Aspergillus fungi (93.2% of correct identifications). PMID:22495559

Iriart, Xavier; Lavergne, Rose-Anne; Fillaux, Judith; Valentin, Alexis; Magnaval, Jean-François; Berry, Antoine; Cassaing, Sophie

2012-04-11

160

Fluorescence-based cloning of a protein tyrosine kinase with a yeast tribrid system.  

PubMed

Post-translational modifications of proteins control myriad biological functions. However, relatively few methods exist for the identification of the enzymes that catalyze these modifications. To expand this repertoire, we report a yeast genetic approach that enables the identification of protein tyrosine kinases (PTKs) from cDNA libraries. Yeasts were transformed with four vectors encoding: 1) a potentially universal PTK substrate fused to the LexA DNA binding domain, 2) the Grb2-SH2 domain fused to the B42 activation domain, 3) a fluorescent reporter gene controlled by LexA DNA sites, and 4) a Jurkat cDNA library. Transient expression of PTKs, such as the lymphocyte-specific kinase Fyn, resulted in phosphorylation of the DNA-bound substrate, recruitment of the Grb2-SH2 domain, and activation of the fluorescent reporter gene. This brief induction of protein expression circumvented the potential toxicity of PTKs to the yeast. Fluorescence activated cell sorting (FACS) enabled isolation of PTKs, and these enzymes were further characterized by flow cytometry and immunoblotting. This approach provides a potentially general method for the identification and evaluation of enzymes involved in the post-translational modification of proteins. PMID:16003805

Clark, Daniel D; Peterson, Blake R

2005-08-01

161

Adaptive system identification using cumulants  

Microsoft Academic Search

A lattice version of the recursive instrumental variable method for adaptive parameter identification of ARMA (autoregressive moving-average) processes is developed. Appropriate choice of the instrumental variables leads to cumulant-based AR parameter estimates. Cumulant-based normal equations may be obtained by using nonconventional orthogonality conditions in the linear prediction problem. The development leads to a pair of lattices, one excited by the

Ananthram Swami; Jerry M. Mendel

1988-01-01

162

Analyzing Fission Yeast Multidrug Resistance Mechanisms to Develop a Genetically Tractable Model System for Chemical Biology  

PubMed Central

SUMMARY Chemical inhibitors can help analyze dynamic cellular processes, particularly when probes are active in genetically tractable model systems. Although fission yeast has served as an important model system, which shares more cellular processes (e.g., RNAi) with humans than budding yeast, its use for chemical biology has been limited by its multidrug resistance (MDR) response. Using genomics and genetics approaches, we identified the key transcription factors and drug-efflux transporters responsible for fission yeast MDR and designed strains sensitive to a wide-range of chemical inhibitors, including commonly used probes. We used this strain, along with acute chemical inhibition and high-resolution imaging, to examine metaphase spindle organization in a “closed” mitosis. Together, our findings suggest that our fission yeast strains will allow the use of several inhibitors as probes, discovery of new inhibitors, and analysis of drug action.

Kawashima, Shigehiro A.; Takemoto, Ai; Nurse, Paul; Kapoor, Tarun M.

2013-01-01

163

Optimization of the preanalytical steps of matrix-assisted laser desorption ionization-time of flight mass spectrometry identification provides a flexible and efficient tool for identification of clinical yeast isolates in medical laboratories.  

PubMed

We report here that modifications of the preanalytical steps of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification of yeasts, with regard to the original protocol provided by the manufacturers, appear to be efficient for the reliable routine identification of clinical yeast isolates in medical laboratories. Indeed, when one colony was sampled instead of five and the protein extraction protocol was modified, the performance of MALDI-TOF MS was superior to that of the API ID 32C method (discrepancies were confirmed by using molecular identification), allowing the correct identification of 94% of the 335 clinical isolates prospectively tested. We then demonstrated that the time for which the primary cultures were preincubated on CHROMagar did not impact the identification of yeasts by MALDI-TOF MS, since 95.1 and 96.2% of the 183 clinical yeast isolates prospectively tested were correctly identified after 48 and 72 h of preincubation, respectively. PMID:22718939

Goyer, Marianne; Lucchi, Geraldine; Ducoroy, Patrick; Vagner, Odile; Bonnin, Alain; Dalle, Frederic

2012-06-20

164

The Crabtree Effect: A Regulatory System in Yeast  

Microsoft Academic Search

SUMMARY When Saccharomyces cerevisiae is growing exponentially on glucose or fructose as carbon plus energy source, and in the presence of air, the glucose degradation proceeds mainly via aerobic fermentation. When the yeast is growing on mannose or galactose, degradation proceeds simultaneously via respiration and fermentation. This situation results from a repression of the of the respiratory enzymes synthesis by

R. H. DE DEKEN

1966-01-01

165

Yeast cells expressing differential levels of human or yeast DNA topoisomerase II: a potent tool for identification and characterization of topoisomerase II-targeting antitumour agents  

Microsoft Academic Search

Purpose: To identify and characterize the specificity and potency of topoisomerase II-interacting antitumour drugs in an in vivo\\u000a model utilizing the yeast Saccharomyces cerevisiae. Methods: Four yeast transformants were selected for the expression of either human or yeast DNA topoisomerase II at different, biologically\\u000a relevant, levels under the tight control of promoters of various strengths. Results: Analyses of 24 drugs

Benoît van Hille; Bridget T. Hill

1998-01-01

166

Isolation of plant transcription factors using a modified yeast one-hybrid system  

Microsoft Academic Search

BACKGROUND: The preparation of expressional cDNA libraries for use in the yeast two-hybrid system is quick and efficient when using the dedicated Clontech™ product, the MATCHMAKER Library Construction and Screening Kit 3. This kit employs SMART technology for the amplification of full-length cDNAs, in combination with cloning using homologous recombination. Unfortunately, such cDNA libraries prepared directly in yeast can not

Sergiy Lopato; Natalia Bazanova; Sarah Morran; Andrew S Milligan; Neil Shirley; Peter Langridge

2006-01-01

167

Saccharomyces cerevisiae Produces a Yeast Substance that Exhibits Estrogenic Activity in Mammalian Systems  

NASA Astrophysics Data System (ADS)

Partially purified lipid extracts of Saccharomyces cerevisiae contain a substance that displaces tritiated estradiol from rat uterine cytosol estrogen receptors. The yeast product induces estrogenic bioresponses in mammalian systems as measured by induction of progesterone receptors in cultured MCF-7 human breast cancer cells and by a uterotrophic response and progesterone receptor induction after administration to ovariectomized mice. The findings raise the possibility that bakers' yeast may be a source of environmental estrogens.

Feldman, David; Stathis, Peter A.; Hirst, Margaret A.; Price Stover, E.; Do, Yung S.; Kurz, Walter

1984-06-01

168

Comprehensive screening of human genes with inhibitory effects on yeast growth and validation of a yeast cell-based system for screening chemicals.  

PubMed

To evaluate yeast as a high-throughput cell-based system for screening chemicals that may lead to drug development, 10,302 full-length human cDNAs (~50% of the total cDNAs) were introduced into yeast. Approximately 5.6% (583 clones) of the cDNAs repressed the growth of yeast. Notably, ~25% of the repressive cDNAs encoded uncharacterized proteins. Small chemicals can be readily surveyed by monitoring their restorative effects on the growth of yeast. The authors focused on protein kinases because protein kinases are involved in various diseases. Among 263 protein kinase cDNAs (~50% of the total) expressed in yeast, 60 cDNAs (~23%), including c-Yes, a member of the Src tyrosine kinase family, inhibited the growth of yeast. Known inhibitors for protein kinases were examined for whether they reversed the c-Yes-induced inhibition of the yeast growth. Among 85 inhibitors tested, 6 compounds (PP2, PP1, SU6656, purvalanol, radicicol, and geldanamycin) reversed the inhibition, indicating a high specificity sufficient for validating this screening system. Human c-Yes was found to interact with Hsc82, one of the yeast chaperones. Radicicol and geldanamycin probably exerted their actions through interactions with Hsc82. These results indicate that when human proteins requiring molecular chaperones for their activities are subjected to the yeast screening system, 2 groups of chemicals may be found. The actions of one group are exerted through direct interactions with the human proteins, whereas those of the other group are mediated through interactions with chaperones. PMID:20237203

Sekigawa, Masayuki; Kunoh, Tatsuki; Wada, Shu-Ichi; Mukai, Yukio; Ohshima, Kazuhiko; Ohta, Shinji; Goshima, Naoki; Sasaki, Ryuzo; Mizukami, Tamio

2010-03-17

169

Isolation and Characterization of a Dibenzofuran-Degrading Yeast: Identification of Oxidation and Ring Cleavage Products  

PubMed Central

We characterized the ability of a yeast to cleave the aromatic structure of the dioxin-like compound dibenzofuran. The yeast strain was isolated from a dioxin-contaminated soil sample and identified as Trichosporon mucoides. During incubation of glucose-pregrown cells with dibenzofuran, six major metabolites were detected by high-performance liquid chromatography. The formation of four different monohydroxylated dibenzofurans was proven by comparison of analytical data (gas chromatography-mass spectrometry) with that for authentic standards. Further oxidation produced 2,3-dihydroxydibenzofuran and its ring cleavage product 2-(1-carboxy methylidene)-2,3-dihydrobenzo[b]furanylidene glycolic acid, which were characterized by mass spectrometry and 1H nuclear magnetic resonance spectroscopy. These two metabolites are derived from 2-hydroxydibenzofuran and 3-hydroxydibenzofuran, as shown by incubation experiments using these monohydroxylated dibenzofurans as substrates.

Hammer, Elke; Krowas, Dirk; Schafer, Annett; Specht, Michael; Francke, Wittko; Schauer, Frieder

1998-01-01

170

Identification of Connexin-Interacting Proteins: Application of the Yeast Two-Hybrid Screen  

Microsoft Academic Search

Protein–protein interactions are recognized as one of the fundamental mechanisms for relaying the intra- and intercellular signals that are required for normal cellular activities affecting growth, development, and maintenance of homeostasis in tissues and organs. The yeast two-hybrid screen has become a valuable tool for identifying protein–protein interactions. The gap junction protein connexin 43 (Cx43) has been implicated in a

Chengshi Jin; Alan F. Lau; Kendra Dean Martyn

2000-01-01

171

Identification of a coffee berry borer-associated yeast: does it break down caffeine?  

Microsoft Academic Search

Two yeasts isolated from laboratory reared adult coffee berry borers ( Hypothenemus hampei (Ferrari) (Coleoptera: Scolytidae)) and from insects collected in the field in Colombia were identified as Pichia burtonii Boidin and Candida fermentati (Saito) Bai, based on sequencing of the nuclear large subunit 26S rDNA variable D1\\/D2 domain. Liquid culture experiments using P. burtonii in media containing different caffeine

Fernando E. Vega; Michael B. Blackburn; Cletus P. Kurtzman; Patrick F. Dowd

2003-01-01

172

Identification of eukaryotic secreted and cell surface proteins using the yeast secretion trap screen  

Microsoft Academic Search

Secreted and cell surface proteins play essential roles in numerous essential biological processes in eukaryotic organisms, but are often more difficult to isolate and identify than proteins that are localized in intracellular compartments. However, several high-throughput 'gene-trap' techniques have been developed to characterize these 'secretomes', including the yeast secretion trap (YST) screen. This method involves fusing cDNA libraries from the

Sang-Jik Lee; Byung-Dong Kim; Jocelyn K C Rose

2006-01-01

173

Aniline blue-containing buffered charcoal-yeast extract medium for presumptive identification of Legionella species  

SciTech Connect

By utilizing buffered charcoal-yeast extract medium containing 0.01% aniline blue in conjunction with a long-wave UV light, the differentiation of five species of Legionella was facilitated. L. pneumophila, when grown on this medium, did not absorb the aniline blue dye; however, L. micdadei, L. dumoffii, L. bozemanii, and L. gormanii absorbed the dye in varying amounts and produced colonies of various shades of blue.

Holmes, R.L.

1982-04-01

174

Determinants of Allosteric Activation of Yeast Pyruvate Kinase and Identification of Novel Effectors Using Computational Screening †  

Microsoft Academic Search

We have analyzed the structural determinants of the allosteric activation of yeast pyruvate kinase (YPK) by mutational and kinetic analysis and initiated a structure-based design project to identify novel effectors that modulate its allosteric response by binding to the allosteric site for fructose-1,6- bisphosphate (FBP). The wild-type enzyme is strongly activated by fructose-1,6-bisphosphate and weakly activated by both fructose-1-phosphate and

Christopher J. Bond; Melissa S. Jurica; Andrew Mesecar; Barry L. Stoddard

2000-01-01

175

Identification of yeasts isolated from wine-related environments and capable of producing 4-ethylphenol  

Microsoft Academic Search

The ability to produce 4-ethylphenol from the substrate p-coumaric acid in synthetic media was evaluated for several yeast species associated with wine production. Molar conversion rates as high as 90% were found by only Dekkera bruxellensis, D. anomala and by some unidentified strains isolated from wine-related environments. Other unidentified strains produced traces of 4-ethylphenol. All unidentified strains showed the same

L. Dias; S. Dias; T. Sancho; H. Stender; A. Querol; M. Malfeito-Ferreira; V. Loureiro

2003-01-01

176

Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast.  

PubMed Central

A gene from Saccharomyces cerevisiae has been mapped, cloned, sequenced and shown to encode a catalytic subunit of an N-terminal acetyltransferase. Regions of this gene, NAT1, and the chloramphenicol acetyltransferase genes of bacteria have limited but significant homology. A nat1 null mutant is viable but exhibits a variety of phenotypes, including reduced acetyltransferase activity, derepression of a silent mating type locus (HML) and failure to enter G0. All these phenotypes are identical to those of a previously characterized mutant, ard1. NAT1 and ARD1 are distinct genes that encode proteins with no obvious similarity. Concomitant overexpression of both NAT1 and ARD1 in yeast causes a 20-fold increase in acetyltransferase activity in vitro, whereas overexpression of either NAT1 or ARD1 alone does not raise activity over basal levels. A functional iso-1-cytochrome c protein, which is N-terminally acetylated in a NAT1 strain, is not acetylated in an isogenic nat1 mutant. At least 20 other yeast proteins, including histone H2B, are not N-terminally acetylated in either nat1 or ard1 mutants. These results suggest that NAT1 and ARD1 proteins function together to catalyze the N-terminal acetylation of a subset of yeast proteins. Images

Mullen, J R; Kayne, P S; Moerschell, R P; Tsunasawa, S; Gribskov, M; Colavito-Shepanski, M; Grunstein, M; Sherman, F; Sternglanz, R

1989-01-01

177

Construction and identification of a yeast two-hybrid bait vector and its effect on the growth of yeast cells and the self-activating function of reporter genes for screening of HPV18 E6-interacting protein  

Microsoft Academic Search

Summary  By using a yeast two-hybrid system, a yeast two-hybrid bait vector was constructed and identified for screening of the HPV18\\u000a E6-interacting proteins, and its effects on the growth of yeast cells and the activation of reporter genes were investigated.\\u000a Total mRNA extracted from Hela cells was reversely transcribed into cDNA. Fragment of HPV18 E6 cDNA was amplified using RT-PCR\\u000a and

Quan Mei; Shuang Li; Ping Liu; Ling Xi; Shixuan Wang; Yuhan Meng; Jie Liu; Xinwei Yang; Yunping Lu; Hui Wang

2010-01-01

178

Talker Identification Using Reverberation Sensing System  

Microsoft Academic Search

In this paper, we propose a robust talker identification (TI) system that can identify speakers in different reverberant environments. We describe a reverberation sensing system (RSS) that determines the approximate reverberation level of the surrounding environment, and then selects a TI engine trained in a similar reverberant environment; greater TI accuracy is achieved when training and test environments are similar.

A. R. Abu-El-Quran; J. S. Gammal; R. A. Goubran; A. D. C. Chan

2007-01-01

179

XC automatic equipment identification (AEI) system  

Microsoft Academic Search

XC AEI system that is researched and manufactured by Lanzhou Yuanwang IT Co. Ltd. is presented. This system has mainly been developed for the automatic electronic identification of freight cars and locomotives on railroads. Its composition, main specifications and technical innovations are introduced in this paper

Xu Yusuo; Ruan Jinping

2000-01-01

180

Simulation of a Radio Frequency Identification System  

Microsoft Academic Search

As supply chains become more complex, RFID deployment is needed for efficient item identification and tracking. A system simulation of RFID is constructed in this paper. RFID systems consist of tags and readers. Tags are components that store the information and are physically attached to each item. The tag transmits information back to the reader by modulating an RF signal

Sara Abou Chakra; Usamah O. Farrukh; B. A. Garcia

2009-01-01

181

Yeast protein synthesis. Preparation and analysis of a highly active cell-free system  

PubMed Central

A detailed description is given of the techniques for preparing, handling and assaying a cell-free protein-synthesizing system from yeast, analogous to crude (S-30) Escherichia coli extracts. Its basic characteristics are described. The rate of poly(U)-directed polyphenylalanine synthesis was at least fivefold higher than in previously reported yeast cell-free systems, approaching that of crude mammalian cell-free systems. Fractionation of the S-30 extracts lowered activity. Organelles and their fragments present in the S-30 extract neither contributed to nor inhibited cytoplasmic protein synthesis. There was a component localized in the high-speed supernatant that caused an inhibition of polyphenylalanine synthesis. Poly(U) programmed the synthesis of long-chain polyphenylalanine, in contrast with the only other yeast system in which this has been examined (Bretthauer & Golichowski, 1968). Preincubation techniques inactivated the system and probably a small proportion only of the ribosomes was active.

Sissons, Christopher H.

1974-01-01

182

Evaluation of a novel rapid detection system for yeasts and molds.  

PubMed

A novel system, the NISSUI rapid detection system, has been developed to rapidly detect yeasts and molds in food. This system consists of a liquid medium containing resazurin as a redox indicator, a unique original micro-well dish containing 676 micro-wells, and a fluorescence-monitoring instrument with an incubator. To evaluate this system, orange juice, milk, and physiological saline solutions artificially inoculated with yeasts or molds were used as samples. Comparison of the new system used at 28ºC for 48 h with a spread-plate method using a potato-dextrose-agar plate at 25ºC for 120 h yielded a correlation coefficient (r) of 0.95. Our data reveal that the new method considerably shortens the time required for detection of yeasts and molds in food. PMID:21212506

Tominaga, Kei; Ii, Toshihiro; Kashiwabara, Fumi; Hara, Ryotaro; Uesaka, Yoshihiko; Kodaka, Hidemasa

2010-12-01

183

Functional Analysis With a Barcoder Yeast Gene Overexpression System  

PubMed Central

Systematic analysis of gene overexpression phenotypes provides an insight into gene function, enzyme targets, and biological pathways. Here, we describe a novel functional genomics platform that enables a highly parallel and systematic assessment of overexpression phenotypes in pooled cultures. First, we constructed a genome-level collection of ~5100 yeast barcoder strains, each of which carries a unique barcode, enabling pooled fitness assays with a barcode microarray or sequencing readout. Second, we constructed a yeast open reading frame (ORF) galactose-induced overexpression array by generating a genome-wide set of yeast transformants, each of which carries an individual plasmid-born and sequence-verified ORF derived from the Saccharomyces cerevisiae full-length EXpression-ready (FLEX) collection. We combined these collections genetically using synthetic genetic array methodology, generating ~5100 strains, each of which is barcoded and overexpresses a specific ORF, a set we termed “barFLEX.” Additional synthetic genetic array allows the barFLEX collection to be moved into different genetic backgrounds. As a proof-of-principle, we describe the properties of the barFLEX overexpression collection and its application in synthetic dosage lethality studies under different environmental conditions.

Douglas, Alison C.; Smith, Andrew M.; Sharifpoor, Sara; Yan, Zhun; Durbic, Tanja; Heisler, Lawrence E.; Lee, Anna Y.; Ryan, Owen; Gottert, Hendrikje; Surendra, Anu; van Dyk, Dewald; Giaever, Guri; Boone, Charles; Nislow, Corey; Andrews, Brenda J.

2012-01-01

184

Identification of triacylglycerol and steryl ester synthases of the methylotrophic yeast Pichia pastoris  

PubMed Central

In yeast like in many other eukaryotes, fatty acids are stored in the biologically inert form of triacylglycerols (TG) and steryl esters (SE) as energy reserve and/or as membrane building blocks. In the present study, we identified gene products catalyzing formation of TG and SE in the methylotrophic yeast Pichia pastoris. Based on sequence homologies to Saccharomyces cerevisiae, the two diacylglycerol acyltransferases Dga1p and Lro1p and one acyl CoA:sterol acyltransferase Are2p from P. pastoris were identified. Mutants bearing single and multiple deletions of the respective genes were analyzed for their growth phenotype, lipid composition and the ability to form lipid droplets. Our results indicate that the above mentioned gene products are most likely responsible for the entire TG and SE synthesis in P. pastoris. Lro1p which has low fatty acid substrate specificity in vivo is the major TG synthase in this yeast, whereas Dga1p contributes less to TG synthesis although with some preference to utilize polyunsaturated fatty acids as substrates. In contrast to S. cerevisiae, Are2p is the only SE synthase in P. pastoris. Also this enzyme exhibits some preference for certain fatty acids as judged from the fatty acid profile of SE compared to bulk lipids. Most interestingly, TG formation in P. pastoris is indispensable for lipid droplet biogenesis. The small amount of SE synthesized by Are2p in a dga1?lro1? double deletion mutant is insufficient to initiate the formation of the storage organelle. In summary, our data provide a first insight into the molecular machinery of non-polar lipid synthesis and storage in P. pastoris and demonstrate specific features of this machinery in comparison to other eukaryotic cells, especially S. cerevisiae.

Ivashov, Vasyl A.; Zellnig, Guenther; Grillitsch, Karlheinz; Daum, Guenther

2013-01-01

185

Identification of Telomerase RNAs from Filamentous Fungi Reveals Conservation with Vertebrates and Yeasts  

PubMed Central

Telomeres are the nucleoprotein complexes at eukaryotic chromosomal ends. Telomeric DNA is synthesized by the ribonucleoprotein telomerase, which comprises a telomerase reverse transcriptase (TERT) and a telomerase RNA (TER). TER contains a template for telomeric DNA synthesis. Filamentous fungi possess extremely short and tightly regulated telomeres. Although TERT is well conserved between most organisms, TER is highly divergent and thus difficult to identify. In order to identify the TER sequence, we used the unusually long telomeric repeat sequence of Aspergillus oryzae together with reverse-transcription-PCR and identified a transcribed sequence that contains the potential template within a region predicted to be single stranded. We report the discovery of TERs from twelve other related filamentous fungi using comparative genomic analysis. These TERs exhibited strong conservation with the vertebrate template sequence, and two of these potentially use the identical template as humans. We demonstrate the existence of important processing elements required for the maturation of yeast TERs such as an Sm site, a 5? splice site and a branch point, within the newly identified TER sequences. RNA folding programs applied to the TER sequences show the presence of secondary structures necessary for telomerase activity, such as a yeast-like template boundary, pseudoknot, and a vertebrate-like three-way junction. These telomerase RNAs identified from filamentous fungi display conserved structural elements from both yeast and vertebrate TERs. These findings not only provide insights into the structure and evolution of a complex RNA but also provide molecular tools to further study telomere dynamics in filamentous fungi.

Kuprys, Paulius V.; Davis, Shaun M.; Hauer, Tyler M.; Meltser, Max; Tzfati, Yehuda; Kirk, Karen E.

2013-01-01

186

Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry  

Microsoft Academic Search

Herewereporttherapididentificationofthe proteins of the spliceosomal U1 small nuclear ribonucleopro- tein (snRNP) from the yeast Saccharomyces cerevisiae by searching mass spectrometric data in genomic sequence da- tabases. The U1 snRNP, containing a histidine-tagged 70K protein, was isolated from cell extracts by anti m3G-cap immunoaffinity and subsequent nickel nitrilotriacetic acid chromatography.AU1snRNPfractioncontaining20proteins was obtained. Further purification by glycerol gradient cen- trifugationidentifiednineU1snRNPspecificandsixcommon proteins. The

A LEXANDERGOTTSCHALK; Emil Mannkopff-Strasse

187

Identification of Malassezia yeast species isolated from patients with pityriasis versicolor.  

PubMed

Pityriasis versicolor (PV) is a disease with worldwide distribution. Twelve different species of Malassezia yeast have been described. The objective of this study was to determine which species of Malassezia are more prevalent in patients with pityriasis versicolor. Samples were collected by scraping the lesions of 87 patients with a clinical suspicion of pityriasis versicolor. The samples were then submitted to fungal microscopy and culture to identify the species. The species found were: Malassezia sympodialis (30%), Malassezia furfur (25.7%), Malassezia globosa (22.7%), Malassezia restricta (12.1%), Malassezia obtusa (7.6%) and Malassezia slooffiae (1.5%). PMID:21987156

Petry, Vanessa; Tanhausen, Fernanda; Weiss, Luciana; Milan, Thais; Mezzari, Adelina; Weber, Magda Blessmann

188

[A study of culture-based easy identification system for Malassezia].  

PubMed

Most species of this genus are lipid-dependent yeasts, which colonize the seborrheic part of the skin, and they have been reported to be associated with pityriasis versicolor, Malassezia folliculitis, seborrheic dermatitis, and atopic dermatitis. Malassezia have been re-classified into 7 species based on molecular biological analysis of nuclear ribosomal DNA/RNA and new Malassezia species were reported. As members of the genus Malassezia share similar morphological and biochemical characteristics, it was thought to be difficult to differentiate between them based on phenotypic features. While molecular biological techniques are the most reliable methods for identification of Malassezia, they are not available in most clinical laboratories. We studied ( i ) development of an efficient isolation media and culture based easy identification system, ( ii ) the incidence of atypical biochemical features in Malassezia species and propose a culture-based easy identification system for clinically important Malassezia species, M. globosa, M. restricta, and M. furfur. PMID:22123328

Kaneko, Takamasa

2011-01-01

189

Identification for disturbed MIMO Wiener systems  

Microsoft Academic Search

The identification of Multi-input Multi-output (MIMO) Wiener systems is concerned in this paper. The system presented is comprised\\u000a of a multi-dimensional linear subsystem and a memory-less nonlinear block which is made of discontinuous asymmetric piece-wise\\u000a linear functions. A recursive algorithm is proposed to estimate all the unknown parameters of the system with interference\\u000a noises. It is shown that the recursive algorithm

Dan Fan; Kueiming Lo

2009-01-01

190

Coated whey protein/alginate microparticles as oral controlled delivery systems for probiotic yeast.  

PubMed

Viable Saccharomyces boulardii, used as a biotherapeutic agent, was encapsulated in food-grade whey protein isolate (WP) and alginate (ALG) microparticles, in order to protect and vehicle them in gastrointestinal environment. Yeast-loaded microparticles with a WP/ALG ratio of 62/38 were produced with high encapsulation efficiency (95%) using an extrusion/cold gelation method and coated with ALG or WP by a simple immersion method. Swelling, yeast survival, WP loss and yeast release in simulated gastric and intestinal fluids (SGF and SIF, pH 1.2 and 7.5) with and without their respective digestive enzymes (pepsin and pancreatin) were investigated. In SGF, ALG network shrinkage limited enzyme diffusion into the WP/ALG matrix. Coated and uncoated WP/ALG microparticles were resistant in SGF even with pepsin. Survival of yeast cells in microparticles was 40% compared to 10% for free yeast cells and was improved to 60% by coating. In SIF, yeast cell release followed coated microparticle swelling with a desirable delay. Coated WP/ALG microparticles appear to have potential as oral delivery systems for Saccharomyces boulardii or as encapsulation means for probiotic cells in pharmaceutical or food processing applications. PMID:20163284

Hébrard, Géraldine; Hoffart, Valérie; Beyssac, Eric; Cardot, Jean-Michel; Alric, Monique; Subirade, Muriel

2010-01-01

191

System identification using nonstationary signals  

Microsoft Academic Search

The conventional method for identifying the transfer function of an unknown linear system consists of a least squares fit of its input to its output. It is equivalent to identifying the frequency response of the system by calculating the empirical cross-spectrum between the system's input and output, divided by the empirical auto-spectrum of the input process. However, if the additive

Ofir Shalvi; Ehud Weinstein

1996-01-01

192

Identification of a tomato gene for the ethylene-forming enzyme by expression in yeast.  

PubMed Central

The ethylene-forming enzyme (EFE), which catalyzes the last step in the biosynthesis of the plant hormone ethylene, has never been purified and no molecular probes are available. Recently, a putative cDNA clone for tomato EFE (pTOM13) has been identified by inhibiting ethylene synthesis with an antisense gene expressed in transgenic plants. A direct test of its function has been made by expression of a pTOM13 gene in Saccharomyces cerevisiae. After cloning artefacts were discovered in the 5' region of the cDNA, a corrected cDNA (pRC13) was created by the fusion of the 5' end of a genomic clone to the 3' end of the cDNA and expressed in S. cerevisiae. Cultures of transformed yeast converted 1-aminocyclopropane-1-carboxylic acid (ACC) to ethylene, whereas control cells did not. This EFE activity displays similar characteristics to EFE found in plant tissue: it converts the trans isomer of the ACC analogue 1-amino-2-ethylcyclopropane-1-carboxylic acid to 1-butene in preference to the cis isomer, and it is strongly inhibited by cobaltous ions and 1,10-phenanthroline. Furthermore, information gained from the activity of effectors on yeast EFE activity supports the hypothesis that EFE is one of a group of hydroxylase enzymes. Images

Hamilton, A J; Bouzayen, M; Grierson, D

1991-01-01

193

Identification of Novel Membrane-binding Domains in Multiple Yeast Cdc42 Effectors  

PubMed Central

The Rho-type GTPase Cdc42 is a central regulator of eukaryotic cell polarity and signal transduction. In budding yeast, Cdc42 regulates polarity and mitogen-activated protein (MAP) kinase signaling in part through the PAK-family kinase Ste20. Activation of Ste20 requires a Cdc42/Rac interactive binding (CRIB) domain, which mediates its recruitment to membrane-associated Cdc42. Here, we identify a separate domain in Ste20 that interacts directly with membrane phospholipids and is critical for its function. This short region, termed the basic-rich (BR) domain, can target green fluorescent protein to the plasma membrane in vivo and binds PIP2-containing liposomes in vitro. Mutation of basic or hydrophobic residues in the BR domain abolishes polarized localization of Ste20 and its function in both MAP kinase–dependent and independent pathways. Thus, Cdc42 binding is required but is insufficient; instead, direct membrane binding by Ste20 is also required. Nevertheless, phospholipid specificity is not essential in vivo, because the BR domain can be replaced with several heterologous lipid-binding domains of varying lipid preferences. We also identify functionally important BR domains in two other yeast Cdc42 effectors, Gic1 and Gic2, suggesting that cooperation between protein–protein and protein–membrane interactions is a prevalent mechanism during Cdc42-regulated signaling and perhaps for other dynamic localization events at the cell cortex.

Takahashi, Satoe

2007-01-01

194

Identification and characterization of major lipid particle proteins of the yeast Saccharomyces cerevisiae.  

PubMed

Lipid particles of the yeast Saccharomyces cerevisiae were isolated at high purity, and their proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Major lipid particle proteins were identified by mass spectrometric analysis, and the corresponding open reading frames (ORFs) were deduced. In silicio analysis revealed that all lipid particle proteins contain several hydrophobic domains but none or only few (hypothetical) transmembrane spanning regions. All lipid particle proteins identified by function so far, such as Erg1p, Erg6p, and Erg7p (ergosterol biosynthesis) and Faa1p, Faa4p, and Fat1p (fatty acid metabolism), are involved in lipid metabolism. Based on sequence homology, another group of three lipid particle proteins may be involved in lipid degradation. To examine whether lipid particle proteins of unknown function are also involved in lipid synthesis, mutants with deletions of the respective ORFs were constructed and subjected to systematic lipid analysis. Deletion of YDL193w resulted in a lethal phenotype which could not be suppressed by supplementation with ergosterol or fatty acids. Other deletion mutants were viable under standard conditions. Strains with YBR177c, YMR313c, and YKL140w deleted exhibited phospholipid and/or neutral lipid patterns that were different from the wild-type strain and thus may be further candidate ORFs involved in yeast lipid metabolism. PMID:10515935

Athenstaedt, K; Zweytick, D; Jandrositz, A; Kohlwein, S D; Daum, G

1999-10-01

195

Identification and Characterization of Major Lipid Particle Proteins of the Yeast Saccharomyces cerevisiae  

PubMed Central

Lipid particles of the yeast Saccharomyces cerevisiae were isolated at high purity, and their proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Major lipid particle proteins were identified by mass spectrometric analysis, and the corresponding open reading frames (ORFs) were deduced. In silicio analysis revealed that all lipid particle proteins contain several hydrophobic domains but none or only few (hypothetical) transmembrane spanning regions. All lipid particle proteins identified by function so far, such as Erg1p, Erg6p, and Erg7p (ergosterol biosynthesis) and Faa1p, Faa4p, and Fat1p (fatty acid metabolism), are involved in lipid metabolism. Based on sequence homology, another group of three lipid particle proteins may be involved in lipid degradation. To examine whether lipid particle proteins of unknown function are also involved in lipid synthesis, mutants with deletions of the respective ORFs were constructed and subjected to systematic lipid analysis. Deletion of YDL193w resulted in a lethal phenotype which could not be suppressed by supplementation with ergosterol or fatty acids. Other deletion mutants were viable under standard conditions. Strains with YBR177c, YMR313c, and YKL140w deleted exhibited phospholipid and/or neutral lipid patterns that were different from the wild-type strain and thus may be further candidate ORFs involved in yeast lipid metabolism.

Athenstaedt, Karin; Zweytick, Dagmar; Jandrositz, Anita; Kohlwein, Sepp Dieter; Daum, Gunther

1999-01-01

196

Frequency-variation method for system identification  

Microsoft Academic Search

A frequency-variation method is established for identifying a linear system transfer function from a single set of frequency response data. The method generally applies three different Cauer continued fraction forms. Based on the real and imaginary parts of the frequency response data, a corresponding transfer function can be identified. The identification processes can be carried out with a digital computer.

Leang-San Shieh; JOSE MARIANO NAVARRO

1974-01-01

197

The yeast tribrid system--genetic detection of trans-phosphorylated ITAM-SH2-interactions.  

PubMed

Protein-protein interactions are often dependent on the post-translational modification of one component of a complex. To facilitate the study of these interactions in signal transduction, we have developed the yeast tribrid system, a modification of the yeast two-hybrid system. We demonstrate that the interactions are dependent upon the presence of a tyrosine kinase, an SH2 domain and a tyrosine containing substrate. Using the gamma subunit of the high-affinity IgE receptor, Fc epsilon RI, this approach has been used to isolate a novel SH2-containing family member. The mRNA encoding this novel protein is differentially expressed in rat tissues. The yeast tribrid system can be readily adapted for the characterization of novel tyrosine kinases or substrates, as well as the study of protein-protein interactions which involve other post-translational modifications. PMID:9636306

Osborne, M A; Dalton, S; Kochan, J P

1995-12-01

198

Using the yeast two-hybrid system to identify protein-protein interactions.  

PubMed

The yeast two-hybrid system is currently one of the most standardized protein interaction mapping techniques. The rationale of the yeast two-hybrid system relies on the physical separation of the DNA-binding domain from the transcriptional activation domain of several transcription factors. The protein of interest (bait) is fused to a DNA-binding domain, and complementary DNA (cDNA) library-encoded proteins are fused to a transcriptional activation domain. When a protein encoded by the cDNA library binds to the bait, both activities of the transcription factor are rejoined resulting in transcription from a reporter gene. Here, we describe protocols to test interactions between two individual proteins and to look for novel interacting partners by screening a single protein or domain against a library of other proteins using a GAL4 based yeast two-hybrid system. PMID:24136527

Rodríguez-Negrete, Edgar; Bejarano, Eduardo R; Castillo, Araceli G

2014-01-01

199

Validation of a Flour-Free Model Dough System for Throughput Studies of Baker's Yeast  

Microsoft Academic Search

Evaluation of gene expression in baker's yeast requires the extraction and collection of pure samples of RNA. However, in bread dough this task is difficult due to the complex composition of the system. We found that a liquid model system can be used to analyze the transcriptional response of industrial strains in dough with a high sugar content. The production

Joaquin Panadero; Francisca Randez-Gil; Jose Antonio Prieto

2005-01-01

200

Reliability of the WIDERYST Susceptibility Testing System for Detection of In Vitro Antifungal Resistance in Yeasts  

Microsoft Academic Search

This study evaluated the WIDERYST system, a commercially available computer-assisted image-processing device for the antifungal susceptibility testing of yeasts. A collection of 90 clinical isolates selected to represent ranges of susceptibilities in vitro as broad as possible was tested. An evaluation compared the results obtained by the new system with those achieved by both the Clinical and Laboratory Standards Institute

Manuel Cuenca-Estrella; Alicia Gomez-Lopez; M. Olga Gutierrez; M. Jose Buitrago; Juan L. Rodriguez-Tudela

2008-01-01

201

21 CFR 880.6300 - Implantable radiofrequency transponder system for patient identification and health information.  

Code of Federal Regulations, 2010 CFR

... false Implantable radiofrequency transponder system for patient identification and...6300 Implantable radiofrequency transponder system for patient identification and...Identification . An implantable radiofrequency transponder system for patient...

2010-04-01

202

21 CFR 880.6300 - Implantable radiofrequency transponder system for patient identification and health information.  

Code of Federal Regulations, 2010 CFR

... false Implantable radiofrequency transponder system for patient identification and...6300 Implantable radiofrequency transponder system for patient identification and...Identification . An implantable radiofrequency transponder system for patient...

2009-04-01

203

Identification of Noncoding Transcripts from within CENP-A Chromatin at Fission Yeast Centromeres*  

PubMed Central

The histone H3 variant CENP-A is the most favored candidate for an epigenetic mark that specifies the centromere. In fission yeast, adjacent heterochromatin can direct CENP-ACnp1 chromatin establishment, but the underlying features governing where CENP-ACnp1 chromatin assembles are unknown. We show that, in addition to centromeric regions, a low level of CENP-ACnp1 associates with gene promoters where histone H3 is depleted by the activity of the Hrp1Chd1 chromatin-remodeling factor. Moreover, we demonstrate that noncoding RNAs are transcribed by RNA polymerase II (RNAPII) from CENP-ACnp1 chromatin at centromeres. These analyses reveal a similarity between centromeres and a subset of RNAPII genes and suggest a role for remodeling at RNAPII promoters within centromeres that influences the replacement of histone H3 with CENP-ACnp1.

Choi, Eun Shik; Stralfors, Annelie; Castillo, Araceli G.; Durand-Dubief, Mickael; Ekwall, Karl; Allshire, Robin C.

2011-01-01

204

Zymological indicators: a new concept applied to the detection of potential spoilage yeast species associated with fruit pulps and concentrates  

Microsoft Academic Search

In a survey of the microbial quality of raw materials used in fruit juice processing, yeast counts in fruit concentrates and pulps were found to range from <1 to 2·9×103cfu g?1. Ascomycetous yeasts were represented by 76% of the isolates while 24% were basidiomycetes. The identification of strains isolated by the simplified identification system (SIM) revealed 19 yeast species representing

T. Sancho; G. Gimenez-Jurado; M. Malfeito-Ferreira; V. Loureiro

2000-01-01

205

Isolation and Identification of Black Yeasts by Enrichment on Atmospheres of Monoaromatic Hydrocarbons  

PubMed Central

Black yeast members of the Herpotrichiellaceae present a complex ecological behavior: They are often isolated from rather extreme environments polluted with aromatic hydrocarbons, while they are also regularly involved in human opportunistic infections. A selective technique to promote the in vitro growth of herpotrichiellaceous fungi was applied to investigate their ecophysiology. Samples from natural ecological niches and man-made environments that might contain black yeasts were enriched on an inert solid support at low humidity and under a controlled atmosphere rich in volatile aromatic hydrocarbons. Benzene, toluene, and xylene were provided separately as the sole carbon and energy source via the gas phase. The assayed isolation protocol was highly specific toward mesophilic Exophiala species (70 strains of this genus out of 71 isolates). Those were obtained predominantly from creosote-treated railway ties (53 strains), but isolates were also found on wild berries (11 strains) and in guano-rich soil samples (six strains). Most of the isolates were obtained on toluene (43 strains), but enrichments on xylene and benzene also yielded herpotrichiellaceous fungi (17 and 10 isolates, respectively). Based upon morphological characterizations and DNA sequences of the full internal transcriber spacers (ITS) and the 8.5S rRNA genes, the majority of the obtained isolates were affiliated to the recently described species Exophiala xenobiotica (32 strains) and Exophiala bergeri (nine strains). Members of two other phylogenetic groups (24 and two strains, respectively) somewhat related to E. bergeri were also found, and a last group (three strains) corresponded to an undescribed Exophiala species.

Zhao, Jingjun; Zeng, Jingsi; de Hoog, G. Sybren; Attili-Angelis, Derlene

2010-01-01

206

Application of the FLP/FRT system for conditional gene deletion in yeast Saccharomyces cerevisiae†  

PubMed Central

The yeast Saccharomyces cerevisiae has proved to be an excellent model organism to study the function of proteins. One of the many advantages of yeast is the many genetic tools available to manipulate gene expression, but there are still limitations. To complement the many methods used to control gene expression in yeast, we have established a conditional gene deletion system by using the FLP/FRT system on yeast vectors to conditionally delete specific yeast genes. Expression of Flp recombinase, which is under the control of the GAL1 promoter, was induced by galactose, which in turn excised FRT sites flanked genes. The efficacy of this system was examined using the FRT site-flanked genes HSP104, URA3 and GFP. The pre-excision frequency of this system, which might be caused by the basal activity of the GAL1 promoter or by spontaneous recombination between FRT sites, was detected ca. 2% under the non-selecting condition. After inducing expression of Flp recombinase, the deletion efficiency achieved ca. 96% of cells in a population within 9 h. After conditional deletion of the specific gene, protein degradation and cell division then diluted out protein that was expressed from this gene prior to its excision. Most importantly, the specific protein to be deleted could be expressed under its own promoter, so that endogenous levels of protein expression were maintained prior to excision by the Flp recombinase. Therefore, this system provides a useful tool for the conditional deletion of genes in yeast. Published in 2011 by John Wiley & Sons, Ltd.

Park, Yang-Nim; Masison, Daniel; Eisenberg, Evan; Greene, Lois E

2011-01-01

207

Large-scale analysis of the yeast proteome by multidimensional protein identification technology  

Microsoft Academic Search

We describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and database searching by the SEQUEST algorithm, named multidimensional protein identification technology (MudPIT). MudPIT was applied to the proteome of the Saccharomyces cerevisiae strain BJ5460 grown to mid-log phase and yielded the largest proteome analysis to date. A total of 1,484

Michael P. Washburn; Dirk Wolters; John R. Yates III

2001-01-01

208

Identification of multivariate linear systems  

SciTech Connect

This paper considers the problem of modeling multivariate linear systems where noisy output measurements are the only available data. The techniques presented are valid for a class of canonical forms. Results from several simulations demonstrate the capability for structure and parameter estimation.

Griffith, J.M.

1981-01-01

209

A new system for comparative functional genomics of Saccharomyces yeasts.  

PubMed

Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var. uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene-expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting data set reveals that gene-expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast. PMID:23852385

Caudy, Amy A; Guan, Yuanfang; Jia, Yue; Hansen, Christina; DeSevo, Chris; Hayes, Alicia P; Agee, Joy; Alvarez-Dominguez, Juan R; Arellano, Hugo; Barrett, Daniel; Bauerle, Cynthia; Bisaria, Namita; Bradley, Patrick H; Breunig, J Scott; Bush, Erin; Cappel, David; Capra, Emily; Chen, Walter; Clore, John; Combs, Peter A; Doucette, Christopher; Demuren, Olukunle; Fellowes, Peter; Freeman, Sam; Frenkel, Evgeni; Gadala-Maria, Daniel; Gawande, Richa; Glass, David; Grossberg, Samuel; Gupta, Anita; Hammonds-Odie, Latanya; Hoisos, Aaron; Hsi, Jenny; Hsu, Yu-Han Huang; Inukai, Sachi; Karczewski, Konrad J; Ke, Xiaobo; Kojima, Mina; Leachman, Samuel; Lieber, Danny; Liebowitz, Anna; Liu, Julia; Liu, Yufei; Martin, Trevor; Mena, Jose; Mendoza, Rosa; Myhrvold, Cameron; Millian, Christian; Pfau, Sarah; Raj, Sandeep; Rich, Matt; Rokicki, Joe; Rounds, William; Salazar, Michael; Salesi, Matthew; Sharma, Rajani; Silverman, Sanford; Singer, Cara; Sinha, Sandhya; Staller, Max; Stern, Philip; Tang, Hanlin; Weeks, Sharon; Weidmann, Maxwell; Wolf, Ashley; Young, Carmen; Yuan, Jie; Crutchfield, Christopher; McClean, Megan; Murphy, Coleen T; Llinás, Manuel; Botstein, David; Troyanskaya, Olga G; Dunham, Maitreya J

2013-07-12

210

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Identification of Yeasts Is Contingent on Robust Reference Spectra  

PubMed Central

Background Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for yeast identification is limited by the requirement for protein extraction and for robust reference spectra across yeast species in databases. We evaluated its ability to identify a range of yeasts in comparison with phenotypic methods. Methods MALDI-TOF MS was performed on 30 reference and 167 clinical isolates followed by prospective examination of 67 clinical strains in parallel with biochemical testing (total n?=?264). Discordant/unreliable identifications were resolved by sequencing of the internal transcribed spacer region of the rRNA gene cluster. Principal Findings Twenty (67%; 16 species), and 24 (80%) of 30 reference strains were identified to species, (spectral score ?2.0) and genus (score ?1.70)-level, respectively. Of clinical isolates, 140/167 (84%) strains were correctly identified with scores of ?2.0 and 160/167 (96%) with scores of ?1.70; amongst Candida spp. (n?=?148), correct species assignment at scores of ?2.0, and ?1.70 was obtained for 86% and 96% isolates, respectively (vs. 76.4% by biochemical methods). Prospectively, species-level identification was achieved for 79% of isolates, whilst 91% and 94% of strains yielded scores of ?1.90 and ?1.70, respectively (100% isolates identified by biochemical methods). All test scores of 1.70–1.90 provided correct species assignment despite being identified to “genus-level”. MALDI-TOF MS identified uncommon Candida spp., differentiated Candida parapsilosis from C. orthopsilosis and C. metapsilosis and distinguished between C. glabrata, C. nivariensis and C. bracarensis. Yeasts with scores of <1.70 were rare species such as C. nivariensis (3/10 strains) and C. bracarensis (n?=?1) but included 4/12 Cryptococcus neoformans. There were no misidentifications. Four novel species-specific spectra were obtained. Protein extraction was essential for reliable results. Conclusions MALDI-TOF MS enabled rapid, reliable identification of clinically-important yeasts. The addition of spectra to databases and reduction in identification scores required for species-level identification may improve its utility.

Pinto, Angie; Halliday, Catriona; Zahra, Melissa; van Hal, Sebastian; Olma, Tom; Maszewska, Krystyna; Iredell, Jonathan R.; Meyer, Wieland; Chen, Sharon C.-A.

2011-01-01

211

Expression of Escherichia coli AppA2 phytase in four yeast systems  

Microsoft Academic Search

To develop an effective fermentation system for producing Escherichia coliphytase AppA2, we expressed the enzyme in three inducible yeast systems: Saccharomyces cerevisiae (pYES2), Schizosaccharomyces pombe (pDS472a), and Pichia pastoris (pPICZ A), and one constitutive system: P. pastoris (pGAPZA). All four systems produced an extracellular functional AppA2 phytase with apparent molecular masses ranging from 51.5 to 56 kDa. During 8-day batch fermentation

Seonho Lee; Taewan Kim; Chad H. Stahl; Xin Gen Lei

2005-01-01

212

Study of amyloids using yeast  

PubMed Central

Summary Saccharomyces cerevisiae has been a useful model organism in such fields as the cell cycle, regulation of transcription, protein trafficking and cell biology, primarily because of its ease of genetic manipulation. This is no less so in the area of amyloid studies. The endogenous yeast amyloids described to date include prions, infectious proteins (Table 1), and some cell wall proteins (1). and amyloids of humans and a fungal prion have also been studied using the yeast system. Accordingly, the emphasis of this chapter will be on genetic, biochemical, cell biological and physical methods particularly useful in the study of yeast prions and other amyloids studied in yeast. We limit our description of these methods to those aspects which have been most useful in studying yeast prions, citing more detailed expositions in the literature. Volumes on yeast genetics methods (2–4), and on amyloids and prions (5, 6) are useful, and Masison has edited a volume of Methods on “Identification, analysis and characterization of fungal prions” which covers some of this territory (7). We also outline some useful physical methods, pointing the reader to more extensive and authoratative descriptions.

Wickner, Reed B.; Kryndushkin, Dmitry; Shewmaker, Frank; McGlinchey, Ryan; Edskes, Herman K.

2012-01-01

213

Identification and nuclear localization of yeast pre-messenger RNA processing components: RNA2 and RNA3 proteins  

PubMed Central

Temperature-sensitive mutations in the RNA2 through RNA11 genes of yeast prevent the processing of nuclear pre-mRNAs. We have raised antisera that detect the RNA2 and RNA3 proteins in immunoblots of extracts of yeast containing high copy number RNA2 and RNA3 plasmids. Subcellular fractionation of yeast cells that overproduce the RNA2 and RNA3 proteins has revealed that these proteins are enriched in nuclear fractions. Indirect immunofluorescence results have indicated that these proteins are localized in yeast nuclei. These localization results are consistent with the fact that these genes have a role in processing yeast pre-mRNA.

1986-01-01

214

Identification of a novel type of spacer element required for imprinting in fission yeast.  

PubMed

Asymmetrical segregation of differentiated sister chromatids is thought to be important for cellular differentiation in higher eukaryotes. Similarly, in fission yeast, cellular differentiation involves the asymmetrical segregation of a chromosomal imprint. This imprint has been shown to consist of two ribonucleotides that are incorporated into the DNA during lagging-strand synthesis in response to a replication pause, but the underlying mechanism remains unknown. Here we present key novel discoveries important for unravelling this process. Our data show that cis-acting sequences within the mat1 cassette mediate pausing of replication forks at the proximity of the imprinting site, and the results suggest that this pause dictates specific priming at the position of imprinting in a sequence-independent manner. Also, we identify a novel type of cis-acting spacer region important for the imprinting process that affects where subsequent primers are put down after the replication fork is released from the pause. Thus, our data suggest that the imprint is formed by ligation of a not-fully-processed Okazaki fragment to the subsequent fragment. The presented work addresses how differentiated sister chromatids are established during DNA replication through the involvement of replication barriers. PMID:21423720

Sayrac, Suha; Vengrova, Sonya; Godfrey, Emma L; Dalgaard, Jacob Z

2011-03-10

215

Identification of Yeast V-ATPase Mutants by Western Blots Analysis of Whole Cell Lysates  

NASA Astrophysics Data System (ADS)

A biochemistry laboratory was designed for an undergraduate course to help students better understand the link between molecular engineering and biochemistry. Students identified unknown yeast strains with high specificity using SDS-PAGE and Western blot analysis of whole cell lysates. This problem-solving exercise is a common application of biochemistry in biotechnology research. Three different strains were used: a wild-type and two mutants for the proton pump vacuolar ATPase (V-ATPase). V-ATPases are multisubunit enzymes and the mutants used were deletion mutants; each lacked one structural gene of the complex. After three, three-hour labs, mutant strains were easily identified by the students and distinguished from wild-type cells analyzing the pattern of SDS-PAGE distribution of proteins. Identifying different subunits of one multimeric protein allowed for discussion of the structure and function of this metabolic enzyme, which captured the interest of the students. The experiment can be adapted to other multimeric protein complexes and shows improvement of the described methodology over previous reports, perhaps because the problem and its solution are representative of the type of techniques currently used in research labs.

Parra-Belky, Karlett

2002-11-01

216

Identification of two species of yeast-like symbiotes in the brown planthopper, Nilaparvata lugens.  

PubMed

To determine the species of the yeast-like symbionts (YLS) in the brown planthoppers (BPH), Nilaparvata lugens, YLS were first isolated and purified by ultracentrifugation from the fat bodies of BPH, and then 18S rDNA and internal transcribed spacer (ITS)-5.8S rDNA sequences of YLS were amplified with the different general primers for fungi. The results showed that the two different 18S and ITS-5.8S rDNA sequences of YLS were obtained. One 2291-bp DNA sequence, which contained 18S and ITS-5.8S rDNA, showed the high similarity to Cryptococcus and was named Cryp-Like symbiotes. Another 1248-bp DNA sequence, which contained a part of 18S and ITS-5.8S rDNA, showed the high similarity to Pichia guilliermondii and was named Pichia-Like symbiotes. It was further proved that Cryp- and Pichia-Like symbiotes existed in BPH through nested PCR with specific primers for two symbiotes and in situ hybridization analysis using digoxigenin-labeled probes. Our results showed that BPH harbored more than one species of eukaryotic YLS, which suggested that diversity of fungal endosymbiotes may be occurred in planthoppers, just like bacterial endosymbiotes. PMID:21153730

Dong, ShengZhang; Pang, Kun; Bai, Xu; Yu, XiaoPing; Hao, PeiYing

2010-12-14

217

The identification and characterization of osmotolerant yeast isolates from chemical wastewater evaporation ponds.  

PubMed

Ramat Hovav is a major chemical industrial park manufacturing pharmaceuticals, pesticides, and various aliphatic and aromatic halogens. All wastewater streams are collected in large evaporation ponds. Salinity in the evaporation ponds fluctuates between 3% (w/v) and saturation and pH values range between 2.0 and 10.0. We looked for microorganisms surviving in these extreme environmental conditions and found that 2 yeast strains dominate this biotope. 18S rDNA sequence analysis identified the isolates as Pichia guilliermondii and Rhodotorula mucilaginosa. Both isolates grew in NaCl concentrations ranging up to 3.5 M and 2.5 M, respectively, and at a pH range of 2-10. There was a distinct difference between the Rhodotorula and Pichia strains and S. cerevisiae RS16 that served as a control strain with respect to accumulation of osmoregulators and internal ion concentrations when exposed to osmotic stress. The Pichia and Rhodotorula strains maintained high glycerol concentration also in media low in NaCl. Utilization of various carbon sources was examined. Using a tetrazolium-based assay we show that the Rhodotorula and Pichia strains are capable of utilizing a wide range of different carbon sources including anthracene, phenanthrene, and other cyclic aromatic hydrocarbons. PMID:12037616

Lahav, R; Fareleira, P; Nejidat, A; Abeliovich, A

2002-03-05

218

Identification of Neuroglobin-interacting Proteins Using Yeast Two-hybrid Screening  

PubMed Central

Neuroglobin (Ngb) is a globin protein that is highly and specifically expressed in brain neurons. A large volume of evidence has proven that Ngb is a neuroprotective molecule against hypoxic/ischemic brain injury and other related neurological disorder; however, the underlying mechanisms remain poorly understood. Aiming to provide more clues in understanding the molecular mechanisms of Ngb’s neuroprotection, we performed yeast two-hybrid screening to search for proteins that interact with Ngb. From a mouse brain cDNA library, we found totally 36 proteins that potentially interact with Ngb, and 10 of them were each identified in multiple positive clones. The shared sequences within these multiple clones are more likely to be Ngb-interacting domains. In primary cultured mouse cortical neurons, immuno-precipitation was performed to confirm the interactions of selected proteins with Ngb. The discovered Ngb-interacting proteins in this study include those involved in energy metabolism, mitochondria function and signaling pathways for cell survival and proliferation. Our findings provide molecular targets for investigating protein interaction-based biological functions and neuroprotective mechanisms of Ngb.

Yu, Zhanyang; Liu, Ning; Wang, Yi; Li, Xiaokun; Wang, Xiaoying

2011-01-01

219

Customer identification system and method  

US Patent & Trademark Office Database

A method and system are presented for identifying a customer in a commercial transaction using less than complete identifying information. A name for the customer is extracted from a credit card during a purchase transaction. A trade area for the point of sale location used to restrict a search of a demographic database to find a list of potential identity matches having names similar to the name on the credit card. A best match generator creates a profile of the expected purchaser of the products in the transaction. Using demographic information about each identity in the list of potential identity matches, each identity is compared to the profile and given a score. The highest scoring identity is then considered the best match. The best match identity is then assumed to be the identity involved in the transaction, and the customer database is updated to reflect this determination.

Anglum; Timothy J. (Chanhassen, MN)

2007-07-31

220

Unique device identification system. Final rule.  

PubMed

The Food and Drug Administration (FDA) is issuing a final rule to establish a system to adequately identify devices through distribution and use. This rule requires the label of medical devices to include a unique device identifier (UDI), except where the rule provides for an exception or alternative placement. The labeler must submit product information concerning devices to FDA's Global Unique Device Identification Database (GUDID), unless subject to an exception or alternative. The system established by this rule requires the label and device package of each medical device to include a UDI and requires that each UDI be provided in a plain-text version and in a form that uses automatic identification and data capture (AIDC) technology. The UDI will be required to be directly marked on the device itself if the device is intended to be used more than once and intended to be reprocessed before each use. PMID:24066364

2013-09-24

221

Proteomics and systems biology to tackle biological complexity: Yeast as a case study.  

PubMed

In this note we discuss how, by using budding yeast as model organism (as has been done in the past for biochemical, genetics and genomic studies), the integration of "omics" sciences and more specifically of proteomics with systems biology offers a very profitable approach to elucidating regulatory circuits of complex biological functions. PMID:21061424

Alberghina, Lilia; Cirulli, Claudia

2010-12-01

222

Power system identification toolbox: Phase two progress  

Microsoft Academic Search

This report describes current progress on a project funded by the Bonneville Power Administration (BPA) to develop a set of state-of-the-art analysis software (termed the Power System Identification [PSI] Toolbox) for fitting dynamic models to measured data. The project is being conducted as a three-phase effort. The first phase, completed in late 1992, involved investigating the characteristics of the analysis

Trudnowski

1994-01-01

223

Reconfigurable control and fault identification system  

Microsoft Academic Search

The integration of health management and reconfigurable flight control is demonstrated in the NAVAIR\\/Boeing Reconfigurable Control and Fault Identification System (RCF1S) Dual Use Science and Technology program (Contract N00421-003-0123). The major research results include: 1) expansion of diagnostic capability by detecting levels of actuator degradation that can be used to reduce could not duplicates and false alarms in the current

S. Black; K. Keller; K. Swearingen; M. Vandernoot; M. Hood; J. Urnes; A. B. Page

2004-01-01

224

New identification system aimed at thwarting theft  

SciTech Connect

A survey of 8500 general contractors showed that in 1980, total losses due to equipment theft represented $403 million. If thefts of other off-road machinery - forestry and agricultural equipment - are added, the total annual loss in the US may be $1 billion. This work discusses the product identification number (PIN) system initiated by John Deere and Co., along with its effectiveness in preventing theft and facilitating recovery of stolen property.

Beek, C.M.

1982-10-01

225

A novel yeast expression/secretion system for the recombinant plant thiol endoprotease propapain.  

PubMed

A new high-yield yeast expression/secretion system has been adapted for the plant thiol endoprotease papain. The propapain gene, obtained from Carica papaya fruit, is expressed in the yeast Saccharomyces cerevisiae. The gene was cloned into a FLAG epitope-tagging expression vector downstream of the yeast alpha mating factor (alpha-factor) secretion signal sequence. Expression of the heterologous propapain in yeast is controlled by the glucose-repressible alcohol dehydrogenase isoenzyme II promoter (ADH2). Glycosylated FLAG-tagged propapain is secreted by a so-called 'super secretor' strain, pmr1 (ssc1), into the culture supernatant where it accumulates to approximately 1.7 mg/l. The proregion contains three consensus N-linked glycosylation sites, whereas there are only two such sites in previously reported cDNA sequences. Removal of this third N-linked glycosylation site results in a drastic reduction in the level of protease activity present in the culture supernatant. Two different types of affinity chromatography were used to purify either propapain or papain. The propapain precursor is autoproteolytically activated to mature papain (M(r) = 24 kDa) using conditions reported previously. The kinetic parameters obtained agree well with the literature values. The yields of active papain are 10-fold higher than those previously reported for propapain in other yeast or bacterial expression systems. This, together with the ease with which mutant proteins can be made, makes this yeast advantageous for a structure-function analysis of recombinant wild-type and mutant papain, and possibly for other related cysteine proteases as well. PMID:8961359

Ramjee, M K; Petithory, J R; McElver, J; Weber, S C; Kirsch, J F

1996-11-01

226

Evaluation of PNA-FISH Yeast Traffic Light for Rapid Identification of Yeast Directly from Positive Blood Cultures and Assessment of Clinical Impact  

PubMed Central

The PNA-FISH Yeast Traffic Light assay was performed on 54 clinical isolates of yeasts inoculated into blood culture bottles. The assay showed high sensitivity (Candida albicans/C. parapsilosis, 100%; C. glabrata/C. krusei, 92.3%; C. tropicalis, 100%) and specificity (C. albicans/C. parapsilosis, 100%; C. glabrata/C. krusei, 94.8%; C. tropicalis, 100%). Case note review estimated a change in therapy in 29% of cases had the PNA-FISH result been available to the clinician.

Gorton, R. L.; Barker, K.; Ramnarain, P.; Kibbler, C. C.

2013-01-01

227

Identification of PDE6D as a molecular target of anecortave acetate via a methotrexate-anchored yeast three-hybrid screen.  

PubMed

Glaucoma and age-related macular degeneration are ocular diseases targeted clinically by anecortave acetate (AA). AA and its deacetylated metabolite, anecortave desacetate (AdesA), are intraocular pressure (IOP)-lowering and angiostatic cortisenes devoid of glucocorticoid activity but with an unknown mechanism of action. We used a methotrexate-anchored yeast three-hybrid (Y3H) technology to search for binding targets for AA in human trabecular meshwork (TM) cells, the target cell type that controls IOP, a major risk factor in glaucoma. Y3H hits were filtered by competitive Y3H screens and coimmunoprecipitation experiments and verified by surface plasmon resonance analysis to yield a single target, phosphodiesterase 6-delta (PDE6D). PDE6D is a prenyl-binding protein with additional function outside the PDE6 phototransduction system. Overexpression of PDE6D in mouse eyes caused elevated IOP, and this elevation was reversed by topical ocular application of either AA or AdesA. The identification of PDE6D as the molecular binding partner of AA provides insight into the role of this drug candidate in treating glaucoma. PMID:23301619

Shepard, Allan R; Conrow, Raymond E; Pang, Iok-Hou; Jacobson, Nasreen; Rezwan, Mandana; Rutschmann, Katrin; Auerbach, Daniel; Sriramaratnam, Rohitha; Cornish, Virginia W

2013-01-09

228

System identification of Drosophila olfactory sensory neurons  

PubMed Central

The lack of a deeper understanding of how olfactory sensory neurons (OSNs) encode odors has hindered the progress in understanding the olfactory signal processing in higher brain centers. Here we employ methods of system identification to investigate the encoding of time-varying odor stimuli and their representation for further processing in the spike domain by Drosophila OSNs. In order to apply system identification techniques, we built a novel low-turbulence odor delivery system that allowed us to deliver airborne stimuli in a precise and reproducible fashion. The system provides a 1% tolerance in stimulus reproducibility and an exact control of odor concentration and concentration gradient on a millisecond time scale. Using this novel setup, we recorded and analyzed the in-vivo response of OSNs to a wide range of time-varying odor waveforms. We report for the first time that across trials the response of OR59b OSNs is very precise and reproducible. Further, we empirically show that the response of an OSN depends not only on the concentration, but also on the rate of change of the odor concentration. Moreover, we demonstrate that a two-dimensional (2D) Encoding Manifold in a concentration-concentration gradient space provides a quantitative description of the neuron’s response. We then use the white noise system identification methodology to construct one-dimensional (1D) and two-dimensional (2D) Linear-Nonlinear-Poisson (LNP) cascade models of the sensory neuron for a fixed mean odor concentration and fixed contrast. We show that in terms of predicting the intensity rate of the spike train, the 2D LNP model performs on par with the 1D LNP model, with a root mean-square error (RMSE) increase of about 5 to 10%. Surprisingly, we find that for a fixed contrast of the white noise odor waveforms, the nonlinear block of each of the two models changes with the mean input concentration. The shape of the nonlinearities of both the 1D and the 2D LNP model appears to be, for a fixed mean of the odor waveform, independent of the stimulus contrast. This suggests that white noise system identification of Or59b OSNs only depends on the first moment of the odor concentration. Finally, by comparing the 2D Encoding Manifold and the 2D LNP model, we demonstrate that the OSN identification results depend on the particular type of the employed test odor waveforms. This suggests an adaptive neural encoding model for Or59b OSNs that changes its nonlinearity in response to the odor concentration waveforms.

Kim, Anmo J.; Slutskiy, Yevgeniy B.

2013-01-01

229

Identification and cloning of two putative subunits of DNA polymerase epsilon in fission yeast  

PubMed Central

DNA polymerase epsilon (Pol ?) is a multi-subunit enzyme required for the initiation of chromosomal DNA replication. Here, we report the cloning of two fission yeast genes, called dpb3+ and dpb4+ that encode proteins homologous to the two smallest subunits of Pol ?. Although Dpb4 is not required for cell viability, ?dpb4 mutants are synthetically lethal with mutations in four genes required for DNA replication initiation, cdc20+ (encoding DNA Pol ?), cut5+ (homologous to DPB11/TopBP1), sna41+ (homologous to CDC45) and cdc21+ (encoding Mcm4, a component of the pre-replicative complex). In contrast to Dpb4, Dpb3 is essential for cell cycle progression. A glutathione S-transferase pull-down assay indicates that Dpb3 physically interacts with both Dpb2 and Dpb4, suggesting that Dpb3 associates with other members of the Pol ? complex. Depletion of Dpb3 leads to an accumulation of cells in S phase consistent with Dpb3 having a role in DNA replication. In addition, many of the cells have a bi-nucleate or multinucleate phenotype, indicating that cell separation is also inhibited. Finally, we have examined in vivo localization of green fluorescent protein (GFP)-tagged Dpb3 and Dpb4 and found that both proteins are localized to the nucleus consistent with their proposed role in DNA replication. However, in the absence of Dpb3, GFP-Dpb4 appears to be more dispersed throughout the cell, suggesting that Dpb3 may be important in establishing or maintaining normal localization of Dpb4.

Spiga, Maria-Grazia; D'Urso, Gennaro

2004-01-01

230

SCiFI - A System for Secure Face Identification  

Microsoft Academic Search

We introduce SCiFI, a system for Secure Computation of Face Identification. The system performs face identification which compares faces of subjects with a database of registered faces. The identification is done in a secure way which protects both the privacy of the subjects and the confidentiality of the database. A specific application of SCiFI is reducing the privacy impact of

Margarita Osadchy; Benny Pinkas; Ayman Jarrous; Boaz Moskovich

2010-01-01

231

Nonlinear system identification using adaptive Chebyshev neural networks  

Microsoft Academic Search

A new adaptive Chebyshev neural networks (ACNN) algorithm for the purpose of complex nonlinear system identification was proposed. In the proposed algorithm, the activation function of hidden units was defined by Chebyshev polynomials in the neural networks. The efficient algorithm for complex nonlinear system identification was constructed, which integrated Chebyshev neural networks with adaptive learning strategy to improve the identification

Mu Li; Yigang He

2010-01-01

232

Identification of the transcription factor Znc1p, which regulates the yeast-to-hypha transition in the dimorphic yeast Yarrowia lipolytica.  

PubMed

The dimorphic yeast Yarrowia lipolytica is used as a model to study fungal differentiation because it grows as yeast-like cells or forms hyphal cells in response to changes in environmental conditions. Here, we report the isolation and characterization of a gene, ZNC1, involved in the dimorphic transition in Y. lipolytica. The ZNC1 gene encodes a 782 amino acid protein that contains a Zn(II)2C6 fungal-type zinc finger DNA-binding domain and a leucine zipper domain. ZNC1 transcription is elevated during yeast growth and decreases during the formation of mycelium. Cells in which ZNC1 has been deleted show increased hyphal cell formation. Znc1p-GFP localizes to the nucleus, but mutations within the leucine zipper domain of Znc1p, and to a lesser extent within the Zn(II)2C6 domain, result in a mislocalization of Znc1p to the cytoplasm. Microarrays comparing gene expression between znc1::URA3 and wild-type cells during both exponential growth and the induction of the yeast-to-hypha transition revealed 1,214 genes whose expression was changed by 2-fold or more under at least one of the conditions analyzed. Our results suggest that Znc1p acts as a transcription factor repressing hyphal cell formation and functions as part of a complex network regulating mycelial growth in Y. lipolytica. PMID:23826133

Martinez-Vazquez, Azul; Gonzalez-Hernandez, Angelica; Domínguez, Angel; Rachubinski, Richard; Riquelme, Meritxell; Cuellar-Mata, Patricia; Guzman, Juan Carlos Torres

2013-06-24

233

Realization-Based System Identification with Applications  

NASA Astrophysics Data System (ADS)

The identification of dynamic system behavior from experimentally measured or computationally simulated data is fundamental to the fields of control system design, modal analysis, and defect detection. In this dissertation, methods for system identification are developed based on classical linear system realization theory. The common methods of state-space realization from a measured, discrete-time impulse response are generalized to the following additional types of experiments: measured step responses, arbitrary sets of input-output data, and estimated cross-covariance functions of input-output data. The methods are particularly well suited to systems with large input and/or output dimension, for which classical system identification methods based on maximum likelihood estimation may fail due to their reliance on non-convex optimizations. The realization-based methods by themselves require a finite number of linear algebraic operations. Because these methods implicitly optimize cost functions that are linear in state-space parameters, they may be augmented with convex constraints to form convex optimization problems. Several common behavioral constraints are translated into eigenvalue constraints stated as linear matrix inequalities, and the realization-based methods are converted into semidefinite programming problems. Some additional constraints on transient and steady-state behavior are derived and incorporated into a quadratic program, which is solved following the semidefinite program. The newly developed realization-based methods are applied to two experiments: the aeroelastic response of a fighter aircraft and the transient thermal behavior of a light-emitting diode. The algorithms for each experiment are implemented in two freely available software packages.

Miller, Daniel N.

234

Mutant yeast on drugs  

Microsoft Academic Search

Analyzing drug-treated and mutant yeast cells with the new tools of genomics enables the identification of drug targets and should improve the odds of developing useful therapeutics (pages 1293–1301).

David J. Lockhart

1998-01-01

235

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2012 CFR

...following: (1) Personnel identification media thatâ (i) Convey a full-face...the individual to whom the identification medium is issued; (ii) Indicate clearly...continuously displays the identification medium issued to that individual on the...

2012-10-01

236

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2011 CFR

...following: (1) Personnel identification media thatâ (i) Convey a full-face...the individual to whom the identification medium is issued; (ii) Indicate clearly...continuously displays the identification medium issued to that individual on the...

2011-10-01

237

Detection and Identification of Yeasts from Formalin-Fixed, Paraffin-Embedded Tissue by Use of PCR-Electrospray Ionization Mass Spectrometry.  

PubMed

Diagnosis of yeast infection is typically accomplished by fungal smear and culture, histopathologic examination, and/or serologic studies. Newer assays based on mass spectrometry may be useful for yeast identification when histologic examination is inconclusive, fungal cultures are not ordered, or cultures fail to yield a causative agent. The purpose of this study was to evaluate the ability of the PLEX-ID broad fungal assay to accurately detect and identify yeasts in formalin-fixed paraffin-embedded (FFPE) tissues. Tissue samples from 78 FFPE specimens with both histopathology and corresponding culture results for a variety of yeasts were tested using the PLEX-ID broad fungal assay. A 40-?m FFPE tissue section from each specimen was digested with proteinase K followed by nucleic acid extraction and PCR using broad-range fungal primers. Yeast DNA in amplified products was identified using electrospray ionization mass spectrometry. Discordant results were resolved by D2 rRNA gene sequencing. PLEX-ID analysis detected yeast DNA in 78.2% (61/78) of the cases, of which 91.8% (56/61) were concordant with culture results. Of the 5 discordant positive results, 4 PLEX-ID results were considered to result from environmental contaminants, while 1 clinically important discrepancy was observed (Blastomyces dermatitidis by culture and Cryptococcus neoformans by PLEX-ID). Sequencing of the discordant sample was unsuccessful. The majority of histopathology results (89.7% [70/78]) correlated with culture results. The PLEX-ID broad fungal assay identifies fungi directly from FFPE tissues and can be a useful adjunct to traditional culture and histopathology tests. PMID:23985922

Simner, Patricia J; Buckwalter, Seanne P; Uhl, James R; Wengenack, Nancy L; Pritt, Bobbi S

2013-08-28

238

Dual Control and Identification Methods for Avionic System. Part II. Optimal Inputs for Linear System Identification.  

National Technical Information Service (NTIS)

The report presents the results of the second part of a one-year study on Dual Control and Identification Methods for Avionic Systems. First, a general theory is developed for designing optimal inputs to identify parameters in linear dynamic systems. It i...

D. E. Stepner J. A. Casti J. S. Tyler R. K. Mehra

1972-01-01

239

Identification and killer activity of a yeast contaminating starter cultures of Saccharomyces cerevisiae strains used in the Turkish baking industry  

Microsoft Academic Search

The yeast contaminating the starter cultures ofSaccharomyces cerevisiaefermentation strains BSP 1–4, used in the Turkish baking industry, was identified asCandida tropicaliswith a killer phenotype. The activity of the killer toxin against the industrial strains was optimum at pH 3.9 and 4.1 at 22–25°C. The activities of some killer toxin-producing yeasts of known phenotypes againstC. tropicaliswere determined. Among the yeasts testedS.

F. Izgü; D. Alt?nbay; A. Yüceli?

1997-01-01

240

Identification of lethal cluster of genes in the yeast transcription network  

NASA Astrophysics Data System (ADS)

Identification of essential or lethal genes would be one of the ultimate goals in drug designs. Here we introduce an in silico method to select the cluster with a high population of lethal genes, called lethal cluster, through microarray assay. We construct a gene transcription network based on the microarray expression level. Links are added one by one in the descending order of the Pearson correlation coefficients between two genes. As the link density p increases, two meaningful link densities p and p are observed. At p, which is smaller than the percolation threshold, the number of disconnected clusters is maximum, and the lethal genes are highly concentrated in a certain cluster that needs to be identified. Thus the deletion of all genes in that cluster could efficiently lead to a lethal inviable mutant. This lethal cluster can be identified by an in silico method. As p increases further beyond the percolation threshold, the power law behavior in the degree distribution of a giant cluster appears at p. We measure the degree of each gene at p. With the information pertaining to the degrees of each gene at p, we return to the point p and calculate the mean degree of genes of each cluster. We find that the lethal cluster has the largest mean degree.

Rho, K.; Jeong, H.; Kahng, B.

2006-05-01

241

Modified MuDPIT separation identified 4488 proteins in a system-wide analysis of quiescence in yeast.  

PubMed

A modified multidimensional protein identification technology (MudPIT) separation was coupled to an LTQ Orbitrap Velos mass spectrometer and used to rapidly identify the near-complete yeast proteome from a whole cell tryptic digest. This modified online two-dimensional liquid chromatography separation consists of 39 strong cation exchange steps followed by a short 18.5 min reversed-phase (RP) gradient. A total of 4269 protein identifications were made from 4189 distinguishable protein families from yeast during log phase growth. The "Micro" MudPIT separation performed as well as a standard MudPIT separation in 40% less gradient time. The majority of the yeast proteome can now be routinely covered in less than a days' time with high reproducibility and sensitivity. The newly devised separation method was used to detect changes in protein expression during cellular quiescence in yeast. An enrichment in the GO annotations "oxidation reduction", "catabolic processing" and "cellular response to oxidative stress" was seen in the quiescent cellular fraction, consistent with their long-lived stress resistant phenotypes. Heterogeneity was observed in the stationary phase fraction with a less dense cell population showing reductions in KEGG pathway categories of "Ribosome" and "Proteasome", further defining the complex nature of yeast populations present during stationary phase growth. In total, 4488 distinguishable protein families were identified in all cellular conditions tested. PMID:23540446

Webb, Kristofor J; Xu, Tao; Park, Sung Kyu; Yates, John R

2013-04-09

242

Yeast Replicative DNA Polymerases and Their Role at the Replication Fork  

Microsoft Academic Search

The budding yeast, Saccharomyces cerevisiae, is an excellent model system for the study of DNA poly- merases and their roles in DNA replication, repair, and recombination. Presently ten DNA polymerases have been purified and characterized from S. cer e- visiae. Rapid advances in g enome sequencing projects for yeast and other organisms have greatly facilitated and accelerated the identification of

Yasuo Kawasaki; Akio Sugino

2001-01-01

243

Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Clinically Important Yeast Species ?  

PubMed Central

We evaluated the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the rapid identification of yeast species. Using Bruker Daltonics MALDI BioTyper software, we created a spectral database library with m/z ratios of 2,000 to 20,000 Da for 109 type and reference strains of yeast (44 species in 8 genera). The database was tested for accuracy by use of 194 clinical isolates (23 species in 6 genera). A total of 192 (99.0%) of the clinical isolates were identified accurately by MALDI-TOF MS. The MALDI-TOF MS-based method was found to be reproducible and accurate, with low consumable costs and minimal preparation time.

Stevenson, Lindsay G.; Drake, Steven K.; Shea, Yvonne R.; Zelazny, Adrian M.; Murray, Patrick R.

2010-01-01

244

IDENTIFICATION OF FUNGAL AND YEAST ISOLATES BY ANALYSIS OF NUCLEAR LARGE SUBUNIT(26S) RIBOSOMAL DNA SEQUENCES  

Technology Transfer Automated Retrieval System (TEKTRAN)

Yeast and fungal strains were isolated from pistachio and almond orchards as single colonies. Yeast cells and fungal mycelia were harvested from cultures medium by centrifugation and DNA were extracted for PCR reaction. A pair of universal primers, NL1 and NL4 were used to generate the fragment of ...

245

Molecular Genetics of the Ubiquitin-Proteasome System: Lessons from Yeast  

Microsoft Academic Search

\\u000a Our studies with the yeast Saccharomyces cerevisiae have uncovered a number of general principles governing substrate selectivity and proteolysis by the ubiquitin-proteasome\\u000a system. The initial work focused on the degradation of a transcription factor, the MAT?2 repressor, but the pathways uncovered\\u000a have a much broader range of targets. At least two distinct ubiquitination mechanisms contribute to ?2 turnover. One of them\\u000a depends on

M. Hochstrasser; M. Deng; A. R. Kusmierczyk; X. Li; S. G. Kreft; T. Ravid; M. Funakoshi; M. Kunjappu; Y. Xie

246

Some properties of an immobilized glycolysis system of yeast in fermentative phosphorylation of nucleotides  

Microsoft Academic Search

Summary  Immobilized dried yeast cells, which contain glycolytic and some other emzymes, required NAD but not ATP for the (e.g. choline\\u000a kinase, pyrophosphorylase) fermentative production of CDP-choline, when washed and reused. The immobilized system was more\\u000a resistant to heat than dried cells, which had previously been used for the same purpose. However, when too many cells were\\u000a immobilized, leakage of the

Akira Kimura; Yoshinori Tatsutomi; Ryu'ichi Matsuno; Atsuo Tanaka; Hirosuke Fukuda

1981-01-01

247

The proteolytic systems and heterologous proteins degradation in the methylotrophic yeast Pichia pastoris  

Microsoft Academic Search

ThePichia pastoris expression system has been successfully used for production of various recombinant heterogeneous proteins. The productivity\\u000a ofP. pastoris can be improved substantially by bioreactor cultivations. However, heterologous proteins degradation increases as well in\\u000a high-cell density culture. Proteolytic degradation is a serious problem since the yeast has been employed to express recombinant\\u000a proteins. In this review, some of the recent

Yewang Zhang; Ruijiang Liu; Xiaoyu Wu

2007-01-01

248

Purification and characterization of bovine adrenal cytochrome b 561 expressed in insect and yeast cell systems  

Microsoft Academic Search

Bovine adrenal chromaffin granule cytochrome (cyt) b561 is a transmembrane hemoprotein that plays a key role in transporting reducing equivalents from ascorbate to dopamine-?-hydroxylase for catecholamine synthesis. We have developed procedures for expression and purification of functional bovine adrenal cyt b561 in insect and yeast cell systems. The bovine cyt b561 coding sequence, with or without a hexahistidine-tag sequence at

Wen Liu; Yury Kamensky; Reva Kakkar; Erin Foley; Richard J. Kulmacz; Graham Palmer

2005-01-01

249

Identification of cultured isolates of clinically important yeast species using fluorescent fragment length analysis of the amplified internally transcribed rRNA spacer 2 region  

PubMed Central

Background The number of patients with yeast infection has increased during the last years. Also the variety of species of clinical importance has increased. Correct species identification is often important for efficient therapy, but is currently mostly based on phenotypic features and is sometimes time-consuming and depends largely on the expertise of technicians. Therefore, we evaluated the feasibility of PCR-based amplification of the internally transcribed spacer region 2 (ITS2), followed by fragment size analysis on the ABI Prism 310 for the identification of clinically important yeasts. Results A rapid DNA-extraction method, based on simple boiling-freezing was introduced. Of the 26 species tested, 22 could be identified unambiguously by scoring the length of the ITS2-region. No distinction could be made between the species Trichosporon asteroides and T. inkin or between T. mucoides and T. ovoides. The two varieties of Cryptococcus neoformans (var. neoformans and var. gattii) could be differentiated from each other due to a one bp length difference of the ITS2 fragment. The three Cryptococcus laurentii isolates were split into two groups according to their ITS2-fragment lengths, in correspondence with the phylogenetic groups described previously. Since the obtained fragment lengths compare well to those described previously and could be exchanged between two laboratories, an internationally usable library of ITS2 fragment lengths can be constructed. Conclusions The existing ITS2 size based library enables identification of most of the clinically important yeast species within 6 hours starting from a single colony and can be easily updated when new species are described. Data can be exchanged between laboratories.

De Baere, Thierry; Claeys, Geert; Swinne, Danielle; Massonet, Caroline; Verschraegen, Gerda; Muylaert, An; Vaneechoutte, Mario

2002-01-01

250

In vitro evaluation of atmospheric particulate matter and sedimentation particles using yeast bioassay system.  

PubMed

Little information on the evaluation of airborne particulate matter (APM) and sedimentation particles from subway stations is available. The thermal metamorphism of train wheels generating toxic particles in subway stations is a possibility. In this study, the toxicity and physiological effects of particles from subway stations were evaluated using a yeast bioassay system. Estrogenic and antiestrogenic activities of APM in APM extracts from subway stations were determined. No estrogenic activity was found in the APM fractions and their S9-activated APM samples. Sedimentation dust samples also showed no estrogen activity. In contrast, extracts from sedimentation dust samples showed antiestrogen activity. Marked yeast toxicity was observed in the samples extracted from sedimentation dust. Potent yeast toxicity was also found in the S9-activated extracts from sedimentation dust. The results suggest that sedimentation dust from a semiclosed area of a subway system has antiestrogen activity, although both the origin and generation system of this activity are uncertain. These pollutants in sedimentation dust may change to a more toxic form in vivo by S9 activation. PMID:17762843

Mori, Taiki; Inudo, Makiko; Takao, Yuji; Koga, Minoru; Takemasa, Takehiro; Shinohara, Ryota; Arizono, Koji

2007-01-01

251

Introduction to Automatic Data Identification Systems  

NSDL National Science Digital Library

Introduction to Automatic Data Identification Systems is composed of distance learning classes offered by Cuesta College. Sample video presentations for Engineering Statics and Strength of Materials I:ENGR50 Engineering Statics Analyzes forces on structures in equilibrium, properties of forces, moments, couples and resultant, conditions for equilibrium, friction, centroids, and area moments of inertia.ENGR52A Strength of Materials IStudy of stresses, strains, and deformations associated with axial, torsional, and flexural loading of bars, shafts, and beams. Includes analysis of elementary determinate and indeterminate mechanical and structural systems.Note: Link below is for the Engineering Statics course. The link for the Strength of Materials course is: http://www.yourotherteacher.com/lecture26498/vuxsq4dnb3a/E52-05-27.html

Jones, Jeff

2010-02-17

252

Cytochrome C oxidase III interacts with hepatitis B virus X protein in vivo by yeast two-hybrid system  

Microsoft Academic Search

AIM: To screen and identify the proteins which interact with hepatitis B virus (HBV) X protein in hepatocytes by yeast two-hybrid system and to explore the effects of X protein in the development of hepatocellular carcinoma (HCC). METHODS: With HBV X gene amplified by polymerase chain reaction (PCR), HBV X bait plasmid, named pAS2-1-X, was constructed by yeast-two hybridization system3

Dan Li; Xiao-Zhong Wang; Jie-Ping Yu; Zhi-Xin Chen; Yue-Hong Huang; Qi-Min Tao

253

Development of a high-throughput yeast two-hybrid screening system to study protein-protein interactions in plants  

Microsoft Academic Search

We have developed a high-throughput yeast two-hybrid screening system (HTP-YTH) that incorporates yeast gap-repair cloning, multiple positive (ADE2, HIS3, lacZ) and negative (URA3-based) selection schemes to reduce the incidence of negative and false positive clones, and automation of laboratory procedures to increase throughput. This HTP-YTH system has been applied to the study of protein-protein interactions that are involved in rice

Y. Fang; D. Macool; Z. Xue; E. Heppard; C. Hainey; S. Tingey; G.-H. Miao

2002-01-01

254

Sorting in the endosomal system in yeast and animal cells  

Microsoft Academic Search

The endosomal system is a major membrane-sorting apparatus. New evidence reveals that novel coat proteins assist specific sorting steps and docking factors ensure the vectorial nature of trafficking in the endosomal compartment. There is also good evidence for ubiquitin regulating passage of certain proteins into multivesicular late endosomes, which mature by accumulating invaginated membrane. Lipids play a central role in

Sandra K Lemmon; Linton M Traub

2000-01-01

255

Checking cell size in budding yeast: a systems biology approach.  

PubMed

The regulation of cell cycle progression via the attainment of a critical cell size is a conserved feature from simpler unicellular organisms to mammalian cells that is obtaining much attention recently. Genome wide analysis of Saccharomyces cerevisiae deletion strains, genetic epistasis, DNA microarray analysis have recently revealed an increasingly complex network of cell size modulation mechanisms. A systems biology-based approach, that is needed to structure the underlying complexity of cell cycle regulatory mechanisms, is described. PMID:12833640

Alberghina, Lilia; Rossi, Riccardo L; Wanke, Valeria; Querin, Lorenzo; Vanoni, Marco

2003-03-01

256

Analysis of substrate specificity of human DHHC protein acyltransferases using a yeast expression system  

PubMed Central

Palmitoylation plays important roles in the regulation of protein localization, stability, and activity. The protein acyltransferases (PATs) have a common DHHC Cys-rich domain. Twenty-three DHHC proteins have been identified in humans. However, it is unclear whether all of these DHHC proteins function as PATs. In addition, their substrate specificities remain largely unknown. Here we develop a useful method to examine substrate specificities of PATs using a yeast expression system with six distinct model substrates. We identify 17 human DHHC proteins as PATs. Moreover, we classify 11 human and 5 yeast DHHC proteins into three classes (I, II, and III), based on the cellular localization of their respective substrates (class I, soluble proteins; class II, integral membrane proteins; class III, lipidated proteins). Our results may provide an important clue for understanding the function of individual DHHC proteins.

Ohno, Yusuke; Kashio, Atsushi; Ogata, Ren; Ishitomi, Akihiro; Yamazaki, Yuki; Kihara, Akio

2012-01-01

257

Microbial exopolymers link predator and prey in a model yeast biofilm system.  

PubMed

Protistan grazing on biofilms is potentially an important conduit enabling energy flow between microbial trophic levels. Contrary to the widely held assumption that protistan feeding primarily involves ingestion of biofilm cells, with negative consequences for the biofilm, this study demonstrated preferential grazing on the noncellular biofilm matrix by a ciliate, with selective ingestion of yeast and bacterial cells of planktonic origin over attached and biofilm-derived planktonic cells. Introducing a ciliate to two biofilm-forming Cryptococcus species, as well as two bacterial species in a model biofilm system, fluorescent probes were applied to determine ingestion of cellular and noncellular biofilm fractions. Fluoromicroscopy, as well as photometric quantification, confirmed that protistan grazing enhanced yeast biofilm metabolism, and an increase in biofilm biomass and viability. We propose that the extracellular polymeric matrix of biofilms may act as an interface regulating interaction between predator and prey, while serving as source of nutrients and energy for protists. PMID:16897306

Joubert, L-M; Wolfaardt, G M; Botha, A

2006-08-08

258

Analysis of substrate specificity of human DHHC protein acyltransferases using a yeast expression system.  

PubMed

Palmitoylation plays important roles in the regulation of protein localization, stability, and activity. The protein acyltransferases (PATs) have a common DHHC Cys-rich domain. Twenty-three DHHC proteins have been identified in humans. However, it is unclear whether all of these DHHC proteins function as PATs. In addition, their substrate specificities remain largely unknown. Here we develop a useful method to examine substrate specificities of PATs using a yeast expression system with six distinct model substrates. We identify 17 human DHHC proteins as PATs. Moreover, we classify 11 human and 5 yeast DHHC proteins into three classes (I, II, and III), based on the cellular localization of their respective substrates (class I, soluble proteins; class II, integral membrane proteins; class III, lipidated proteins). Our results may provide an important clue for understanding the function of individual DHHC proteins. PMID:23034182

Ohno, Yusuke; Kashio, Atsushi; Ogata, Ren; Ishitomi, Akihiro; Yamazaki, Yuki; Kihara, Akio

2012-10-03

259

Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae  

PubMed Central

Background Scheffersomyces stipitis is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as Saccharomyces cerevisiae, the onset of fermentation in S. stipitis is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though S. stipitis has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of S. stipitis during aerobic growth on glucose under batch and chemostat cultivations. Results Starting from the analysis of physiological data, we confirmed through 13C-based flux analysis the fully respiratory metabolism of S. stipitis when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for S. cerevisiae under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with S. cerevisiae. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through in silico transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways. Conclusions The work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for S. stipitis under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for S. cerevisiae under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, in silico analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of S. stiptis is investigated in details and is compared to S. cerevisiae. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of S. stipitis as cell factory.

2012-01-01

260

Single cell adhesion force measurement for viability identification using nanorobotic manipulation system inside ESEM  

Microsoft Academic Search

Cell viability identification is the first step for single cell analysis. In this paper, a novel cell viability identification method was proposed based on the cell adhesion force measure- ment. Living and dead yeast cell samples were prepared using the stain method. The micro puller for adhesion force measurement was fabricated from atomic force microscopy (AFM) cantilever by focused ion

Yajing Shen; Masahiro Nakajima; Seiji Kojima; Michio Homma; Toshio Fukuda

2011-01-01

261

Identification of a CAP (adenylyl-cyclase-associated protein) homologous gene in Lentinus edodes and its functional complementation of yeast CAP mutants.  

PubMed

The adenylyl-cyclase-associated protein, CAP, was originally identified in yeasts as a protein that functions in both signal transduction and cytoskeletal organization. This paper reports the identification of a cDNA and genomic DNA that encodes a CAP homologue from the mushroom Lentinus edodes. The L. edodes cap gene contains eight introns and an ORF encoding a 518 amino acid protein. The L. edodes CAP is 35.5% and 40.9% identical at the amino acid level with Saccharomyces cerevisiae CAP and Schizosaccharomyces pombe CAP, respectively. The C-terminal domain shows greater homology (39-46% identity) with yeast CAPs than does the N-terminal domain (27-35% identity). Southern blotting and Northern blotting results suggest that L. edodes cap is a single-copy gene and uniformly expressed. Expression of the L. edodes CAP in both Schiz. pombe and Sacch. cerevisiae complemented defects associated with the loss of the C-terminal domain function of the endogenous CAP. By using a yeast two-hybrid assay, an interaction was demonstrated between the L. edodes CAP and Schiz. pombe actin. This result and the functional complementation test indicate that CAP from L. edodes has a conserved C-terminal domain function. PMID:9579081

Zhou, G L; Miyazaki, Y; Nakagawa, T; Tanaka, K; Shishido, K; Matsuda, H; Kawamukai, M

1998-04-01

262

Performance Assessment of the CapitalBio Mycobacterium Identification Array System for Identification of Mycobacteria  

PubMed Central

The CapitalBio Mycobacterium identification microarray system is a rapid system for the detection of Mycobacterium tuberculosis. The performance of this system was assessed with 24 reference strains, 486 Mycobacterium tuberculosis clinical isolates, and 40 clinical samples and then compared to the “gold standard” of DNA sequencing. The CapitalBio Mycobacterium identification microarray system showed highly concordant identification results of 100% and 98.4% for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM), respectively. The sensitivity and specificity of the CapitalBio Mycobacterium identification array for identification of Mycobacterium tuberculosis isolates were 99.6% and 100%, respectively, for direct detection and identification of clinical samples, and the overall sensitivity was 52.5%. It was 100% for sputum, 16.7% for pleural fluid, and 10% for bronchoalveolar lavage fluid, respectively. The total assay was completed in 6 h, including DNA extraction, PCR, and hybridization. The results of this study confirm the utility of this system for the rapid identification of mycobacteria and suggest that the CapitalBio Mycobacterium identification array is a molecular diagnostic technique with high sensitivity and specificity that has the capacity to quickly identify most mycobacteria.

Liu, Jingbo; Yan, Zihe; Han, Min; Han, Zhijun; Jin, Lingjie; Zhao, Yanlin

2012-01-01

263

Membrane Delivery to the Yeast Autophagosome from the Golgi-Endosomal System  

PubMed Central

While many of the proteins required for autophagy have been identified, the source of the membrane of the autophagosome is still unresolved with the endoplasmic reticulum (ER), endosomes, and mitochondria all having been evoked. The integral membrane protein Atg9 is delivered to the autophagosome during starvation and in the related cytoplasm-to-vacuole (Cvt) pathway that occurs constitutively in yeast. We have examined the requirements for delivery of Atg9-containing membrane to the yeast autophagosome. Atg9 does not appear to originate from mitochondria, and Atg9 cannot reach the forming autophagosome directly from the ER or early Golgi. Components of traffic between Golgi and endosomes are known to be required for the Cvt pathway but do not appear required for autophagy in starved cells. However, we find that pairwise combinations of mutations in Golgi-endosomal traffic components apparently only required for the Cvt pathway can cause profound defects in Atg9 delivery and autophagy in starved cells. Thus it appears that membrane that contains Atg9 is delivered to the autophagosome from the Golgi-endosomal system rather than from the ER or mitochondria. This is underestimated by examination of single mutants, providing a possible explanation for discrepancies between yeast and mammalian studies on Atg9 localization and autophagosome formation.

Ohashi, Yohei

2010-01-01

264

Comparison of enzymatic antioxidant defence systems in different metabolic types of yeasts.  

PubMed

The enzymatic defence system in the 2 yeasts Kluyveromyces marxianus and Rhodotorula glutinis, differing in their mode of oxygen uptake and energy generation, was characterized and compared with the well-studied facultatively fermentative Crabtree-positive Saccharomyces cerevisiae strain. Twofold higher superoxide dismutase (SOD) and catalase activities were detected in K. marxianus and R. glutinis when cells were cultured on glucose. Further increases of 10%-15% in SOD activity and 30%-50% in catalase were measured in all studied yeasts strains after transfer to media containing ethanol. An evaluation of the ratio of Cu/Zn SOD / Mn SOD was performed as a measure of the oxidative metabolism. A 20% decrease was observed when the respiratory source of energy was ethanol, with the lowest ratio being observed for the oxidative type of K. marxianus yeasts. Electrophoretic analysis revealed that all tested strains possess active Cu/Zn and Mn SODs. A reverse electrophoretic mobility pattern of K. marxianus and R. glutinis SOD enzymes was observed in comparison with the same couple in S. cerevisiae. The investigation of electrophoretic profile of catalase enzymes showed that alongside their different taxonomic status and fermentative capacity, all tested strains possess 2 separate catalases. The role of antioxidant enzymes in preventing oxidant-induced cytotoxicity (treatment with hydrogen peroxide, paraquat, and menadione) was shown. PMID:18997852

Koleva, Dafinka I; Petrova, Ventsislava Y; Kujumdzieva, Anna V

2008-11-01

265

Reduction of distributed system identification complexity using intelligent sensors  

Microsoft Academic Search

The identification problems of distributed-parameter systems (DPS) is dealt with, A special method of data collection by using moving sensors is proposed. The sensors are ‘intelligent’ in the sense that they are able to track the positions of the exiremum values of a system state at each time instant. It is shown how to reduce the identification problem for DPS

EWARYST RAFAJ?OWICZ

1989-01-01

266

An Analytic Geometry Approach to Wiener System Frequency Identification  

Microsoft Academic Search

This paper addresses the problem of Wiener system identification. The underlying linear subsystem is stable but not necessarily parametric. The nonlinear element in turn is allowed to be nonparametric, noninvertible, and nonsmooth. As Wiener models are uniquely defined up to an uncertain multiplicative factor, it makes sense to start the frequency identification process estimating the system phase (which is common

Fouad Giri; Youssef Rochdi; Fatima-Zahra Chaoui

2009-01-01

267

System identification technology for estimating reentry vehicle aerodynamic coefficients  

Microsoft Academic Search

This paper describes the development and application of a system identification technology to obtain accurate estimates of maneuvering reentry vehicle aerodynamic coefficients from flight data. The impact of the specific maneuvering reentry vehicle characteristics on system identification is described and appropriate solutions are proposed. Examples illustrate the effectiveness of the technology.

Narendra K. Gupta; W. Earl Hall

1977-01-01

268

Modeling emotional content of music using system identification  

Microsoft Academic Search

Research was conducted to develop a methodology to model the emotional content of music as a function of time and musical features. Emotion is quantified using the dimensions valence and arousal, and system-identification techniques are used to create the models. Results demonstrate that system identification provides a means to generalize the emotional content for a genre of music. The average

Mark D. Korhonen; David A. Clausi; M. Ed Jernigan

2006-01-01

269

Information-Dependent Switching of Identification Criteria in a Genetic Programming System for System Identification  

Microsoft Academic Search

\\u000a Genetic Programming (GP) can be used to identify the nonlinear differential equations of dynamical systems. If, however, the\\u000a fitness function is chosen in a classical way, the optimization will not work very well. In this article, we explain the reasons\\u000a for the failure of the GP approach and present a solution strategy for improving performance. Using more than one identification

Thomas Buchsbaum; Siegfried Vössner

2006-01-01

270

49 CFR 1544.231 - Airport-approved and exclusive area personnel identification systems.  

Code of Federal Regulations, 2011 CFR

...personnel identification system for identification media that are airport-approved, or identification media that are issued for use in an exclusive area...following: (1) Personnel identification media thatâ (i) Convey a full face...

2011-10-01

271

49 CFR 1544.231 - Airport-approved and exclusive area personnel identification systems.  

Code of Federal Regulations, 2012 CFR

...personnel identification system for identification media that are airport-approved, or identification media that are issued for use in an exclusive area...following: (1) Personnel identification media thatâ (i) Convey a full face...

2012-10-01

272

Identification of two hydrophilins that contribute to the desiccation and freezing tolerance of yeast (Saccharomyces cerevisiae) cells.  

PubMed

Hydrophilins are a group of proteins that are present in all organisms and that have been defined as being highly hydrophilic and rich in glycine. They are assumed to play important roles in cellular dehydration tolerance. There are 12 genes in the yeast Saccharomyces cerevisiae that encode hydrophilins and most of these genes are stress responsive. However, the functional role of yeast hydrophilins, especially in desiccation and freezing tolerance, is largely unknown. Here, we selected six candidate hydrophilins for further analysis. All six proteins were predicted to be intrinsically disordered, i.e. to have no stable structure in solution. The contribution of these proteins to the desiccation and freezing tolerance of yeast was investigated in the respective knock-out strains. Only the disruption of the genes YJL144W and YMR175W (SIP18) resulted in significantly reduced desiccation tolerance, while none of the strains was affected in its freezing tolerance under our experimental conditions. Complementation experiments showed that yeast cells overexpressing these two genes were both more desiccation and freezing tolerant, confirming the role of these two hydrophilins in yeast dehydration stress tolerance. PMID:21420397

Dang, Nghiem X; Hincha, Dirk K

2011-03-21

273

Capability of yeast derivatives to adhere enteropathogenic bacteria and to modulate cells of the innate immune system.  

PubMed

Yeast derivatives including yeast cell wall components are promising alternatives to antibiotics with respect to the promotion of health and performance in livestock, based on their capacity to bind enteropathogenic bacteria and to beneficially modulate the immune system. However, these mode(s) of action both in vitro and in vivo are still not well understood. Furthermore, standardization and reproducibility of in vitro techniques (microbiology, cell culture assays) are critical features for the application of yeast derivatives as well as for the proof of effectiveness. Yeast cell wall products are suggested as anti-adhesive agents and are thus proposed to prevent attachment of certain intestinal bacteria by providing alternative adhesion sites to enterobacteria, which contain mannose-specific type I fimbriae such as Escherichia coli or Salmonella spp. and which is well documented. Various in vitro assay techniques have become of paramount importance for biotechnological research since they allow for determination and quantification of potential mode(s) of action. However, in vitro assays may be criticized by product end users as not accurately reflecting in vivo responses. Pro and cons of different assays and their bias will be discussed specifically regarding yeast cell wall components and adhesion of enteropathogenic bacteria. Immunomodulation is a therapeutic approach intervening in auto-regulating processes of the defense system. Yeast derivatives such as beta-glucans are proposed to interact with cells of the innate immune system by receptor recognition. Controversial data in literature and mode(s) of action are reviewed and discussed here. PMID:22615053

Ganner, Anja; Schatzmayr, Gerd

2012-05-22

274

Design and evaluation of a microfluidic system for inhibition studies of yeast cell signaling  

NASA Astrophysics Data System (ADS)

In cell signaling, different perturbations lead to different responses and using traditional biological techniques that result in averaged data may obscure important cell-to-cell variations. The aim of this study was to develop and evaluate a four-inlet microfluidic system that enables single-cell analysis by investigating the effect on Hog1 localization post a selective Hog1 inhibitor treatment during osmotic stress. Optical tweezers was used to position yeast cells in an array of desired size and density inside the microfluidic system. By changing the flow rates through the inlet channels, controlled and rapid introduction of two different perturbations over the cell array was enabled. The placement of the cells was determined by diffusion rates flow simulations. The system was evaluated by monitoring the subcellular localization of a fluorescently tagged kinase of the yeast "High Osmolarity Glycerol" (HOG) pathway, Hog1-GFP. By sequential treatment of the yeast cells with a selective Hog1 kinase inhibitor and sorbitol, the subcellular localization of Hog1-GFP was analysed on a single-cell level. The results showed impaired Hog1-GFP nuclear localization, providing evidence of a congenial design. The setup made it possible to remove and add an agent within 2 seconds, which is valuable for investigating the dynamic signal transduction pathways and cannot be done using traditional methods. We are confident that the features of the four-inlet microfluidic system will be a valuable tool and hence contribute significantly to unravel the mechanisms of the HOG pathway and similar dynamic signal transduction pathways.

Hamngren, Charlotte; Dinér, Peter; Grøtli, Morten; Goksör, Mattias; Adiels, Caroline B.

2012-10-01

275

Identification of a drought-induced rice gene, OsSAP, that suppresses Bax-induced cell death in yeast.  

PubMed

We identified rice genes that might be involved in drought stress tolerance by virtue of their anti-apoptotic activity. Potential anti-apoptosis related genes were identified by screening an Oryza sativa cDNA library derived from drought stressed tissues in a yeast functional assay. About 28 O. sativa cDNAs promoted yeast survival following engagement of Bax-induced apoptosis. An O. sativa cDNA encoding R12H780 was a highly conserved putative senescence-associated-protein (OsSAP). OsSAP was both highly and rapidly expressed in response to drought stress. Additionally, OsSAP was found to be localized to the mitochondria. Overall, OsSAP represents a new type of Bax suppressor related gene and endows multiple stress tolerance in yeast. PMID:24096889

Ubaidillah, Mohammad; Kim, Kyung-A; Kim, Yoon Ha; Lee, In-Jung; Yun, Byung-Wook; Kim, Doh Hoon; Loake, Gary J; Kim, Kyung-Min

2013-10-05

276

Emergent system identification using particle swarm optimization  

NASA Astrophysics Data System (ADS)

Complex Adaptive Structures can be viewed as a combination of Complex Adaptive Systems and fully integrated autonomous Smart Structures. Traditionally when designing a structure, one combines rules of thumb with theoretical results to develop an acceptable solution. This methodology will have to be extended for Complex Adaptive Structures, since they, by definition, will participate in their own design. In this paper we introduce a new methodology for Emergent System Identification that is concerned with combining the methodologies of self-organizing functional networks (GMDH - Alexy G. Ivakhnenko), Particle Swarm Optimization (PSO - James Kennedy and Russell C. Eberhart) and Genetic Programming (GP - John Koza). This paper will concentrate on the utilization of Particle Swarm Optimization in this effort and discuss how Particle Swarm Optimization relates to our ultimate goal of emergent self-organizing functional networks that can be used to identify overlapping internal structural models. The ability for Complex Adaptive Structures to identify emerging internal models will be a key component for their success.

Voss, Mark S.; Feng, Xin

2001-10-01

277

Cumulant based identification approaches for nonminimum phase FIR systems  

Microsoft Academic Search

Recursive and least squares methods for identification of non-minimum-phase linear time-invariant (NMP-LTI) FIR systems are developed. The methods utilize the second- and third-order cumulants of the output of the FIR system whose input is an independent, identically distributed (i.i.d.) non-Gaussian process. Since knowledge of the system order is of utmost importance to many system identification algorithms, new procedures for determining

Saleh A. Alshebeili; A. N. Venetsanopoulos; A. Enis Cetin

1993-01-01

278

Nonlinear system identification by fuzzy piecewise affine models  

Microsoft Academic Search

In this paper, a new identification method of a piecewise affine model for a nonlinear system based on input-output data measurements is presented. In particular the identification of piecewise affine models of nonlinear single-input-single-output systems through Takagi-Sugeno models is considered. The basic idea in this paper is to decompose the nonlinear system into a set of piecewise affine systems. First,

Haider A. F. Mohamed; Masood Askari; M. Moghavvemi; S. S. Yang

2008-01-01

279

78 FR 46940 - Hazardous and Solid Waste Management System: Identification and Listing of Special Wastes...  

Federal Register 2010, 2011, 2012, 2013

...2050-AE81 Hazardous and Solid Waste Management System: Identification and...proposed rule: Hazardous and Solid Waste Management System: Identification and...comments to Hazardous and Solid Waste Management System: Identification...

2013-08-02

280

Exploiting input cyclostationarity for blind channel identification in OFDM systems  

Microsoft Academic Search

Transmitter-induced cyclostationarity has been explored previously as an alternative to fractional sampling and antenna array methods for blind identification of FIR communication channels. An interesting application of these ideas is in OFDM systems, which induce cyclostationarity due to the cyclic prefix. We develop a novel subspace approach for blind channel identification using cyclic correlations at the OFDM receiver. Even channels

Georgios B. Giannakis

1999-01-01

281

Validation of a Flour-Free Model Dough System for Throughput Studies of Baker's Yeast  

PubMed Central

Evaluation of gene expression in baker's yeast requires the extraction and collection of pure samples of RNA. However, in bread dough this task is difficult due to the complex composition of the system. We found that a liquid model system can be used to analyze the transcriptional response of industrial strains in dough with a high sugar content. The production levels of CO2 and glycerol by two commercial strains in liquid and flour-based doughs were correlated. We extracted total RNA from both a liquid and a flour-based dough. We used Northern blotting to analyze mRNA levels of three stress marker genes, HSP26, GPD1, and ENA1, and 10 genes in different metabolic subcategories. All 13 genes had the same transcriptional profile in both systems. Hence, the model appears to effectively mimic the environment encountered by baker's yeast in high-sugar dough. The liquid dough can be used to help understand the connections between technological traits and biological functions and to facilitate studies of gene expression under commercially important, but experimentally intractable, conditions.

Panadero, Joaquin; Randez-Gil, Francisca; Prieto, Jose Antonio

2005-01-01

282

Isolation, Identification and Growth of some Soil Hyphomycetes and YeastLike Fungi which Utilize Aromatic Compounds Related to Lignin  

Microsoft Academic Search

SUMMARY Fungi were isolated from soil under several vegetational types by an enrichment technique with vanillin or p-hydroxybenzaldehyde as sole source of carbon. Although similar morphologically, the isolates obtained are classified in two separate groups, yeasts and hyphomycetes. A study was made of the growth in pure culture of representative species, namely, Pullularia pullulans, Margarinomyces hetero- morpha and M. mutabilis

MOIRA E. K. HENDERSON

1961-01-01

283

Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences  

Microsoft Academic Search

Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1\\/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among

Cletus P. Kurtzman; Christie J. Robnett

1998-01-01

284

Identification of yeast MAS17 encoding the functional counterpart of the mitochondrial receptor complex protein MOM22 of Neurospora crassa  

Microsoft Academic Search

MOM22 of Neurospora crassa was suggested to be required for the transfer of mitochondrial precursor proteins from the receptors to the protein translocation machinery. We isolated a yeast mutant the viability of which depended on the expression of the introduced N. crassa MOM22 gene. The mutant cells showed defects in protein import into mitochondria when the cells were depleted of

Masato Nakai; Toshiya Endo

1995-01-01

285

Fission yeast cell morphogenesis: identification of new genes and analysis of their role during the cell cycle  

Microsoft Academic Search

To identify new genes involved in the control of cell morphogenesis in the fission yeast Schizosaccha- romyces pombe we have visually screened for tempera- ture-sensitive mutants that show defects in cell mor- phology. We have isolated and characterized 64 mutants defining 19 independent genes, 10 of which have not been previously described. One class of mu- tants, defining 12 orb

Fulvia Verde; Juan Mata; Paul Nurse

1995-01-01

286

A yeast secretion trap assay for identification of secreted proteins from eukaryotic phytopathogens and their plant hosts.  

PubMed

Secreted proteins from plants and phytopathogens play important roles in their interactions and contribute to elaborate mechanisms of attack, defense, and counter-defense, as well as surveillance and signaling. There is therefore considerable interest in developing techniques to characterize "secretomes." Here, we describe the use of the yeast secretion trap (YST) functional screen to isolate and identify secreted proteins that are accumulated and detected in the extracellular matrix of eukaryotes. This method involves fusing cDNAs generated or derived from plants, pathogens, or infected tissue to a yeast (Saccharomyces cerevisiae) invertase (suc2) reporter gene lacking its signal peptide, transforming the resulting fusion library into an invertase-deficient yeast strain, and plating the transformants on a sucrose selection medium. A yeast transformant containing a cDNA that encodes a secreted protein can rescue the mutant and the plasmid DNA can then be sequenced to identify the secreted protein. The YST screen can be a very powerful tool in the study of dynamics of plant host-pathogen interactions. PMID:22183675

Lee, Sang-Jik; Rose, Jocelyn K C

2012-01-01

287

UASIS: Universal Automatic SNP Identification System  

PubMed Central

Background SNP (Single Nucleotide Polymorphism), the most common genetic variations between human beings, is believed to be a promising way towards personalized medicine. As more and more research on SNPs are being conducted, non-standard nomenclatures may generate potential problems. The most serious issue is that researchers cannot perform cross referencing among different SNP databases. This will result in more resources and time required to track SNPs. It could be detrimental to the entire academic community. Results UASIS (Universal Automated SNP Identification System) is a web-based server for SNP nomenclature standardization and translation at DNA level. Three utilities are available. They are UASIS Aligner, Universal SNP Name Generator and SNP Name Mapper. UASIS maps SNPs from different databases, including dbSNP, GWAS, HapMap and JSNP etc., into an uniform view efficiently using a proposed universal nomenclature and state-of-art alignment algorithms. UASIS is freely available at http://www.uasis.tk with no requirement of log-in. Conclusions UASIS is a helpful platform for SNP cross referencing and tracking. By providing an informative, unique and unambiguous nomenclature, which utilizes unique position of a SNP, we aim to resolve the ambiguity of SNP nomenclatures currently practised. Our universal nomenclature is a good complement to mainstream SNP notations such as rs# and HGVS guidelines. UASIS acts as a bridge to connect heterogeneous representations of SNPs.

2011-01-01

288

Frequency-domain subspace identification for nonlinear mechanical systems  

NASA Astrophysics Data System (ADS)

This paper introduces a new frequency-domain subspace-based method for the identification of nonlinear mechanical systems. The technique exploits frequency-domain data and interprets nonlinearities as feedback forces exciting the underlying linear system. It is first demonstrated using two academic examples, namely a Duffing oscillator and a five-degree-of-freedom system comprising two nonlinearities. The identification of an experimental beam exhibiting geometrically nonlinear behaviour is then addressed.

Noël, J. P.; Kerschen, G.

2013-11-01

289

Stochastic structural system identification . Part 2: Variance parameter estimation  

NASA Astrophysics Data System (ADS)

This paper suggests a variance parameter's identification technique based on the stochastic structural system analysis method and the multidimensional optimisation algorithm. On combining the technique with the mean parameter identification method, proposed in the first part of this paper, a stochastic structural system modelling scheme is presented. The simulation results show that the scheme can produce a good estimation of mean parameters and variance parameters of stochastic structural system simultaneously.

Li, J.; Roberts, J. B.

290

BioID: A Multimodal Biometric Identification System  

Microsoft Academic Search

accurate identification.BioID is the first identification system we know of thatuses a dynamic feature, lip movement.1This featuremakes BioID more secure against fraud than systemsusing only static features such as fingerprints.Commercially available since 1998, the system hasdemonstrated its reliability in many installationsaround the world.SYSTEM FUNCTIONSFigure 1 diagrams BioID's functions. The systemacquires (records), preprocesses, and classifies eachbiometric feature...

Robert Frischholz; Ulrich Dieckmann

2000-01-01

291

Mammalian ribosomal and chaperone protein RPS3A counteracts ?-synuclein aggregation and toxicity in a yeast model system  

PubMed Central

Accumulation of aggregated forms of ?Syn (?-synuclein) into Lewy bodies is a known hallmark associated with neuronal cell death in Parkinson's disease. When expressed in the yeast Saccharomyces cerevisiae, ?Syn interacts with the plasma membrane, forms inclusions and causes a concentration-dependent growth defect. We have used a yeast mutant, cog6?, which is particularly sensitive to moderate ?Syn expression, for screening a mouse brain-specific cDNA library in order to identify mammalian proteins that counteract ?Syn toxicity. The mouse ribosomal and chaperone protein RPS3A was identified as a suppressor of ?Syn [WT (wild-type) and A53T] toxicity in yeast. We demonstrated that the 50 N-terminal amino acids are essential for this function. The yeast homologues of RPS3A were not effective in suppressing the ?Syn-induced growth defect, illustrating the potential of our screening system to identify modifiers that would be missed using yeast gene overexpression as the first screening step. Co-expression of mouse RPS3A delayed the formation of ?Syn–GFP inclusions in the yeast cells. The results of the present study suggest that the recently identified extraribosomal chaperonin function of RPS3A also acts on the neurodegeneration-related protein ?Syn and reveal a new avenue for identifying promising candidate mammalian proteins involved in ?Syn functioning.

De Graeve, Stijn; Marinelli, Sarah; Stolz, Frank; Hendrix, Jelle; Vandamme, Jurgen; Engelborghs, Yves; Van Dijck, Patrick; Thevelein, Johan M.

2013-01-01

292

Mammalian ribosomal and chaperone protein RPS3A counteracts ?-synuclein aggregation and toxicity in a yeast model system.  

PubMed

Accumulation of aggregated forms of ?Syn (?-synuclein) into Lewy bodies is a known hallmark associated with neuronal cell death in Parkinson's disease. When expressed in the yeast Saccharomyces cerevisiae, ?Syn interacts with the plasma membrane, forms inclusions and causes a concentration-dependent growth defect. We have used a yeast mutant, cog6?, which is particularly sensitive to moderate ?Syn expression, for screening a mouse brain-specific cDNA library in order to identify mammalian proteins that counteract ?Syn toxicity. The mouse ribosomal and chaperone protein RPS3A was identified as a suppressor of ?Syn [WT (wild-type) and A53T] toxicity in yeast. We demonstrated that the 50 N-terminal amino acids are essential for this function. The yeast homologues of RPS3A were not effective in suppressing the ?Syn-induced growth defect, illustrating the potential of our screening system to identify modifiers that would be missed using yeast gene overexpression as the first screening step. Co-expression of mouse RPS3A delayed the formation of ?Syn-GFP inclusions in the yeast cells. The results of the present study suggest that the recently identified extraribosomal chaperonin function of RPS3A also acts on the neurodegeneration-related protein ?Syn and reveal a new avenue for identifying promising candidate mammalian proteins involved in ?Syn functioning. PMID:23924367

De Graeve, Stijn; Marinelli, Sarah; Stolz, Frank; Hendrix, Jelle; Vandamme, Jurgen; Engelborghs, Yves; Van Dijck, Patrick; Thevelein, Johan M

2013-11-01

293

Field Study of an Iris Identification System.  

National Technical Information Service (NTIS)

We conducted a field trial of a commercial iris identification scanner at the US Navy Fleet Numerical Meterology and Oceanography Center (FNMOC) in Monterey, CA. Scans were performed by US military guards who had received approximately 20 minutes of train...

S. McLaren S. L. Garfinkel

2008-01-01

294

A Multiparameter Oil Pollution Source Identification System.  

National Technical Information Service (NTIS)

The feasibility of oil pollution source identification is demonstrated on eighty crude oils from the world's major oil fields. Measurements of fifteen diagnostic parameters were made on the 600+F fraction of the crude oil samples. Of the fifteen parameter...

J. W. Miller

1973-01-01

295

Requirements for Biological Threat Identification Systems  

Microsoft Academic Search

Rapid identification of bioterrorism or biological warfare agents is most urgent within the first 24 h after an attack (1–3). After that period, the ability to affect the prognosis of patients that have been infected with a highly virulent organism,\\u000a such as Bacillus anthracis, sharply declines (2). For less virulent organisms, identification during the pre-symptomatic stage is critical because the

Erik A. Henchal; George V. Ludwig

296

A yeast three-hybrid system that reconstitutes mammalian hypoxia inducible factor regulatory machinery  

PubMed Central

Background Several human pathologies, including neoplasia and ischemic cardiovascular diseases, course with an unbalance between oxygen supply and demand (hypoxia). Cells within hypoxic regions respond with the induction of a specific genetic program, under the control of the Hypoxia Inducible Factor (HIF), that mediates their adaptation to the lack of oxygen. The activity of HIF is mainly regulated by the EGL-nine homolog (EGLN) enzymes that hydroxylate the alpha subunit of this transcription factor in an oxygen-dependent reaction. Hydroxylated HIF is then recognized and ubiquitinilated by the product of the tumor suppressor gene, pVHL, leading to its proteosomal degradation. Under hypoxia, the hydroxylation of HIF by the EGLNs is compromised due to the lack of oxygen, which is a reaction cosubstrate. Thus, HIF escapes degradation and drives the transcription of its target genes. Since the progression of the aforementioned pathologies might be influenced by activation of HIF-target genes, development of small molecules with the ability to interfere with the HIF-regulatory machinery is of great interest. Results Herein we describe a yeast three-hybrid system that reconstitutes mammalian HIF regulation by the EGLNs and VHL. In this system, yeast growth, under specific nutrient restrictions, is driven by the interaction between the ? domain of VHL and a hydroxyproline-containing HIF? peptide. In turn, this interaction is strictly dependent on EGLN activity that hydroxylates the HIF? peptide. Importantly, this system accurately preserves the specificity of the hydroxylation reaction toward specific substrates. We propose that this system, in combination with a matched control, can be used as a simple and inexpensive assay to identify molecules that specifically modulate EGLN activity. As a proof of principle we show that two known EGLN inhibitors, dimethyloxaloylglycine (DMOG) and 6-chlor-3-hydroxychinolin-2-carbonic acid-N-carboxymethylamide (S956711), have a profound and specific effect on the yeast HIF/EGLN/VHL system. Conclusion The system described in this work accurately reconstitutes HIF regulation while preserving EGLN substrate specificity. Thus, it is a valuable tool to study HIF regulation, and particularly EGLN biochemistry, in a cellular context. In addition, we demonstrate that this system can be used to identify specific inhibitors of the EGLN enzymes.

Alcaide-German, Maria L; Vara-Vega, Alicia; Garcia-Fernandez, Luis F; Landazuri, Manuel O; del Peso, Luis

2008-01-01

297

Yeast two-hybrid screening using constitutive-active caspase-7 as bait in the identification of PA28? as an effector caspase substrate  

Microsoft Academic Search

Caspase-3 and -7 represent executioner\\/effector caspases that directly cause apoptotic morphological changes by cleaving various death substrates. The substrates for caspases generally interact with active caspases, but not with inactive zymogens of caspase or procaspases. Here, to isolate proteins that interact with caspase-7, we established a yeast two-hybrid screening system using reversed-caspase-7, a constitutive active mutant of caspase-7 as a

R Araya; R Takahashi; Y Nomura

2002-01-01

298

Evaluation of Candida ID, a New Chromogenic Medium for Fungal Isolation and Preliminary Identification of Some Yeast Species  

PubMed Central

Candida ID, a new chromogenic medium, allows identification of Candida albicans (blue colonies) and preliminary identification into a group of four species (pink colonies). In comparison with Albicans ID2 and Sabouraud gentamicin chloramphenicol on 446 fungal strains, Candida ID allowed the isolation of more species than Albicans ID 2 (95.5% versus 91.2%).

Fricker-Hidalgo, H.; Orenga, S.; Lebeau, B.; Pelloux, H.; Brenier-Pinchart, M. P.; Ambroise-Thomas, P.; Grillot, R.

2001-01-01

299

Engineered Saccharomyces cerevisiae strain for improved xylose utilization with a three-plasmid SUMO yeast expression system.  

PubMed

A three-plasmid yeast expression system utilizing the portable small ubiquitin-like modifier (SUMO) vector set combined with the efficient endogenous yeast protease Ulp1 was developed for production of large amounts of soluble functional protein in Saccharomyces cerevisiae. Each vector has a different selectable marker (URA, TRP, or LEU), and the system provides high expression levels of three different proteins simultaneously. This system was integrated into the protocols on a fully automated plasmid-based robotic platform to screen engineered strains of S. cerevisiae for improved growth on xylose. First, a novel PCR assembly strategy was used to clone a xylose isomerase (XI) gene into the URA-selectable SUMO vector and the plasmid was placed into the S. cerevisiae INVSc1 strain to give the strain designated INVSc1-XI. Second, amino acid scanning mutagenesis was used to generate a library of mutagenized genes encoding the bioinsecticidal peptide lycotoxin-1 (Lyt-1) and the library was cloned into the TRP-selectable SUMO vector and placed into INVSc1-XI to give the strain designated INVSc1-XI-Lyt-1. Third, the Yersinia pestis xylulokinase gene was cloned into the LEU-selectable SUMO vector and placed into the INVSc1-XI-Lyt-1 yeast. Yeast strains expressing XI and xylulokinase with or without Lyt-1 showed improved growth on xylose compared to INVSc1-XI yeast. PMID:18831987

Hughes, Stephen R; Sterner, David E; Bischoff, Kenneth M; Hector, Ronald E; Dowd, Patrick F; Qureshi, Nasib; Bang, Sookie S; Grynaviski, Nicole; Chakrabarty, Tania; Johnson, Eric T; Dien, Bruce S; Mertens, Jeffrey A; Caughey, Robert J; Liu, Siqing; Butt, Tauseef R; LaBaer, Joshua; Cotta, Michael A; Rich, Joseph O

2008-10-26

300

Species-specific identification of Dekkera/Brettanomyces yeasts by fluorescently labeled DNA probes targeting the 26S rRNA.  

PubMed

Sequencing of the complete 26S rRNA genes of all Dekkera/Brettanomyces species colonizing different beverages revealed the potential for a specific primer and probe design to support diagnostic PCR approaches and FISH. By analysis of the complete 26S rRNA genes of all five currently known Dekkera/Brettanomyces species (Dekkera bruxellensis, D. anomala, Brettanomyces custersianus, B. nanus and B. naardenensis), several regions with high nucleotide sequence variability yet distinct from the D1/D2 domains were identified. FISH species-specific probes targeting the 26S rRNA gene's most variable regions were designed. Accessibility of probe targets for hybridization was facilitated by the construction of partially complementary 'side'-labeled probes, based on secondary structure models of the rRNA sequences. The specificity and routine applicability of the FISH-based method for yeast identification were tested by analyzing different wine isolates. Investigation of the prevalence of Dekkera/Brettanomyces yeasts in the German viticultural regions Wonnegau, Nierstein and Bingen (Rhinehesse, Rhineland-Palatinate) resulted in the isolation of 37 D. bruxellensis strains from 291 wine samples. PMID:17596183

Röder, Christoph; König, Helmut; Fröhlich, Jürgen

2007-06-27

301

Renewable Identification Number System and U.S. Biofuel Mandates.  

National Technical Information Service (NTIS)

The Renewable Fuel Standard (RFS) sets annual mandates for renewable transportation fuels sold or introduced into commerce in the United States. The current RFS sets mandates through 2022. The Renewable Identification Number (RIN) system was created by th...

H. Lutman L. McPhail P. Westoctt

2011-01-01

302

47 CFR 25.281 - Automatic Transmitter Identification System (ATIS).  

Code of Federal Regulations, 2011 CFR

...CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Technical Operations...Identification System (ATIS). All satellite uplink transmissions carrying broadband... (a) Effective March 1, 1991, all satellite video uplink facilities shall be...

2011-10-01

303

Non-Linear Systems Identification Using Radial Basis Functions.  

National Technical Information Service (NTIS)

The identification of discrete-time nonlinear systems is investigated using radial basis functions. A forward regression algorithm based on an orthogonal decomposition of the regression matrix is employed. A set of radial basis function centers is selecte...

S. Chen S. A. Billings C. F. N. Cowan P. M. Grant

1989-01-01

304

Contribution of yeast models to neurodegeneration research.  

PubMed

As a model organism Saccharomyces cerevisiae has greatly contributed to our understanding of many fundamental aspects of cellular biology in higher eukaryotes. More recently, engineered yeast models developed to study endogenous or heterologous proteins that lay at the root of a given disease have become powerful tools for unraveling the molecular basis of complex human diseases like neurodegeneration. Additionally, with the possibility of performing target-directed large-scale screenings, yeast models have emerged as promising first-line approaches in the discovery process of novel therapeutic opportunities against these pathologies. In this paper, several yeast models that have contributed to the uncovering of the etiology and pathogenesis of several neurodegenerative diseases are described, including the most common forms of neurodegeneration worldwide, Alzheimer's, Parkinson's, and Huntington's diseases. Moreover, the potential input of these cell systems in the development of more effective therapies in neurodegeneration, through the identification of genetic and chemical suppressors, is also addressed. PMID:22910375

Pereira, Clara; Bessa, Cláudia; Soares, Joana; Leão, Mariana; Saraiva, Lucília

2012-07-15

305

Identification of Mating Type Genes in the Bipolar Basidiomycetous Yeast Rhodosporidium toruloides: First Insight into the MAT Locus Structure of the Sporidiobolales? †  

PubMed Central

Rhodosporidium toruloides is a heterothallic, bipolar, red yeast that belongs to the Sporidiobolales, an order within a major lineage of basidiomycetes, the Pucciniomycotina. In contrast to other basidiomycetes, considerably less is known about the nature of the mating type (MAT) loci that control sexual reproduction in this lineage. Three genes (RHA1, RHA2, and RHA3) encoding precursors of the MAT A1 pheromone (rhodotorucine A) were previously identified and formed the basis for a genome walking approach that led to the identification of additional MAT genes in complementary mating strains of R. toruloides. Two mating type-specific alleles encoding a p21-activated kinase (PAK; Ste20 homolog) were found between the RHA2 and RHA3 genes, and identification in MAT A2 strains of a gene encoding a presumptive pheromone precursor enabled prediction of the structure of rhodotorucine a. In addition, a putative pheromone receptor gene (STE3 homolog) was identified upstream of RHA1. Analyses of genomic data from two closely related species, Sporobolomyces roseus and Sporidiobolus salmonicolor, identified syntenic regions that contain homologs of all the above-mentioned genes. Notably, six novel pheromone precursor genes were uncovered, which encoded, similarly to the RHA genes, multiple tandem copies of the peptide moiety. This suggests that this structure, which is unique among fungal lipopeptide pheromones, seems to be prevalent in red yeasts. Species comparisons provided evidence for a large, multigenic MAT locus structure in the Sporidiobolales, but no putative homeodomain transcription factor genes (which are present in all basidiomycetous MAT loci characterized thus far) could be found in any of the three species in the vicinity of the MAT genes identified.

Coelho, Marco A.; Rosa, Andre; Rodrigues, Nadia; Fonseca, Alvaro; Goncalves, Paula

2008-01-01

306

Identification of mating type genes in the bipolar basidiomycetous yeast Rhodosporidium toruloides: first insight into the MAT locus structure of the Sporidiobolales.  

PubMed

Rhodosporidium toruloides is a heterothallic, bipolar, red yeast that belongs to the Sporidiobolales, an order within a major lineage of basidiomycetes, the Pucciniomycotina. In contrast to other basidiomycetes, considerably less is known about the nature of the mating type (MAT) loci that control sexual reproduction in this lineage. Three genes (RHA1, RHA2, and RHA3) encoding precursors of the MAT A1 pheromone (rhodotorucine A) were previously identified and formed the basis for a genome walking approach that led to the identification of additional MAT genes in complementary mating strains of R. toruloides. Two mating type-specific alleles encoding a p21-activated kinase (PAK; Ste20 homolog) were found between the RHA2 and RHA3 genes, and identification in MAT A2 strains of a gene encoding a presumptive pheromone precursor enabled prediction of the structure of rhodotorucine a. In addition, a putative pheromone receptor gene (STE3 homolog) was identified upstream of RHA1. Analyses of genomic data from two closely related species, Sporobolomyces roseus and Sporidiobolus salmonicolor, identified syntenic regions that contain homologs of all the above-mentioned genes. Notably, six novel pheromone precursor genes were uncovered, which encoded, similarly to the RHA genes, multiple tandem copies of the peptide moiety. This suggests that this structure, which is unique among fungal lipopeptide pheromones, seems to be prevalent in red yeasts. Species comparisons provided evidence for a large, multigenic MAT locus structure in the Sporidiobolales, but no putative homeodomain transcription factor genes (which are present in all basidiomycetous MAT loci characterized thus far) could be found in any of the three species in the vicinity of the MAT genes identified. PMID:18408057

Coelho, Marco A; Rosa, André; Rodrigues, Nádia; Fonseca, Alvaro; Gonçalves, Paula

2008-04-11

307

Evaluation of Pyrosequencing® technology for the identification of clinically relevant non-dematiaceous yeasts and related species  

Microsoft Academic Search

Pyrosequencing was used to identify 133 isolates of clinically relevant non-dematiaceous yeasts. These included 97 ATCC strains\\u000a (42 type strains), seven UAMH strains, and 29 clinical isolates. Isolates belonged to the following genera: Candida (18 species), Trichosporon (10), Cryptococcus (7), Malassezia (3), Rhodotorula (2), Geotrichum (1), Blastoschizomyces (1), and Kodamaea (1). Amplicons of a hyper-variable ITS region were obtained and

C. I. Montero; Y. R. Shea; P. A. Jones; S. M. Harrington; N. E. Tooke; F. G. Witebsky; P. R. Murray

2008-01-01

308

Application of PCR-DGGE for the identification of lactic acid bacteria in acitve dry wine yeasts  

Microsoft Academic Search

In this work a Polymerase Chain Reaction (PCR)-Denaturing Gradient Gel Electrophoresis (DGGE) protocol was used to identify\\u000a the Lactic Acid Bacteria (LAB) contaminants in enological active dry yeasts routinely used in the wine production. The method\\u000a is based on the PCR amplification of a DNA fragment from the region V1 of 16S rDNA gene followed by a DGGE technique. The

Cristina Giusto; Dagmara Medrala; Giuseppe Comi; Marisa Manzano

2007-01-01

309

Identification of multiple interacting bad data via power system decomposition  

SciTech Connect

This paper presents a new, highly robust bad data identification algorithm for electric power system state estimation. A system decomposition scheme is coupled with the least median of squares estimator to allow identification of multiple interacting bad data even in cases of conforming errors. The algorithm is inherently resistant to bad measurements in positions of leverage, makes no a priori measurement error probability distribution assumptions, and is applicable in a real-time environment.

Cheniae, M.G.; Mili, L. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Bradley Dept. of Electrical Engineering; Rousseeuw, P.J. [Univ. Instelling Antwerpen (Belgium). Mathematics Dept.

1996-08-01

310

Test for Success: Next Generation Aircraft Identification System RF Simulation  

Microsoft Academic Search

Advancements in Identification Friend or Foe (IFF) systems are generating a variety of signals operating with a common purpose and often over common radio frequency (RF) spectrum. This paper will describe the top level characteristics of each of the following IFF\\/Surveillance systems and the plans and challenges of modeling these systems in ViaSat's RF stimulator systems. (1.) Mark XIIA, Mode

M. L. Garcia; J. M. Hoffman; J. L. Rowley; D. L. Stone

2007-01-01

311

A computerized bacterial identification system as applied to planetary quarantine  

Microsoft Academic Search

A system has been developed to identify the samples obtained from Apollo spacecraft which uses a computer to process laboratory test results. This system is described in detail. The results of using the system with the available data are presented compared with conventional laboratory identifications. As a result of the performance with these comparisons, the system has been incorporated into

R. T. Dillon; Diane Holdridge; J. R. Puleo; G. S. Oxborrow

1971-01-01

312

National identification and recording systems for contagious animal disease control  

Microsoft Academic Search

A conceptual framework was described for national identification and recording (I&R) systems, especially referring to the role in the control of highly contagious diseases in pigs. Subsequently, four different concepts of I&R systems were described: a current system meeting EU minimum standards, a revised system that will be introduced in several countries in the near future and two future concepts,

H. W. Saatkamp; R. Geers; J. P. T. M. Noordhuizen; A. A. Dijkhuizen; R. B. M. Huirne; V. Goedseels

1995-01-01

313

Identification and characterization of a cDNA encoding mouse CAP: a homolog of the yeast adenylyl cyclase associated protein.  

PubMed

CAP, an adenylyl cyclase associated protein, is present in Saccharomyces cerevisiae and Schizosaccharomyces pombe. In both organisms, CAP is bifunctional: the N-terminal domain binds to adenylyl cyclase, thereby enabling adenylyl cyclase to respond appropriately to upstream regulatory signals, such as RAS in S. cerevisiae; the C-terminal domain is required for cellular morphogenesis. Here, we describe the isolation of a cDNA encoding a CAP homolog from a higher eukaryote. The mouse CAP cDNA contains an open reading frame capable of encoding a 474 amino acid protein. The protein encoded by the mouse CAP cDNA shows extensive homology to the yeast CAP proteins, particularly in the central poly-proline rich region and in the C-terminal domain. By northern analysis, the CAP message appears to be ubiquitous, but not uniform. By indirect immunofluorescence, ectopically expressed mouse CAP protein is found in the cytoplasm of fibroblasts and, in migrating cells, at the leading edge. Expression of the mouse CAP cDNA in S. cerevisiae complements defects associated with loss of the yeast CAP carboxy-terminal domain. Hence, the function of the CAP carboxy-terminal domain has been conserved from yeast to mouse. PMID:7691848

Vojtek, A B; Cooper, J A

1993-07-01

314

Identification of Human Intracellular Targets of the Medicinal Herb St. John's Wort by Chemical-Genetic Profiling in Yeast  

PubMed Central

St. John’s Wort (SJW; Hypericum perforatum L.) is commonly known for its antidepressant properties and was traditionally used to promote wound healing, but its molecular mechanism of action is not known. Here, chemical-genetic profiling in yeast was used to predict the human intracellular targets of an aqueous extract of SJW. SJW source material was authenticated by TLC, digital microscopy, and HPLC, and further characterized by colorimetric methods for antioxidant activity, protein content, and total soluble phenolic content. SJW extract contained 1.76µg/mL hyperforin, 10.14µg/mL hypericin, and 46.05µg/mL pseudohypericin. The effect of SJW extract on ~5900 barcoded heterozygous diploid deletion strains of Saccharomyces cerevisiae was investigated using high-density oligonucleotide microarrays. Seventy-eight (78) yeast genes were identified as sensitive to SJW and were primarily associated with vesicle-mediated transport and signal transduction pathways. Potential human intracellular targets were identified using sequence-based comparisons and included proteins associated with neurological disease and angiogenesis-related pathways. Selected human targets were confirmed by cell-based immunocytochemical assays. The comprehensive and systematic nature of chemical-genetic profiling in yeast makes this technique attractive for elucidating the potential molecular mechanisms of action of botanical medicines and other bioactive dietary plants.

Phang, James M.

2008-01-01

315

Automatic Parameters Identification of Groundwater Model using Expert System  

NASA Astrophysics Data System (ADS)

Conventionally, parameters identification of groundwater model can be classified into manual parameters identification and automatic parameters identification using optimization method. Parameter searching in manual parameters identification requires heavily interaction with the modeler. Therefore, the identified parameters value is interpretable by the modeler. However, manual method is a complicated and time-consuming work and requires groundwater modeling practice and parameters identification experiences to performing the task. Optimization-based identification is more efficient and convenient comparing to the manual one. Nevertheless, the parameters search in the optimization approach can not directly interactive with modeler and one can only examine the final results. Moreover, because of the simplification of the optimization model, the parameters value obtained by optimization-based identification may not be feasible in reality. In light of previous discussion, this study integrates a rule-based expert system and a groundwater simulation model, MODFLOW 2000, to develop an automatic groundwater parameters identification system. The hydraulic conductivity and specific yield are the parameters to be calibrated in the system. Since the parameter value is automatic searched according the rules that are specified by modeler, it is efficient and the identified parameters value is more interpretable than that by optimized based approach. Beside, since the rules are easy to modify and adding, the system is flexible and can accumulate the expertise experiences. Several hypothesized cases were used to examine the system validity and capability. The result shows a good agreement between the identified and given parameter values and also demonstrates a great potential for extending the system to a fully function and practical field application system.

Tsai, P. J.; Chen, Y.; Chang, L.

2011-12-01

316

Evaluation of Accuracy and Repeatability of Identification of Food-Borne Pathogens by Automated Bacterial Identification Systems  

PubMed Central

The performances of five automated microbial identification systems, relative to that of a reference identification system, for their ability to accurately and repeatedly identify six common food-borne pathogens were assessed. The systems assessed were the MicroLog system (Biolog Inc., Hayward, Calif.), the Microbial Identification System (MIS; MIDI Inc., Newark, Del.), the VITEK system (bioMérieux Vitek, Hazelwood, Mo.), the MicroScan WalkAway 40 system (Dade-MicroScan International, West Sacramento, Calif.), and the Replianalyzer system (Oxoid Inc., Nepean, Ontario, Canada). The sensitivities and specificities of these systems for the identification of food-borne isolates of Bacillus cereus, Campylobacter jejuni, Listeria monocytogenes, Staphylococcus aureus, Salmonella spp., and verotoxigenic Escherichia coli were determined with 40 reference positive isolates and 40 reference negative isolates for each pathogen. The sensitivities of these systems for the identification of these pathogens ranged from 42.5 to 100%, and the specificities of these systems for the identification of these pathogens ranged from 32.5 to 100%. Some of the systems had difficulty correctly identifying the reference isolates when the results were compared to those from the reference identification tests. The sensitivity of MIS for the identification of S. aureus, B. cereus, E. coli, and C. jejuni, for example, ranged from 47.5 to 72.5%. The sensitivity of the Microlog system for the identification of E. coli was 72.5%, and the sensitivity of the VITEK system for the identification of B. cereus was 42.5%. The specificities of four of the five systems for the identification of all of the species tested with the available databases were greater than or equal to 97.5%; the exception was MIS for the identification of C. jejuni, which displayed a specificity of 32.5% when it was tested with reference negative isolates including Campylobacter coli and other Campylobacter species. All systems had >80% sensitivities for the identification of Salmonella species and Listeria species at the genus level. The repeatability of these systems for the identification of test isolates ranged from 30 to 100%. Not all systems included all six pathogens in their databases; thus, some species could not be tested with all systems. The choice of automated microbial identification system for the identification of a food-borne pathogen would depend on the availability of identification libraries within the systems and the performance of the systems for the identification of the pathogen.

Odumeru, Joseph A.; Steele, Marina; Fruhner, Lynne; Larkin, Carolyn; Jiang, Jiangdong; Mann, Elroy; McNab, W. Bruce

1999-01-01

317

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2010 CFR

...that each individual in the secured area or SIDA continuously displays the identification...unescorted access to secured areas and SIDA's to ascertain the authority of any...unescorted access authority to a secured area or SIDA thatâ (1) Ensure that only...

2009-10-01

318

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2010 CFR

...that each individual in the secured area or SIDA continuously displays the identification...unescorted access to secured areas and SIDA's to ascertain the authority of any...unescorted access authority to a secured area or SIDA thatâ (1) Ensure that only...

2010-10-01

319

System identification with generalized orthonormal basis functions  

Microsoft Academic Search

A least-squares identification method is studied that estimates a finite number of expansion coefficients in the series expansion of a transfer function, where the expansion is in terms of recently introduced generalized basis functions. The basis functions are orthogonal in H2, and generalize the pulse, Laguerre and Kautz bases. One of their important properties is that, when chosen properly, they

Peter S. C. Heuberger; József Bokor

1995-01-01

320

A portable system for nuclear, chemical agent, and explosives identification  

NASA Astrophysics Data System (ADS)

The FRIS/PINS hybrid integrates the LLNL-developed Field Radionuclide Identification System (FRIS) with the INEEL-developed Portable Isotopic Neutron Spectroscopy (PINS) chemical assay system to yield a combined general radioisotope, special nuclear material, and chemical weapons/explosives detection and identification system. The PINS system uses a neutron source and a high-purity germanium ?-ray detector. The FRIS system uses an electromechanically cooled germanium detector and its own analysis software to detect and identify special nuclear material and other radioisotopes. The FRIS/PINS combined system also uses the electromechanically-cooled germanium detector. There is no other currently available integrated technology that can combine a prompt-gamma neutron-activation analysis capability for CWE with a passive radioisotope measurement and identification capability for special nuclear material. .

Parker, W. E.; Buckley, W. M.; Kreek, S. A.; Caffrey, A. J.; Mauger, G. J.; Lavietes, A. D.; Dougan, A. D.

2001-07-01

321

Portable system for nuclear, chemical agent, and explosives identification  

NASA Astrophysics Data System (ADS)

The FRIS/PINS hybrid integrates the LLNL-developed Field Radionuclide Identification System (FRIS) with the INEEL- developed Portable Isotopic Neutron Spectroscopy (PINS) chemical assay system to yield a combined general radioisotope, special nuclear material (SNM), and chemical weapons/explosives (CWE) detection and identification system. The PINS system uses a neutron source and a high- purity germanium (gamma) -ray detector. The FRIS system uses an electromechanically cooled germanium detector and its own analysis software to detect and identify SNM and other radioisotopes. The FRIS/PINS combined system also uses the electromechanically-cooled germanium detector. There is no other currently available integrated technology that can combine an active neutron interrogation and analysis capability for CWE with a passive radioisotope measurement and identification capability for SNM.

Parker, Winifred E.; Buckley, W. M.; Kreek, S. A.; Caffrey, A. J.; Mauger, George J.; Lavietes, Anthony D.; Dougan, Arden D.

1999-10-01

322

A portable air jet actuator device for mechanical system identification  

NASA Astrophysics Data System (ADS)

System identification of limb mechanics can help diagnose ailments and can aid in the optimization of robotic limb control parameters and designs. An interesting fluid phenomenon--the Coand? effect--is utilized in a portable actuator to provide a stochastic binary force disturbance to a limb system. The design of the actuator is approached with the goal of creating a portable device which could be deployed on human or robotic limbs for in situ mechanical system identification. The viability of the device is demonstrated by identifying the parameters of an underdamped elastic beam system with fixed inertia and stiffness and variable damping. The nonparametric compliance impulse response yielded from the system identification is modeled as a second-order system and the resultant parameters are found to be in excellent agreement with those found using more traditional system identification techniques. The current design could be further miniaturized and developed as a portable, wireless, unrestrained mechanical system identification instrument for less intrusive and more widespread use.

Belden, Jesse; Staats, Wayne L.; Mazumdar, Anirban; Hunter, Ian W.

2011-03-01

323

A Functional Genomic Yeast Screen to Identify Pathogenic Bacterial Proteins  

PubMed Central

Many bacterial pathogens promote infection and cause disease by directly injecting into host cells proteins that manipulate eukaryotic cellular processes. Identification of these translocated proteins is essential to understanding pathogenesis. Yet, their identification remains limited. This, in part, is due to their general sequence uniqueness, which confounds homology-based identification by comparative genomic methods. In addition, their absence often does not result in phenotypes in virulence assays limiting functional genetic screens. Translocated proteins have been observed to confer toxic phenotypes when expressed in the yeast Saccharomyces cerevisiae. This observation suggests that yeast growth inhibition can be used as an indicator of protein translocation in functional genomic screens. However, limited information is available regarding the behavior of non-translocated proteins in yeast. We developed a semi-automated quantitative assay to monitor the growth of hundreds of yeast strains in parallel. We observed that expression of half of the 19 Shigella translocated proteins tested but almost none of the 20 non-translocated Shigella proteins nor ?1,000 Francisella tularensis proteins significantly inhibited yeast growth. Not only does this study establish that yeast growth inhibition is a sensitive and specific indicator of translocated proteins, but we also identified a new substrate of the Shigella type III secretion system (TTSS), IpaJ, previously missed by other experimental approaches. In those cases where the mechanisms of action of the translocated proteins are known, significant yeast growth inhibition correlated with the targeting of conserved cellular processes. By providing positive rather than negative indication of activity our assay complements existing approaches for identification of translocated proteins. In addition, because this assay only requires genomic DNA it is particularly valuable for studying pathogens that are difficult to genetically manipulate or dangerous to culture.

Slagowski, Naomi L; Kramer, Roger W; Morrison, Monica F; LaBaer, Joshua; Lesser, Cammie F

2008-01-01

324

Growth control of the eukaryote cell: a systems biology study in yeast  

PubMed Central

Background Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. Results Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.

Castrillo, Juan I; Zeef, Leo A; Hoyle, David C; Zhang, Nianshu; Hayes, Andrew; Gardner, David CJ; Cornell, Michael J; Petty, June; Hakes, Luke; Wardleworth, Leanne; Rash, Bharat; Brown, Marie; Dunn, Warwick B; Broadhurst, David; O'Donoghue, Kerry; Hester, Svenja S; Dunkley, Tom PJ; Hart, Sarah R; Swainston, Neil; Li, Peter; Gaskell, Simon J; Paton, Norman W; Lilley, Kathryn S; Kell, Douglas B; Oliver, Stephen G

2007-01-01

325

Decentralized system identification using stochastic subspace identification on wireless smart sensor networks  

NASA Astrophysics Data System (ADS)

Wireless Smart Sensor Networks (WSSNs) facilitates a new paradigm to structural identification and monitoring for civil infrastructure. Conventional monitoring systems based on wired sensors and centralized data acquisition and processing have been considered to be challenging and costly due to cabling and expensive equipment and maintenance costs. WSSNs have emerged as a technology that can overcome such difficulties, making deployment of a dense array of sensors on large civil structures both feasible and economical. However, as opposed to wired sensor networks in which centralized data acquisition and processing is common practice, WSSNs require decentralized computing algorithms to reduce data transmission due to the limitation associated with wireless communication. Thus, several system identification methods have been implemented to process sensor data and extract essential information, including Natural Excitation Technique with Eigensystem Realization Algorithm, Frequency Domain Decomposition (FDD), and Random Decrement Technique (RDT); however, Stochastic Subspace Identification (SSI) has not been fully utilized in WSSNs, while SSI has the strong potential to enhance the system identification. This study presents a decentralized system identification using SSI in WSSNs. The approach is implemented on MEMSIC's Imote2 sensor platform and experimentally verified using a 5-story shear building model.

Sim, Sung-Han; Spencer, Billie F., Jr.; Park, Jongwoong; Jung, Hyungjo

2012-03-01

326

Blackbox model identification of a magnetically levitated microrobotic system  

Microsoft Academic Search

Magnetically levitated microrobotic systems have shown a great deal of promise for micromanipulation and biomedical applications. This paper discusses the identification of the vertical and horizontal motion models for a large-gap magnetic suspension system developed by the authors. The suspension system consists of six electromagnets attached to a soft iron pole piece, which levitate a small microrobot prototype manufactured from

David Craig; Mir Behrad Khamesee

2007-01-01

327

Web based image database system for ballistic firearm identification  

Microsoft Academic Search

Computerised ballistic identification system can be used to streamline the process and increase the efficiency and accuracy. Web base FireBall aims to provide such system via Internet. This web application development is a practical approach to extend the formal desktop Fireball system to web application by using web database and web programming mechanism. The goal of this research is to

T. C. Chase; Dongguang Li

2001-01-01

328

Identification of Yeast Rho1p GTPase as a Regulatory Subunit of 1,3-\\/beta-Glucan Synthase  

Microsoft Academic Search

1,3-beta-D-Glucan synthase [also known as beta(1-->3)glucan synthase] is a multi-enzyme complex that catalyzes the synthesis of 1,3-beta-linked glucan, a major structural component of the yeast cell wall. Temperature-sensitive mutants in the essential Rho-type guanosine triphosphatase (GTPase), Rho1p, displayed thermolabile glucan synthase activity, which was restored by the addition of recombinant Rho1p. Glucan synthase from mutants expressing constitutively active Rho1p did

Hiroshi Qadota; Christophe P. Python; Shunsuke B. Inoue; Mikio Arisawa; Yasuhiro Anraku; Yi Zheng; Takahide Watanabe; David E. Levin; Yoshikazu Ohya

1996-01-01

329

[Aspects of yeast biodiversity].  

PubMed

Yeast biodiversity represents a dynamic scientific domain characterized by permanent emerging theories and accumulation of new data. Identification of genome structure for a number of yeast species and elucidation of regulatory pathways for species-specific metabolic networks, lead to development of numerous applications of yeasts in industry, biotechnology, therapeutics and bioremediation. The studies of the scientific community were long time focused on Saccharomyces cerevisae due mainly to its use in food production. Therefore, the species belonging to Saccharomyces genus became reference points for genomics and biodiversity studies. During last decades there is a growing interest for yeast species able to produce biomass by assimilating or degrading various compounds such as methanol, hydrocarbons, wood hydrolisates and other residues or by-products from different industries. PMID:23745219

Csutak, Ortansa; Vassu, Tatiana

330

Genome-wide system analysis reveals stable yet flexible network dynamics in yeast.  

PubMed

Recently, important insights into static network topology for biological systems have been obtained, but still global dynamical network properties determining stability and system responsiveness have not been accessible for analysis. Herein, we explore a genome-wide gene-to-gene regulatory network based on expression data from the cell cycle in Saccharomyces cerevisae (budding yeast). We recover static properties like hubs (genes having several out-going connections), network motifs and modules, which have previously been derived from multiple data sources such as whole-genome expression measurements, literature mining, protein-protein and transcription factor binding data. Further, our analysis uncovers some novel dynamical design principles; hubs are both repressed and repressors, and the intra-modular dynamics are either strongly activating or repressing whereas inter-modular couplings are weak. Finally, taking advantage of the inferred strength and direction of all interactions, we perform a global dynamical systems analysis of the network. Our inferred dynamics of hubs, motifs and modules produce a more stable network than what is expected given randomised versions. The main contribution of the repressed hubs is to increase system stability, while higher order dynamic effects (e.g. module dynamics) mainly increase system flexibility. Altogether, the presence of hubs, motifs and modules induce few flexible modes, to which the network is extra sensitive to an external signal. We believe that our approach, and the inferred biological mode of strong flexibility and stability, will also apply to other cellular networks and adaptive systems. PMID:19640161

Gustafsson, M; Hörnquist, M; Björkegren, J; Tegnér, J

2009-07-01

331

MAC, A System for Automatically IPR Identification, Collection and Distribution  

NASA Astrophysics Data System (ADS)

Controlling Intellectual Property Rights (IPR) in the Digital World is a very hard challenge. The facility to create multiple bit-by-bit identical copies from original IPR works creates the opportunities for digital piracy. One of the most affected industries by this fact is the Music Industry. The Music Industry has supported huge losses during the last few years due to this fact. Moreover, this fact is also affecting the way that music rights collecting and distributing societies are operating to assure a correct music IPR identification, collection and distribution. In this article a system for automating this IPR identification, collection and distribution is presented and described. This system makes usage of advanced automatic audio identification system based on audio fingerprinting technology. This paper will present the details of the system and present a use-case scenario where this system is being used.

Serrão, Carlos

332

Nonlinear identification of a brushless excitation system via field tests  

Microsoft Academic Search

In this paper, nonlinear identification of the excitation system (EXS) in the gas unit #2 of Rajaee power plant in Iran is presented. Two methods of modeling, i.e., grey-box and black-box modeling are used and compared. In the grey-box (classical) approach, first a block-diagram for the EXS is suggested, then a test procedure for identification of its parameters is outlined.

M. Rasouli; M. Karrari

2004-01-01

333

Neuro-fuzzy methods for nonlinear system identification  

Microsoft Academic Search

Most processes in industry are characterized by nonlinear and time-varying behavior. Nonlinear system identification is becoming an important tool which can be used to improve control performance and achieve robust fault-tolerant behavior. Among the different nonlinear identification techniques, methods based on neuro-fuzzy models are gradually becoming established not only in the academia but also in industrial applications. Neuro-fuzzy modeling can

Robert Babuška; Henk Verbruggen

2003-01-01

334

Source options for nuclear weapons identification system  

Microsoft Academic Search

This report briefly presents the advantages and disadvantages of two timed sources of neutrons that can be used with the source-driven noise analysis method: (1) ²⁵²Cf in an ionization chamber and (2) an associated-particle sealed tube neutron generator (APSTNG). These sources can be used with frequency and time analysis methods for nuclear weapons identification, quality assurance in production, special nuclear

J. T. Mihalczo; P. E. Koehler; T. E. Valentine; L. D. Phillips

1995-01-01

335

Identification of furfural as a key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain.  

PubMed

The production of fuel ethanol from low-cost lignocellulosic biomass currently suffers from several limitations. One of them is the presence of inhibitors in lignocellulosic hydrolysates that are released during pre-treatment. These compounds inhibit growth and hamper the production of ethanol, thereby affecting process economics. To delineate the effects of such complex mixtures, we conducted a chemical analysis of four different real-world lignocellulosic hydrolysates and determined their toxicological effect on yeast. By correlating the potential inhibitor abundance to the growth-inhibiting properties of the corresponding hydrolysates, we identified furfural as an important contributor to hydrolysate toxicity for yeast. Subsequently, we conducted a targeted evolution experiment to improve growth behaviour of the half industrial Saccharomyces cerevisiae strain TMB3400 in the hydrolysates. After about 300 generations, representative clones from these evolved populations exhibited significantly reduced lag phases in medium containing the single inhibitor furfural, but also in hydrolysate-supplemented medium. Furthermore, these strains were able to grow at concentrations of hydrolysates that effectively killed the parental strain and exhibited significantly improved bioconversion characteristics under industrially relevant conditions. The improved resistance of our evolved strains was based on their capacity to remain viable in a toxic environment during the prolonged, furfural induced lag phase. PMID:21261870

Heer, Dominik; Sauer, Uwe

2008-08-04

336

Identification of the Yeast R-SNARE Nyv1p as a Novel Longin Domain-containing Protein  

PubMed Central

Using nuclear magnetic resonance spectroscopy, we establish that the N-terminal domain of the yeast vacuolar R-SNARE Nyv1p adopts a longin-like fold similar to those of Sec22b and Ykt6p. Nyv1p is sorted to the limiting membrane of the vacuole via the adaptor protein (AP)3 adaptin pathway, and we show that its longin domain is sufficient to direct transport to this location. In contrast, we found that the longin domains of Sec22p and Ykt6p were not sufficient to direct their localization. A YXX?-like adaptin-dependent sorting signal (Y31GTI34) unique to the longin domain of Nyv1p mediates interactions with the AP3 complex in vivo and in vitro. We show that amino acid substitutions to Y31GTI34 (Y31Q;I34Q) resulted in mislocalization of Nyv1p as well as reduced binding of the mutant protein to the AP3 complex. Although the sorting of Nyv1p to the limiting membrane of the vacuole is dependent upon the Y31GTI34 motif, and Y31 in particular, our findings with structure-based amino acid substitutions in the mu chain (Apm3p) of yeast AP3 suggest a mechanistically distinct role for this subunit in the recognition of YXX?-like sorting signals.

Wen, Wenyu; Chen, Lu; Wu, Hao; Sun, Xin; Zhang, Mingjie

2006-01-01

337

Identification of amino acid residues essential for the yeast N-acetyltransferase Mpr1 activity by site-directed mutagenesis.  

PubMed

We previously discovered that the budding yeast Saccharomyces cerevisiae Sigma1278b has the MPR1 gene that confers resistance to the proline analogue azetidine-2-carboxylate (AZC). The MPR1-encoded protein (Mpr1) is an N-acetyltransferase that detoxifies AZC and is a novel member of the GCN5-related N-acetyltransferase (GNAT) superfamily. Mpr1 can reduce intracellular oxidation levels and protect yeast cells from oxidative stress, heat shock, freezing, or ethanol treatment. Here, we analyzed the amino acid residues in Mpr1 involved in substrate binding and catalysis by site-directed mutagenesis. The mutated genes were expressed in Escherichia coli, and the recombinant Strep-tagged fusion proteins were analyzed in terms of AZC resistance and acetyltransferase activity. The replacement of Arg145, which is conserved in the GNAT superfamily, by Ala, Asp, Glu, Gly, or Trp led to a growth defect of transformants grown in the presence of AZC. Kinetic studies demonstrated that these mutations caused a large reduction in the affinity for AZC and acetyl-CoA, suggesting that Arg145 interacts with both substrates. Among seven conserved Tyr residues, one of which may be a catalytic residue in the GNAT superfamily, Tyr166Ala- showed no detectable activity and Tyr166Phe-Mpr1, a remarkable decrease of the k(cat)/K(m) value. This result suggests that Tyr166 is critical for the catalysis. PMID:18373682

Kotani, Tetsuya; Takagi, Hiroshi

2008-03-27

338

Online identification of nonlinear spatiotemporal systems using kernel learning approach.  

PubMed

The identification of nonlinear spatiotemporal systems is of significance to engineering practice, since it can always provide useful insight into the underlying nonlinear mechanism and physical characteristics under study. In this paper, nonlinear spatiotemporal system models are transformed into a class of multi-input-multi-output (MIMO) partially linear systems (PLSs), and an effective online identification algorithm is therefore proposed by using a pruning error minimization principle and least square support vector machines. It is shown that many benchmark physical and engineering systems can be transformed into MIMO-PLSs which keep some important physical spatiotemporal relationships and are very helpful in the identification and analysis of the underlying system. Compared with several existing methods, the advantages of the proposed method are that it can make full use of some prior structural information about system physical models, can realize online estimation of the system dynamics, and achieve accurate characterization of some important nonlinear physical characteristics of the system. This would provide an important basis for state estimation, control, optimal analysis, and design of nonlinear distributed parameter systems. The proposed algorithm can also be applied to identification problems of stochastic spatiotemporal dynamical systems. Numeral examples and comparisons are given to demonstrate our results. PMID:21788186

Ning, Hanwen; Jing, Xingjian; Cheng, Li

2011-07-22

339

Identification of Medically Relevant Nocardia Species with an Abbreviated Battery of Tests  

Microsoft Academic Search

Identification of Nocardia to the species level is useful for predicting antimicrobial susceptibility patterns and defining the pathogenicity and geographic distribution of these organisms. We sought to develop an identification method which was accurate, timely, and employed tests which would be readily available in most clinical laboratories. We evaluated the API 20C AUX yeast identification system as well as several

Deanna L. Kiska; Karen Hicks; David J. Pettit

2002-01-01

340

Yarrowia lipolytica, a yeast genetic system to study mitochondrial complex I  

Microsoft Academic Search

The obligate aerobic yeast Yarrowia lipolytica is introduced as a powerful new model for the structural and functional analysis of mitochondrial complex I. A brief introduction into the biology and the genetics of this nonconventional yeast is given and the relevant genetic tools that have been developed in recent years are summarized. The respiratory chain of Y. lipolytica contains complexes

Stefan Kerscher; Stefan Dröse; Klaus Zwicker; Volker Zickermann; Ulrich Brandt

2002-01-01

341

Statistics for sparse, high-dimensional, and nonparametric system identification  

Microsoft Academic Search

Local linearization techniques are an important class of nonparametric system identification. Identifying local linearizations in practice involves solving a linear regression problem that is ill-posed. The problem can be ill-posed either if the dynamics of the system lie on a manifold of lower dimension than the ambient space or if there are not enough measurements of all the modes of

Anil Aswani; Peter Bickel; Claire Tomlin

2009-01-01

342

An overview of backscattered radio frequency identification system (RFID)  

Microsoft Academic Search

A radio frequency identification (RFID) system is a wireless communication system in which the radio link between the base station and the transponders are furnished by the modulated backscattered waves. The present paper is intended to provide a brief description of various subsystems of the RFID. The various applications of RFID are discussed. Sample results on read\\/write range for a

K. V. S. Rao

1999-01-01

343

Performance of an optical identification and interrogation system  

NASA Astrophysics Data System (ADS)

A free space optics based identification and interrogation system has been designed. The applications of the proposed system lie primarily in areas which require a secure means of mutual identification and information exchange between optical readers and tags. Conventional RFIDs raise issues regarding security threats, electromagnetic interference and health safety. The security of RF-ID chips is low due to the wide spatial spread of radio waves. Malicious nodes can read data being transmitted on the network, if they are in the receiving range. The proposed system provides an alternative which utilizes the narrow paraxial beams of lasers and an RSA-based authentication scheme. These provide enhanced security to communication between a tag and the base station or reader. The optical reader can also perform remote identification and the tag can be read from a far off distance, given line of sight. The free space optical identification and interrogation system can be used for inventory management, security systems at airports, port security, communication with high security systems, etc. to name a few. The proposed system was implemented with low-cost, off-the-shelf components and its performance in terms of throughput and bit error rate has been measured and analyzed. The range of operation with a bit-error-rate lower than 10-9 was measured to be about 4.5 m. The security of the system is based on the strengths of the RSA encryption scheme implemented using more than 1024 bits.

Venugopalan, A.; Ghosh, A. K.; Verma, P.; Cheng, S.

2008-05-01

344

An information theoretic approach to dynamical systems modeling and identification  

Microsoft Academic Search

The identification and modeling of dynamical systems in a practical situation, where the model set under consideration does not necessarily include the observed system, are treated. A measure of the relevant information in a sequence of observations is shown to possess useful properties, such as the metric property on the parameter set. It is then shown that maximum likelihood and

YORAM BARAM

1978-01-01

345

Systems Identification by Quasilinearization and by Evolutionary Programming  

Microsoft Academic Search

Two new methods for obtaining the values of the coefficients in the differential equations describing the dynamics of a system are developed. The first method is based on a quasilinearization procedure and is applicable in parameter identification problems where the plant is modeled by a system of linear differential equations, and noisy measurements of state and control variables are available.

George H. Burgin

1973-01-01

346

Interaction of the mixed yeast culture in the autotroph-heterotroph system with a closed gas cycle and spatially separated components  

NASA Astrophysics Data System (ADS)

The study considers the experimental model of the "autotroph-heterotroph" system with a closed gas cycle, in which the heterotrophic link is a mixed yeast population. The autotrophic link is represented by the algae Chlorella vulgaris and the heterotrophic link by the yeasts Candida utilis and Candida guilliermondii. The controls are separate links of Chlorella and yeasts isolated from the atmosphere. It has been shown that the outcome of the competition in the heterotrophic link depends on the strategy of the yeast population towards the substrate and oxygen. The C. utilis population quickly utilizes the substrate as it is an R-strategist and is less sensitive to oxygen deficiency. The C. guilliermondii population consumes low concentrations of the substrate because it is a K-strategist, but it is more sensitive to oxygen deficiency. That is why, in the "autotroph-heterotroph" system with a closed gas cycle, after a considerable amount of the substrate has been consumed, the C. guilliermondii population becomes more competitive that the C. utilis population. In the culture of a separate yeast link, isolated from the atmosphere, the C. utilis population finds itself in more favorable conditions due to oxygen deficiency. The system with a complex heterotrophic component exists longer than the system whose heterotrophic component is represented by one yeast species. This is accounted for by the positive metabolite interaction of yeasts and a more complete utilization of the substrate by a mixed culture of yeasts featuring different strategies towards the substrate.

Pisman, T.; Somova, L.

347

Interaction of a mixed yeast culture in an ``autotroph-heterotroph'' system with a closed atmosphere cycle and spatially separated components  

NASA Astrophysics Data System (ADS)

The study considers an experimental model of the "autotroph-heterotroph" system with a closed atmosphere cycle, in which the heterotrophic link is a mixed yeast population. The autotrophic link is represented by the algae Chlorella vulgaris and the heterotrophic link by the yeasts Candida utilis and Candida guilliermondii. The controls are populations of Chlorella and the same yeasts isolated from the atmosphere. It has been shown that the outcome of competition in the heterotrophic link depends on the strategy of the yeast population towards the substrate and oxygen. The C. utilis population quickly utilizes the substrate as it is an r-strategist and is less sensitive to oxygen deficiency. The C. guilliermondii population consumes low concentrations of the substrate because it is a K-strategist, but it is more sensitive to oxygen deficiency. That is why, in the "autotroph-heterotroph" system with a closed gas cycle, after a considerable amount of the substrate has been consumed, the C. guilliermondii population becomes more competitive that the C. utilis population. In the culture of yeasts, isolated from the atmosphere, the C. utilis population finds itself in more favorable conditions due to oxygen deficiency. The system with a complex heterotrophic component survive longer than a system whose heterotrophic component is represented by only one yeast species. This is explained for by the positive metabolite interaction of yeasts and a more complete utilization of the substrate by a mixed culture of yeasts featuring different strategies towards the substrate.

Pisman, T. I.; Somova, L. A.

348

Interaction of a mixed yeast culture in an "autotroph-heterotroph" system with a closed atmosphere cycle and spatially separated components.  

PubMed

The study considers an experimental model of the "autotroph-heterotroph" system with a closed atmosphere cycle, in which the heterotrophic link is a mixed yeast population. The autotrophic link is represented by the algae Chlorella vulgaris and the heterotrophic link by the yeasts Candida utilis and Candida guilliermondii. The controls are populations of Chlorella and the same yeasts isolated from the atmosphere. It has been shown that the outcome of competition in the heterotrophic link depends on the strategy of the yeast population towards the substrate and oxygen. The C. utilis population quickly utilizes the substrate as it is an r-strategist and is less sensitive to oxygen deficiency. The C. guilliermondii population consumes low concentrations of the substrate because it is a K-strategist, but it is more sensitive to oxygen deficiency. That is why, in the "autotroph-heterotroph" system with a closed gas cycle, after a considerable amount of the substrate has been consumed, the C. guilliermondii population becomes more competitive that the C. utilis population. In the culture of yeasts, isolated from the atmosphere, the C. utilis population finds itself in more favorable conditions due to oxygen deficiency. The system with a complex heterotrophic component survive longer than a system whose heterotrophic component is represented by only one yeast species. This is explained for by the positive metabolite interaction of yeasts and a more complete utilization of the substrate by a mixed culture of yeasts featuring different strategies towards the substrate. PMID:14503513

Pisman, T I; Somova, L A

2003-01-01

349

Identification of a group-I intron within the 25S rDNA from the yeast Arxula adeninivorans.  

PubMed

The 25S rDNA of the yeast Arxula adeninivorans LS3 has been closed from a genomic library and sequenced. This DNA could be localized on chromosome 1 from A. adeninivorans and comprised 3790 bp. The DNA sequence from this rDNA of the strain LS3 is very similar to the 25S rDNA of Candida albicans (91.7%), Saccharomyces cerevisiae (90.5%), Schizosaccharomyces pombe (83.8%) and Mucor racemosus (79.2%). Additionally a 411 bp insertion could be localized within the 25S rDNA. This intervening sequence, which is devoid of any long open reading frame, is a group-IC intron as revealed from its site of insertion, predicted secondary structure, and its self-splicing capability. The Arxula intron is intermediate in structure and sequence between the ribosomal introns of Tetrahymena thermophila and C. albicans. PMID:8905924

Rösel, H; Kunze, G

1996-09-30

350

Identification of Methylated Proteins in the Yeast Small Ribosomal Subunit: A Role for SPOUT Methyltransferases in Protein Arginine Methylation†  

PubMed Central

We have characterized the posttranslational methylation of Rps2, Rps3, and Rps27a, three small ribosomal subunit proteins in the yeast Saccharomyces cerevisiae, using mass spectrometry and amino acid analysis. We found that Rps2 is substoichiometrically modified at arginine-10 by the Rmt1 methyltransferase. We demonstrated that Rps3 is stoichiometrically modified by ?-monomethylation at arginine-146 by mass spectrometric and site-directed mutagenic analyses. Substitution of alanine for arginine at position 146 is associated with slow cell growth, suggesting that the amino acid identity at this site may influence ribosomal function and/or biogenesis. Analysis of the three-dimensional structure of Rps3 in S. cerevisiae shows that arginine-146 makes contacts with the small subunit rRNA. Screening of deletion mutants encoding potential yeast methyltransferases revealed that the loss of the YOR021C gene results in the absence of methylation on Rps3. We demonstrated that recombinant Yor021c catalyzes ?-monomethylarginine formation when incubated with S-adenosylmethionine and hypomethylated ribosomes prepared from a YOR021C deletion strain. Interestingly, Yor021c belongs to the family of SPOUT methyltransferases that, to date, have only been shown to modify RNA substrates. Our findings suggest a wider role for SPOUT methyltransferases in nature. Finally, we have demonstrated the presence of a stoichiometrically methylated cysteine residue at position 39 of Rps27a in a zinc-cysteine cluster. The discovery of these three novel sites of protein modification within the small ribosomal subunit will now allow for an analysis of their functional roles in translation and possibly other cellular processes.

Young, Brian D.; Weiss, David I.; Zurita-Lopez, Cecilia I.; Webb, Kristofor J.; Clarke, Steven G.; McBride, Anne E.

2012-01-01

351

[An intron-free methyl jasmonate inducible geranylgeranyl diphosphate synthase gene from Taxus media and its functional identification in yeast].  

PubMed

Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for diterpenes including Taxol, one of the most potent antitumor drugs. In order to investigate the role of GGPP synthase in taxol biosynthesis, we cloned, characterized and functionally expressed the GGPP synthase gene from Taxus media. A 3743-bp genomic sequence of T. media was isolated by genome walking strategy which contained an 1182-bp open reading frame (ORF) encoding a 393-amino acid polypeptide that showed high similarity to other plant GGPPSs. Subsequently the full-length cDNA of the GGPPS gene of T. media (designated TmGGPPS) was amplified by RACE. Bioinformatic analysis showed that TmGGPPS was an intron-free gene and its deduced polypeptide contained all the five conserved domains and functional aspartate-rich motifs of the prenyltransferases. By constructing the phylogenetic tree of plant GGPPSs, it was found that plant-derived GGPPSs could be divided into two classes, angiosperm and gymnosperm classes, which might have evolved in parallel from the same ancestor. To our knowledge this was the first report that the geranylgeranyl diphosphate synthase genes were free of intron and evolved in parallel between angiosperms and gymnosperms. The coding sequence of TmGGPPS was expressed in yeast mutant (SFNY368) lacking of GGPP synthase activity through functional complementation, and the transgenic yeast showed to have activity of GGPP synthase. This was also the first time to use SFNY368 to identify the function of plant-derived GGPPSs. Furthermore, investigation of the impact of methyl jasmonate (MeJA) on the expression of TmGGPPS revealed that MeJA-treated T. media cultured cells had much higher expression of TmGGPPS than untreated cells. PMID:15773543

Liao, Zhihua; Gong, Yifu; Kai, Guoyin; Zuo, Kaijing; Chen, Min; Tan, Qiumin; Wei, Yamin; Guo, Liang; Tan, Feng; Sun, Xiaofen; Tang, Kexuan

352

Detecting Protein-Protein Interactions in Vesicular Stomatitis Virus Using a Cytoplasmic Yeast Two Hybrid System  

PubMed Central

Summary Protein-protein interactions play an important role in many virus-encoded functions and in virus-host interactions. While a “classical” yeast two-hybrid system (Y2H) is one of the most common techniques to detect such interactions, it has a number of limitations, including a requirement for the proteins of interest to be relocated to the nucleus. Modified Y2H, such as the Sos recruitment system (SRS), which detect interactions occurring in the cytoplasm rather than the nucleus, allow proteins from viruses replicating in the cytoplasm to be tested in a more natural context. In this study, a SRS was used to detect interactions involving proteins from vesicular stomatitis virus (VSV), a prototypic non-segmented negative strand RNA (NNS) virus. All five full-length VSV proteins, as well as several truncated proteins, were screened against each other. Using the SRS, most interactions demonstrated previously involving VSV phosphoprotein, nucleocapsid (N) and large polymerase proteins were confirmed independently, while difficulties were encountered using the membrane associated matrix and glycoproteins. A human cDNA library was also screened against VSV N protein and one cellular protein, SFRS18, was identified which interacted with N in this context. The system presented can be redesigned easily for studies in other less tractable NNS viruses.

Moerdyk-Schauwecker, Megan; DeStephanis, Darla; Hastie, Eric; Grdzelishvili, Valery Z.

2011-01-01

353

Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle  

PubMed Central

Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified, understanding their functional interrelationships has been a challenge. Here we construct a comprehensive network of the mitochondrial system. We integrated genome-wide datasets to generate an accurate and inclusive mitochondrial parts list. Together with benchmarked measures of protein interactions, a network of mitochondria was constructed in their cellular context, including extra-mitochondrial proteins. This network also integrates data from different organisms to expand the known mitochondrial biology beyond the information in the existing databases. Our network brings together annotated and predicted functions into a single framework. This enabled, for the entire system, a survey of mutant phenotypes, gene regulation, evolution, and disease susceptibility. Furthermore, we experimentally validated the localization of several candidate proteins and derived novel functional contexts for hundreds of uncharacterized proteins. Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders.

Perocchi, Fabiana; Jensen, Lars J; Gagneur, Julien; Ahting, Uwe; von Mering, Christian; Bork, Peer; Prokisch, Holger; Steinmetz, Lars M

2006-01-01

354

Assessing systems properties of yeast mitochondria through an interaction map of the organelle.  

PubMed

Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified, understanding their functional interrelationships has been a challenge. Here we construct a comprehensive network of the mitochondrial system. We integrated genome-wide datasets to generate an accurate and inclusive mitochondrial parts list. Together with benchmarked measures of protein interactions, a network of mitochondria was constructed in their cellular context, including extra-mitochondrial proteins. This network also integrates data from different organisms to expand the known mitochondrial biology beyond the information in the existing databases. Our network brings together annotated and predicted functions into a single framework. This enabled, for the entire system, a survey of mutant phenotypes, gene regulation, evolution, and disease susceptibility. Furthermore, we experimentally validated the localization of several candidate proteins and derived novel functional contexts for hundreds of uncharacterized proteins. Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders. PMID:17054397

Perocchi, Fabiana; Jensen, Lars J; Gagneur, Julien; Ahting, Uwe; von Mering, Christian; Bork, Peer; Prokisch, Holger; Steinmetz, Lars M

2006-10-20

355

A deceptive pollination system targeting drosophilids through olfactory mimicry of yeast.  

PubMed

In deceptive pollination, insects are bamboozled into performing nonrewarded pollination. A prerequisite for the evolutionary stability in such systems is that the plants manage to generate a perfect sensory impression of a desirable object in the insect nervous system [1]. The study of these plants can provide important insights into sensory preference of their visiting insects. Here, we present the first description of a deceptive pollination system that specifically targets drosophilid flies. We show that the examined plant (Arum palaestinum) accomplishes its deception through olfactory mimicry of fermentation, a strategy that represents a novel pollination syndrome. The lily odor is composed of volatiles characteristic of yeast, and produces in Drosophila melanogaster an antennal detection pattern similar to that elicited by a range of fermentation products. By functional imaging, we show that the lily odors target a specific subset of odorant receptors (ORs), which include the most conserved OR genes in the drosophilid olfactome. Furthermore, seven of eight visiting drosophilid species show a congruent olfactory response pattern to the lily, in spite of comprising species pairs separated by ?40 million years [2], showing that the lily targets a basal function of the fly nose, shared by species with similar ecological preference. PMID:20933425

Stökl, Johannes; Strutz, Antonia; Dafni, Amots; Svatos, Ales; Doubsky, Jan; Knaden, Markus; Sachse, Silke; Hansson, Bill S; Stensmyr, Marcus C

2010-10-07

356

Resolving the network of cell signaling pathways using the evolving yeast two-hybrid system  

PubMed Central

In 1983, while investigators had identified a few human proteins as important regulators of specific biological outcomes, how these proteins acted in the cell was essentially unknown in almost all cases. 25 years on, our knowledge of the mechanistic basis of protein action has been transformed by our increasingly detailed understanding of protein-protein interactions, which have allowed us to define cellular machines. The advent of the yeast two-hybrid (Y2H) system in 1989 marked a milestone in the field of proteomics. Exploiting the modular nature of transcription factors, the Y2H system allows facile measurement of the activation of reporter genes based on interactions between two chimeric or “hybrid” proteins of interest. After a decade of service as a leading platforms for individual investigators to use in exploring the interaction properties of interesting target proteins, the Y2H system has increasing been applied in high throughput applications intended to map genome-scale protein-protein interactions for model organisms and humans. Although some significant technical limitations apply, the Y2H has made a great contribution to our general understanding of the topology of cellular signaling networks.

Ratushny, Vladimir; Golemis, Erica A.

2008-01-01

357

Power System Dynamic Equivalents Using Identification Techniques.  

National Technical Information Service (NTIS)

This report describes the development and demonstration of an equivalent mathematical model for the representation of the external system dynamics at the boundary buses of an internal system. These equivalents are needed for different system studies in wh...

M. A. H. Ibrahim

1976-01-01

358

Subspace identification of Hammerstein systems using B-splines.  

PubMed

This paper presents an algorithm for the identification of Hammerstein cascades with hard nonlinearities. The nonlinearity of the cascade is described using a B-spline basis with fixed knot locations; the linear dynamics are described using a state-space model. The algorithm automatically estimates both the order of the linear system and the number and locations of the knots used to characterize the nonlinearity. Therefore, it significantly reduces the a priori knowledge about the underlying system required for identification. A simulation study on a model of reflex stiffness shows that the new method estimates the nonlinearity accurately in the presence of output noise. PMID:23366635

Jalaleddini, K; Westwick, D T; Kearney, R E

2012-01-01

359

RNA-protein interactions in the yeast three-hybrid system: Affinity, sensitivity, and enhanced library screening  

Microsoft Academic Search

The yeast three-hybrid system has become a useful tool in analyzing RNA-protein interactions. An RNA sequence is tested in combination with an RNA-binding protein linked to a transcription activation domain (AD). A productive RNA-protein inter- action activates a reporter gene in vivo. The system has been used to test candidate RNA-protein pairs, to isolate mutations in each interacting partner, and

BRAD HOOK; DAVID BERNSTEIN; BEILIN ZHANG; MARVIN WICKENS

2005-01-01

360

A yeast expression system for functional and pharmacological studies of the malaria parasite Ca2+/H+ antiporter  

PubMed Central

Background Calcium (Ca2+) signalling is fundamental for host cell invasion, motility, in vivo synchronicity and sexual differentiation of the malaria parasite. Consequently, cytoplasmic free Ca2+ is tightly regulated through the co-ordinated action of primary and secondary Ca2+ transporters. Identifying selective inhibitors of Ca2+ transporters is key towards understanding their physiological role as well as having therapeutic potential, therefore screening systems to facilitate the search for potential inhibitors are a priority. Here, the methodology for the expression of a Calcium membrane transporter that can be scaled to high throughputs in yeast is presented. Methods The Plasmodium falciparum Ca2+/H+ antiporter (PfCHA) was expressed in the yeast Saccharomyces cerevisiae and its activity monitored by the bioluminescence from apoaequorin triggered by divalent cations, such as calcium, magnesium and manganese. Results Bioluminescence assays demonstrated that PfCHA effectively suppressed induced cytoplasmic peaks of Ca2+, Mg2+ and Mn2+ in yeast mutants lacking the homologue yeast antiporter Vcx1p. In the scalable format of 96-well culture plates pharmacological assays with a cation antiporter inhibitor allowed the measurement of inhibition of the Ca2+ transport activity of PfCHA conveniently translated to the familiar concept of fractional inhibitory concentrations. Furthermore, the cytolocalization of this antiporter in the yeast cells showed that whilst PfCHA seems to locate to the mitochondrion of P. falciparum, in yeast PfCHA is sorted to the vacuole. This facilitates the real-time Ca2+-loading assays for further functional and pharmacological studies. Discussion The functional expression of PfCHA in S. cerevisiae and luminescence-based detection of cytoplasmic cations as presented here offer a tractable system that facilitates functional and pharmacological studies in a high-throughput format. PfCHA is shown to behave as a divalent cation/H+ antiporter susceptible to the effects of cation/H+ inhibitors such as KB-R7943. This type of gene expression systems should advance the efforts for the screening of potential inhibitors of this type of divalent cation transporters as part of the malaria drug discovery initiatives and for functional studies in general. Conclusion The expression and activity of the PfCHA detected in yeast by a bioluminescence assay that follows the levels of cytoplasmic Ca2+ as well as Mg2+ and Mn2+ lend itself to high-throughput and quantitative settings for pharmacological screening and functional studies.

2012-01-01

361

Music identification system using MPEG-7 audio signature descriptors.  

PubMed

This paper describes a multiresolution system based on MPEG-7 audio signature descriptors for music identification. Such an identification system may be used to detect illegally copied music circulated over the Internet. In the proposed system, low-resolution descriptors are used to search likely candidates, and then full-resolution descriptors are used to identify the unknown (query) audio. With this arrangement, the proposed system achieves both high speed and high accuracy. To deal with the problem that a piece of query audio may not be inside the system's database, we suggest two different methods to find the decision threshold. Simulation results show that the proposed method II can achieve an accuracy of 99.4% for query inputs both inside and outside the database. Overall, it is highly possible to use the proposed system for copyright control. PMID:23533359

You, Shingchern D; Chen, Wei-Hwa; Chen, Woei-Kae

2013-03-07

362

Music Identification System Using MPEG-7 Audio Signature Descriptors  

PubMed Central

This paper describes a multiresolution system based on MPEG-7 audio signature descriptors for music identification. Such an identification system may be used to detect illegally copied music circulated over the Internet. In the proposed system, low-resolution descriptors are used to search likely candidates, and then full-resolution descriptors are used to identify the unknown (query) audio. With this arrangement, the proposed system achieves both high speed and high accuracy. To deal with the problem that a piece of query audio may not be inside the system's database, we suggest two different methods to find the decision threshold. Simulation results show that the proposed method II can achieve an accuracy of 99.4% for query inputs both inside and outside the database. Overall, it is highly possible to use the proposed system for copyright control.

You, Shingchern D.; Chen, Wei-Hwa; Chen, Woei-Kae

2013-01-01

363

Revisiting the Two-Stage Algorithm for Hammerstein system identification  

Microsoft Academic Search

The Two-Stage Algorithm (TSA) has been extensively used and adapted for the identification of block-oriented nonlinear systems including Hammerstein systems. This paper revisits an optimality result established by Bai in 1998 showing that the TSA provides the optimal estimation of a bilinearly parameterized Hammerstein system in the sense of a weighted nonlinear least-squares (LS) criterion formulated with some special weighting

Jiandong Wang; Qinghua Zhang; LLennart. Ljung

2009-01-01

364

Identification of Prp40, a novel essential yeast splicing factor associated with the U1 small nuclear ribonucleoprotein particle.  

PubMed Central

We have used suppressor genetics to identify factors that interact with Saccharomyces cerevisiae U1 small nuclear RNA (snRNA). In this way, we isolated PRP40-1, a suppressor that restores growth at 18 degrees C to a strain bearing a cold-sensitive mutation in U1 RNA. A gene disruption experiment shows that PRP40 is an essential gene. To study the role of PRP40 in splicing, we created a pool of temperature-sensitive prp40 strains. Primer extension analysis of intron-containing transcripts in prp40 temperature-sensitive strains reveals a splicing defect, indicating that Prp40 plays a direct role in pre-mRNA splicing. In addition, U1 RNA coimmunoprecipitates with Pro40, indicating that Prp40 is bound to the U1 small nuclear ribonucleoprotein particle in vivo. Therefore, we conclude that PRP40 encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle.

Kao, H Y; Siliciano, P G

1996-01-01

365

Identification of the second chromophore of Escherichia coli and yeast DNA photolyases as 5,10-methenyltetrahydrofolate.  

PubMed Central

Denaturation of DNA photolyase (deoxyribodipyrimidine photolyase, EC 4.1.99.3) from Escherichia coli with guanidine hydrochloride or acidification to pH 2 released, in addition to FAD, a chromophore with the spectral and chromatographic properties of a reduced pterin. Treatment of the enzyme with iodine prior to acidification converted the chromophore to a stable, oxidized derivative, which was resolved by HPLC into four species with identical spectral properties. The same species, in the same distribution, were obtained from the yeast enzyme. The material isolated from the iodine-oxidized enzyme was shown to be a pterin by conversion to pterin-6-carboxylic acid with alkaline permanganate and was found to release glutamate upon acid hydrolysis. The presence of 10-formylfolate in the isolated, oxidized chromophore was demonstrated by absorption and fluorescence spectroscopy and by deformylation and conversion to folic acid. Analysis of the distribution of polyglutamates revealed that the four species identified by HPLC corresponded to the tri-, tetra-, penta-, and hexaglutamate derivatives of 10-formylfolate. The results were consistent with gamma linkages in the triglutamate derivative with additional glutamates linked via the alpha-carboxyl group of the preceding residue. Treatment with rat plasma hydrolase produced the monoglutamate derivative of 10-formylfolate. The native, enzyme-bound form of the folate cofactor was identified as 5,10-methenyltetrahydrofolylpolyglutamate by effecting release and isolation at low pH to protect the 5,10-methenyl bridge and preserve the reduced pyrazine ring structure.

Johnson, J L; Hamm-Alvarez, S; Payne, G; Sancar, G B; Rajagopalan, K V; Sancar, A

1988-01-01

366

Identification of act2, an essential gene in the fission yeast Schizosaccharomyces pombe that encodes a protein related to actin.  

PubMed Central

Actins are a family of highly conserved proteins that are ubiquitously found among eukaryotic organisms. All actins that have previously been identified, including those of animals, plants, fungi, and protozoa, are 374-376 amino acids long and exhibit at least 70% amino acid sequence identity when compared with one another. We have cloned a gene from the fission yeast Schizosaccharomyces pombe that encodes a distantly related member of the actin protein family, herein referred to as act2. In contrast to all other actins, the derived amino acid sequence reveals that act2 is 427 residues long and exhibits only 35-40% identity to actins, including act1 from Sch. pombe. Comparison to the known x-ray crystallographic structure of rabbit skeletal muscle actin indicates that the ATP and divalent metal ion binding sites are largely conserved in act2, while regions involved in actin-actin and actin-myosin interactions are relatively divergent. Disruption of the act2 gene demonstrated that this gene encodes a function essential for germination of haploid spores. These findings indicate that while act2 and act1 are related proteins, they appear to have distinct functions. In addition, they demonstrate that the actin protein family is more diverse than was previously thought. Images

Lees-Miller, J P; Henry, G; Helfman, D M

1992-01-01

367

Identification of high gamma-aminobutyric acid producing marine yeast strains by physiological and biochemical characteristics and gene sequence analyses.  

PubMed

Four marine yeasts isolated from the Pacific Ocean off Japan (Siki No. 4, Siki No. 15, Hach No. 6, and Inub No. 11), which showed high gamma-aminobutyric acid (GABA) producing abilities, were identified and classified by physiological and biochemical characteristics and gene sequence analyses. Analysis of biochemical data suggested that while Siki No. 15 was identical to Candida, the remaining three isolates belonged to the genus Pichia. However, these data were insufficient to resolve their identity at the species level. Subsequently, analysis of the 5.8S rRNA genes and the two internal transcribed spacer regions (ITS) sequences revealed that Siki No. 15 belongs to Pichia guilliermondii, while the remaining three isolates corresponded to Pichia anomala. Since Siki No. 4 showed slightly different biochemical properties than the other two isolates, which were otherwise identical, we sought to investigate the sequences of the intergenic spacer region 1 (IGS1). We observed few nucleotide changes, suggesting that the Hach No. 6 and Inub No. 11 isolates belong to different but new strains for which we propose the names P. anomola MR-1 and MR-2 respectively. PMID:19584549

Guo, Xiao-feng; Aoki, Hitoshi; Hagiwara, Toshihiko; Masuda, Kazuaki; Watabe, Shugo

2009-07-07

368

Writer Identification for Smart Meeting Room Systems  

Microsoft Academic Search

In this paper we present a text independent on-line writer identifica- tion system based on Gaussian Mixture Models (GMMs). This system has been developed in the context of research on Smart Meeting Rooms. The GMMs in our system are trained using two sets of features extracted from a text line. The first feature set is similar to feature sets used

Marcus Liwicki; Andreas Schlapbach; Horst Bunke; Samy Bengio; Johnny Mariéthoz; Jonas Richiardi

2006-01-01

369

In vivo identification of essential nucleotides in tRNALeu to its functions by using a constructed yeast tRNALeu knockout strain  

PubMed Central

The fidelity of protein biosynthesis requires the aminoacylation of tRNA with its cognate amino acid catalyzed by aminoacyl-tRNA synthetase with high levels of accuracy and efficiency. Crucial bases in tRNALeu to aminoacylation or editing functions of leucyl-tRNA synthetase have been extensively studied mainly by in vitro methods. In the present study, we constructed two Saccharomyces cerevisiae tRNALeu knockout strains carrying deletions of the genes for tRNALeu(GAG) and tRNALeu(UAG). Disrupting the single gene encoding tRNALeu(GAG) had no phenotypic consequence when compared to the wild-type strain. While disrupting the three genes for tRNALeu(UAG) had a lethal effect on the yeast strain, indicating that tRNALeu(UAG) decoding capacity could not be compensated by another tRNALeu isoacceptor. Using the triple tRNA knockout strain and a randomly mutated library of tRNALeu(UAG), a selection to identify critical tRNALeu elements was performed. In this way, mutations inducing in vivo decreases of tRNA levels or aminoacylation or editing ability by leucyl-tRNA synthetase were identified. Overall, the data showed that the triple tRNA knockout strain is a suitable tool for in vivo studies and identification of essential nucleotides of the tRNA.

Huang, Qian; Yao, Peng; Eriani, Gilbert; Wang, En-Duo

2012-01-01

370

A combined database related and de novo MS-identification of yeast mannose-1-phosphate guanyltransferase PSA1 interaction partners at different phases of batch cultivation  

NASA Astrophysics Data System (ADS)

Mass spectrometry-based proteomic research has become one of the main methods in protein-protein interaction research. Several high throughput studies have established an interaction landscape of exponentially growing Baker's yeast culture. However, many of the protein-protein interactions are likely to change in different environmental conditions. In order to examine the dynamic nature of the protein interactions we isolated the protein complexes of mannose-1-phosphate guanyltransferase PSA1 from Saccharomyces cerevisiae at four different time points during batch cultivation. We used the tandem affinity purification (TAP)-method to purify the complexes and subjected the tryptic peptides to LC-MS/MS. The resulting peak lists were analyzed with two different methods: the database related protein identification program X!Tandem and the de novo sequencing program Lutefisk. We observed significant changes in the interactome of PSA1 during the batch cultivation and identified altogether 74 proteins interacting with PSA1 of which only six were found to interact during all time points. All the other proteins showed a more dynamic nature of binding activity. In this study we also demonstrate the benefit of using both database related and de novo methods in the protein interaction research to enhance both the quality and the quantity of observations.

Parviainen, Ville; Joenväärä, Sakari; Peltoniemi, Hannu; Mattila, Pirkko; Renkonen, Risto

2009-04-01

371

Identification and cloning in yeast artificial chromosomes of a region of elevated loss of heterozygosity on chromosome 1p31.1 in human breast cancer  

SciTech Connect

We have mapped a region of high loss of heterozygosity in breast cancer to a 2-cM interval between the loci D1S430 and D1S465 on chromosome 1p31.1. This region shows allelic imbalance in around 60% of breast tumors. As part of a strategy to clone the target gene(s) within this interval, we have generated a yeast artificial chromosome contig spanning over 7 Mb. YACs from the CEPH and Zeneca (formerly ICI) libraries have been obtained by screening with PCR-based STSs from the region for both previously identified loci and newly isolated STSs. The YACs have been assembled into a contig by a combination of approaches, including analysis of their STS content, generation of new STSs from the ends of key YACs, and long-range restriction mapping. These YAC clones provide the basis for complete characterization of the region of high loss in breast cancer and for the ultimate identification of the target gene(s). 84 refs., 3 figs., 3 tabs.

Hoggard, N.; Hey, Y.; Brintnell, B.; James, L. [Paterson Inst. for Cancer Research, Manchester (United Kingdom)] [and others

1995-11-20

372

A switchable light-input, light-output system modelled and constructed in yeast  

Microsoft Academic Search

BACKGROUND: Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidopsis proteins PHYTOCHROME A and FAR-RED ELONGATED HYPOCOTYL 1-LIKE. Light input to this regulatory module allows dynamic control of a light-emitting LUCIFERASE reporter gene, which we detect by real-time imaging of yeast colonies

Oxana Sorokina; Anita Kapus; Kata Terecskei; Laura E Dixon; Laszlo Kozma-Bognar; Ferenc Nagy; Andrew J Millar

2009-01-01

373

An effective iris recognition system for identification of humans  

Microsoft Academic Search

In this paper, identification and verification approach based on human iris pattern is presented. The system is based on several steps from capturing the iris pattern, determining and localizing the iris boundaries, transformation of localized iris into rectangular and polar components, extracting the features from the image, based on wavelet transformation and at the end the matching of the iris.

Muhaminad Khurrarn Khan; Jiashu Zhang; Shi-Jinn Horng

2004-01-01

374

Time-varying system identification and model validation using wavelets  

Microsoft Academic Search

Parametric identification of time-varying (TV) systems is possible if each TV coefficient can be expanded onto a finite set of basis sequences. The problem then becomes time invariant with respect to the parameters of the expansion. The authors address the question of selecting this set of basis sequences. They advocate the use of a wavelet basis because of its flexibility

Michail K. Tsatsanis; Georgios B. Giannakis

1993-01-01

375

Digital identification of voltage sag in distribution system  

Microsoft Academic Search

Voltage sags in distribution system occur more frequently and devastatingly than other power quality problems. Voltage sags due to line faults, transformer energizing and induction motor starting are the main interference sources. The reasons leading to these sags are analyzed and simulation result are presented by an EMTP model in this paper. A new identification method to sag waveforms is

Wang Kexing; Song Zhengxiang; Chen Degui; Wang Jianhua; Geng Yingsan

2002-01-01

376

Nonlinear system identification and model reduction using artificial neural networks  

Microsoft Academic Search

We present a technique for nonlinear system identification and model reduction using artificial neural networks (ANNs). The ANN is used to model plant input–output data, with the states of the model being represented by the outputs of an intermediate hidden layer of the ANN. Model reduction is achieved by applying a singular value decomposition (SVD)-based technique to the weight matrices

Vinay Prasad; B. Wayne Bequette

2003-01-01

377

A novel direct sequence spread spectrum automatic vehicle identification system  

Microsoft Academic Search

Due to a world wide surge in the intelligent vehicle highway system (IVHS), the field of automatic vehicle identification (AVI) has been rapidly growing. The use of spread spectrum communications has not yet pervaded the AVI market. However, in the already cramped electromagnetic environment, spread spectrum techniques have gained significant popularity in many growing areas of wireless communication. AVI is

Brad Hamant; B. Kamali

1996-01-01

378

Pattern identification in dynamical systems via symbolic time series analysis  

Microsoft Academic Search

This paper presents symbolic time series analysis (STSA) of multi-dimensional measurement data for pattern identification in dynamical systems. The proposed methodology is built upon concepts derived from Information Theory and Automata Theory. The objective is not merely to classify the time series patterns but also to identify the variations therein. To achieve this goal, a symbol alphabet is constructed from

Venkatesh Rajagopalan; Asok Ray; Rohan Samsi; Jeffrey Mayer

2007-01-01

379

Reaching beyond Identification through the "Identi-Form" System.  

ERIC Educational Resources Information Center

|The "Identi-Form," a system that includes defensible identification and prescriptive programing for gifted students, utilizes a holistic, multidimensional approach which incorporates test performance and ancedotal data in a total assessment package for each child. Sample case studies illustrate the approach. (Author/CL)|

Weber, Patricia; Battaglia, Catherine

1985-01-01

380

Parameter Identification of PM Motor System at Standstill  

NASA Astrophysics Data System (ADS)

This paper proposes the on-line parameter identification method of PM motor system including inverter. The d and q-axis inductances, phase resistance and voltage drop of inverter can be identified from the detected currents and voltage references at standstill. The validity of the proposed method is confirmed by experimental results.

Morimoto, Shigeo; Kozaki, Masayuki; Takeda, Yoji

381

An experimental study of nonlinear dynamic system identification  

Microsoft Academic Search

A technique for robust identification of nonlinear dynamic systems is developed and illustrated using both digital simulations and analog experiments. The technique is based on the Minimum Model Error optimal estimation approach. A detailed literature review is included in which fundamental differences between the current approach and previous work is described. The most significant feature of the current work is

Greselda I. Stry; D. Joseph Mook

1992-01-01

382

Identification of nonlinear dynamic systems using a rapid neural network  

Microsoft Academic Search

This paper presents the application of a rapid neural network for identification of unknown nonlinear dynamic systems when the inputs and outputs are accessible for measurements. The learning algorithm of the rapid neural network does not need an iterative procedure as in most learning algorithms such as the well known back-propagation algorithm. It is able to achieve a solution in

Refaat S. Ahmed

2001-01-01

383

Benchmarking the operational search accuracy of a national identification system  

Microsoft Academic Search

This paper reports on some of the challenges associated with setting up and conducting a full operational benchmark of a palm and fingerprint identification system, based on PITO's own recent experience in this field. The tests described were undertaken as part of the overall evaluation of suppliers tendering for a multi million pound contract to deliver a new national automated

Ambika Suman; Geoff Whitaker

2005-01-01

384

A single chip computational sensor system for gamma isotope identification  

Microsoft Academic Search

This paper presents the design and test results of a computational radiation sensor system based on a single chip solution that can perform standalone gamma isotope identification. A low power sensor front end with a charge sensitive amplifier, an event driven analog-to-digital converter, and a dedicated microcontroller are integrated on the same chip to process and bin the isotope data

Nathan Schemm; Bo Liang; Sina Balkir; Michael W. Hoffman; Mark Bauer

2010-01-01

385

System Identification and Multi-Level Optimization of Integrated Ground Water Systems.  

National Technical Information Service (NTIS)

Conjunctive surface water and ground water systems are analyzed using the techniques of system identification and multi-level optimization. Mathematical models describing the behavior of the ground water regime are developed. Given historic ground water l...

J. A. Dracup

1974-01-01

386

DNA barcode-based molecular identification system for fish species.  

PubMed

In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp . PMID:21110132

Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

2010-11-23

387

Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.  

PubMed

Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule that participates in various cellular regulatory events and that has been implicated in disease. Deciphering ceramide signaling is challenging because multiple ceramide species exist, and many of them may have distinct functions. We applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast Saccharomyces cerevisiae and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We found that during heat stress, distinct metabolic mechanisms controlled the abundance of different groups of ceramide species and provided experimental support for the importance of the dihydroceramidase Ydc1 in mediating the decrease in dihydroceramides during heat stress. Additionally, distinct groups of ceramide species, with different N-acyl chains and hydroxylations, regulated different sets of functionally related genes, indicating that the structural complexity of these lipids produces functional diversity. The transcriptional modules that we identified provide a resource to begin to dissect the specific functions of ceramides. PMID:24170935

Montefusco, David J; Chen, Lujia; Matmati, Nabil; Lu, Songjian; Newcomb, Benjamin; Cooper, Gregory F; Hannun, Yusuf A; Lu, Xinghua

2013-10-29

388

S-adenosyl-L-homocysteine hydrolase and methylation disorders: Yeast as a model system  

PubMed Central

S-adenosyl-L-methionine (AdoMet)-dependent methylation is central to the regulation of many biological processes: more than 50 AdoMet-dependent methyltransferases methylate a broad spectrum of cellular compounds including nucleic acids, proteins and lipids. Common to all AdoMet-dependent methyltransferase reactions is the release of the strong product inhibitor S-adenosyl-L-homocysteine (AdoHcy), as a by-product of the reaction. S-adenosyl-L-homocysteine hydrolase is the only eukaryotic enzyme capable of reversible AdoHcy hydrolysis to adenosine and homocysteine and, thus, relief from AdoHcy inhibition. Impaired S-adenosyl-L-homocysteine hydrolase activity in humans results in AdoHcy accumulation and severe pathological consequences. Hyperhomocysteinemia, which is characterized by elevated levels of homocysteine in blood, also exhibits a similar phenotype of AdoHcy accumulation due to the reversal of the direction of the S-adenosyl-L-homocysteine hydrolase reaction. Inhibition of S-adenosyl-L-homocysteine hydrolase is also linked to antiviral effects. In this review the advantages of yeast as an experimental system to understand pathologies associated with AdoHcy accumulation will be discussed.

Tehlivets, Oksana; Malanovic, Nermina; Visram, Myriam; Pavkov-Keller, Tea; Keller, Walter

2013-01-01

389

Development and application of a DNA microarray-based yeast two-hybrid system  

PubMed Central

The yeast two-hybrid (Y2H) system is the most widely applied methodology for systematic protein–protein interaction (PPI) screening and the generation of comprehensive interaction networks. We developed a novel Y2H interaction screening procedure using DNA microarrays for high-throughput quantitative PPI detection. Applying a global pooling and selection scheme to a large collection of human open reading frames, proof-of-principle Y2H interaction screens were performed for the human neurodegenerative disease proteins huntingtin and ataxin-1. Using systematic controls for unspecific Y2H results and quantitative benchmarking, we identified and scored a large number of known and novel partner proteins for both huntingtin and ataxin-1. Moreover, we show that this parallelized screening procedure and the global inspection of Y2H interaction data are uniquely suited to define specific PPI patterns and their alteration by disease-causing mutations in huntingtin and ataxin-1. This approach takes advantage of the specificity and flexibility of DNA microarrays and of the existence of solid-related statistical methods for the analysis of DNA microarray data, and allows a quantitative approach toward interaction screens in human and in model organisms.

Suter, Bernhard; Fontaine, Jean-Fred; Yildirimman, Reha; Rasko, Tamas; Schaefer, Martin H.; Rasche, Axel; Porras, Pablo; Vazquez-Alvarez, Blanca M.; Russ, Jenny; Rau, Kirstin; Foulle, Raphaele; Zenkner, Martina; Saar, Kathrin; Herwig, Ralf; Andrade-Navarro, Miguel A.; Wanker, Erich E.

2013-01-01

390

Yeasts associated with the infrabuccal pocket and colonies of the carpenter ant Camponotus vicinus.  

PubMed

After scanning electron microscopy indicated that the infrabuccal pockets of carpenter ants (Camponotus vicinus) contained numerous yeast-like cells, yeast associations were examined in six colonies of carpenter ants from two locations in Benton County in western Oregon. Samples from the infrabuccal-pocket contents and worker ant exoskeletons, interior galleries of each colony, and detritus and soil around the colonies were plated on yeast-extract/ malt-extract agar augmented with 1 M hydrochloric acid and incubated at 25 C. Yeasts were identified on the basis of morphological characteristics and physiological attributes with the BIOLOG(®) microbial identification system. Yeast populations from carpenter ant nest material and material surrounding the nest differed from those obtained from the infrabuccal pocket. Debaryomyces polymorphus was isolated more often from the infrabuccal pocket than from other material. This species has also been isolated from other ant species, but its role in colony nutrition is unknown. PMID:21148849

Mankowski, M E; Morrell, J J

391

Optimal inputs for linear system identification  

Microsoft Academic Search

This paper considers the design of optimal inputs for identifying parameters in linear dynamic systems. The criterion used for optimization is the sensitivity of the system output to the unknown parameters as expressed by the weighted trace of the Fisher information matrix. It is shown that the optimal energy constrained input is an eigenfunction of a positive self-adjoint operator corresponding

R. Mehra

1974-01-01

392

Dynamic response simulation through system identification  

NASA Astrophysics Data System (ADS)

Nonlinear dynamic systems, such as those associated with structural testing of vehicles, are considered. The vehicle, or a substructure, is mounted in a test rig that is normally driven by servo-hydraulic actuators. The specimen and test rig form a nonlinear dynamic system. These test systems assure the durability of vehicles by reproducing a structural response time history that has been measured in a road test of a vehicle. For this, a force or displacement input to the actuators’ control system must be determined as a function of time. Current practice employs an iterative algorithm, using a frequency response function to represent the system. The conventional iteration is a particular version of well established numerical techniques for solving nonlinear systems. However, the success of the iteration is dependent on the degree of nonlinearity and on the level of noise in the signals coming from the system. This paper advocates identifying the system to improve its representation in the iterative algorithm. The theory underpinning the alternative algorithm is presented and a comparison is made between the performances of the two algorithms, using computer simulations based on Duffing's equation. These simulations show that, even for this simple model, the alternative algorithm is faster, more reliable and more tolerant of response noise.

Roberts, D. E.; Hay, N. C.

2006-08-01

393

A Method of Visualizing Three-Dimensional Distribution of Yeast in Bread Dough  

NASA Astrophysics Data System (ADS)

A novel technique was developed to monitor the change in three-dimensional (3D) distribution of yeast in frozen bread dough samples in accordance with the progress of mixing process. Application of a surface engineering technology allowed the identification of yeast in bread dough by bonding EGFP (Enhanced Green Fluorescent Protein) to the surface of yeast cells. The fluorescent yeast (a biomarker) was recognized as bright spots at the wavelength of 520 nm. A Micro-Slicer Image Processing System (MSIPS) with a fluorescence microscope was utilized to acquire cross-sectional images of frozen dough samples sliced at intervals of 1 ?m. A set of successive two-dimensional images was reconstructed to analyze 3D distribution of yeast. Samples were taken from each of four normal mixing stages (i.e., pick up, clean up, development, and final stages) and also from over mixing stage. In the pick up stage yeast distribution was uneven with local areas of dense yeast. As the mixing progressed from clean up to final stages, the yeast became more evenly distributed throughout the dough sample. However, the uniformity in yeast distribution was lost in the over mixing stage possibly due to the breakdown of gluten structure within the dough sample.

Maeda, Tatsurou; Do, Gab-Soo; Sugiyama, Junichi; Oguchi, Kosei; Shiraga, Seizaburou; Ueda, Mitsuyoshi; Takeya, Koji; Endo, Shigeru

394

PICK1: a perinuclear binding protein and substrate for protein kinase C isolated by the yeast two-hybrid system  

Microsoft Academic Search

Abstract. Protein kinase C (PKC) plays a central role in the control of proliferation and differentiation of a wide range of cell types by mediating,the signal trans- duction response to hormones,and growth,factors. Upon activation by diacylglycerol, PKC translocates to different subcellular sites where,it phosphorylates numerous proteins, most of which are unidentified. We used the yeast two-hybrid system to identify pro-

J. Staudinger; J Zhou; R Burgess; Sj Elledge; En Olson

1995-01-01

395

Parametric Identification of a Power-System Emulator  

Microsoft Academic Search

\\u000a This paper presents the modeling and parametric identification of a motor-generator set. Our aim is to obtain a model including\\u000a the corresponding parameters for experimental research in power systems. The long term objective would be to have a turbine-generator\\u000a emulator as an experimental tool for studying the transient behavior of a power system when small disturbances appear. The\\u000a electric machines

Rubén Salas-Cabrera; Oscar Martínez-Hernández; Julio C. Rosas-Caro; Jonathan C. Mayo-Maldonado; E. Nacú Salas-Cabrera; Aaron González-Rodríguez; Hermenegildo Cisneros-Villegas; Rafael Castillo-Gutierrez; Gregorio Hernández-Palmer; Rodolfo Castillo-Ibarra

396

Soldier Identification System utilizing low probability of intercept (LPI) techniques  

Microsoft Academic Search

This paper documents the design of a laser\\/radio frequency (RF) Soldier Identification (ID) System developed by Dynetics, Inc., Harris, Corp., and the US Army Communications and Electronics Command (CECOM). The Soldier ID system includes an Interrogation Unit with a programmable activation code. The Interrogation Unit consists of a directive, eye-safe laser and a spread-spectrum RF transceiver. This allows for a

Michael C. Zari; Anthony F. Zwilling; David A. Hess; Jino Jo; Chris S. Anderson; Dave Chiang

1997-01-01

397

Toward Automated Anomaly Identification in Large-Scale Systems  

Microsoft Academic Search

When a system fails to function properly, health-related data are collected for troubleshooting. However, it is challenging to effectively identify anomalies from the voluminous amount of noisy, high-dimensional data. The traditional manual approach is time-consuming, error-prone, and even worse, not scalable. In this paper, we present an automated mechanism for node-level anomaly identification in large-scale systems. A set of techniques

Zhiling Lan; Ziming Zheng; Yawei Li

2010-01-01

398

Material Outgassing, Identification and Deposition, Molidep System.  

National Technical Information Service (NTIS)

The outgassing tests are performed employing a modified vacuum operated Cahn analytical microbalance, identified as the MOLIDEP system. The test measures under high vacuum, the time varying Molecular mass loss of a material sample held at a chosen tempera...

J. J. Scialdone A. F. Montoya

2002-01-01

399

Emotional System for Military Target Identification.  

National Technical Information Service (NTIS)

The thought of man-made systems and machines having emotions sounds like science fiction, however, few decades ago the idea of machines with intelligence seemed also like fiction, but today we are developing intelligent machines and using them successfull...

A. Khashman

2009-01-01

400

A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast  

Technology Transfer Automated Retrieval System (TEKTRAN)

A linear discrete dynamic system model is constructed to represent the temporal interactions among significantly expressed genes in response to bioethanol conversion inhibitor 5-hydroxymethylfurfural for ethanologenic yeast Saccharomyces cerevisiae. This study identifies the most significant linear...

401

Gene Engineering in Yeast for Biodegradation: Immunological Cross-Reactivity among Cytochrome P-450 System Proteins of 'Saccharomyces cerevisiae' and 'Candida tropicalis'.  

National Technical Information Service (NTIS)

Yeasts are eukaryotic microorganisms whose cytochrome P-450 monooxygenase systems may be amenable to genetic engineering for the hydroxylation and detoxication of polychlorinated aromatic hydrocarbons. The molecular genetic properties of strains of bakers...

J. C. Loper C. Chen C. R. Dey

1993-01-01

402

76 FR 63252 - Hazardous and Solid Waste Management System: Identification and Listing of Special Wastes...  

Federal Register 2010, 2011, 2012, 2013

...2050-AE81 Hazardous and Solid Waste Management System: Identification and...proposed rule: Hazardous and Solid Waste Management System: Identification and...residuals (CCRs); Facility and waste management unit data; Information on...

2011-10-12

403

21 CFR 880.6300 - Implantable radiofrequency transponder system for patient identification and health information.  

Code of Federal Regulations, 2013 CFR

...transponder system for patient identification and health information. 880.6300 Section 880...AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL...transponder system for patient identification and health information. (a)...

2013-04-01

404

Yeast screening system for the detection of mutation, recombination, and aneuploidy  

SciTech Connect

Two strains of the yeast Saccharomyces cerevisiae were constructed to detect genetic damage. Strain XD99 can detect chromosome loss, important in the induction of teratogenesis, aneuploidy, and possibly carcinogenesis. Two positive selection techniques were developed which select for the simultaneous loss of both arms of chromosome X. Confirmation of chromosome loss using a centromere-linked marker was found to be essential for distinguishing chromosome loss from coincident crossing-over. The high selectivity of strain XD99 allowed the development of a spot test for chromosome loss. Methyl benzimidazole-2-yl-carbamate and ethyl methanesulfonate induced chromosome loss in the spot test. The two carcinogens 4-nitroquinoline-N-oxide and N-methyl-N'-nitro-N-nitrosoguanidine also induced chromosome loss. Chromosome X monosomics were found to be unstable and were restored to euploidy. This restoration of euploidy may have important implications regarding chromosome loss as a mechanism of promotion. Strain XD83 can detect multiple genetic changes: nuclear frameshift and base pair substitution mutations, nuclear mitotic crossing-over and gene conversion and mitochondrial large deletions and forward point mutations. Ethyl methanesulfonate, ICR-170, N-methyl-N'-nitro-N-nitrosoguanidine, 4-nitroquinoline-N-oxide, ultraviolet light and ethidium bromide were tested. None of the carcinogens were specific in their induced spectrum of damage. Only ethidium bromide induced a highly specific spectrum of damage: petite induction. The variety of endpoints monitored here may allow the detection of certain carcinogens and other genetically toxic agents which have escaped detection in other systems. This system may be useful in the study of possible mechanisms of carcinogenesis and aneuploidy.

Dixon, M.L.

1983-09-01

405

A Yeast-Based Genetic System for Functional Analysis of Viral mRNA Capping Enzymes  

PubMed Central

Virus-encoded mRNA capping enzymes are attractive targets for antiviral therapy, but functional studies have been limited by the lack of genetically tractable in vivo systems that focus exclusively on the RNA-processing activities of the viral proteins. Here we have developed such a system by engineering a viral capping enzyme—vaccinia virus D1(1-545)p, an RNA triphosphatase and RNA guanylyltransferase—to function in the budding yeast Saccharomyces cerevisiae in lieu of the endogenous fungal triphosphatase (Cet1p) and guanylyltransferase (Ceg1p). This was accomplished by fusion of D1(1-545)p to the C-terminal guanylyltransferase domain of mammalian capping enzyme, Mce1(211-597)p, which serves as a vehicle to target the viral capping enzyme to the RNA polymerase II elongation complex. An inactivating mutation (K294A) of the mammalian guanylyltransferase active site in the fusion protein had no impact on genetic complementation of cet1?ceg1? cells, thus proving that (i) the viral guanylyltransferase was active in vivo and (ii) the mammalian domain can serve purely as a chaperone to direct other proteins to the transcription complex. Alanine scanning had identified five amino acids of vaccinia virus capping enzyme—Glu37, Glu39, Arg77, Glu192, and Glu194—that are essential for ? phosphate cleavage in vitro. Here we show that the introduction of mutation E37A, R77A, or E192A into the fusion protein abrogates RNA triphosphatase function in vivo. The essential residues are located within three motifs that define a family of viral and fungal metal-dependent phosphohydrolases with a distinctive capacity to hydrolyze nucleoside triphosphates to nucleoside diphosphates in the presence of manganese or cobalt. The acidic residues Glu37, Glu39, and Glu192 likely comprise the metal-binding site of vaccinia virus triphosphatase, insofar as their replacement by glutamine abolishes the RNA triphosphatase and ATPase activities.

Ho, C. Kiong; Martins, Alexandra; Shuman, Stewart

2000-01-01

406

System Identification with Information Theoretic Criteria  

Microsoft Academic Search

Attention is focused in this paper on the approximation problem of system identificationwith information theoretic criteria. For a class of problems it is shown thatthe criterion of mutual information rate is identical to the criterion of exponentialof-quadratic cost and to H1 entropy. In addition the relation between the likelihoodfunction and divergence is explored. As a consequence of these relations a

A. a. Stoorvogel; J. h. Van Schuppen

1996-01-01

407

Generalized Sensitivity Functions in Physiological System Identification  

Microsoft Academic Search

Parameters of physiological models are commonly associated in an input–output experiment with a specific pattern of the system response. This association is often made on an intuitive basis by traditional sensitivity analysis, i.e., by inspecting the variations of model output trajectories with respect to parameter variations. However, this approach provides limited information since, for instance, it ignores correlation among parameters.

Karl Thomaseth; Claudio Cobelli

1999-01-01

408

Evaluation of risk factors in patients with vulvovaginal candidiasis and the value of chromID Candida agar versus CHROMagar Candida for recovery and presumptive identification of vaginal yeast species.  

PubMed

Vulvovaginal candidiasis (VVC), particularly the recurrent form, remains an intractable problem for clinicians, microbiologists, and patients. It is essential to confirm the clinical diagnosis by mycological methods and avoid empirical therapy. The recovery of yeast in fungal culture, such as on Sabouraud dextrose agar, remains the gold standard for diagnosis. In this investigation, we examined 474 participants, including 122 (25.7%) with acute VVC cases, 249 (52.5%) who had recurrent VVC (RVVC) cases, and 103 (21.7%) healthy controls. We also administered a questionnaire to obtain information on patient lifestyle and medical, gynecological, and sexual history. In addition, we compared the performance of chromID Candida agar (CAN2) to CHROMagar Candida (CAC) and Sabouraud dextrose agar with gentamicin and chloramphenicol (SGC2). The yeasts were identified by conventional methods including the germ tube test, microscopic morphology on cornmeal-Tween 80 agar, and the commercial API 20C AUX system. We detected yeasts in 60 of 122 (49.2%) patients with acute VVC cases, 110 of 249 (44.2%) with RVVC cases, and in 35 of 103 (34%) healthy controls (P = 0.07). A total of 205 samples were found to be positive for fungi (43.2%), of which 176 (85.9%) were monofungal, and 29 (14.1%) were polyfungal. In addition, 198 of these samples (96.6%) were positive on CAN2, 195 (95.1%) on CAC, 189 (92.2%) on SGC2, and 183 (89.3%) samples on all three (P = 0.17). The 234 yeast isolates recovered were C. albicans (n = 118), C. glabrata (n = 82), C. kefyr (n = 11), C. krusei (n = 9), C. lipolytica (n = 3), C. colliculosa (n = 2), C. parapsilosis (n = 2), C. pelliculosa (n = 2), C. tropicalis (n = 2), and other species of Candida (n = 3). Of the 29 polyfungal populations, 28 (96.6%) were detected in CAN2, 25 in (86.2%) CAC, and 25 (86.2%) on both (P = 0.35). Notably, we detected the high predominance of C. albicans+C. glabrata (86.2%) in polyfungal populations. Briefly, the detection of C. albicans after 24 h of incubation was easier on CAN2 (64.4%) than on CAC (25.4%). This study showed that CAN2 is a rapid and reliable medium for immediate identification of C. albicans and for detecting polyfungal populations in vaginal specimens. We observed that the use of antibiotics, intrauterine devices, as well as, perineal laceration, short anovaginal distance (< 3 cm), and genital epilation in common areas are predisposing factors for RVVC (P < 0.001). In addition, we detected that the use of menstrual pad, using an (IUD), and having a history of childbirth increased the risk of both acute and recurrent VVC (P < 0.01), whereas the use of a daily pad and walking daily significantly decreased the risk of both acute and recurrent VVC (P < 0.01). PMID:20608776

Guzel, Ahmet Bari?; Ilkit, Macit; Akar, Tuba; Burgut, Refik; Demir, S Cansun

2010-07-07

409

TRP channels in yeast.  

PubMed

Microbes have made numerous contributions to the study of biology and medicine. Those contributions also include many original discovery's in the study of ion channels often thought as the province of neuroscientists or cardiophysiologists. Yeast have long been used as a model organism and TRP channel genes and their transmembrane products touted as the "vanguards of the sensory system" can be identified in the genomes of many yeasts. This article aims to review the study of these TRP channels in yeast their discovery, electrophysiological properties and physiological function. PMID:21290303

Kaleta, Marta; Palmer, Christopher

2011-01-01

410

Linear and nonlinear system identification of autonomic heart-rate modulation  

Microsoft Academic Search

The authors' findings show that system identification provides a useful, noninvasive, and quantitative means for evaluating cardiovascular regulatory mechanisms. With combinations of linear and nonlinear identification, new insights about the cardiovascular regulatory dynamics were obtained. System identification provides a new way of studying and monitoring cardiovascular function. Instead of just studying the signals generated by the cardiovascular regulatory system, the

Ki. H. Chon; Ramakrishna Mukkamala; Karin Toska; Thomas J. Mullen; A. A. Armoundas; R. J. Cohen

1997-01-01

411

System and method for radioisotope identification  

US Patent & Trademark Office Database

A system and method are providing for analyzing radiation signature data (i.e., spectral data) produced by a detector device against stored data representing the computed interaction of known radioisotopic spectra with a representative cross section for each of a small number of material groups. Each material group comprises materials expected to be in a detection path of the detector and which exhibit similar cross sections. Comparative analysis is made of the spectral data received from the detector for threat materials to determine whether the spectral data indicates presence of a threat material in the interrogated space. The system and method is not limited to any particular detector type, and may be used with any detector that produces spectral data.

2013-06-11

412

Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range  

PubMed Central

Although the proteins comprising many signaling systems are known, less is known about their numbers per cell. Existing measurements often vary by more than 10-fold. Here, we devised improved quantification methods to measure protein abundances in the Saccharomyces cerevisiae pheromone response pathway, an archetypical signaling system. These methods limited variation between independent measurements of protein abundance to a factor of two. We used these measurements together with quantitative models to identify and investigate behaviors of the pheromone response system sensitive to precise abundances. The difference between the maximum and basal signaling output (dynamic range) of the pheromone response MAPK cascade was strongly sensitive to the abundance of Ste5, the MAPK scaffold protein, and absolute system output depended on the amount of Fus3, the MAPK. Additional analysis and experiment suggest that scaffold abundance sets a tradeoff between maximum system output and system dynamic range, a prediction supported by recent experiments.

Thomson, Ty M.; Benjamin, Kirsten R.; Bush, Alan; Love, Tonya; Pincus, David; Resnekov, Orna; Yu, Richard C.; Gordon, Andrew; Colman-Lerner, Alejandro; Endy, Drew; Brent, Roger

2011-01-01

413

Evolutionary program for the identification of dynamical systems  

NASA Astrophysics Data System (ADS)

Various forms of neural networks have been applied to identification of non-linear dynamical systems. In most of these methods, the network architecture is set prior to training. In this paper, a method that evolves a symbolic solution for plant models is described. This method uses a evolutionary program to manipulate collections of parse trees expressed in a task specific language. Experiments performed on two unknown plants show this method is competitive with those that train neural networks for similar problems.

Angeline, Peter J.; Fogel, David B.

1997-04-01

414

Terahertz imaging system performance model for concealed-weapon identification  

Microsoft Academic Search

The U.S. Army Night Vision and Electronic Sensors Directorate (NVESD) and the U.S. Army Research Laboratory have developed a terahertz (THz) -band imaging system performance model for detection and identification of concealed weaponry. The MATLAB-based model accounts for the effects of all critical sensor and display components and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination.

Steven R. Murrill; Eddie L. Jacobs; Steven K. Moyer; Carl E. Halford; Steven T. Griffin; Frank C. De Lucia; Douglas T. Petkie; Charmaine C. Franck

2008-01-01

415

Terahertz imaging system performance model for concealed weapon identification  

Microsoft Academic Search

The U.S. Army Night Vision and Electronic Sensors Directorate and the U.S. Army Research Laboratory have developed a terahertz-band imaging system performance model for detection and identification of concealed weaponry. The MATLAB-based model accounts for the effects of all critical sensor and display components, and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination. The model is

Steven R. Murrill; Eddie L. Jacobs; Steven K. Moyer; Carl E. Halford; Steven T. Griffin; Frank C. De Lucia; Douglas T. Petkie; Charmaine C. Franck

2005-01-01

416

Isolation and identification of yeast strains capable of producing single cell protein from whey in co-cultures with Saccharomyces cerevisiae  

Microsoft Academic Search

In this study, twenty-five whey samples collected from dairy industries in the city of Isfahan. The samples were cultured on malt extract broth (MEB) and yeast extract glucose chloramphenicol agar (YGCA) media. Eleven yeast strains (designated M1 to M11) were iso- lated from the culture. The strains were identified by their morphological and physiological properties. Beta- galactosidase activity in the

Hassan Moeini; Sadeq Vallian; Iraj Nahvi

2004-01-01

417

Dry yeast  

NSDL National Science Digital Library

Yeast is a type of eukaryotic organism that can live in a dormant state. It can be activated from its dormant state by water and sugar. The yeast uses the sugar to grow and produces carbon dioxide gas as a byproduct.

Ranveig Thattai (None;)

2005-09-27

418

A yeast surface display system for the discovery of ligands that trigger cell activation  

Microsoft Academic Search

Opposing cells often communicate signalling events using multivalent interactions between receptors present on their cell surface. For example, T cells are typically activated when the T cell receptor (TCR) and its associated costimulatory molecules are multivalently engaged by the appropriate ligands present on an antigen presenting cell. In this report, yeast expressing high cell-surface levels of a TCR ligand (a

Bryan K. Cho; Michele C. Kieke; Eric T. Boder; K. Dane Wittrup; David M. Kranz

1998-01-01

419

Cloning and Expression in Yeast of a Plant Potassium Ion Transport System  

Microsoft Academic Search

A membrane polypeptide involved in K^+ transport in a higher plant was cloned by complementation of a yeast mutant defective in K^+ uptake with a complementary DNA library from Arabidopsis thaliana. A 2.65-kilobase complementary DNA conferred ability to grow on media with K^+ concentration in the micromolar range and to absorb K^+ (or 86Rb^+) at rates similar to those in

Herve Sentenac; Nathalie Bonneaud; Michele Minet; Francois Lacroute; Jean-Michel Salmon; Frederic Gaymard; Claude Grignon

1992-01-01

420

Vaginal Yeast Infections  

MedlinePLUS

... HIV/AIDS Sexually transmitted infections fact sheet Vaginal yeast infections fact sheet What is a vaginal yeast ... on vaginal yeast infections What is a vaginal yeast infection? A vaginal yeast infection is irritation of ...

421

The Alcohol Dehydrogenase System in the Xylose-Fermenting Yeast Candida maltosa  

PubMed Central

Background The alcohol dehydrogenase (ADH) system plays a critical role in sugar metabolism involving in not only ethanol formation and consumption but also the general “cofactor balance” mechanism. Candida maltosa is able to ferment glucose as well as xylose to produce a significant amount of ethanol. Here we report the ADH system in C. maltosa composed of three microbial group I ADH genes (CmADH1, CmADH2A and CmADH2B), mainly focusing on its metabolic regulation and physiological function. Methodology/Principal Findings Genetic analysis indicated that CmADH2A and CmADH2B tandemly located on the chromosome could be derived from tandem gene duplication. In vitro characterization of enzymatic properties revealed that all the three CmADHs had broad substrate specificities. Homo- and heterotetramers of CmADH1 and CmADH2A were demonstrated by zymogram analysis, and their expression profiles and physiological functions were different with respect to carbon sources and growth phases. Fermentation studies of ADH2A-deficient mutant showed that CmADH2A was directly related to NAD regeneration during xylose metabolism since CmADH2A deficiency resulted in a significant accumulation of glycerol. Conclusions/Significance Our results revealed that CmADH1 was responsible for ethanol formation during glucose metabolism, whereas CmADH2A was glucose-repressed and functioned to convert the accumulated ethanol to acetaldehyde. To our knowledge, this is the first demonstration of function separation and glucose repression of ADH genes in xylose-fermenting yeasts. On the other hand, CmADH1 and CmADH2A were both involved in ethanol formation with NAD regeneration to maintain NADH/NAD ratio in favor of producing xylitol from xylose. In contrast, CmADH2B was expressed at a much lower level than the other two CmADH genes, and its function is to be further confirmed.

Lin, Yuping; He, Peng; Wang, Qinhong; Lu, Dajun; Li, Zilong; Wu, Changsheng; Jiang, Ning

2010-01-01

422

Release of Ca2+ and Mg2+ from yeast mitochondria is stimulated by increased ionic strength  

Microsoft Academic Search

BACKGROUND: Divalent cations are required for many essential functions of mitochondrial metabolism. Yet the transporters that mediate the flux of these molecules into and out of the mitochondrion remain largely unknown. Previous studies in yeast have led to the molecular identification of a component of the major mitochondrial electrophoretic Mg2+ uptake system in this organism as well as a functional

Patrick C Bradshaw; Douglas R Pfeiffer

2006-01-01

423

Identification of biochemically atypical Staphylococcus aureus clinical isolates with three automated identification systems.  

PubMed

Between January and April 2002, a total of 271 strains of Staphylococcus aureus were isolated from clinical specimens at Toho University Omori Hospital, Japan, including 201 (74.2 %) which were identified as meticillin-resistant S. aureus (MRSA). However, 34 (12.5 %) were biochemically atypical, because they did not produce acid on mannitol salt agar or did not agglutinate in Staphaurex testing but were categorized as MRSA by PCR analysis and by antibiotic susceptibility. Three automatic identification systems, AutoScan-4 (Dade Behring), BD Phoenix (Becton Dickinson) and Vitek 2 (bioMérieux), were evaluated by testing these atypical S. aureus isolates. The AutoScan-4 and Phoenix systems identified all 34 isolates as S. aureus. Without additional tests such as Staphaurex, observation of colony pigment and haemolysins on sheep blood agar, Vitek 2 identified only 16 isolates (47.1 %) as S. aureus with good or better confidence levels and misidentified one of the remaining isolates as Staphylococcus chromogenes. This study shows that it is possible to identify these physiologically atypical S. aureus isolates correctly by using the Phoenix and AutoScan-4 fully automatic identification systems. PMID:16533985

Ishii, Yoshikazu; Alba, Jimena; Maehara, Chikako; Murakami, Hinako; Matsumoto, Tetsuya; Tateda, Kazuhiro; Furuya, Nobuhiko; Iwata, Morihiro; Yamaguchi, Keizo

2006-04-01

424

Advanced system identification techniques for wind turbine structures with special emphasis on modal parameters.  

National Technical Information Service (NTIS)

The goal of this research is to develop advanced system identification techniques that can be used to accurately measure the frequency response functions of a wind-turbine structure immersed in wind noise. To allow for accurate identification, the authors...

J. T. Bialasiewicz

1995-01-01

425

Characterization of identity, metabolism and androgenic activity of 17-hydroxyandrosta-3,5-diene by GC-MS and a yeast transactivation system.  

PubMed

Anabolic-androgenic steroids are frequently misused compounds in sports, and they belong to the controlled substances according to the requirements of the World Anti-Doping Agency. The classical techniques of steroid detection are mass spectrometry coupled to gas or liquid chromatography. Biological methods that base on the ability of substances to bind the steroid receptor are not applied in routine doping control procedures so far, but they appear to be useful for characterization of steroid androgenic potential. In this study we used the yeast androgen receptor reporter system (YAS), which in the past has already successfully been applied to both various androgenic substances and also urine samples. Giving attention to the androgenic potential of steroidal dietary supplements, we exemplified the analysis using both mass spectrometry techniques and the YAS-based assay on the product "Syntrax Tetrabol" which was a confiscated dietary supplement and marketed as a steroid precursor. Identification, structure and the kinetic behavior of its excreted metabolites were analyzed by NMR, GC-MS and LC-MS/MS. The androgenic potential of the parent compound as well as its metabolites in urine was evaluated with the help of the YAS. The application of urine samples with a previous deconjugation and the inclusion of urine density values were carried out and led to increased responses on the YAS. Further, the possibility of a complementary application of structure-based instrumental analysis and biological detection of androgenicity with the help of the YAS seems to be desirable and is discussed. PMID:22811023

Bauer, Anne; Rataj, Felicitas; Zierau, Oliver; Anielski, Patricia; Große, Joachim; Parr, Maria-Kristina; Vollmer, Günter; Thieme, Detlef

2012-07-19

426

Non-parametric identification of non-linear oscillating systems  

NASA Astrophysics Data System (ADS)

The problem of system identification from a time series of measurements is solved by using non-parametric additive models. Having only few structural information about the system, a non-parametric approach may be more appropriate than a parametric one for which detailed prior knowledge is needed. Based on non-parametric regression, the functions in the additive models are estimated by a penalized least-squares approach using backfitting. The optimal smoothing parameters are determined via generalized cross-validation, making this approach completely adaptive to the data. The procedure is applied to identify the non-linear restoring force of vibrationally excited helical wire rope isolators.

Peifer, M.; Timmer, J.; Voss, H. U.

2003-11-01

427

Yeast and Mammals Utilize Similar Cytosolic Components to Drive Protein Transport through the Golgi Complex  

NASA Astrophysics Data System (ADS)

Vesicular transport between successive compartments of the mammalian Golgi apparatus has recently been reconstituted in a cell-free system. In addition to ATP, transport requires both membrane-bound and cytosolic proteins. Here we report that the cytosol fraction from yeast will efficiently substitute for mammalian cytosol. Mammalian cytosol contains several distinct transport factors, which we have distinguished on the basis of gel filtration and ion-exchange chromatography. Yeast cytosol appears to contain the same collection of transport factors. Resolved cytosol factors from yeast and mammals complement each other in a synergistic manner. These findings suggest that the molecular mechanisms of intracellular protein transport have been conserved throughout evolution. Moreover, this hybrid cell-free system will enable the application of yeast genetics to the identification and isolation of cytosolic proteins that sustain intracellular protein transport.

Dunphy, William G.; Pfeffer, Suzanne R.; Clary, Douglas O.; Wattenberg, Binks W.; Glick, Benjamin S.; Rothman, James E.

1986-03-01

428

Nonlinear stochastic system identification of skin using volterra kernels.  

PubMed

Volterra kernel stochastic system identification is a technique that can be used to capture and model nonlinear dynamics in biological systems, including the nonlinear properties of skin during indentation. A high bandwidth and high stroke Lorentz force linear actuator system was developed and used to test the mechanical properties of bulk skin and underlying tissue in vivo using a non-white input force and measuring an output position. These short tests (5 s) were conducted in an indentation configuration normal to the skin surface and in an extension configuration tangent to the skin surface. Volterra kernel solution methods were used including a fast least squares procedure and an orthogonalization solution method. The practical modifications, such as frequency domain filtering, necessary for working with low-pass filtered inputs are also described. A simple linear stochastic system identification technique had a variance accounted for (VAF) of less than 75%. Representations using the first and second Volterra kernels had a much higher VAF (90-97%) as well as a lower Akaike information criteria (AICc) indicating that the Volterra kernel models were more efficient. The experimental second Volterra kernel matches well with results from a dynamic-parameter nonlinearity model with fixed mass as a function of depth as well as stiffness and damping that increase with depth into the skin. A study with 16 subjects showed that the kernel peak values have mean coefficients of variation (CV) that ranged from 3 to 8% and showed that the kernel principal components were correlated with location on the body, subject mass, body mass index (BMI), and gender. These fast and robust methods for Volterra kernel stochastic system identification can be applied to the characterization of biological tissues, diagnosis of skin diseases, and determination of consumer product efficacy. PMID:23264003

Chen, Yi; Hunter, Ian W

2012-12-22

429

A versatile overexpression strategy in the pathogenic yeast Candida albicans: identification of regulators of morphogenesis and fitness.  

PubMed

Candida albicans is the most frequently encountered human fungal pathogen, causing both superficial infections and life-threatening systemic diseases. Functional genomic studies performed in this organism have mainly used knock-out mutants and extensive collections of overexpression mutants are still lacking. Here, we report the development of a first generation C. albicans ORFeome, the improvement of overexpression systems and the construction of two new libraries of C. albicans strains overexpressing genes for components of signaling networks, in particular protein kinases, protein phosphatases and transcription factors. As a proof of concept, we screened these collections for genes whose overexpression impacts morphogenesis or growth rates in C. albicans. Our screens identified genes previously described for their role in these biological processes, demonstrating the functionality of our strategy, as well as genes that have not been previously associated to these processes. This article emphasizes the potential of systematic overexpression strategies to improve our knowledge of regulatory networks in C. albicans. The C. albicans plasmid and strain collections described here are available at the Fungal Genetics Stock Center. Their extension to a genome-wide scale will represent important resources for the C. albicans community. PMID:23049891

Chauvel, Murielle; Nesseir, Audrey; Cabral, Vitor; Znaidi, Sadri; Goyard, Sophie; Bachellier-Bassi, Sophie; Firon, Arnaud; Legrand, Mélanie; Diogo, Dorothée; Naulleau, Claire; Rossignol, Tristan; d'Enfert, Christophe

2012-09-25

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Identification of power system load dynamics using artificial neural networks  

SciTech Connect

Power system loads are important for planning and operation of an electric power system. Load characteristics can significantly influence the results of synchronous stability and voltage stability studies. This paper presents a methodology for identification of power system load dynamics using neural networks. Input-output data of a power system dynamic load is used to design a neural network model which comprises delayed inputs and feedback connections. The developed neural network model can predict the future power system dynamic load behavior for arbitrary inputs. In particular, a third-order induction motor load neural network model is developed to verify the methodology. Neural network simulation results are illustrated and compared with the induction motor load response.

Bostanci, M.; Koplowitz, J.; Taylor, C.W. [Clarkson Univ., Potsdam, NY (United States)]|[Bonneville Power Administration, Portland, OR (United States)

1997-11-01