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1

Evaluation of Automated Yeast Identification System  

NASA Technical Reports Server (NTRS)

One hundred and nine teleomorphic and anamorphic yeast isolates representing approximately 30 taxa were used to evaluate the accuracy of the Biolog yeast identification system. Isolates derived from nomenclatural types, environmental, and clinica isolates of known identity were tested in the Biolog system. Of the isolates tested, 81 were in the Biolog database. The system correctly identified 40, incorrectly identified 29, and was unable to identify 12. Of the 28 isolates not in the database, 18 were given names, whereas 10 were not. The Biolog yeast identification system is inadequate for the identification of yeasts originating from the environment during space program activities.

McGinnis, M. R.

1996-01-01

2

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

3

Rapid Identification of Candida dubliniensis with Commercial Yeast Identification Systems  

PubMed Central

Candida dubliniensis is a newly described species that is closely related phylogenetically to Candida albicans and that is commonly associated with oral candidiasis in human immunodeficiency virus-positive patients. Several recent studies have attempted to elucidate phenotypic and genotypic characteristics of use in separating the two species. However, results obtained with simple phenotypic tests were too variable and tests that provided more definitive data were too complex for routine use in the clinical laboratory setting. The objective of this study was to determine if reproducible identification of C. dubliniensis could be obtained with commercial identification kits. The substrate reactivity profiles of 80 C. dubliniensis isolates were obtained by using the API 20C AUX, ID 32 C, RapID Yeast Plus, VITEK YBC, and VITEK 2 ID-YST systems. The percentages of C. dubliniensis isolates capable of assimilating or hydrolyzing each substrate were compared with the percentages from the C. albicans profiles in each kit's database, and the results were expressed as percent C. dubliniensis and percent C. albicans. Any substrate that showed >50% difference in reactivity was considered useful in differentiating the species. In addition, assimilation of methyl-?-d-glucoside (MDG), d-trehalose (TRE), and d-xylose (XYL) by the same isolates was investigated by the traditional procedure of Wickerham and Burton (L. J. Wickerham and K. A. Burton, J. Bacteriol. 56:363–371, 1948). At 48 h (the time recommended by the manufacturer for its new database), we found that the assimilation of four carbohydrates in the API 20C AUX system could be used to distinguish the species, i.e., glycerol (GLY; 88 and 14%), XYL (0 and 88%), MDG (0 and 85%), and TRE (15 and 97%). Similarly, results with the ID 32 C system at 48 h showed that XYL (0 and 98%), MDG (0 and 98%), lactate (LAT; 0 and 96%), and TRE (30 and 96%) could be used to separate the two species. Phosphatase (PHS; 9 and 76%) and ?-d-glucosidase (23 and 94%) proved to be the most useful for separation of the species in the RapID Yeast Plus system. While at 24 h the profiles obtained with the VITEK YBC system showed that MDG (10 and 95%), XYL (0 and 95%), and GLY (26 and 80%) could be used to separate the two species, at 48 h only XYL (6 and 95%) could be used to separate the two species. The most useful substrates in the VITEK 2 ID-YST system were TRE (1 and 89%), MDG (1 and 99%), LAT (4 and 98%), and PHS (83 and 1%). While the latter kit was not yet commercially available at the time of the study, it would appear to be the most valuable for the identification of C. dubliniensis. Although assimilation of MDG, TRE, and XYL proved to be the most useful for species differentiation by the majority of commercial systems, the results with these carbohydrates by the Wickerham and Burton procedure were essentially the same for both species, albeit following protracted incubation. Thus, it is the rapidity of the assimilation achieved with the commercial systems that allows the differentiation of C. dubliniensis from C. albicans.

Pincus, D. H.; Coleman, D. C.; Pruitt, W. R.; Padhye, A. A.; Salkin, I. F.; Geimer, M.; Bassel, A.; Sullivan, D. J.; Clarke, M.; Hearn, V.

1999-01-01

4

Comparison of RapID Yeast Plus System with API 20C System for Identification of Common, New, and Emerging Yeast Pathogens  

PubMed Central

The ability to identify yeast isolates by the new enzymatic RapID Yeast Plus System was compared to the ability to identify yeast isolates by the API 20C system. A total of 447 yeast isolates representing Blastoschizomyces capitatus, 17 Candida spp., 5 Cryptococcus spp., Geotrichum spp., 2 Hanseniaspora spp., Hansenula anomala, Hansenula wingei, 3 Rhodotorula spp., Saccharomyces cerevisiae, Sporobolomyces salmonicolor, Trichosporon beigelii, and 2 Prototheca spp. were evaluated. Also, five quality control strains (Candida spp. and Cryptococcus laurentii) with well-documented reactivities by the RapID Yeast Plus System were used. Each isolate was evaluated by both methods with a 48-h culture grown at 30°C on Sabouraud dextrose agar (Emmons modification) by following the recommendations of the manufacturers. The RapID Yeast Plus System enzymatic reactions were read after 4 h of incubation, and the API 20C carbohydrate assimilation identification profiles were obtained after 72 h of incubation. There was good (95.7%) agreement between the identifications obtained by the two methods with the eight common Candida spp. and with Cryptococcus neoformans. The agreement was lower when the emerging Candida spp. and other yeast-like pathogens were tested (79.1 and 75.2%, respectively). These preliminary data suggest the potential utility of the RapID Yeast Plus System for use in the clinical laboratory for the rapid identification of common yeast pathogens as well as certain new and emerging species.

Espinel-Ingroff, A.; Stockman, L.; Roberts, G.; Pincus, D.; Pollack, J.; Marler, J.

1998-01-01

5

Comparative Evaluation of Three Commercial Identification Systems Using Common and Rare Bloodstream Yeast Isolates?  

PubMed Central

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.

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

2011-01-01

6

Evaluation of VITEK 2 and RapID Yeast Plus Systems for Yeast Species Identification: Experience at a Large Clinical Microbiology Laboratory?  

PubMed Central

A total of 750 clinical yeast isolates were evaluated by two identification systems, VITEK 2 and RapID Yeast Plus, using sequence analysis of the rRNA gene internal transcribed spacer regions as the reference method. The VITEK 2 and RapID systems correctly identified 737 (98.2%) and 716 (95.5%) isolates, respectively.

Sanguinetti, Maurizio; Porta, Rosaria; Sali, Michela; La Sorda, Marilena; Pecorini, Giovanni; Fadda, Giovanni; Posteraro, Brunella

2007-01-01

7

[Rapid identification and susceptibility to killer toxins of yeasts isolated from non-systemic mycoses].  

PubMed

Rapid identification and susceptibility to killer toxins of yeasts isolated from non-systemic mycoses. The use of quick and reliable yeast identification methods, as well as the development of new antifungal agents with more specific targets, will enable a more efficient treatment of mycoses. In the present work, a total of 53 clinical isolates obtained from non-systemic infections in Neuquén Hospitals and an ophthalmologic clinic in Buenos Aires during 2005, were identified by means of a rapid molecular method (ITS1-5.8S ADNr-ITS2 PCR-RFLP). Additionally, the killer susceptibility of the isolates was tested against reference and indigenous killer yeasts on plate tests. Eight yeast species were identified among the clinical isolates: Candida albicans (52%), Candida parapsilosis (17%), Candida tropicalis (10%), Candida krusei (5%), Candida glabrata (4%), Candida guilliermondii (4%), Kluyveromyces lactis (4%) and Saccharomyces cerevisiae (4%). Sixty-nine percent of the isolates corresponding to the predominant species (C. albicans) were related to vaginal infections. On the other hand, 61% of the yeasts associated with ocular infections were identified as C. parapsilosis. Two indigenous killer isolates DVMais5 and HCMeiss5, belonging to Pichia anomala and P. kluyveri respectively, exhibited the broadest killer spectrum against clinical isolates. PMID:18390160

Sangorrín, M P; Lopes, C A; Rivero, A; Caballero, A C

2007-01-01

8

Evaluation of the Biolog MicroStation system for yeast identification  

NASA Technical Reports Server (NTRS)

One hundred and fifty-nine isolates representing 16 genera and 53 species of yeasts were processed with the Biolog MicroStation System for yeast identification. Thirteen genera and 38 species were included in the Biolog database. For these 129 isolates, correct identifications to the species level were 13.2, 39.5 and 48.8% after 24, 48 and 72 hours incubation at 30 degrees C, respectively. Three genera and 15 species which were not included in the Biolog database were also tested. Of the 30 isolates studied, 16.7, 53.3 and 56.7% of the isolates were given incorrect names from the system's database after 24,48 and 72 h incubation at 30 degrees C, respectively. The remaining isolates of this group were not identified.

McGinnis, M. R.; Molina, T. C.; Pierson, D. L.; Mishra, S. K.

1996-01-01

9

Comparison of the new API Candida system to the ID 32C system for identification of clinically important yeast species.  

PubMed Central

API Candida was evaluated in comparison with the ID 32C system for the identification of 619 yeast isolates. The sensitivity of API Candida for the identification of the 15 species it claims to identify with and without additional tests was 97.4% (593 of 609) and 75.2% (458 of 609), respectively. The API Candida system is easy to use and rapid (result in 18 to 24 h).

Fricker-Hidalgo, H; Vandapel, O; Duchesne, M A; Mazoyer, M A; Monget, D; Lardy, B; Lebeau, B; Freney, J; Ambroise-Thomas, P; Grillot, R

1996-01-01

10

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

11

Identification of clinical yeasts by Vitek MS system compared with API ID 32 C.  

PubMed

We performed a clinical evaluation of the Vitek MS matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) system with the commercial database version 2.0 for rapid identification of medically important yeasts as compared with the conventional phenotypic method API ID 32 C. We tested 161 clinical isolates, nine isolates from culture collections and five reference strains. In case of discrepant results or no identification with one or both methods, molecular identification techniques were employed. Concordance between both methods was observed with 160/175 isolates (91.42%) and misidentifications by both systems occurred only when taxa were not included in the respective databases, i.e., one isolate of Candida etchellsii was identified as C. globosa by Vitek MS and two isolates of C. orthopsilosis were identified as C. parapsilosis by API ID 32 C. Vitek MS could not identify nine strains (5.14%) and API ID 32 C did not identify 13 (7.42%). Vitek MS was more reliable than API ID 32 C and reduced the time required for the identification of clinical isolates to only a few minutes. PMID:24782106

Durán-Valle, M Teresa; Sanz-Rodríguez, Nuria; Muñoz-Paraíso, Carmen; Almagro-Moltó, María; Gómez-Garcés, José Luis

2014-05-01

12

Evaluation of possibilities in identification and susceptibility testing for Candida glabrata clinical isolates with the Integral System Yeast Plus (ISYP).  

PubMed

The aim of this study was to evaluate possibilities of correct identification and susceptibility testing of C. glabrata clinical isolates with Integral System Yeast Plus (ISYP). For species identification, as the reference method, API Candida test and species-specific PCR reactions were used. The potential of antifungal susceptibility testing by the ISYP test was compared with the Sensititre Yeast One. Whilst the reference methods confirmed that the received population (n = 65 isolates) represented only C. glabrata, identification with the ISYP system showed correct data only in the case of 18 strains tested (27.7%). Species identification of the other 47 strains with the ISYP test was not possible at all. Significant differences were also observed for drug susceptibility testing carried out by the ISYP and the Sensititre Yeast One. The highest level of disagreement in classifying strains as resistant or susceptible estimated, as 73.9% and 40.0%, was observed for itraconazole and amphotericin B, respectively. Satisfactory results were only obtained for 5-fluorocytosine with 93.8% agreement between both methods. In our opinion the idea of the ISYP system is certainly good. The combination of identification ability and drug susceptibility testing in one test is very important, especially from a clinical point of view. However, the current version of the ISYP has many disadvantages. We would like to encourage the manufacturer to make an effort and develop a new, more accurate version of the test. PMID:24939684

Szweda, Piotr; Gucwa, Katarzyna; Naumiuk, Lukasz; Romanowska, Ewa; Dzierzanowska-Fangrat, Katarzyna; Brillowska-Dabrowska, Anna; Wojciechowska-Koszko, Iwona; Milewski, Slawomir

2014-06-01

13

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

PubMed Central

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.

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

2013-01-01

14

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

2013-11-01

15

[Identification of therapeutic and diagnostic targets through yeast two hybrid system: molecular biology in medicine].  

PubMed

In the last decades, molecular biology development was driven medicine, mainly in identification of novel therapeutic and diagnostics targets. In cells, proteins are the main responsible for the functioning of all cellular processes, from DNA synthesis to RNA and protein production, transport of cellular components and structural composition of the cell. Proteins are also an important component of signaling pathways between cells. Studies show that proteins normally do not function as singular units but as protein complexes. Understand protein interactions and discover compounds that interfere with such protein complexes are important to develop new pharmacologic treatments. There are already some drugs with such characteristics. Trichostatin A, a histone diacetilase, acts in Phosphatase protein 1 - Histone diacetilase complex, being a good target for anti-cancer therapy. In 1989, in a revolutionary way, Fields and Songs developed the Yeast Two Hybrid system (YTH). This method is based in the genetic properties of Saccharomyces cerevisiae and allows the detection of protein interactions in vivo. Since its development it suffered a few modifications that allowed its application in translational medicine. For example, this technique allows a high throughput screening to assess if a drug can interfere with a protein interaction. In the other hand, YTH can be used to ascertain which proteins interact with a protein of interest in a specific tissue (for example, brain or testis). Thus it is possible to unveil protein functions, signaling pathways and tissue functions. The great amount of data produced with YTH allows the identification and validation of diagnostic and therapeutic targets and also the development of new drugs. This review has the purpose to clarify the YTH system function and its contribution in identification of new pharmacologic treatments. PMID:23534595

Freitas, Maria João; Korrodi-Gregório, Luís; Esteves, Sara; Fardilha, Margarida

2012-01-01

16

Yeast One-Hybrid G? Recruitment System for Identification of Protein Lipidation Motifs  

PubMed Central

Fatty acids and isoprenoids can be covalently attached to a variety of proteins. These lipid modifications regulate protein structure, localization and function. Here, we describe a yeast one-hybrid approach based on the G? recruitment system that is useful for identifying sequence motifs those influence lipid modification to recruit proteins to the plasma membrane. Our approach facilitates the isolation of yeast cells expressing lipid-modified proteins via a simple and easy growth selection assay utilizing G-protein signaling that induces diploid formation. In the current study, we selected the N-terminal sequence of G? subunits as a model case to investigate dual lipid modification, i.e., myristoylation and palmitoylation, a modification that is widely conserved from yeast to higher eukaryotes. Our results suggest that both lipid modifications are required for restoration of G-protein signaling. Although we could not differentiate between myristoylation and palmitoylation, N-terminal position 7 and 8 play some critical role. Moreover, we tested the preference for specific amino-acid residues at position 7 and 8 using library-based screening. This new approach will be useful to explore protein-lipid associations and to determine the corresponding sequence motifs.

Fukuda, Nobuo; Doi, Motomichi; Honda, Shinya

2013-01-01

17

Evaluation of the updated Vitek yeast identification data base.  

PubMed Central

Using 398 isolates of yeasts and yeastlike fungi comprising 9 genera and 26 species, as well as the hyphomycete Geotrichum candidum and the achlorophyllous alga Prototheca wickerhamii, we compared the API 20C yeast identification system with the modified Vitek yeast identification system with an expanded data base. We found 11 discrepancies between the two systems: five (1.3%) of the isolates (Blastoschizomyces capitatus, 1; Candida albicans, 1; Hansenula anomala, 1; Rhodotorula minuta, 2) had biocodes not included in the expanded Vitek data base, and six (1.5%) of the isolates (Candida lusitaniae, 1; Candida parapsilosis, 1; Cryptococcus uniguttulatus, 1; H. anomala, 1; Torulopsis candida, 2) were misidentified by the Vitek system. Overall, the efficacy of the Vitek system compares favorably with that of the API 20C in the identification of clinically important yeasts.

el-Zaatari, M; Pasarell, L; McGinnis, M R; Buckner, J; Land, G A; Salkin, I F

1990-01-01

18

Identification of antituberculosis agents that target ribosomal protein interactions using a yeast two-hybrid system  

PubMed Central

Mycobacterium tuberculosis kills about 2 million people annually and antibiotic resistance is a cause of increased mortality. Therefore, development of new antituberculosis drugs is urgent for the control of widespread tuberculosis infections. For this purpose, we performed an innovative screen to identify new agents that disrupt the function of ribosomes in M. tuberculosis. Two bacterial ribosomal proteins L12 and L10 interact with each other and constitute the stalk of the 50S ribosomal subunit, which recruits initiation and elongation factors (EFs) during translation. Therefore, the L12–L10 interaction should be essential for ribosomal function and protein synthesis. We established a yeast two-hybrid system to identify small molecules that block the interaction between L12 and L10 proteins from M. tuberculosis. Using this system, we identified two compounds T766 and T054 that show strong bactericidal activity against tuberculosis but with low toxicity to mice and other bacterial strains. Moreover, using surface plasmon resonance (SPR) assay, we have demonstrated that these compounds bind specifically to L12 to disrupt L12–L10 interaction. Overproduction of L12 protein, but not L10, lowers the antibacterial activity of T766 and T054, indicating that the ribosome is likely the cellular target. Therefore, our data demonstrate that this yeast two-hybrid system is a useful tool to identify unique antituberculosis agents targeting the ribosomal protein L12–L10 interaction.

Lin, Yuan; Li, Yan; Zhu, Yuanjun; Zhang, Jing; Li, Yongzhen; Liu, Xiao; Jiang, Wei; Yu, Shishan; You, Xue-Fu; Xiao, Chunling; Hong, Bin; Wang, Yanchang; Jiang, Jian-Dong; Si, Shuyi

2012-01-01

19

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

20

Evaluation of the BD Phoenix system for identification of a wide spectrum of clinically important yeast species: a comparison with Vitek 2-YST.  

PubMed

The Phoenix Yeast ID and Vitek 2-YST panels were compared using 351 molecularly identified yeast isolates. The Phoenix showed a comparable rate of correct identification for 4 common (Phoenix, 98%; Vitek, 94%) and 45 uncommon species (Phoenix, 70%; Vitek, 64%) and had a shorter mean identification time (6-7 h). PMID:24952986

Won, Eun Jeong; Shin, Jong Hee; Kim, Mi-Na; Choi, Min Ji; Joo, Min Young; Kee, Seung Jung; Shin, Myung Geun; Suh, Soon Pal; Ryang, Dong Wook

2014-08-01

21

Improved identification of yeast species directly from positive blood culture media by combining Sepsityper specimen processing and Microflex analysis with the matrix-assisted laser desorption ionization Biotyper system.  

PubMed

Current methods for identification of yeast from blood cultures may take several days after these microorganisms have been observed by Gram stain smears from positive blood cultures. We explored the use of a matrix-assisted laser desorption ionization (MALDI) Biotyper system in combination with Sepsityper specimen processing and Microflex analysis for improved detection and identification of yeast species directly from positive blood culture specimens demonstrating yeast-like organisms by Gram stain. The limit of detection of yeast species in blood culture medium was determined to be 5.9 × 10(5) CFU, with intra- and interstrain coefficients of variation of 1.8 to 3.6% and 2.9%, respectively. A total of 42 yeast-containing positive blood culture specimens were processed, and the identification results were compared to those obtained by routinely used phenotypic methods. Specimens with discrepant results between the Biotyper and phenotypic methods were identified on the basis of internal transcribed spacer region sequencing. The MALDI Biotyper system correctly identified the 42 specimens to species level, including 28 (66.7%) Candida albicans, 8 (19.0%) Candida parapsilosis, and 5 (11.9%) Candida tropicalis isolates and 1 (2.4%) Cryptococcus neoformans isolate. The entire procedure, from specimen extraction to final result reporting, can be completed within 1 h. Our data indicated that the Sepsityper specimen processing and Microflex analysis by the MALDI Biotyper system provide a rapid and reliable tool for yeast species identification directly from positive blood culture media. PMID:21543564

Yan, Yingjun; He, Ying; Maier, Thomas; Quinn, Criziel; Shi, Gongyi; Li, Haijing; Stratton, Charles W; Kostrzewa, Markus; Tang, Yi-Wei

2011-07-01

22

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

23

Accuracy of Species-Level Identification of Yeast Isolates from Blood Cultures from 10 University Hospitals in South Korea by Use of the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Vitek MS System  

PubMed Central

We assessed the accuracy of yeast bloodstream isolate identification performed over a 1-year period at 10 South Korean hospitals, using the matrix-assisted laser desorption ionization–time of flight (MALDI-TOF)-based Vitek MS system. The overall phenotypic misidentification rate was 3.4% (18/533), with considerable variation between hospitals (0.0% to 19.0%), compared to 1.1% (6/533) for the Vitek MS system.

Won, Eun Jeong; Lee, Kyungwon; Kim, Mi-Na; Lee, Hye Soo; Park, Yeon-Joon; Joo, Min Young; Kim, Soo Hyun; Shin, Myung Geun; Suh, Soon Pal; Ryang, Dong Wook

2013-01-01

24

Accuracy of species-level identification of yeast isolates from blood cultures from 10 university hospitals in South Korea by use of the matrix-assisted laser desorption ionization-time of flight mass spectrometry-based Vitek MS system.  

PubMed

We assessed the accuracy of yeast bloodstream isolate identification performed over a 1-year period at 10 South Korean hospitals, using the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)-based Vitek MS system. The overall phenotypic misidentification rate was 3.4% (18/533), with considerable variation between hospitals (0.0% to 19.0%), compared to 1.1% (6/533) for the Vitek MS system. PMID:23784123

Won, Eun Jeong; Shin, Jong Hee; Lee, Kyungwon; Kim, Mi-Na; Lee, Hye Soo; Park, Yeon-Joon; Joo, Min Young; Kim, Soo Hyun; Shin, Myung Geun; Suh, Soon Pal; Ryang, Dong Wook

2013-09-01

25

Yeast identification algorithm based on use of the Vitek MS system selectively supplemented with ribosomal DNA sequencing: proposal of a reference assay for invasive fungal surveillance programs in China.  

PubMed

Sequence analysis of the internal transcribed spacer (ITS) region was employed as the gold standard method for yeast identification in the China Hospital Invasive Fungal Surveillance Net (CHIF-NET). It has subsequently been found that matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is potentially a more practical approach for this purpose. In the present study, the performance of the Vitek MS v2.0 system for the identification of yeast isolates collected from patients with invasive fungal infections in the 2011 CHIF-NET was evaluated. A total of 1,243 isolates representing 31 yeast species were analyzed, and the identification results by the Vitek MS v2.0 system were compared to those obtained by ITS sequence analysis. By the Vitek MS v2.0 system, 96.7% (n = 1,202) of the isolates were correctly assigned to the species level and 0.2% (n = 2) of the isolates were identified to the genus level, while 2.4% (n = 30) and 0.7% (n = 9) of the isolates were unidentified and misidentified, respectively. After retesting of the unidentified and misidentified strains, 97.3% (n = 1,209) of the isolates were correctly identified to the species level. Based on these results, a testing algorithm that combines the use of the Vitek MS system with selected supplementary ribosomal DNA (rDNA) sequencing was developed and validated for yeast identification purposes. By employing this algorithm, 99.7% (1,240/1,243) of the study isolates were accurately identified with the exception of two isolates of Candida fermentati and one isolate of Cryptococcus gattii. In conclusion, the proposed identification algorithm could be practically implemented in strategic programs of fungal infection surveillance. PMID:24478490

Zhang, Li; Xiao, Meng; Wang, He; Gao, Ran; Fan, Xin; Brown, Mitchell; Gray, Timothy J; Kong, Fanrong; Xu, Ying-Chun

2014-02-01

26

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

Microsoft Academic Search

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

A. Kaya; Huseyin C. Karakaya; Dmitri E. Fomenko; Vadim N. Gladyshev; A. Koc

2009-01-01

27

Identification of Protein Components of Yeast Telomerase.  

National Technical Information Service (NTIS)

Telomere length is tightly regulated in Saccharomycetes. This lengthening is dependent on TLC1, which encodes the RNA component of telomerase but independent of RAD52, which encodes a protein required for most recombination events in mitotic yeast cells. ...

S. Teng

1999-01-01

28

Identification of a novel system for boron transport: Atr1 is a main boron exporter in yeast.  

PubMed

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 atr1Delta mutants were highly sensitive to boron treatment, whereas cells overexpressing ATR1 were boron resistant. In addition, atr1Delta cells accumulated boron, whereas ATR1-overexpressing cells had low intracellular levels of the element. Furthermore, atr1Delta 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. PMID:19414602

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

2009-07-01

29

System identification using identification patterns  

Microsoft Academic Search

In this paper, system identification techniques using identification patterns are developed for use in on-line, in-situ monitoring of sensors and systems. The dynamic properties of sensors play an essential role in the performance of measurement and control systems. Both the single-frequency identification pattern (SIP) of the squarewave and the compact multifrequency identification pattern (MIP) for other test signals are examined

Ian A. Henderson; Lidia Jackowska-Strummillo; Joseph McGhee; Phillip McGlone; Dominik Sankowski

1999-01-01

30

Molecular Biological Identification of Malassezia Yeasts Using Pyrosequencing  

PubMed Central

Background A Pyrosequencing assay has been used in identification of fungal species such as Candida or Aspergillus and diagnosis of pathogenic bacteria such as Helicobacter pylori but there has been no report on successful isolation and identification of Malassezia yeasts using the pyrosequencing method. Objective Examine the applicability and plausibility of the pyrosequencing method in identification of the Malassezia species. Methods At internal transcribed spacer (ITS) sites 1 and 2, three primers were developed using Pyrosequencing Assay Design Software (Biotage AB). Pyrosequencing was performed on 11 standard strains and 83 genomic DNA samples obtained from 66 healthy controls aged from 1 to 80. Results The eleven Malassezia standard species and 83 genomic DNA samples were successfully identified using the pyrosequencing assay. Conclusion The pyrosequencing method is a new tool for analysis of Malassezia yeasts, and its precision and rapidity suggests its clinical applicability.

Kim, Ji Young; Hahn, Hyung Jin; Choe, Yong Beom; Ahn, Kyu Joong; Moon, Kee Chan

2013-01-01

31

[Evaluation of Vitek 2 for the identification of Candida yeasts].  

PubMed

The aim of this investigation was to evaluate the performance of Vitek 2 YST cards (bioMérieux, Inc., Hazelwood, MO, USA) for the identification of yeasts of the genus Candida. A total of 168 isolates were analyzed and the results were compared to those of the API 20 C AUX (24%) o API ID 32 C (76%) kits (bioMérieux, Marcy L'Etoile, France). Each isolate was grown in chromogenic agar and in corn meal agar (Oxoid, UK) to observe its micromorphology. C. albicans and C. dublininesis were identified by additional biochemical and molecular tests. The agreement observed was 98.3%. Only three isolates were incorrectly identified by Vitek 2: one strain of C .tropicalis and one strain of C. krusei were identified as C. parapsilosis by YST while one strain of C. krusei was identified with low discrimination. The average time for obtaining results was 18.25 h. Vitek 2 is a simple, safe and useful system for the identification of significant Candida species. PMID:25011593

Ochiuzzi, María E; Cataldi, Silvana; Guelfand, Liliana; Maldonado, Ivana; Arechavala, Alicia

2014-01-01

32

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

33

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

2013-04-01

34

Differential identification of Candida species and other yeasts by analysis of (/sup 35/S)methionine-labeled polypeptide profiles  

SciTech Connect

This paper describes a scheme for differential identification of Candida species and other yeasts based on autoradiographic analysis of protein profiles of (/sup 35/S)methionine-labeled cellular proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Using ATCC strains as references, protein profile analysis showed that different Candida and other yeast species produced distinctively different patterns. Good agreement in results obtained with this approach and with other conventional systems was observed. Being accurate and reproducible, this approach provides a basis for the development of an alternative method for the identification of yeasts isolated from clinical specimens.

Shen, H.D.; Choo, K.B.; Tsai, W.C.; Jen, T.M.; Yeh, J.Y.; Han, S.H.

1988-12-01

35

Role of Yeasts and Clostridia in Silage Deterioration: Identification and Ecology.  

National Technical Information Service (NTIS)

Conditions influencing the growth of yeasts and clostridia during fermentation and deterioration of grass silage were studied. Methods for quantification and identification for these organisms were developed and evaluated. Lactate-assimilating yeasts were...

A. Jonsson

1989-01-01

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

Internal Transcribed Spacer Sequencing versus Biochemical Profiling for Identification of Medically Important Yeasts  

PubMed Central

In this study, we established an in-house database of yeast internal transcribed spacer (ITS) sequences. This database includes medically important as well as colonizing yeasts that frequently occur in the diagnostic laboratory. In a prospective study, we compared molecular identification with phenotypic identification by using the ID32C system (bioMérieux) for yeast strains that could not be identified by a combination of CHROMagar Candida and morphology on rice agar. In total, 113 yeast strains were included in the study. By sequence analysis, 98% of all strains were identified correctly to the species level. With the ID32C, 87% of all strains were identified correctly to the species or genus level, 7% of the isolates could not be identified, and 6% of the isolates were misidentified, most of them as Candida rugosa or Candida utilis. For a diagnostic algorithm, we suggest a three-step procedure which integrates morphological criteria, biochemical investigation, and sequence analysis of the ITS region.

Ciardo, D. E.; Schar, G.; Bottger, E. C.; Altwegg, M.; Bosshard, P. P.

2006-01-01

38

Molecular Identification of Unusual Pathogenic Yeast Isolates by Large Ribosomal Subunit Gene Sequencing: 2 Years of Experience at the United Kingdom Mycology Reference Laboratory?  

PubMed Central

Rapid identification of yeast isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. We present here an analysis of the utility of PCR amplification and sequence analysis of the hypervariable D1/D2 region of the 26S rRNA gene for the identification of yeast species submitted to the United Kingdom Mycology Reference Laboratory over a 2-year period. A total of 3,033 clinical isolates were received from 2004 to 2006 encompassing 50 different yeast species. While more than 90% of the isolates, corresponding to the most common Candida species, could be identified by using the AUXACOLOR2 yeast identification kit, 153 isolates (5%), comprised of 47 species, could not be identified by using this system and were subjected to molecular identification via 26S rRNA gene sequencing. These isolates included some common species that exhibited atypical biochemical and phenotypic profiles and also many rarer yeast species that are infrequently encountered in the clinical setting. All 47 species requiring molecular identification were unambiguously identified on the basis of D1/D2 sequences, and the molecular identities correlated well with the observed biochemical profiles of the various organisms. Together, our data underscore the utility of molecular techniques as a reference adjunct to conventional methods of yeast identification. Further, we show that PCR amplification and sequencing of the D1/D2 region reliably identifies more than 45 species of clinically significant yeasts and can also potentially identify new pathogenic yeast species.

Linton, Christopher J.; Borman, Andrew M.; Cheung, Grace; Holmes, Ann D.; Szekely, Adrien; Palmer, Michael D.; Bridge, Paul D.; Campbell, Colin K.; Johnson, Elizabeth M.

2007-01-01

39

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

40

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

PubMed Central

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 identified representing 11 different genera. Distribution of the species was considerably different depending on the type of sample. Fourteen different species were identified from pasteurized single-strength orange juice that had been contaminated after pasteurization (PSOJ), while only six species were isolated from fresh-squeezed, unpasteurized orange juice (FSOJ). Among PSOJ isolates, Candida intermedia and Candida parapsilosis were the predominant species. Hanseniaspora occidentalis and Hanseniaspora uvarum represented up to 73% of total FSOJ isolates. Partial sequence of the 26S rRNA gene yielded the best results in terms of correct identification, followed by classical techniques and 5.8S-ITS analysis. The commercial identification kits RapID Yeast Plus system and API 20C AUX were able to correctly identify only 35 and 13% of the isolates, respectively. Six new 5.8S-ITS profiles were described, corresponding to Clavispora lusitaniae, Geotrichum citri-aurantii, H. occidentalis, H. vineae, Pichia fermentans, and Saccharomycopsis crataegensis. With the addition of these new profiles to the existing database, the use of 5.8S-ITS sequence became the best tool for rapid and accurate identification of yeast isolates from orange juice.

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

2002-01-01

41

Yeast Functional Genomic Screens Lead to Identification of a Role for a Bacterial Effector in Innate Immunity Regulation  

Microsoft Academic Search

Numerous bacterial pathogens manipulate host cell processes to promote infection and ultimately cause disease through the action of proteins that they directly inject into host cells. Identification of the targets and molecular mechanisms of action used by these bacterial effector proteins is critical to understanding pathogenesis. We have developed a systems biological approach using the yeast Saccharomyces cerevisiae that can

Roger W. Kramer; Naomi L. Slagowski; Ngozi A. Eze; Kara S. Giddings; Monica F. Morrison; Keri A. Siggers; Michael N. Starnbach; Cammie F. Lesser

2007-01-01

42

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

PubMed Central

Using fluorescent membrane potential sensing dyes to stain budding yeast, mitochondria are resolved as tubular organelles aligned in radial arrays that converge at the bud neck. Time-lapse fluorescence microscopy reveals region-specific, directed mitochondrial movement during polarized yeast cell growth and mitotic cell division. Mitochondria in the central region of the mother cell move linearly towards the bud, traverse the bud neck, and progress towards the bud tip at an average velocity of 49 +/- 21 nm/sec. In contrast, mitochondria in the peripheral region of the mother cell and at the bud tip display significantly less movement. Yeast strains containing temperature sensitive lethal mutations in the actin gene show abnormal mitochondrial distribution. No mitochondrial movement is evident in these mutants after short-term shift to semi-permissive temperatures. Thus, the actin cytoskeleton is important for normal mitochondrial movement during inheritance. To determine the possible role of known myosin genes in yeast mitochondrial motility, we investigated mitochondrial inheritance in myo1, myo2, myo3 and myo4 single mutants and in a myo2, myo4 double mutant. Mitochondrial spatial arrangement and motility are not significantly affected by these mutations. We used a microfilament sliding assay to examine motor activity on isolated yeast mitochondria. Rhodamine-phalloidin labeled yeast actin filaments bind to immobilized yeast mitochondria, as well as unilamellar, right- side-out, sealed mitochondrial outer membrane vesicles. In the presence of low levels of ATP (0.1-100 microM), we observed F-actin sliding on immobilized yeast mitochondria. In the presence of high levels of ATP (500 microM-2 mM), bound filaments are released from mitochondria and mitochondrial outer membranes. The maximum velocity of mitochondria- driven microfilament sliding (23 +/- 11 nm/sec) is similar to that of mitochondrial movement in living cells. This motor activity requires hydrolysis of ATP, does not require cytosolic extracts, is sensitive to protease treatment, and displays an ATP concentration dependence similar to that of members of the myosin family of actin-based motors. This is the first demonstration of an actin-based motor activity in a defined organelle population.

1995-01-01

43

Evaluation of New Colorimetric Vitek 2 Yeast Identification Card by Use of Different Source Media ?  

PubMed Central

The new colorimetric Vitek 2 YST card was evaluated for identification of yeasts (136 strains) with respect to the influence of different source media. The Vitek 2 YST card achieved satisfactory results for all yeast species tested, with the exception of Candida guilliermondii, Candida norvegensis, Candida parapsilosis, Candida rugosa, and Candida tropicalis. After simple additional tests, 93.7% of all the strains tested were correctly identified. A significant influence of the isolation medium on the identification rate could not be observed.

Valenza, Giuseppe; Strasen, Jorn; Schafer, Frauke; Frosch, Matthias; Kurzai, Oliver; Abele-Horn, Marianne

2008-01-01

44

Evaluation and Reliability of a Simplified Method for Identification of Food-Borne Yeasts  

PubMed Central

A simplified identification key described by Deak and Beuchat (T. Deak and L. R. Beuchat, J. Food Prot. 50:243-264, 1987) and the computer method of Barnett et al. (J. A. Barnett, R. W. Payne, and D. Yarrow, Yeast Identification Program, 1985) were used to identify 12 reference strains and 382 yeasts isolated from cultured milk products. Because the simplified key failed to account for species variability with regard to physiological, morphological, and sexual reproduction characteristics, poor agreement of the identification results was obtained. A reevaluation of the basic theoretical assumptions of the simplified key only confirmed the practical results and indicates that this identification method is unsatisfactory

Rohm, Harald; Lechner, Frieda

1990-01-01

45

Performance of mass spectrometric identification of bacteria and yeasts routinely isolated in a clinical microbiology laboratory using MALDI-TOF MS  

PubMed Central

Background Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is an emerging technology newly applied to identifying bacterial and yeast strains. The aim of this study was to evaluate the clinical performance of the VITEK® MS system in the identification of bacteria and yeast strains routinely isolated from clinical samples. Methods We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria and yeasts regardless of phylum or source of isolation. Discordant results were resolved with 16S rDNA or internal transcribed spacer (ITS) gene sequencing. Colonies (a single deposit on a MALDI disposable target without any prior extraction step) were analyzed using the VITEK® MS system. Peptide spectra acquired by the system were compared with the VITEK® MS IVD database Version 2.0, and the identification scores were recorded. Results Of the 1,181 isolates (1,061 bacterial isolates and 120 yeast isolates) analyzed, 99.5% were correctly identified by MALDI-TOF mass spectrometry; 95.7% identified to the species level, 3.6% identified to the genus level, and 0.3% identified within a range of species belonging to different genera. Conversely, 0.1% of isolates were misidentified and 0.4% were unidentified, partly because the species were not included in the database. Re-testing using a second deposit provided a successful identification for 0.5% of isolates unidentified with the first deposit. Our results show that the VITEK® MS system has exceptional performance in identifying bacteria and yeast by comparing acquired peptide spectra to those contained in its database. Conclusions MALDI-TOF mass spectrometry is a rapid, accurate, and relatively inexpensive method for bacterial and yeast identification. Our results demonstrate that the VITEK® MS system is a fast and reliable technique, and has the potential to replace conventional phenotypic identification for most bacterial and yeast strains routinely isolated in clinical microbiology laboratories.

Wang, Weiping; Xi, Haiyan; Huang, Mei; Wang, Jie; Fan, Ming; Chen, Yong; Shao, Haifeng

2014-01-01

46

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

2013-07-01

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 Central

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).

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

2013-01-01

48

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

PubMed

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 MicroLog system from Biolog (USA). Genetic diversity was investigated by randomly amplified polymorphic DNA fingerprinting and mitochondrial-DNA restriction enzyme analysis. Sequences of the internal transcribed spacers between 18S and 26S rDNA genes were analysed. Candida humilis was the predominant species (56% of isolates), whereas the remaining strains (44%) were related to the Saccharomyces cerevisiae sensu stricto group. Identification systems based on phenotypic analysis proved to be unreliable to identify yeasts from sourdough. Either RAPD-PCR or mtDNA restriction analysis showed to be suitable for the identification of species, but could not be used to differentiate among the isolates at the strain level. Sequencing of the ITS region permitted a consistent classification of the sourdough yeasts. PMID:15040949

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

2004-03-01

49

Prospective evaluation of the VITEK MS for the routine identification of bacteria and yeast in the clinical microbiology laboratory: assessment of accuracy of identification and turnaround time.  

PubMed

This study assessed the accuracy of bacterial and yeast identification using the VITEK MS, and the time to reporting of isolates before and after its implementation in routine clinical practice. Three hundred and sixty-two isolates of bacteria and yeast, consisting of a variety of clinical isolates and American Type Culture Collection strains, were tested. Results were compared with reference identifications from the VITEK 2 system and with 16S rRNA sequence analysis. The VITEK MS provided an acceptable identification to species level for 283 (78?%) isolates. Considering organisms for which genus-level identification is acceptable for routine clinical care, 315 isolates (87?%) had an acceptable identification. Six isolates (2?%) were identified incorrectly, five of which were Shigella species. Finally, the time for reporting the identifications was decreased significantly after implementation of the VITEK MS for a total mean reduction in time of 10.52 h (P<0.0001). Overall, accuracy of the VITEK MS was comparable or superior to that from the VITEK 2. The findings were also comparable to other studies examining the accuracy of the VITEK MS, although differences exist, depending on the diversity of species represented as well as on the versions of the databases used. The VITEK MS can be incorporated effectively into routine use in a clinical microbiology laboratory and future expansion of the database should provide improved accuracy for the identification of micro-organisms. PMID:24227878

Charnot-Katsikas, Angella; Tesic, Vera; Boonlayangoor, Sue; Bethel, Cindy; Frank, Karen M

2014-02-01

50

Advantages of Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry as a Rapid Diagnostic Tool for Identification of Yeasts and Mycobacteria in the Clinical Microbiological Laboratory  

PubMed Central

Yeast and mycobacteria can cause infections in immunocompromised patients and normal hosts. The rapid identification of these organisms can significantly improve patient care. There has been an increasing number of studies on using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for rapid yeast and mycobacterial identifications. However, studies on direct comparisons between the Bruker Biotyper and bioMérieux Vitek MS systems for the identification of yeast and mycobacteria have been limited. This study compared the performance of the two systems in their identification of 98 yeast and 102 mycobacteria isolates. Among the 98 yeast isolates, both systems generated species-level identifications in >70% of the specimens, of which Candida albicans was the most commonly cultured species. At a genus-level identification, the Biotyper system identified more isolates than the Vitek MS system for Candida (75/78 [96.2%]versus 68/78 [87.2%], respectively; P = 0.0426) and non-Candida yeasts (18/20 [90.0%]versus 7/20 [35.0%], respectively; P = 0.0008). For mycobacterial identification, the Biotyper system generated reliable identifications for 89 (87.3%) and 64 (62.8%) clinical isolates at the genus and species levels, respectively, from solid culture media, whereas the Vitek MS system did not generate any reliable identification. The MS method differentiated 12/21 clinical species, despite the fact that no differentiation between Mycobacterium abscessus and Mycobacterium chelonae was found by using 16S rRNA gene sequencing. In summary, the MALDI-TOF MS method provides short turnaround times and a standardized working protocol for the identification of yeast and mycobacteria. Our study demonstrates that MALDI-TOF MS is suitable as a first-line test for the identification of yeast and mycobacteria in clinical laboratories.

Chen, Jonathan H. K.; Yam, Wing-Cheong; Ngan, Antonio H. Y.; Fung, Ami M. Y.; Woo, Wai-Lan; Yan, Mei-Kum; Choi, Garnet K. Y.; Ho, Pak-Leung; Cheng, Vincent C. C.

2013-01-01

51

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

2013-05-01

52

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

53

Quantum identification system  

NASA Astrophysics Data System (ADS)

A secure quantum identification system combining a classical identification procedure and quantum key distribution is proposed. Each identification sequence is always used just once and sequences are ``refueled'' from a shared provably secret key transferred through the quantum channel. Two identification protocols are devised. The first protocol can be applied when legitimate users have an unjammable public channel at their disposal. The deception probability is derived for the case of a noisy quantum channel. The second protocol employs unconditionally secure authentication of information sent over the public channel, and thus can be applied even in the case when an adversary is allowed to modify public communications. An experimental realization of a quantum identification system is described.

Dušek, Miloslav; Haderka, Ond?ej; Hendrych, Martin; Myška, Robert

1999-07-01

54

Simplified techniques for identifying foodborne yeasts.  

PubMed

Four problematic areas associated with the identification of foodborne yeasts are discussed. These consist of (1) the inability of conventional identification tests to recognize some common and important foodborne yeasts characterized by genomic differences (e.g., Saccharomyces cerevisiae, S. bayanus and S. pastorianus); (2) the delay in application of non-traditional identification methods such as DNA fingerprinting, chromosome karyotyping, protein electrophoretic patterns and fatty acid profiles for routine identification purposes; (3) the lack of commercially available manual or automated identification systems dedicated to the diagnosis of foodborne yeasts; and (4) the disregard for considering ecological frequency of yeasts in computerized probabilistic identification systems. PMID:8357753

Deák, T

1993-06-25

55

Assessment of Accuracy of Identification of Pathogenic Yeasts in Microbiology Laboratories in the United Kingdom  

PubMed Central

Rapid, accurate identification of yeast isolates from clinical samples has always been important given their innately variable antifungal susceptibility profiles. Recently, this has become paramount with the proposed introduction of species-specific interpretive breakpoints for MICs obtained in yeast antifungal susceptibility tests (M. A. Pfaller, D. Andes, D. J. Diekema, A. Espinel–Ingroff, D. Sheehan, and CLSI Subcommittee for Antifungal Susceptibility Testing, Drug Resist. Updat. 13:180–195, 2010). Here, we present the results of a 12-month evaluation of the accuracy of identifications that accompany yeast isolates submitted to the Mycology Reference Laboratory (United Kingdom) for either confirmation of identity or susceptibility testing. In total, 1,781 yeast isolates were analyzed, and the robustness of prior identifications obtained in microbiology laboratories throughout the United Kingdom was assessed using a combination of culture on chromogenic agar, morphology on cornmeal agar, and molecular identification by pyrosequencing. Over 40% of isolates (755) were submitted without any suggested identification. Of those isolates with a prior identification, 100 (9.7%) were incorrectly identified. Error rates ranged from 5.2% (for organisms submitted for antifungal susceptibility testing) to 18.2% (for organisms requiring confirmation of identity) and varied in a strictly species-specific manner. At least 50% of identification errors would be likely to affect interpretation of MIC data, with a possible impact on patient management. In addition, 2.3% of submitted cultures were found to contain mixtures of at least two yeast species. The vast majority of mixtures had gone undetected in the referring laboratory and would have impacted the interpretation of antifungal susceptibility profiles and patient management. Some of the more common misidentifications are discussed according to the identification method employed, with suggestions for avoiding such misinterpretations.

Szekely, Adrien; Palmer, Michael D.; Johnson, Elizabeth M.

2012-01-01

56

Evaluation of new colorimetric vitek 2 yeast identification card by use of different source media.  

PubMed

The new colorimetric Vitek 2 YST card was evaluated for identification of yeasts (136 strains) with respect to the influence of different source media. The Vitek 2 YST card achieved satisfactory results for all yeast species tested, with the exception of Candida guilliermondii, Candida norvegensis, Candida parapsilosis, Candida rugosa, and Candida tropicalis. After simple additional tests, 93.7% of all the strains tested were correctly identified. A significant influence of the isolation medium on the identification rate could not be observed. PMID:18799700

Valenza, Giuseppe; Strasen, Jörn; Schäfer, Frauke; Frosch, Matthias; Kurzai, Oliver; Abele-Horn, Marianne

2008-11-01

57

Optimized System Identification  

NASA Technical Reports Server (NTRS)

In system identification, one usually cares most about finding a model whose outputs are as close as possible to the true system outputs when the same input is applied to both. However, most system identification algorithms do not minimize this output error. Often they minimize model equation error instead, as in typical least-squares fits using a finite-difference model, and it is seen here that this distinction is significant. Here, we develop a set of system identification algorithms that minimize output error for multi-input/multi-output and multi-input/single-output systems. This is done with sequential quadratic programming iterations on the nonlinear least-squares problems, with an eigendecomposition to handle indefinite second partials. This optimization minimizes a nonlinear function of many variables, and hence can converge to local minima. To handle this problem, we start the iterations from the OKID (Observer/Kalman Identification) algorithm result. Not only has OKID proved very effective in practice, it minimizes an output error of an observer which has the property that as the data set gets large, it converges to minimizing the criterion of interest here. Hence, it is a particularly good starting point for the nonlinear iterations here. Examples show that the methods developed here eliminate the bias that is often observed using any system identification methods of either over-estimating or under-estimating the damping of vibration modes in lightly damped structures.

Juang, Jer-Nan; Longman, Richard W.

1999-01-01

58

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

59

Identification and characterization of antimicrobial activity in two yeast genera.  

PubMed Central

A general screening test for the expression of antibacterial activity was performed on over 400 cultures belonging to 31 yeast genera. Of these cultures, only two, Kluyveromyces thermotolerans and Kloeckera apiculata, were found to produce zones of inhibition of bacterial growth on Diagnostic Sensitivity Test Agar medium supplemented with 0.002% methylene blue. Of nine bacteria used as test organisms, only Lactobacillus plantarum and Bacillus megaterium were inhibited. No antibacterial activity was evident against four gram-negative bacteria used in this study. Optimal activities were found to be expressed after yeasts were grown at pH 6. A requirement for cultivation in the presence of methylene blue added to culture media for the expression of apparent antibacterial activity was demonstrated. Images

Bilinski, C A; Innamorato, G; Stewart, G G

1985-01-01

60

Yeasts from kefir grains: isolation, identification, and probiotic characterization.  

PubMed

Kefir-a traditional beverage whose consumption has been associated with health benefits-is a logical natural product to investigate for new probiotic strains. The aim of the present work was to isolate and identify kefir yeasts and select those with acid and bile tolerance to study their adhesion to epithelial cells and their transit through mouse gut. From 4 milky and 3 sugary kefir grains, 34 yeast strains were isolated and identified by means of classical microbiological and molecular-genetic methods (whole-cell protein pattern, internal-transcribed-spacer amplification, and analysis of restriction-fragment-length polymorphisms). We identified 4 species belonging to 3 genera-Saccharomyces cerevisiae (15 strains), Saccharomyces unisporus (6 strains), Issatchenkia occidentalis (4 strains), and Kluyveromyces marxianus (9 strains)-and selected 13 strains on the basis of resistance to low pH and bile salts. Among the strains selected, Kluyveromyces marxianus CIDCA 8154 and Saccharomyces cerevisiae CIDCA 8112 were further studied. Both strains evidenced the capacity to adhere to epithelial intestine-derived cells in vitro and to survive passage through the gastrointestinal tract of BALB/c mice. The investigation of the potential probiotic features of these kefir-yeast strains should be useful for the development of novel functional foods. PMID:23824665

Diosma, Gabriela; Romanin, David E; Rey-Burusco, María F; Londero, Alejandra; Garrote, Graciela L

2014-01-01

61

Identification of indigenous yeast flora isolated from the five winegrape varieties harvested in Xiangning, China.  

PubMed

Inoculated fermentation by selected indigenous yeast strains from a specific location could provide the wine with unique regional sensory characteristics. The identification and differentiation of local yeasts are the first step to understand the function of yeasts and develop a better strain-selection program for winemaking. The indigenous yeasts in five grape varieties, Chardonnay, Cabernet Franc, Cabernet Sauvignon, Marselan, and Merlot cultivated in Xiangning, Shanxi, China were investigated. Eight species of seven genera including Aureobasidium pullulans, Candida zemplinina, Hanseniaspora uvarum, Hanseniaspora occidentalis, Issatchenkia terricola, Metschnikowia pulcherrima, Pichia kluyveri, and Saccharomyces cerevisiae were identified using Wallerstein Laboratory Nutrient medium with sequencing of the 26S rDNA D1/D2 domain. H. uvarum and S. cerevisiae were the predominant species, while most non-Saccharomyces species were present in the whole fermentation process at different levels among the grape varieties. The genotypes of S. cerevisiae from each microvinification were determined by using interdelta sequence analysis. The 102 isolates showed eight different genotypes, and genotype III was the predominant genotype found. The distribution of S. cerevisiae strains during the fermentation of Marselan was also studied. Six genotypes were observed among the 92 strains with different genotypes of competitiveness at different sampling stages. Genotype V demonstrated the potential for organizing starter strains and avoiding inefficient fermentation. In general, this study explored the yeast species in the grapes grown in Xiangning County and provided important information of relationship of local yeast diversity and its regional wine sensory characteristics. PMID:24395034

Sun, Yue; Guo, Jingjing; Liu, Fubing; Liu, Yanlin

2014-03-01

62

Automated Microbiological Detection/Identification System  

PubMed Central

An automated, computerized system, the AutoMicrobic System, has been developed for the detection, enumeration, and identification of bacteria and yeasts in clinical specimens. The biological basis for the system resides in lyophilized, highly selective and specific media enclosed in wells of a disposable plastic cuvette; introduction of a suitable specimen rehydrates and inoculates the media in the wells. An automated optical system monitors, and the computer interprets, changes in the media, with enumeration and identification results automatically obtained in 13 h. Sixteen different selective media were developed and tested with a variety of seeded (simulated) and clinical specimens. The AutoMicrobic System has been extensively tested with urine specimens, using a urine test kit (Identi-Pak) that contains selective media for Escherichia coli, Proteus species, Pseudomonas aeruginosa, Klebsiella-Enterobacter species, Serratia species, Citrobacter freundii, group D enterococci, Staphylococcus aureus, and yeasts (Candida species and Torulopsis glabrata). The system has been tested with 3,370 seeded urine specimens and 1,486 clinical urines. Agreement with simultaneous conventional (manual) cultures, at levels of 70,000 colony-forming units per ml (or more), was 92% or better for seeded specimens; clinical specimens yielded results of 93% or better for all organisms except P. aeruginosa, where agreement was 86%. System expansion in progress includes antibiotic susceptibility testing and compatibility with most types of clinical specimens. Images

Aldridge, C.; Jones, P. W.; Gibson, S.; Lanham, J.; Meyer, M.; Vannest, R.; Charles, R.

1977-01-01

63

Yeast bioassay for identification of inositol depleting compounds.  

PubMed

Bipolar affective disorder is a chronic, severe, debilitating illness affecting 1-2% of the population. Valproate, along with lithium and carbamazepine, are the only drugs for which long-term efficacy has been established. However, these drugs are ineffective for, and not well tolerated by, a large number of patients and are also associated with teratogenicity and reproductive defects. Therefore, there is a substantial need to develop more effective anti-bipolar drugs. We have previously shown that valproate, like lithium, decreases intracellular inositol, which supports the inositol depletion hypothesis. We employed inositol depletion in yeast as a screening tool to identify potential new anti-bipolar medications. We show here that hexanoic acid, heptanoic acid, octanoic acid, nonanoic acid, decanoic acid, ethylhexanoate, and methyloctanoate decrease intracellular inositol levels and increase the expression of INO1, the gene encoding myo-inositol-3-phosphate synthase (MIPS). Similar to valproate, these inositol-depleting carboxylic acids inhibited MIPS indirectly. A correlation was shown between cell growth inhibition and the increase in INO1 expression by the carboxylic acids, factors that were reversed in the presence of inositol. Inositol depletion in yeast may be exploited as an easy and inexpensive screening test for potential new inositol depleting anti-bipolar drugs. PMID:18979283

Ding, Daobin; Shi, Yihui; Shaltiel, Galit; Azab, Abed N; Pullumbi, Ervin; Campbell, Adam; Mehta, Dhara V; Agam, Galila; Greenberg, Miriam L

2009-01-01

64

Identification of Holliday junction resolvases from humans and yeast.  

PubMed

Four-way DNA intermediates, also known as Holliday junctions, are formed during homologous recombination and DNA repair, and their resolution is necessary for proper chromosome segregation. Here we identify nucleases from Saccharomyces cerevisiae and human cells that promote Holliday junction resolution, in a manner analogous to that shown by the Escherichia coli Holliday junction resolvase RuvC. The human Holliday junction resolvase, GEN1, and its yeast orthologue, Yen1, were independently identified using two distinct experimental approaches: GEN1 was identified by mass spectrometry following extensive fractionation of HeLa cell-free extracts, whereas Yen1 was detected by screening a yeast gene fusion library for nucleases capable of Holliday junction resolution. The eukaryotic Holliday junction resolvases represent a new subclass of the Rad2/XPG family of nucleases. Recombinant GEN1 and Yen1 resolve Holliday junctions by the introduction of symmetrically related cuts across the junction point, to produce nicked duplex products in which the nicks can be readily ligated. PMID:19020614

Ip, Stephen C Y; Rass, Ulrich; Blanco, Miguel G; Flynn, Helen R; Skehel, J Mark; West, Stephen C

2008-11-20

65

Molecular-based identification of yeasts isolated from bovine clinical mastitis in Japan.  

PubMed

This study analyzed molecular-based identification of yeasts that associated with bovine clinical mastitis in Japan. Over 3,200 quarter milk samples from Holstein dairy cows collected in 2011 on Hokkaido and Honshu islands were examined. Yeast isolates were characterized by polymerase chain reaction amplification and sequencing of the D1/D2 region of the 26S rDNA. Molecular characterization confirmed that Candida spp. and Pichia spp. were most frequently isolated species. Our molecular analysis of mastitic milk samples demonstrated the prevalence of Pichia kudriavzevii(22/58) and Candida tropicalis(14/58). In addition, we demonstrated that molecular analysis of the D1/D2 region of the 26S rDNA is a rapid and reliable method for identifying clinically significant yeasts in dairy hygiene, including potentially new or emerging pathogenic species. PMID:23100116

Hayashi, Tomohito; Sugita, Takashi; Hata, Eiji; Katsuda, Ken; Zhang, Enshi; Kiku, Yoshio; Sugawara, Kazue; Ozawa, Tomomi; Matsubara, Tomoko; Ando, Takaaki; Obayashi, Tetsu; Ito, Takaaki; Yabusaki, Takahiro; Kudo, Katsunori; Yamamoto, Hiroshi; Koiwa, Masateru; Oshida, Toshio; Tagawa, Yuichi; Kawai, Kazuhiro

2013-01-01

66

Molecular identification of yeast species associated with ‘Hamei’ — A traditional starter used for rice wine production in Manipur, India  

Microsoft Academic Search

In Manipur state of North-Eastern India, wine from glutinous rice using traditional solid state starter called ‘Hamei’ is particularly interesting because of its unique flavour. A total of 163 yeast isolates were obtained from fifty four ‘Hamei’ samples collected from household rice wine preparations in tribal villages of Manipur. Molecular identification of yeast species was carried out by analysis of

K. Jeyaram; W. Mohendro Singh; Angela Capece; Patrizia Romano

2008-01-01

67

Yeast Transcriptional Module Identification Based on Line Manifold  

Microsoft Academic Search

A living cell can carry out complex biological functions dependent on its transcriptional regulatory modules. Therefore, identifying transcriptional regulatory modules is very important for understanding cell function and its transcription mechanism. In this paper, a novel algorithm based on line manifold clusters and a linear mixture framework is presented for transcriptional regulatory module identification. A combined dissimilarity is constructed by

Gangguo Li; Zhengzhi Wang

2010-01-01

68

Rapid Identification of Candida Species and Other Clinically Important Yeast Species by Flow Cytometry†  

PubMed Central

Two rapid diagnostic assays, utilizing two different Luminex flow cytometry methods, were developed for identification of clinically important ascomycetous yeast species. Direct hybridization and allele-specific primer extension methods were both successful in establishing a DNA-based assay that can rapidly and accurately identify Candida albicans, Candida krusei, Candida parapsilosis, Candida glabrata, and Candida tropicalis as well as other clinical species. The direct hybridization assay was designed to identify a total of 19 ascomycetous yeast species, and the allele-specific primer extension assay was designed to identify a total of 34 species. Probes were validated against 438 strains representing 303 species. From culture to identification, the allele-specific primer extension method takes 8 h and the direct hybridization method takes less than 5 h to complete. These assays represent comprehensive, rapid tests that are well suited for the clinical laboratory.

Page, Brent T.; Kurtzman, Cletus P.

2005-01-01

69

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

70

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Fast and Reliable Identification of Clinical Yeast Isolates?  

PubMed Central

The clinical impact of severe infections with yeasts and yeast-like fungi has increased, especially in immunocompromised hosts. In recent years, new antifungal agents with different and partially species-specific activity patterns have become available. Therefore, rapid and reliable species identification is essential for antifungal treatment; however, conventional biochemical methods are time-consuming and require considerable expertise. We evaluated matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the rapid routine identification of clinical yeast isolates. A total of 18 type collection strains and 267 recent clinical isolates of Candida (n = 250), Cryptococcus, Saccharomyces, Trichosporon, Geotrichum, Pichia, and Blastoschizomyces spp. were identified by MALDI-TOF MS. The results were compared with those obtained by conventional phenotyping and biochemical tests, including the API ID 32C system (bioMérieux, Nürtingen, Germany). Starting with cells from single colonies, accurate species identification by MALDI-TOF MS was achieved for 247 of the clinical isolates (92.5%). The remaining 20 isolates required complementation of the reference database with spectra for the appropriate reference strains which were obtained from type culture collections or identified by 26S rRNA gene sequencing. The absence of a suitable reference strain from the MALDI-TOF MS database was clearly indicated by log(score) values too low for the respective clinical isolates; i.e., no false-positive identifications occurred. After complementation of the database, all isolates were unambiguously identified. The established API ID 32C biochemical diagnostic system identified 244 isolates in the first round. Overall, MALDI-TOF MS proved a most rapid and reliable tool for the identification of yeasts and yeast-like fungi, with the method providing a combination of the lowest expenditure of consumables, easy interpretation of results, and a fast turnaround time.

Marklein, G.; Josten, M.; Klanke, U.; Muller, E.; Horre, R.; Maier, T.; Wenzel, T.; Kostrzewa, M.; Bierbaum, G.; Hoerauf, A.; Sahl, H.-G.

2009-01-01

71

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

72

Yeast cell cycle transcription factors identification by variable selection criteria.  

PubMed

Identifying cell cycle transcription factors (TFs) is important for understanding the transcriptional regulation of the cell cycle process which controls the growth and development of all organisms. Existing computational approaches for identifying cell cycle TFs are mainly based on methods with a fixed selection criterion. That is, the same criterion was applied to each TF to determine whether it is a cell cycle TF or not. Since the characteristic of each TF may be quite different, it is not suitable to use a fixed selection criterion in identifying cell cycle TFs. Instead of using a fixed selection criterion, we propose a method with variable selection criteria to identify cell cycle TFs in yeast by integrating the ChIP-chip and cell cycle gene expression data. Our method is shown to outperform five existing methods which used the same ChIP-chip dataset as we did. Fifteen cell cycle TFs were identified by our approach, 12 of which are known cell cycle TFs, while the remaining three (Hap4, Reb1 and Tye7) are novel cell cycle TFs. The biological significance of our predictions is shown by four lines of indirect evidence derived from the protein-protein interaction data, TF mutant data, ChIP-chip data and the results of the previous computational studies. PMID:21703335

Wang, Hsiuying; Wang, Yu-Han; Wu, Wei-Sheng

2011-10-10

73

Identification of a possible MAP kinase cascade in Arabidopsis thaliana based on pairwise yeast two-hybrid analysis and functional complementation tests of yeast mutants  

Microsoft Academic Search

A possible MAP kinase (MAPK) cascade of Arabidopsis thaliana was identified on the basis of both yeast 2-hybrid analysis and complementation analysis of yeast mutants. Specific protein-protein interactions between ATMPK4 (a MAPK) and MEK1 (a MAPKK) and interactions between MEK1 and ATMEKK1 (a MAPKKK) were detected by using the 2-hybrid system. A growth defect of the yeast mpk1? mutant was

Tsuyoshi Mizoguchi; Kazuya Ichimura; Kenji Irie; Peter Morris; Jérôme Giraudat; Kunihiro Matsumoto; Kazuo Shinozaki

1998-01-01

74

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

75

A yeast homolog of the human UEF stimulates transcription from the adenovirus 2 major late promoter in yeast and in mammalian cell-free systems.  

PubMed Central

We report the identification and purification of a yeast factor functionally homologous to the human upstream element factor (UEFh). Although the yeast protein (UEFy) has a higher molecular weight than the HeLa UEF (60 kD versus 45 kD) both have identical DNA-binding properties: the purified UEFy recognizes the Adenovirus 2 (Ad2) major late promoter upstream element (MLP-UE; from nucleotide -49 to -67) as well as the IVa2 upstream element (IVa2-UE; from nucleotide -98 to -122) with a higher affinity for the MLP-UE than for the IVa2-UE. Based on its DNA binding specificity, size and thermostability, the UEFy protein appears also similar or equivalent to the centromere binding protein CP1. In a competition assay with oligonucleotides containing the MLP-UE binding site, a drastic reduction of Ad2 MLP transcription was observed both in a HeLa and in a yeast cell free system, which was restored by addition of either the purified UEFh or UEFy proteins. We conclude that both UEFh and UEFy activate transcription from the Ad2 MLP upon binding to the upstream element, whatever is the in vitro cell-free system (yeast or HeLa). This indicate that some regulatory function represented by the upstream element and its cognate factor, is well conserved between human and yeast. Images

Moncollin, V; Stalder, R; Verdier, J M; Sentenac, A; Egly, J M

1990-01-01

76

High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories ?  

PubMed Central

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory.

van Veen, S. Q.; Claas, E. C. J.; Kuijper, Ed J.

2010-01-01

77

Comparison of Nested PCR and RFLP for Identification and Classification of Malassezia Yeasts from Healthy Human Skin  

PubMed Central

Background Malassezia yeasts are normal flora of the skin found in 75~98% of healthy subjects. The accurate identification of the Malassezia species is important for determining the pathogenesis of the Malassezia yeasts with regard to various skin diseases such as Malassezia folliculitis, seborrheic dermatitis, and atopic dermatitis. Objective This research was conducted to determine a more accurate and rapid molecular test for the identification and classification of Malassezia yeasts. Methods We compared the accuracy and efficacy of restriction fragment length polymorphism (RFLP) and the nested polymerase chain reaction (PCR) for the identification of Malassezia yeasts. Results Although both methods demonstrated rapid and reliable results with regard to identification, the nested PCR method was faster. However, 7 different Malassezia species (1.2%) were identified by the nested PCR compared to the RFLP method. Conclusion Our results show that RFLP method was relatively more accurate and reliable for the detection of various Malassezia species compared to the nested PCR. But, in the aspect of simplicity and time saving, the latter method has its own advantages. In addition, the 26S rDNA, which was targeted in this study, contains highly conserved base sequences and enough sequence variation for inter-species identification of Malassezia yeasts.

Oh, Byung Ho; Song, Young Chan; Choe, Yong Beom; Ahn, Kyu Joong

2009-01-01

78

A shuttle mutagenesis system for tagging genes in the yeast Yarrowia lipolytica.  

PubMed

A shuttle mutagenesis system was developed for the dimorphic yeast Yarrowia lipolytica. This system combines transposon insertions generated in Escherichia coli with the transformation of yeast with the Tn-mutagenized DNA. The mini-transposon mTn-3xHA/GFP, used in Saccharomyces cerevisiae for producing stable insertions, was adapted for use in the yeast Y. lipolytica. The mTnYl1 transposon (for mini-Tn of Y. lipolytica) confers resistance to tetracycline in E. coli. It also contains the Y. lipolytica URA3 gene for selection of yeast transformants, and the coding sequence for the S65T mutant form of GFP. The rare cutter endonuclease, I-SceI, restriction site, which enables identification of the chromosomal localization of mutagenized genes, was also incorporated. mTnYl1 was first tested on the ACO1 gene, which encodes an Acyl CoA oxidase isozyme. The mutagenesis system was further validated on a Y. lipolytica genomic DNA library constructed in a pHSS6 derivative vector. Mutants with a particular morphology or defective for alkane, fatty acids and oil degradation were obtained. PMID:9630501

Neuvéglise, C; Nicauda, J M; Ross-Macdonald, P; Gaillardin, C

1998-06-15

79

Discrete Dynamical System Modeling for Gene Regulatory Networks of HMF Tolerance for Ethanologenic Yeast  

Microsoft Academic Search

Abstract Composed of linear difference equations, a discrete dynamical system model was designed,to reconstruct,transcriptional regulations,in gene,regulatory,networks,for ethanologenic yeast Saccharomyces cerevisiae in response to 5-hydroxymethylfurfural, a bioethanol,conversion,inhibitor. The modeling,aims,at identification of a system of linear difference equations,to represent temporal,interactions among,significantly expressed,genes. Power-stability is imposed,on a system,model,under,the normal condition in the absence of the inhibitor. Non-uniform sampling, typical in a time course

Zhengyu Ouyang; Z. Lewis Liu

80

System identification of jet engines  

Microsoft Academic Search

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

N. Sugiyama

2000-01-01

81

Yeast Augmented Network Analysis (YANA): a new systems approach to identify therapeutic targets for human genetic diseases  

PubMed Central

Genetic interaction networks that underlie most human diseases are highly complex and poorly defined. Better-defined networks will allow identification of a greater number of therapeutic targets. Here we introduce our Yeast Augmented Network Analysis (YANA) approach and test it with the X-linked spinal muscular atrophy (SMA) disease gene UBA1. First, we express UBA1 and a mutant variant in fission yeast and use high-throughput methods to identify fission yeast genetic modifiers of UBA1. Second, we analyze available protein-protein interaction network databases in both fission yeast and human to construct UBA1 genetic networks. Third, from these networks we identified potential therapeutic targets for SMA. Finally, we validate one of these targets in a vertebrate (zebrafish) SMA model. This study demonstrates the power of combining synthetic and chemical genetics with a simple model system to identify human disease gene networks that can be exploited for treating human diseases.

Wiley, David J.; Juan, Ilona; Le, Hao; Cai, Xiaodong; Baumbach, Lisa; Beattie, Christine; D'Urso, Gennaro

2014-01-01

82

Leon County Service Identification System.  

National Technical Information Service (NTIS)

The Human Services Coordination Alliance Services Identification System was developed as a means of identifying, defining, and classifying human services. In this report, the system is first briefly described and an effort is made to explain how it was de...

1977-01-01

83

Clinical Evaluation of the FilmArray Blood Culture Identification Panel in Identification of Bacteria and Yeasts from Positive Blood Culture Bottles  

PubMed Central

The FilmArray platform (FA; BioFire, Salt Lake City, UT) is a closed diagnostic system allowing high-order multiplex PCR analysis with automated readout of results directly from positive blood cultures in 1 h. In the present study, we evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel, which includes 19 bacteria, five yeasts, and three antibiotic resistance genes. In total, 206 blood culture bottles were included in the study. The FilmArray could identify microorganisms in 153/167 (91.6%) samples with monomicrobial growth. Thirteen of the 167 (7.8%) microorganisms were not covered by the FilmArray BCID panel. In 6/167 (3.6%) samples, the FilmArray detected an additional microorganism compared to blood culture. When polymicrobial growth was analyzed, the FilmArray could detect all target microorganisms in 17/24 (71%) samples. Twelve blood culture bottles that yielded a positive signal but showed no growth were also negative by FilmArray. In 3/206 (1.5%) bottles, the FilmArray results were invalid. The results of the FilmArray were reproducible, as demonstrated by the testing and retesting of five bottles in the same day and a longitudinal follow-up of five other blood cultures up to 4 weeks. The present study shows that the FilmArray is a rapid identification method with high performance in direct identification of bacteria and yeasts from positive blood culture bottles.

Altun, Osman; Almuhayawi, Mohammed; Ullberg, Mans

2013-01-01

84

Preliminary identification and classification of five new yeast strains isolated from oil-polluted environment.  

PubMed

Bioremediation is a very interesting alternative for restoring the oil-polluted ecosystems. Many studies concerning the possibility of using microorganisms (bacteria and yeasts) in the degradation of oil compounds have as starting point the isolation and taxonomical identification of new species and strains with degradative abilities. Our study focusses on the preliminary classification of five yeast strains (D1, D2, D3, D4 and D6) isolated from oil-polluted environments. The strains were characterized by conventional taxonomical techniques: microscopical and macroscopical appearance, fermentation abilities, assimilation of various carbon or nitrogen compounds, growth under stress conditions (non-permissive temperatures, high glucose concentration) and urea degradation. According to these tests, D1, D2 and D4 showed great similarity to Rhodotorula glutinis, D3 to Candida parapsilosis and D6 to Candida tropicalis. Further supplementary tests were performed in order to establish their ability to degrade hydrocarbons, by observing growth in media with n-alkanes (n-decane, n-dodecane, n-tetradecane, n-hexadecane). Thus, D1, D2 and D4 were the best alkane-consuming strains, presenting possible similar degrading abilities and pathways, which correlates well to our identification as Rhodotorula strains. For D3 and D6 the growth was not so spectacular as for D1, D2 and D4, but continuous along the entire experiment. The resemblance between the curves profiles confirms the idea that both belong to the same genus, Candida. PMID:17405317

Csutak, Ortansa; Ghindea, Raluca; Stoica, Ileana; Soare, Simona; Ionescu, Robertina; Creanga, Oana; Vassu, Tatiana

2005-01-01

85

Identification of multivariate linear systems  

SciTech Connect

Multivariate identification problems are treated with a least-squares approach. A chapter on scalar problems focuses attention on the classical parameter-estimate bias problem caused by measurement noise and develops a straightforward and effective way to remove the bias. A chapter on multivariate problems generalizes the bias removal method and develops a form selection procedure. The form selection procedure generally ensures more accurate identification than is possible with identification methods which rely on a fixed form. The concept of a form selection procedure is new to this work. A results chapter presents four example problems. Each example illustrates specific features of the identification technique. As a collection the examples emphasize the complexity of system identification and demonstrate that identification techniques will perform well when carefully applied.

Griffith, J.M.

1982-04-01

86

Isolation and identification of L-dopa decarboxylase as a protein that binds to and enhances transcriptional activity of the androgen receptor using the repressed transactivator yeast two-hybrid system.  

PubMed Central

The AR (androgen receptor) is a ligand-regulated transcription factor, which belongs to the steroid receptor family and plays an essential role in growth and development of the prostate. Transcriptional activity of steroid receptors is modulated by interaction with co-regulator proteins and yeast two-hybrid analysis is commonly used to identify these steroid receptor-interacting proteins. However, a limitation of conventional two-hybrid systems for detecting AR protein partners has been that they only allow for analysis of the ligand- and DNA-binding domains of the receptor, as its NTD (N-terminal domain) possesses intrinsic transactivation activity. To identify AR N-terminus-interacting proteins, its NTD was used in the RTA (repressed transactivator) system, which is specifically designed for transactivator bait proteins and was shown to be suitable for two-hybrid analysis with the AR NTD. DDC (L-dopa decarboxylase) was detected multiple times as a novel AR-interacting protein, which was subsequently confirmed in vitro and in vivo. Furthermore, transient transfection of DDC in prostate cancer cells strongly enhanced ligand-dependent AR transcriptional activity, an effect that was antagonized using high concentrations of the anti-androgen bicalutamide. Glucocorticoid receptor activity was also strongly enhanced with DDC co-transfection, while oestrogen receptor activity was only mildly affected. Together, our data demonstrate that DDC interacts with AR to enhance steroid receptor transactivation, which may have important implications in prostate cancer progression.

Wafa, Latif A; Cheng, Helen; Rao, Mira A; Nelson, Colleen C; Cox, Michael; Hirst, Martin; Sadowski, Ivan; Rennie, Paul S

2003-01-01

87

Novel System for Monitoring Autophagy in the Yeast Saccharomyces cerevisiae  

Microsoft Academic Search

The yeast S. cerevisiae imports cytosolic components into the vacuole non-selectively by autophagy and degrades them by vacuolar hydrolases under nutrient starvation conditions. We developed a novel system for monitoring autophagy by constructing cells in which modified vacuolar alkaline phosphatase is expressed as an inactive precursor form in the cytosol. Under starvation conditions, the processing of the precursor to the

T. Noda; A. Matsuura; Y. Wada; Y. Ohsumi

1995-01-01

88

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

89

Multisensor fusion for system identification  

NASA Astrophysics Data System (ADS)

System identification is a fundamental process for developing a numerical model of a physical structure. The system identification process typically involves in data acquisition; particularly in civil engineering applications accelerometers are preferred due to its cost-effectiveness, low noise, and installation convenience. Because the measured acceleration responses result in translational degrees of freedom (DOF) in the numerical model, moment-resisting structures such as beam and plate are not appropriately represented by the models. This study suggests a system identification process that considers both translational and rotational DOFs by using accelerometers and gyroscopes. The proposed approach suggests a systematic way of obtaining dynamic characteristics as well as flexibility matrix from two different measurements of acceleration and angular velocity. Numerical simulation and laboratory experiment are conducted to validate the efficacy of the proposed system identification process.

Sim, Sung-Han; Cho, Soojin; Park, Jong-Woong; Kim, Hyunjun

2014-04-01

90

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

Microsoft Academic Search

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

Mercedes Villa-Carvajal; Juan José R. Coque; Mar??a Lu??sa Álvarez-Rodr??guez; Federico Uruburu; Carmela Belloch

2004-01-01

91

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

92

Mated Tag Identification System.  

National Technical Information Service (NTIS)

Human errors occur at the rate of one in every one thousand blood transfusions. A small mechanical device capable of limiting errors in sample and patient identification has been devised and improved. It functions by comparing an embossed plastic card who...

H. O. Conde

1973-01-01

93

Interlaboratory comparison of sample preparation methods, database expansions, and cutoff values for identification of yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry using a yeast test panel.  

PubMed

An interlaboratory study using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to determine the identification of clinically important yeasts (n = 35) was performed at 11 clinical centers, one company, and one reference center using the Bruker Daltonics MALDI Biotyper system. The optimal cutoff for the MALDI-TOF MS score was investigated using receiver operating characteristic (ROC) curve analyses. The percentages of correct identifications were compared for different sample preparation methods and different databases. Logistic regression analysis was performed to analyze the association between the number of spectra in the database and the percentage of strains that were correctly identified. A total of 5,460 MALDI-TOF MS results were obtained. Using all results, the area under the ROC curve was 0.95 (95% confidence interval [CI], 0.94 to 0.96). With a sensitivity of 0.84 and a specificity of 0.97, a cutoff value of 1.7 was considered optimal. The overall percentage of correct identifications (formic acid-ethanol extraction method, score ? 1.7) was 61.5% when the commercial Bruker Daltonics database (BDAL) was used, and it increased to 86.8% by using an extended BDAL supplemented with a Centraalbureau voor Schimmelcultures (CBS)-KNAW Fungal Biodiversity Centre in-house database (BDAL+CBS in-house). A greater number of main spectra (MSP) in the database was associated with a higher percentage of correct identifications (odds ratio [OR], 1.10; 95% CI, 1.05 to 1.15; P < 0.01). The results from the direct transfer method ranged from 0% to 82.9% correct identifications, with the results of the top four centers ranging from 71.4% to 82.9% correct identifications. This study supports the use of a cutoff value of 1.7 for the identification of yeasts using MALDI-TOF MS. The inclusion of enough isolates of the same species in the database can enhance the proportion of correctly identified strains. Further optimization of the preparation methods, especially of the direct transfer method, may contribute to improved diagnosis of yeast-related infections. PMID:24920782

Vlek, Anneloes; Kolecka, Anna; Khayhan, Kantarawee; Theelen, Bart; Groenewald, Marizeth; Boel, Edwin; Boekhout, Teun

2014-08-01

94

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

95

Structure errors in system identification  

NASA Technical Reports Server (NTRS)

An approach to system identification is presented which explicitly takes structure errors into account and hence provides a systematic way for answering questions concerning the magnitude of estimated parameter errors resulting from structural errors. It is indicated that, from this point of view, it is possible to define near equivalence between process and model and to obtain meaningful theoretical results on solution error system identification. It remains to apply these results to large realistic problems such as those involving models of complex man machine systems.

Bekey, G. A.; Hadaegh, F. Y.

1984-01-01

96

Identification of Essential Host Factors Affecting Tombusvirus RNA Replication Based on the Yeast Tet Promoters Hughes Collection†  

PubMed Central

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 p92pol viral replication proteins, (ii) the standard 10 to 20:1 ratio between p33 and p92pol 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 ?5,600 genes that represent ?95% of all the known and predicted yeast genes) that affected the accumulation of tombusvirus RNA.

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

2006-01-01

97

Systems identification - reprise and projections  

NASA Technical Reports Server (NTRS)

A state-of-the-arts review is given for the field of system identification. Progress in the field is traced from the early models of dynamic systems by Sir Isaac Newton up to the present day use of advanced techniques for numerous applications.

Taylor, L. W., Jr.

1974-01-01

98

Evaluation of MALDI-TOF mass spectrometry for identification of environmental yeasts and development of supplementary database.  

PubMed

Yeast identification using traditional methods which employ morphological, physiological, and biochemical characteristics can be considered a hard task as it requires experienced microbiologists and a rigorous control in culture conditions that could implicate in different outcomes. Considering clinical or industrial applications, the fast and accurate identification of microorganisms is a crescent demand. Hence, molecular biology approaches has been extensively used and, more recently, protein profiling using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proved to be an even more efficient tool for taxonomic purposes. Nonetheless, concerning to mass spectrometry, data available for the differentiation of yeast species for industrial purpose is limited and reference databases commercially available comprise almost exclusively clinical microorganisms. In this context, studies focusing on environmental isolates are required to extend the existing databases. The development of a supplementary database and the assessment of a commercial database for taxonomic identifications of environmental yeast are the aims of this study. We challenge MALDI-TOF MS to create protein profiles for 845 yeast strains isolated from grape must and 67.7 % of the strains were successfully identified according to previously available manufacturer database. The remaining 32.3 % strains were not identified due to the absence of a reference spectrum. After matching the correct taxon for these strains by using molecular biology approaches, the spectra concerning the missing species were added in a supplementary database. This new library was able to accurately predict unidentified species at first instance by MALDI-TOF MS, proving it is a powerful tool for the identification of environmental yeasts. PMID:24687751

Agustini, Bruna Carla; Silva, Luciano Paulino; Bloch, Carlos; Bonfim, Tania M B; da Silva, Gildo Almeida

2014-06-01

99

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

100

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

Microsoft Academic Search

BackgroundMatrix-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.MethodsMALDI-TOF MS was performed on 30 reference and 167 clinical isolates followed by prospective examination

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

2011-01-01

101

Yeast as an expression system for the production of bacterial and viral antigens.  

PubMed

To develop a yeast system that expresses bacterial and viral antigens in the future, we analyzed yeast secretion with a reporter system based on the cc1A gene of Clostridium thermocellum that encodes endoglucanase A. Sequences coding for the mature CelA protein were fused in frame to yeast promoters and secretion signals, introduced into different vectors and analyzed biochemically in yeast secretory mutants. Gene dosage had little effect, whereas expression from a weak promoter enhanced endoglucanase A secretion. In yeast secretory mutants, a major fraction of endoglucanase A piled up in the endoplasmic reticulum as a core glycosylated protein. PMID:7858405

Silva, A; Benítez, J

1994-01-01

102

Development and characterization of a reconstituted yeast translation initiation system.  

PubMed Central

To provide a bridge between in vivo and in vitro studies of eukaryotic translation initiation, we have developed a reconstituted translation initiation system using components from the yeast Saccharomyces cerevisiae. We have purified a minimal set of initiation factors (elFs) that, together with yeast 80S ribosomes, GTP, and initiator methionyl-tRNA, are sufficient to assemble active initiation complexes on a minimal mRNA template. The kinetics of various steps in the pathway of initiation complex assembly and the formation of the first peptide bond in vitro have been explored. The formation of active initiation complexes in this system is dependent on ribosomes, mRNA, Met-tRNAi, GTP hydrolysis, elF1, elF1A, elF2, elF5, and elF5B. Our data indicate that elF1 and elF1A both facilitate the binding of the elF2 x GTP x Met-tRNAi complex to the 40S ribosomal subunit to form the 43S complex. elF5 stimulates a step after 43S complex formation, consistent with its proposed role in activating GTP hydrolysis by elF2 upon initiation codon recognition. The presence of elF5B is required for the joining of the 40S and 60S subunits to form the 80S initiation complex. The step at which each of these factors acts in this reconstituted system is in agreement with previous data from in vivo studies and work using reconstituted mammalian systems, indicating that the system recapitulates fundamental events in translation initiation in eukaryotic cells. This system should allow us to couple powerful yeast genetic and molecular biological experiments with in vitro kinetic and biophysical experiments, yielding a better understanding of the molecular mechanics of this central, complex process.

Algire, Mikkel A; Maag, David; Savio, Peter; Acker, Michael G; Tarun, Salvador Z; Sachs, Alan B; Asano, Katsura; Nielsen, Klaus H; Olsen, Deanne S; Phan, Lon; Hinnebusch, Alan G; Lorsch, Jon R

2002-01-01

103

An Efficient Ear Identification System  

Microsoft Academic Search

This paper proposes a robust ear identification system which is developed by fusing SIFT features of color segmented slice regions of an ear. It makes use of Gaussian mixture model (GMM) to build ear model with mixture of Gaussian using vector quantization algorithm and K-L divergence is applied to the GMM framework for recording the color similarity in the specified

Dakshina Ranjan Kisku; S. Gupta; P. Gupta; J. K. Sing

2010-01-01

104

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

105

Ras Signaling in Yeast  

PubMed Central

Since the study of yeast RAS and adenylate cyclase in the early 1980s, yeasts including budding and fission yeasts contributed significantly to the study of Ras signaling. First, yeast studies provided insights into how Ras activates downstream signaling pathways. Second, yeast studies contributed to the identification and characterization of GAP and GEF proteins, key regulators of Ras. Finally, the study of yeast provided many important insights into the understanding of C-terminal processing and membrane association of Ras proteins.

Tamanoi, Fuyuhiko

2011-01-01

106

Automated Hardware-Identification System  

NASA Technical Reports Server (NTRS)

"Compressed symbology" emerging technology involving one- and two-dimensional arrays of surface depressions to form optically readable dots. Patterns more durable and denser than common bar codes. Convey identification data in binary form and read by optoelectric sensors. Computers and compressed-symbology engraving machines they control constitute subsystems of "paperless" hardware-tracking and -identification systems coordinating flows of both identifying information and identified parts themselves, along with ancillary information like work orders. Modifications of software expected to accelerate marking operations, eliminate need for trial or practice marking, and reduce incidence of errors.

Schramm, Harry F., Jr.; Roxby, Donald L.

1995-01-01

107

Molecular Identification of Unusual Pathogenic Yeast Isolates by Large Ribosomal Subunit Gene Sequencing: 2 Years of Experience at the United Kingdom Mycology Reference Laboratory  

Microsoft Academic Search

Rapid identification of yeast isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. We present here an analysis of the utility of PCR amplification and sequence analysis of the hypervariable D1\\/D2 region of the 26S rRNA gene for the identification of yeast species submitted to the United Kingdom Mycology Reference Laboratory over a 2-year period.

Christopher J. Linton; Andrew M. Borman; Grace Cheung; Ann D. Holmes; Adrien Szekely; Michael D. Palmer; Paul D. Bridge; Colin K. Campbell; Elizabeth M. Johnson

108

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

109

Screening and identification of yeast strains from fruits and vegetables: Potential for biological control of postharvest chilli anthracnose ( Colletotrichum capsici)  

Microsoft Academic Search

Yeasts antagonistic to Colletotrichum capsici were isolated from Thai fruits and vegetables. Four antagonists (R13, R6, ER1, and L2) were found that inhibited C. capsici growth with biocontrol efficacies of 93.3%, 83.1%, 76.6%, and 66.4%, respectively. Identification by 26S rDNA, and ITS region sequence together with physiological and morphological characteristics, showed them to be Pichia guilliermondii, Candida musae, Issatchenkia orientalis,

Arun Chanchaichaovivat; Pintip Ruenwongsa; Bhinyo Panijpan

2007-01-01

110

A bimodal biometric identification system  

NASA Astrophysics Data System (ADS)

Biometrics consists of methods for uniquely recognizing humans based upon one or more intrinsic physical or behavioral traits. Physicals are related to the shape of the body. Behavioral are related to the behavior of a person. However, biometric authentication systems suffer from imprecision and difficulty in person recognition due to a number of reasons and no single biometrics is expected to effectively satisfy the requirements of all verification and/or identification applications. Bimodal biometric systems are expected to be more reliable due to the presence of two pieces of evidence and also be able to meet the severe performance requirements imposed by various applications. This paper presents a neural network based bimodal biometric identification system by using human face and handwritten signature features.

Laghari, Mohammad S.; Khuwaja, Gulzar A.

2013-03-01

111

Identification of uric acid as the redox molecule secreted by the yeast Arxula adeninivorans.  

PubMed

The yeast Arxula adeninivorans has been previously shown to secrete a large amount of an electro-active molecule. The molecule was produced by cells that had been cultivated in a rich medium, harvested, washed and then suspended in phosphate-buffered saline (PBS). The molecule was easily detectable after 60 min of incubation in PBS, and the cells continued to produce the molecule in these conditions for up to 3 days. The peak anodic potential of the oxidation peak was 0.42 V, and it was shown to be a solution species rather than a cell-attached species. We have optimised the production of the molecule, identified it by high-pressure liquid chromatography (HPLC) fractionation and high-resolution mass spectrometric analysis and determined the pathway involved in its synthesis. It has a mass/charge ratio that corresponds to uric acid, and this identification was supported by comparing UV spectra and cyclic voltammograms of the samples to those of uric acid. An A. adeninivorans xanthine oxidase gene disruption mutant failed to produce uric acid, which added further validity to this identification. It also demonstrated that the purine catabolism pathway is involved in its production. A transgenic A. adeninivorans strain with a switchable urate oxidase gene (AUOX) accumulated uric acid when the gene was switched off but did not when the gene was switched on. Cultivation of cells on amino acid and purine-free minimal media with an inorganic nitrogen source suggests that the cells synthesise purines from inorganic nitrogen and proceed to degrade them via the normal purine degradation pathway. PMID:24407453

Williams, Jonathan; Trautwein-Schult, Anke; Jankowska, Dagmara; Kunze, Gotthard; Squire, Marie A; Baronian, Keith

2014-03-01

112

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

2012-10-01

113

Dissecting a known RNA-protein interaction using a yeast three-hybrid system.  

PubMed

The yeast three-hybrid system has been applied to known protein-RNA interactions for a variety of purposes. For instance, protein and RNA mutants with altered or relaxed binding specificities can be identified. Mutant RNAs can also be analyzed to better understand RNA-binding specificity of a specific protein. Furthermore, this system complements other biochemical techniques, for example, SELEX, co-immunoprecipitation and cross-linking experiments (see UV crosslinking of interacting RNA and protein in cultured cells and PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins). PMID:24581444

Koh, Yvonne Y; Wickens, Marvin

2014-01-01

114

Identification and Characterization of Ixodes scapularis Antigens That Elicit Tick Immunity Using Yeast Surface Display  

PubMed Central

Repeated exposure of rabbits and other animals to ticks results in acquired resistance or immunity to subsequent tick bites and is partially elicited by antibodies directed against tick antigens. In this study we demonstrate the utility of a yeast surface display approach to identify tick salivary antigens that react with tick-immune serum. We constructed an Ixodes scapularis nymphal salivary gland yeast surface display library and screened the library with nymph-immune rabbit sera and identified five salivary antigens. Four of these proteins, designated P8, P19, P23 and P32, had a predicted signal sequence. We generated recombinant (r) P8, P19 and P23 in a Drosophila expression system for functional and immunization studies. rP8 showed anti-complement activity and rP23 demonstrated anti-coagulant activity. Ixodes scapularis feeding was significantly impaired when nymphs were fed on rabbits immunized with a cocktail of rP8, rP19 and rP23, a hall mark of tick-immunity. These studies also suggest that these antigens may serve as potential vaccine candidates to thwart tick feeding.

Daffre, Sirlei; DePonte, Kathleen; Hovius, Joppe W. R.; Veer, Cornelis van't; van der Poll, Tom; Bakhtiari, Kamran; Meijers, Joost C. M.; Boder, Eric T.; van Dam, Alje P.; Fikrig, Erol

2011-01-01

115

Rapid Identification of Ascomycetous Yeasts from Clinical Specimens by a Molecular Method Based on Flow Cytometry and Comparison with Identifications from Phenotypic Assays†  

PubMed Central

This study was designed to compare the identification of ascomycetous yeasts recovered from clinical specimens by using phenotypic assays (PA) and a molecular flow cytometric (FC) method. Large-subunit rRNA domains 1 and 2 (D1/D2) gene sequence analysis was also performed and served as the reference for correct strain identification. A panel of 88 clinical isolates was tested that included representatives of nine commonly encountered species and six infrequently encountered species. The PA included germ tube production, fermentation of seven carbohydrates, morphology on corn meal agar, urease and phenoloxidase activities, and carbohydrate assimilation tests when needed. The FC method (Luminex) employed species-specific oligonucleotides attached to polystyrene beads, which were hybridized with D1/D2 amplicons from the unidentified isolates. The PA identified 81 of 88 strains correctly but misidentified 4 of Candida dubliniensis, 1 of C. bovina, 1 of C. palmioleophila, and 1 of C. bracarensis. The FC method correctly identified 79 of 88 strains and did not misidentify any isolate but did not identify nine isolates because oligonucleotide probes were not available in the current library. The FC assay takes approximately 5 h, whereas the PA takes from 2 h to 5 days for identification. In conclusion, PA did well with the commonly encountered species, was not accurate for uncommon species, and takes significantly longer than the FC method. These data strongly support the potential of FC technology for rapid and accurate identification of medically important yeasts. With the introduction of new antifungals, rapid, accurate identification of pathogenic yeasts is more important than ever for guiding antifungal chemotherapy.

Page, Brent T.; Shields, Christine E.; Merz, William G.; Kurtzman, Cletus P.

2006-01-01

116

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

117

Nonlinear system identification technique validation  

NASA Astrophysics Data System (ADS)

This final technical report describes the results obtained by SIGNATRON, Inc. of Lexington MA on Air Force Contract F30602-80-C-0104 for Rome Air Development Center. The objective of this effort is to develop a technique for identifying system response of nonlinear circuits by measurements of output response to known inputs. The report describes results of a study into the system identification technique based on the pencil-of-function method previously explored by Jain (1974) and Ewen (1979). The procedure identified roles of the linear response and is intended as a first step in nonlinear response and is intended as a first step in nonlinear circuit identification. There are serious implementation problems associated with the original approach such as loss of accuracy due to repeated integrations, lack of good measures of accuracy and computational iteration to identify the number of poles.

Rudko, M.; Bussgang, J. J.

1982-01-01

118

Identification of material flow systems.  

PubMed

Material Flow Analysis (MFA) has become an important instrument in environmental science and pollution research. In this paper, we look at the MFA problem as a particularly structured system identification problem. Special emphasis is given to the linear, static case, where we describe a procedure for reconciliating the flow measurements and for estimating the unmeasured flows and the transfer coefficients by taking into account a priori restrictions such as balance equations. PMID:19005792

Bauer, G; Deistler, M; Gleiss, A; Glenck, E; Matyus, T

1997-01-01

119

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

PubMed Central

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%.

Thornton, Mark A.; Thornton, Roy J.

2013-01-01

120

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

121

On-orbit system parameter identification  

NASA Technical Reports Server (NTRS)

Viewgraphs and discussion on on-orbit system parameter identification are included. Topics covered include: dynamic programming filter (DPF); cost function and estimator; frequency domain formulation structrual dynamic identification; and attributes of DPF.

Simonian, Stepan S.

1988-01-01

122

The MICE Particle Identification System  

NASA Astrophysics Data System (ADS)

The Muon Ionization Cooling Experiment (MICE) at the ISIS accelerator located at the Rutherford Appleton Laboratory, UK, will be the first experiment to study muon cooling at high precision. Demonstration of muon ionization cooling is a major technological step towards the construction of a neutrino factory or a muon collider. A muon beam is produced via pion decay in the MICE beam line within a range of emittances and momenta. Muon purity is assured by a system of detectors for particle identification (PID). We describe briefly the PID system here.

Bogomilov, M.; MICE Collaboration

123

Receptor-mediated mitophagy in yeast and mammalian systems  

PubMed Central

Mitophagy, or mitochondria autophagy, plays a critical role in selective removal of damaged or unwanted mitochondria. Several protein receptors, including Atg32 in yeast, NIX/BNIP3L, BNIP3 and FUNDC1 in mammalian systems, directly act in mitophagy. Atg32 interacts with Atg8 and Atg11 on the surface of mitochondria, promoting core Atg protein assembly for mitophagy. NIX/BNIP3L, BNIP3 and FUNDC1 also have a classic motif to directly bind LC3 (Atg8 homolog in mammals) for activation of mitophagy. Recent studies have shown that receptor-mediated mitophagy is regulated by reversible protein phosphorylation. Casein kinase 2 (CK2) phosphorylates Atg32 and activates mitophagy in yeast. In contrast, in mammalian cells Src kinase and CK2 phosphorylate FUNDC1 to prevent mitophagy. Notably, in response to hypoxia and FCCP treatment, the mitochondrial phosphatase PGAM5 dephosphorylates FUNDC1 to activate mitophagy. Here, we mainly focus on recent advances in our understanding of the molecular mechanisms underlying the activation of receptor-mediated mitophagy and the implications of this catabolic process in health and disease.

Liu, Lei; Sakakibara, Kaori; Chen, Quan; Okamoto, Koji

2014-01-01

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

Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs.  

PubMed

The cell cycle-dependent nucleocytoplasmic transport of proteins is predominantly regulated by CDK kinase activities; however, it is currently difficult to predict the proteins thus regulated, largely because of the low prediction efficiency of the motifs involved. Here, we report the successful prediction of CDK1-regulated nucleocytoplasmic shuttling proteins using a prediction system for nuclear localization signals (NLSs). By systematic amino acid replacement analyses in budding yeast, we created activity-based profiles for different classes of importin-alpha-dependent NLSs that represent the functional contributions of different amino acids at each position within an NLS class. We then developed a computer program for prediction of the classical importin-alpha/beta pathway-specific NLSs (cNLS Mapper, available at http//nls-mapper.iab.keio.ac.jp/) that calculates NLS activities by using these profiles and an additivity-based motif scoring algorithm. This calculation method achieved significantly higher prediction accuracy in terms of both sensitivity and specificity than did current methods. The search for NLSs that overlap the consensus CDK1 phosphorylation site by using cNLS Mapper identified all previously reported and 5 previously uncharacterized yeast proteins (Yen1, Psy4, Pds1, Msa1, and Dna2) displaying CDK1- and cell cycle-regulated nuclear transport. CDK1 activated or repressed their nuclear import activity, depending on the position of CDK1-phosphorylation sites within NLSs. The application of this strategy to other functional linear motifs should be useful in systematic studies of protein-protein networks. PMID:19520826

Kosugi, Shunichi; Hasebe, Masako; Tomita, Masaru; Yanagawa, Hiroshi

2009-06-23

126

Substructure system identification and synthesis  

NASA Technical Reports Server (NTRS)

This paper explores the possibility of performing system identification at the substructure level and then synthesizing the results to obtain a mathematical model for the assembled structure. The study here shows that in order to enforce interface compatibility and equilibrium conditions to the substructure test data, it is necessary to place collocated actuator/sensor pair at every interface degree-of-freedom. Procedures for assembling substructure transfer function data, substructure state-space models, and substructure Markov parameters are presented. Testing difficulties and possible solutions are also discussed. A numerical simulation example is included to illustrate the proposed substructure synthesis methods.

Su, Tzu-Jeng; Juang, Jer-Nan

1993-01-01

127

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

128

Bimodal Biometric Person Identification System Under Perturbations  

Microsoft Academic Search

Multibiometric person identification systems play a crucial role in environments where security must be ensured. However, build- ing such systems must jointly encompass a good compromise between computational costs and overall performance. These systems must also be robust against inherent or potential noise on the data-acquisition ma- chinery. In this respect, we proposed a bimodal identification system that combines two

Miguel Carrasco; Luis Pizarro; Domingo Mery

2007-01-01

129

Nonlinear system identification based on ANFIS  

Microsoft Academic Search

System identification is the basis of designing control system, and it is very difficulty to identify the nonlinear system today. A method of fuzzy identification had been provided in reference 1, and another method of using neural networks to identify system had been provided in reference 2. In this paper, Author points out the disadvantages of those methods and a

Zhixiang Hou; Quntai Shen; Heqing Li

2003-01-01

130

Sex-Determination System in the Diploid Yeast Zygosaccharomyces sapae  

PubMed Central

Sexual reproduction and breeding systems are driving forces for genetic diversity. The mating-type (MAT) locus represents a mutation and chromosome rearrangement hotspot in yeasts. Zygosaccharomyces rouxii complex yeasts are naturally faced with hostile low water activity (aw) environments and are characterized by gene copy number variation, genome instability, and aneuploidy/allodiploidy. Here, we investigated sex-determination system in Zygosaccharomyces sapae diploid strain ABT301T, a member of the Z. rouxii complex. We cloned three divergent mating type-like (MTL) ?-idiomorph sequences and designated them as ZsMTL? copies 1, 2, and 3. They encode homologs of Z. rouxii CBS 732T MAT?2 (amino acid sequence identities spanning from 67.0 to 99.5%) and MAT?1 (identity range 81.5–99.5%). ABT301T possesses two divergent HO genes encoding distinct endonucleases 100% and 92.3% identical to Z. rouxii HO. Cloning of MATa-idiomorph resulted in a single ZsMTLa locus encoding two Z. rouxii-like proteins MATa1 and MATa2. To assign the cloned ZsMTL? and ZsMTLa idiomorphs as MAT, HML, and HMR cassettes, we analyzed their flanking regions. Three ZsMTL? loci exhibited the DIC1-MAT-SLA2 gene order canonical for MAT expression loci. Furthermore, four putative HML cassettes were identified, two containing the ZsMTL? copy 1 and the remaining harboring ZsMTL? copies 2 and 3. Finally, the ZsMTLa locus was 3?-flanked by SLA2, suggesting the status of MAT expression locus. In conclusion, Z. sapae ABT301T displays an a??? genotype missing of the HMR silent cassette. Our results demonstrated that mating-type switching is a hypermutagenic process in Z. rouxii complex that generates genetic diversity de novo. This error-prone mechanism could be suitable to generate progenies more rapidly adaptable to hostile environments.

Solieri, Lisa; Dakal, Tikam Chand; Giudici, Paolo; Cassanelli, Stefano

2014-01-01

131

Sex-Determination System in the Diploid Yeast Zygosaccharomyces sapae.  

PubMed

Sexual reproduction and breeding systems are driving forces for genetic diversity. The mating-type (MAT) locus represents a mutation and chromosome rearrangement hotspot in yeasts. Zygosaccharomyces rouxii complex yeasts are naturally faced with hostile low water activity (aw) environments and are characterized by gene copy number variation, genome instability, and aneuploidy/allodiploidy. Here, we investigated sex-determination system in Zygosaccharomyces sapae diploid strain ABT301(T), a member of the Z. rouxii complex. We cloned three divergent mating type-like (MTL) ?-idiomorph sequences and designated them as ZsMTL? copies 1, 2, and 3. They encode homologs of Z. rouxii CBS 732(T) MAT?2 (amino acid sequence identities spanning from 67.0 to 99.5%) and MAT?1 (identity range 81.5-99.5%). ABT301(T) possesses two divergent HO genes encoding distinct endonucleases 100% and 92.3% identical to Z. rouxii HO. Cloning of MATA: -idiomorph resulted in a single ZsMTLA: locus encoding two Z. rouxii-like proteins MATA: 1 and MATA: 2. To assign the cloned ZsMTL? and ZsMTLA: idiomorphs as MAT, HML, and HMR cassettes, we analyzed their flanking regions. Three ZsMTL? loci exhibited the DIC1-MAT-SLA2 gene order canonical for MAT expression loci. Furthermore, four putative HML cassettes were identified, two containing the ZsMTL? copy 1 and the remaining harboring ZsMTL? copies 2 and 3. Finally, the ZsMTLA: locus was 3'-flanked by SLA2, suggesting the status of MAT expression locus. In conclusion, Z. sapae ABT301(T) displays an a??? genotype missing of the HMR silent cassette. Our results demonstrated that mating-type switching is a hypermutagenic process in Z. rouxii complex that generates genetic diversity de novo. This error-prone mechanism could be suitable to generate progenies more rapidly adaptable to hostile environments. PMID:24939186

Solieri, Lisa; Dakal, Tikam Chand; Giudici, Paolo; Cassanelli, Stefano

2014-01-01

132

Molecular Identification of Veterinary Yeast Isolates by Use of Sequence-Based Analysis of the D1/D2 Region of the Large Ribosomal Subunit?  

PubMed Central

Conventional methods of yeast identification are often time-consuming and difficult; however, recent studies of sequence-based identification methods have shown promise. Additionally, little is known about the diversity of yeasts identified from various animal species in veterinary diagnostic laboratories. Therefore, in this study, we examined three methods of identification by using 109 yeast samples isolated during a 1-year period from veterinary clinical samples. Comparison of the three methods—traditional substrate assimilation, fatty acid profile analysis, and sequence-based analysis of the region spanning the D1 and D2 regions (D1/D2) of the large ribosomal subunit—showed that sequence analysis provided the highest percent identification among the three. Sequence analysis identified 87% of isolates to the species level, whereas substrate assimilation and fatty acid profile analysis identified only 54% and 47%, respectively. Less-stringent criteria for identification increased the percentage of isolates identified to 98% for sequence analysis, 62% for substrate assimilation, and 55% for fatty acid profile analysis. We also found that sequence analysis of the internal transcribed spacer 2 (ITS2) region provided further identification for 36% of yeast not identified to the species level by D1/D2 sequence analysis. Additionally, we identified a large variety of yeast from animal sources, with at least 30 different species among the isolates tested, and with the majority not belonging to the common Candida spp., such as C. albicans, C. glabrata, C. tropicalis, and the C. parapsilosis group. Thus, we determined that sequence analysis of the D1/D2 region was the best method for identification of the variety of yeasts found in a veterinary population.

Garner, Cherilyn D.; Starr, Jennifer K.; McDonough, Patrick L.; Altier, Craig

2010-01-01

133

Molecular identification of veterinary yeast isolates by use of sequence-based analysis of the D1/D2 region of the large ribosomal subunit.  

PubMed

Conventional methods of yeast identification are often time-consuming and difficult; however, recent studies of sequence-based identification methods have shown promise. Additionally, little is known about the diversity of yeasts identified from various animal species in veterinary diagnostic laboratories. Therefore, in this study, we examined three methods of identification by using 109 yeast samples isolated during a 1-year period from veterinary clinical samples. Comparison of the three methods-traditional substrate assimilation, fatty acid profile analysis, and sequence-based analysis of the region spanning the D1 and D2 regions (D1/D2) of the large ribosomal subunit-showed that sequence analysis provided the highest percent identification among the three. Sequence analysis identified 87% of isolates to the species level, whereas substrate assimilation and fatty acid profile analysis identified only 54% and 47%, respectively. Less-stringent criteria for identification increased the percentage of isolates identified to 98% for sequence analysis, 62% for substrate assimilation, and 55% for fatty acid profile analysis. We also found that sequence analysis of the internal transcribed spacer 2 (ITS2) region provided further identification for 36% of yeast not identified to the species level by D1/D2 sequence analysis. Additionally, we identified a large variety of yeast from animal sources, with at least 30 different species among the isolates tested, and with the majority not belonging to the common Candida spp., such as C. albicans, C. glabrata, C. tropicalis, and the C. parapsilosis group. Thus, we determined that sequence analysis of the D1/D2 region was the best method for identification of the variety of yeasts found in a veterinary population. PMID:20392917

Garner, Cherilyn D; Starr, Jennifer K; McDonough, Patrick L; Altier, Craig

2010-06-01

134

Triclabendazole protects yeast and mammalian cells from oxidative stress: Identification of a potential neuroprotective compound  

PubMed Central

The Prestwick and NIH chemical libraries were screened for drugs that protect baker’s yeast from sugar-induced cell death (SICD). SICD is triggered when stationary-phase yeast cells are transferred from spent rich medium into water with 2% glucose and no other nutrients. The rapid, apoptotic cell death occurs because reactive oxygen species (ROS) accumulate. We found that triclabendazole, which is used to treat liver flukes in cattle and man, partially protects against SICD. Characterization of triclabendazole revealed that it also protects yeast cells from death induced by the Parkinson’s disease-related protein alpha-synuclein (?-syn), which is known to induce the accumulation of ROS.

Lee, Yong Joo; Burlet, Elodie; Wang, Shaoxiao; Xu, Baoshan; Huang, Shile; Galiano, Floyd J.; Witt, Stephan N.

2011-01-01

135

Current status of system identification methodology  

NASA Technical Reports Server (NTRS)

Large space structures, system identification, model formulation, experimental design, model order and structure determination, parameter estimation, reduced order modeling, and closed loops are considered.

Larimore, W. E.; Mehra, R. K.; Gustafson, D. E.; Baillieul, J.

1983-01-01

136

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

2013-03-10

137

System/Observer/Controller Identification Toolbox.  

National Technical Information Service (NTIS)

System Identification is the process of constructing a mathematical model from input and output data for a system under testing, and characterizing the system uncertainties and measurement noises. The mathematical model structure can take various forms de...

J. Juang L. G. Horta M. Phan

1992-01-01

138

Identification of She3 as an SCFGrr1 Substrate in Budding Yeast  

PubMed Central

The highly orchestrated progression of the cell cycle depends on the degradation of many regulatory proteins at different cell cycle stages. One of the key cell cycle ubiquitin ligases is the Skp1-cullin-F-box (SCF) complex. Acting in concert with the substrate-binding F-box protein Grr1, SCFGrr1 promotes the degradation of cell cycle regulators as well as various metabolic enzymes. Using a yeast two-hybrid assay with a Grr1 derivative as the bait, we identified She3, which is an adaptor protein in the asymmetric mRNA transport system, as a novel Grr1 substrate. We generated stabilized She3 mutants, which no longer bound to Grr1, and found that the degradation of She3 is not required for regulating asymmetric mRNA transport. However, She3 stabilization leads to slower growth compared to wild-type cells in a co-culture assay, demonstrating that the degradation of She3 by Grr1 is required for optimal cell growth.

Wang, Ruiwen; Solomon, Mark J.

2012-01-01

139

Nanogold labeling of the yeast endosomal system for ultrastructural analyses.  

PubMed

Endosomes are one of the major membrane sorting checkpoints in eukaryotic cells and they regulate recycling or destruction of proteins mostly from the plasma membrane and the Golgi. As a result the endosomal system plays a central role in maintaining cell homeostasis, and mutations in genes belonging to this network of organelles interconnected by vesicular transport, cause severe pathologies including cancer and neurobiological disorders. It is therefore of prime relevance to understand the mechanisms underlying the biogenesis and organization of the endosomal system. The yeast Saccharomyces cerevisiae has been pivotal in this task. To specifically label and analyze at the ultrastructural level the endosomal system of this model organism, we present here a detailed protocol for the positively charged nanogold uptake by spheroplasts followed by the visualization of these particles through a silver enhancement reaction. This method is also a valuable tool for the morphological examination of mutants with defects in endosomal trafficking. Moreover, it is not only applicable for ultrastructural examinations but it can also be combined with immunogold labelings for protein localization investigations. PMID:25046212

Mari, Muriel; Griffith, Janice; Reggiori, Fulvio

2014-01-01

140

Structural system identification of a composite shell  

SciTech Connect

Structural system identification is undergoing a period of renewed interest. Probabilistic approaches to physical parameter identification in analysis finite element models make uncertainty in test results an important issue. In this paper, we investigate this issue with a simple, though in many ways representative, structural system. The results of two modal parameter identification techniques are compared and uncertainty estimates, both through bias and random errors, are quantified. The importance of the interaction between test and analysis is also highlighted. 25 refs.

Red-Horse, J.R.; Carne, T.G.; James, G.H.; Witkowski, W.R.

1991-01-01

141

Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5.  

PubMed

Transcriptional adaptor proteins are required for full function of higher eukaryotic acidic activators in the yeast Saccharomyces cerevisiae, suggesting that this pathway of activation is evolutionarily conserved. Consistent with this view, we have identified possible human homologs of yeast ADA2 (yADA2) and yeast GCN5 (yGCN5), components of a putative adaptor complex. While there is overall sequence similarity between the yeast and human proteins, perhaps more significant is conservation of key sequence features with other known adaptors. We show several functional similarities between the human and yeast adaptors. First, as shown for yADA2 and yGCN5, human ADA2 (hADA2) and human GCN5 (hGCN5) interacted in vivo in a yeast two-hybrid assay. Moreover, hGCN5 interacted with yADA2 in this assay, suggesting that the human proteins form similar complexes. Second, both yADA2 and hADA2 contain cryptic activation domains. Third, hGCN5 and yGCN5 had similar stabilizing effects on yADA2 in vivo. Furthermore, the region of yADA2 that interacted with yGCN5 mapped to the amino terminus of yADA2, which is highly conserved in hADA2. Most striking, is the behavior of the human proteins in human cells. First, GAL4-hADA2 activated transcription in HeLa cells, and second, either hADA2 or hGCN5 augmented GAL4-VP16 activation. These data indicated that the human proteins correspond to functional homologs of the yeast adaptors, suggesting that these cofactors play a key role in transcriptional activation. PMID:8552087

Candau, R; Moore, P A; Wang, L; Barlev, N; Ying, C Y; Rosen, C A; Berger, S L

1996-02-01

142

Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5.  

PubMed Central

Transcriptional adaptor proteins are required for full function of higher eukaryotic acidic activators in the yeast Saccharomyces cerevisiae, suggesting that this pathway of activation is evolutionarily conserved. Consistent with this view, we have identified possible human homologs of yeast ADA2 (yADA2) and yeast GCN5 (yGCN5), components of a putative adaptor complex. While there is overall sequence similarity between the yeast and human proteins, perhaps more significant is conservation of key sequence features with other known adaptors. We show several functional similarities between the human and yeast adaptors. First, as shown for yADA2 and yGCN5, human ADA2 (hADA2) and human GCN5 (hGCN5) interacted in vivo in a yeast two-hybrid assay. Moreover, hGCN5 interacted with yADA2 in this assay, suggesting that the human proteins form similar complexes. Second, both yADA2 and hADA2 contain cryptic activation domains. Third, hGCN5 and yGCN5 had similar stabilizing effects on yADA2 in vivo. Furthermore, the region of yADA2 that interacted with yGCN5 mapped to the amino terminus of yADA2, which is highly conserved in hADA2. Most striking, is the behavior of the human proteins in human cells. First, GAL4-hADA2 activated transcription in HeLa cells, and second, either hADA2 or hGCN5 augmented GAL4-VP16 activation. These data indicated that the human proteins correspond to functional homologs of the yeast adaptors, suggesting that these cofactors play a key role in transcriptional activation.

Candau, R; Moore, P A; Wang, L; Barlev, N; Ying, C Y; Rosen, C A; Berger, S L

1996-01-01

143

Monitoring polyglutamine toxicity in yeast.  

PubMed

Experiments in yeast have significantly contributed to our understanding of general aspects of biochemistry, genetics, and cell biology. Yeast models have also delivered deep insights in to the molecular mechanism underpinning human diseases, including neurodegenerative diseases. Many neurodegenerative diseases are associated with the conversion of a protein from a normal and benign conformation into a disease-associated and toxic conformation - a process called protein misfolding. The misfolding of proteins with abnormally expanded polyglutamine (polyQ) regions causes several neurodegenerative diseases, such as Huntington's disease and the Spinocerebellar Ataxias. Yeast cells expressing polyQ expansion proteins recapitulate polyQ length-dependent aggregation and toxicity, which are hallmarks of all polyQ-expansion diseases. The identification of modifiers of polyQ toxicity in yeast revealed molecular mechanisms and cellular pathways that contribute to polyQ toxicity. Notably, several of these findings in yeast were reproduced in other model organisms and in human patients, indicating the validity of the yeast polyQ model. Here, we describe different expression systems for polyQ-expansion proteins in yeast and we outline experimental protocols to reliably and quantitatively monitor polyQ toxicity in yeast. PMID:21144902

Duennwald, Martin L

2011-03-01

144

Comparison between multiplex PCR and phenotypic systems for Candida spp. identification.  

PubMed

This study evaluated the performances of three phenotypic systems (RapID Yeast panel, Vitek2 YST card, and API 20 C AUX) and multiplex PCR for Candida spp. identification. Four-hundred and fifty clinical strains of Candida spp. were identified with the four systems and results of multiplex PCR were compared with those of phenotypic methods. The best correspondence was obtained between Multiplex PCR and API 20 C AUX (83.7%), but the other comparisons showed similar values (81.7% and 79.3% for Vitek2 and RapID Yeast panel respectively). The correspondence was lower for all the methods in identification of C. krusei; this may be of concern in addition to the azole resistance and the often endogenous origin of this yeast. In the comparison with the three phenotypic methods, multiplex PCR could be reliable and time-saving in the identification of Candida spp. for diagnostics purposes. Nowadays, a large variety of both traditional and molecular methods for Candida spp. identification are commercially available. Multiplex PCR applied in this study may be more rapid and sensitive than phenotypic systems, and less expensive than other molecular methods. PMID:20402415

Liguori, Giorgio; Gallé, Francesca; Lucariello, Angela; Di Onofrio, Valeria; Albano, Luciana; Mazzarella, Gennaro; D'Amora, Maurizio; Rossano, Fabio

2010-01-01

145

FAST SYSTEM IDENTIFICATION AND MODEL REDUCTION SOLVERS  

Microsoft Academic Search

Efficient numerical techniques for multivariable system identification and model reduction are investigated. The techniques are implemented in the system identification and model reduction toolboxes based on the Fortran 77 Subroutine Library in Control Theory (SLICOT). Besides highly performant Fortran drivers and computational routines, these toolboxes provide MATLAB or Scilab interfaces, implementing several algorithmic approaches. Extensive numerical testing and comparisons with

Vasile Sima; Peter Benner

146

Laser\\/rf personnel identification system  

Microsoft Academic Search

This paper documents the design of a Laser\\/RF Personnel Identification System developed for the US Army Communications and Electronics Command (CECOM) for soldier identification. The system has dual use applications, including law enforcement officer protection, and includes a laser interrogation unit with a programmable activation code. The interrogation unit is very directive for low probability of intercept (LPI), which is

Michael C. Zari; Reeder N. Ward; David A. Hess; Christopher S. Anderson

1995-01-01

147

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

148

Identification of enzyme responsible for erythritol utilization and reaction product in yeast Lipomyces starkeyi.  

PubMed

We have identified the enzyme responsible for erythritol utilization and its reaction product in the yeast Lipomyces starkeyi CBS 1807. The enzyme, a polyol dehydrogenase requiring NAD+ as a coenzyme, was induced by erythritol in this yeast. We confirmed that the enzyme product was L-erythrulose by MS, NMR, and polarimeter analyses, meaning that we clarified the first step of erythritol utilization in yeasts for the first time. In the case of the oxidative reaction, D-threitol, (2R,3R)-2,3-butanediol, and erythritol were much better substrates than 21 other polyols tested. These three substrates are tetroses and have an R configuration at C-3, and whose third carbon results in easiest oxidation in this enzyme. The research of the substrate specificity in the reductive reaction demonstrated that L-erythrulose and dihydroxyacetone were better substrates, that D-acetoin was inactive and L-erythrose (aldose) was slightly active. PMID:16716937

Nishimura, Katsushi; Harada, Teiko; Arita, Yasukazu; Watanabe, Hisayuki; Iwabuki, Hidehiko; Terada, Asako; Naganuma, Takafumi; Uzuka, Yasuyuki

2006-04-01

149

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

PubMed

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 microflora of rennet and acid cured cheeses were similar, but the cheeses had clearly different yeast populations. Debaryomyces hansenii and Galactomyces geotrichum prevailed in rennet cheeses while Kluyveromyces marxianus and Pichia membranaefaciens were the main species found in acid cured cheese. The dominance of Yarrowia lipolytica probably indicates an improper yeast population, resulting in poor cheese quality. Some of the species identified are potential candidates for designing a defined ripening culture for rennet red smear cheese. PMID:9039559

Valdés-Stauber, N; Scherer, S; Seiler, H

1997-02-01

150

Isolation and identification of yeasts and yeastlike organisms from clinical veterinary sources.  

PubMed Central

A total of 229 isolates of yeasts and yeastlike organisms recovered from a variety of clinical specimens were identified by using the API 20C microsystem in conjunction with morphological characteristics and urea hydrolysis. Of the 229, 218 (95.1%) were from bovine, porcine, canine, and equine species and the remaining 11 (4.9%) were from feline and avian species. The gastrointestinal and reproductive tracts were the major sources of yeasts and yeastlike organisms, representing 60 (26.2%) and 28 (12.2%) isolates, respectively.

Chengappa, M M; Maddux, R L; Greer, S C; Pincus, D H; Geist, L L

1984-01-01

151

Rapid identification and differentiation of yeasts by DNA and PCR fingerprinting.  

PubMed

We have used the techniques of DNA fingerprinting and polymerase chain reaction (PCR) with probes specific for hypervariable repetitive DNA sequences (mini- and microsatellite DNAs) to analyze 36 yeast strains belonging to 10 species and 2 genera. Using (GTG)5, (GACA)4, phage M13 DNA and the M13 sequence GAGGGTGGCGGTTCT as probes and primers, respectively, we obtained DNA polymorphisms which allowed us to discriminate 23 biotechnologically important strains of the yeast Saccaromyces cerevisiae and to distinguish them from strains of S. pastorianus, S. bayanus and S. willianus. Our results demonstrate that both DNA and PCR fingerprinting are suitable tools for an easy, fast and reliable molecular typing of yeasts. The DNA fingerprinting method seems to be more sensitive than PCR fingerprinting with respect to the individualization of strains. Nevertheless, using the PCR fingerprinting technique we were able to unambigously discriminate between genotypes of different species. Therefore, PCR fingerprinting might become a useful tool in the classification of yeasts on the basis of phylogenetic relatedness. PMID:8271158

Lieckfeldt, E; Meyer, W; Börner, T

1993-01-01

152

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

153

Comparison of the lysis centrifugation and radiometric blood culture systems for recovery of yeast  

Microsoft Academic Search

The performance of the Isolator (lysis centrifugation) and Bactec (radiometric) detection systems for the recovery of fungi from blood was studied prospectively by comparison of 2,188 paired cultures obtained at two geographically separated teaching hospitals. Eighty-three yeast isolates were recovered from 78 (3.6%) cultures that were obtained from 43 patients. Seventy-three (88%) yeast strains were recovered using the Isolator system,

B. A. Body; M. A. Pfaller; J. Durrer; F. Koontz; D. H. M. Gröschel

1988-01-01

154

Identification and characterisation of xylanolytic yeasts isolated from decaying wood and sugarcane bagasse in Brazil.  

PubMed

In this study, yeasts associated with lignocellulosic materials in Brazil, including decaying wood and sugarcane bagasse, were isolated, and their ability to produce xylanolytic enzymes was investigated. A total of 358 yeast isolates were obtained, with 198 strains isolated from decaying wood and 160 strains isolated from decaying sugarcane bagasse samples. Seventy-five isolates possessed xylanase activity in solid medium and were identified as belonging to nine species: Candida intermedia, C. tropicalis, Meyerozyma guilliermondii, Scheffersomyces shehatae, Sugiyamaella smithiae, Cryptococcus diffluens, Cr. heveanensis, Cr. laurentii and Trichosporon mycotoxinivorans. Twenty-one isolates were further screened for total xylanase activity in liquid medium with xylan, and five xylanolytic yeasts were selected for further characterization, which included quantitative analysis of growth in xylan and xylose and xylanase and ?-D-xylosidase activities. The yeasts showing the highest growth rate and cell density in xylan, Cr. laurentii UFMG-HB-48, Su. smithiae UFMG-HM-80.1 and Sc. shehatae UFMG-HM-9.1a, were, simultaneously, those exhibiting higher xylanase activity. Xylan induced the highest level of (extracellular) xylanase activity in Cr. laurentii UFMG-HB-48 and the highest level of (intracellular, extracellular and membrane-associated) ?-D-xylosidase activity in Su. smithiae UFMG-HM-80.1. Also, significant ?-D-xylosidase levels were detected in xylan-induced cultures of Cr. laurentii UFMG-HB-48 and Sc. shehatae UFMG-HM-9.1a, mainly in extracellular and intracellular spaces, respectively. Under xylose induction, Cr. laurentii UFMG-HB-48 showed the highest intracellular ?-D-xylosidase activity among all the yeast tested. C. tropicalis UFMG-HB 93a showed its higher (intracellular) ?-D-xylosidase activity under xylose induction and higher at 30 °C than at 50 °C. This study revealed different xylanolytic abilities and strategies in yeasts to metabolise xylan and/or its hydrolysis products (xylo-oligosaccharides and xylose). Xylanolytic yeasts are able to secrete xylanolytic enzymes mainly when induced by xylan and present different strategies (intra- and/or extracellular hydrolysis) for the metabolism of xylo-oligosaccharides. Some of the unique xylanolytic traits identified here should be further explored for their applicability in specific biotechnological processes. PMID:24748334

Lara, Carla A; Santos, Renata O; Cadete, Raquel M; Ferreira, Carla; Marques, Susana; Gírio, Francisco; Oliveira, Evelyn S; Rosa, Carlos A; Fonseca, César

2014-06-01

155

Validation of a modified algorithm for the identification of yeast isolates using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS).  

PubMed

Optimising antifungal treatment requires the fast and species-specific identification of yeast isolates. We evaluated a modified protocol for the rapid identification of clinical yeast isolates using matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) technology. First, we evaluated a simplified extraction procedure using 54 clinical yeast isolates. Second, we validated a new protocol with this simplified extraction procedure and lower identification threshold by analysing 167 isolates with either MALDI-TOF or conventional identification techniques. MALDI-TOF analysis with both the standard and short extraction procedure yielded identical identification results, although the log-scores were lower with the latter. With the modified protocol, 163/167 (97.6%) isolates showed a correct identification as compared to conventional identification techniques. A total of 135 out of the 163 (82.8%) correct identifications showed log-scores above 1.7, which we considered as the minimum log-score for secure species identification. The rapid identification of clinical yeast isolates is crucial in patient management. The MALDI-TOF technique using a short extraction procedure can be an alternative for the labourious standard procedure, although the log-scores will be lower. The identification of clinical yeast isolates with the modified protocol is a practical and accurate alternative for conventional identification techniques. If the isolate shows a log-score below 1.7, the standard extraction procedure should be used. PMID:21861205

Van Herendael, B H; Bruynseels, P; Bensaid, M; Boekhout, T; De Baere, T; Surmont, I; Mertens, A H

2012-05-01

156

JX401, A p38alpha inhibitor containing a 4-benzylpiperidine motif, identified via a novel screening system in yeast.  

PubMed

In vivo screening of compounds for potential pharmacological activity is more advantageous than in vitro screening. In vivo screens eliminate the isolation of compounds that cannot cross biological membranes, are cytotoxic, or are not specific to the target. However, animal-based or even cell-based systems are usually expensive, time-consuming, and laborious. Here we describe the identification of inhibitors of the mitogen-activated protein kinase p38alpha via a high throughput screen using yeast cells. p38alpha is hyperactive in inflammatory diseases, and various indications suggest that its inhibition would reverse inflammation. However, there are currently no p38alpha inhibitors in clinical use. Because the human p38alpha imposes severe growth retardation when expressed in yeast, we screened a library of 40,000 randomly selected small molecules for compounds that would restore a normal growth rate. We identified two compounds; both share a structural motif of 4-benzylpiperidine, and both were shown to be efficient and selective p38alpha inhibitors in vitro. They were also active in mammalian cells, as manifested by their ability to reversibly inhibit myoblast differentiation. Thus, the yeast screen identified efficient and specific p38alpha inhibitors that are capable of crossing biological membranes, are not toxic, and function in mammalian cells. The rapid and cost-efficient high-throughput screening used here could be applied for isolation of inhibitors of various targets. PMID:16847144

Friedmann, Yael; Shriki, Anat; Bennett, Estelle R; Golos, Stella; Diskin, Ron; Marbach, Irit; Bengal, Eyal; Engelberg, David

2006-10-01

157

Identification of piecewise affine and hybrid systems  

Microsoft Academic Search

We focus on the identification of discrete time hybrid systems in the piecewise affine (PWA) form. This problem can be formulated as the reconstruction of a possibly discontinuous PWA map with a multidimensional domain. In order to achieve our goal, we propose an algorithm that exploits the combined use of clustering, linear identification, and classification techniques. This allows one to

Giancarlo Ferrari-Trecate; Marco Musellit; Diego Liberatis; Manfred Morarit

2001-01-01

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

Identification of the Molecular Mechanisms for Cell-Fate Selection in Budding Yeast through Mathematical Modeling  

PubMed Central

The specification and maintenance of cell fates is essential to the development of multicellular organisms. However, the precise molecular mechanisms in cell fate selection are, to our knowledge, poorly understood due to the complexity of multiple interconnected pathways. In this study, model-based quantitative analysis is used to explore how to maintain distinguished cell fates between cell-cycle commitment and mating arrest in budding yeast. We develop a full mathematical model of an interlinked regulatory network based on the available experimental data. By theoretically defining the Start transition point, the model is able to reproduce many experimental observations of the dynamical behaviors in wild-type cells as well as in Ste5-8A and Far1-S87A mutants. Furthermore, we demonstrate that a moderate ratio between Cln1/2?Far1 inhibition and Cln1/2?Ste5 inhibition is required to ensure a successful switch between different cell fates. We also show that the different ratios of the mutual Cln1/2 and Far1 inhibition determine the different cell fates. In addition, based on a new, definition of network entropy, we find that the Start point in wild-type cells coincides with the system’s point of maximum entropy. This result indicates that Start is a transition point in the network entropy. Therefore, we theoretically explain the Start point from a network dynamics standpoint. Moreover, we analyze the biological bistablity of our model through bifurcation analysis. We find that the Cln1/2 and Cln3 production rates and the nonlinearity of SBF regulation on Cln1/2 production are potential determinants for irreversible entry into a new cell fate. Finally, the quantitative computations further reveal that high specificity and fidelity of the cell-cycle and mating pathways can guarantee specific cell-fate selection. These findings show that quantitative analysis and simulations with a mathematical model are useful tools for understanding the molecular mechanisms in cell-fate decisions.

Li, Yongkai; Yi, Ming; Zou, Xiufen

2013-01-01

160

Caller Identification System in the Internet Environment  

Microsoft Academic Search

The Caller Identification System is a security system designed to strengthen the security measuresalready present in the SNU(Seoul National University) local area network. It is a system made up of twomain components and they are (1) an Extended TCP Wrapper(ETCPW ) and (2) a Caller IdentificationServer(CIS). The Extended TCP Wrapper(ETCPW ) is, as its name suggests, a TCP Wrapper[1] with

Chong Sang Kim; Ghun Choe; Hae Lyong Kim; Hyun Tae Jung; Sang Lyul Min; Yang Min Seo

1993-01-01

161

Comparison of Vitek identification and antifungal susceptibility testing methods to DNA sequencing and Sensititre YeastOne antifungal testing.  

PubMed

The colorimetric Vitek 2 YST card and the yeast susceptibility test (AST-YS01) were evaluated for their identification efficacy and their use in assessing the in vitro susceptibility of Candida spp. to fluconazole, voriconazole and amphotericin B. Ninety-one percent or 62 of 68 Candida isolates from blood specimens were correctly identified, as compared to determinations of the ITS2 fragment length. The overall essential agreements between Vitek 2 and the Sensititre YeastOne (SYO) colorimetric method were 78.4%, 84.6% and 90.8%, for fluconazole, voriconazole and amphotericin B, respectively. The overall categorical agreements between Vitek 2 and SYO for fluconazole and voriconazole were 76.9% and 96.9%, respectively. The poorest agreement between Vitek 2 and SYO was seen with C. glabrata (n = 27), particularly for fluconazole. The MIC values of 2 C. glabrata strains (3%) could not be determined with the Vitek 2 due to an insufficient growth in the control well. For other Candida species (n = 38) Vitek 2 and SYO showed acceptable agreements. PMID:20560861

Vijgen, Sara; Nys, Sita; Naesens, Reinout; Magerman, Koen; Boel, An; Cartuyvels, Reinoud

2011-01-01

162

Yeast "N"-hybrid systems for protein-protein and drug-protein interaction discovery.  

PubMed

The majority of small molecule drugs act on protein targets to exert a therapeutic function. It has become apparent in recent years that many small molecule drugs act on more than one particular target and consequently, approaches which profile drugs to uncover their target binding spectrum have become increasingly important. Classical yeast two-hybrid systems have mainly been used to discover and characterize protein-protein interactions, but recent modifications and improvements have opened up new routes towards screening for small molecule-protein interactions. Such yeast "n"-hybrid systems hold great promise for the development of drugs which interfere with protein-protein interactions and for the discovery of drug-target interactions. In this review, we discuss several yeast two-hybrid based approaches with applications in drug discovery and describe a protocol for yeast three-hybrid screening of small molecules to identify their direct targets. PMID:22728036

Rezwan, Mandana; Auerbach, Daniel

2012-08-01

163

Identification of a rice APETALA3 homologue by yeast two-hybrid screening  

Microsoft Academic Search

A cDNA clone OsMADS16 was isolated from the rice young inflorescence cDNA expression library by the yeast two-hybrid screening method with OsMADS4 as bait. We have previously shown that the OsMADS4 gene is a member of the PI family and that the MADS-box gene is involved in controlling development of the second and third whorls of rice flowers. The sequence

Yong-Hwan Moon; Ji-Young Jung; Hong-Gyu Kang; Gynheung An

1999-01-01

164

Identification of a rice APETALA3 homologue by yeast two-hybrid screening  

Microsoft Academic Search

Ac DNA cloneOsMADS16was isolated from the rice young inflorescence cDNA expression library by the yeast two-hybrid screening method with OsMADS4 as bait. We have previously shown that the OsMADS4 gene is a member of the PI family and that the MADS-box gene is involved in controlling development of the second and third whorls of rice flowers. The sequence comparison indicated

Yong-Hwan Moon; Ji-Young Jung; Hong-Gyu Kang

1999-01-01

165

Screening and identification of yeast sequences that cause growth inhibition when overexpressed  

Microsoft Academic Search

To isolate genes that negatively regulate cell growth, we constructed a galactose-inducible expression library with partially\\u000a digested Saccharomyces cerevisiae genomic DNA fragments inserted downstream of the GAL10 promoter. In all, 240 000 yeast transformants were screened for lethality on galactose medium. From 17 such transformants\\u000a identified, 16 nonoverlapping DNA sequences were obtained. Restriction mapping and determination of DNA sequences adjacent

R. Akada; J. Yamamoto; I. Yamashita

1997-01-01

166

FASTA barcodes: a simple method for the identification of yeast ORF deletions.  

PubMed

A consortium of yeast geneticists have created -6000 individual ORF deletions, representing > 96% of the currently verified or predicted ORFs in S. cerevisiae. Importantly, molecular barcodes (each a unique 20 bp sequence termed either Uptag or Downtag) were used as identifiers for every ORF deletion. Microarray analyses of pooled yeast deletions has been used to identify thousands of genes involved in general fitness, haploinsufficiency, drug resistance and DNA damage repair. However, application of this powerful technology requires considerable expense, expertise and specialized equipment. While standard PCR techniques and specifically designed PCR primers can be used to confirm that a given ORF is in fact deleted, this procedure cannot be used to identify unknown deletions. In theory, every ORF deletion could be determined by barcode sequencing. However, neither a consolidated barcode database nor a reliable search engine is currently available for this purpose. To address this need, we have adapted a FASTA sequence program that utilizes the unique barcode database to allow users to identify individual ORF deletions, based upon simple sequencing reactions of PCR amplifications of either Uptag or Downtag barcodes. In silico and practical testing of this application reveals that it is an inexpensive, reliable and reproducible method for rapidly identifying unknown deletions. This approach allows laboratories to conduct small- or large-scale genetic screens with pooled yeast deletion strains and identify or verify any ORF deletion without the need for microarray technology. PMID:21809386

McMahon, K Wyatt; Manukyan, Arkadi; Dungrawala, Huzefa; Montgomery, Micah; Nordstrom, Brian; Wright, Jill; Abraham, Lesley; Schneider, Brandt L

2011-09-01

167

Identification of Inhibitors of V-ATPase Pumps in Yeast by HTS Flow Cytometry  

PubMed Central

Fluorescence intensity of the pH-sensitive carboxyfluorescein derivative BCECF was monitored by high throughput flow cytometry in living yeast cells. We measured fluorescence intensity of BCECF trapped in yeast vacuoles, acidic compartments equivalent to lysosomes where V-ATPases are abundant. Because V-ATPases maintain a low pH in the vacuolar lumen, V-ATPase inhibition by concanamycin A alkalinized the vacuole and increased BCECF fluorescence. Likewise, V-ATPase deficient mutant cells had greater fluorescence intensity than wild-type cells. Thus, we detected an increase of fluorescence intensity after short-term and long-term inhibition of V-ATPase function. We used yeast cells loaded with BCECF to screen a small chemical library of structurally diverse compounds in order to identify V-ATPase inhibitors. One compound, disulfiram, enhanced BCECF fluorescence intensity (although to a degree beyond anticipated for pH changes alone in the mutant cells). Once confirmed by dose response assays (EC50=26 ?M), we verified V-ATPase inhibition by disulfiram in secondary assays which measured ATP hydrolysis in vacuolar membranes. The inhibitory action of disulfiram against V-ATPase pumps revealed a novel effect previously unknown for this compound. Because V-ATPases are highly conserved, new inhibitors identified could be used as research and therapeutic tools in cancer, viral infections, and other diseases where V-ATPases are involved.

Johnson, Rebecca M.; Allen, Chris; Melman, Sandra D.; Waller, Anna; Young, Susan M.; Sklar, Larry A.; Parra, Karlett J.

2010-01-01

168

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

169

Automatic Identification System (AIS) User Requirements.  

National Technical Information Service (NTIS)

Automatic Identification System (AIS) is a new technology that should improve situational awareness for the mariner by providing navigation information such as the names, positions, courses, and speeds of vessels in the immediate vicinity. Over the past d...

M. Edwards D. Pietraswski

2000-01-01

170

Performance characterization of material identification systems  

NASA Astrophysics Data System (ADS)

In recent years a number of analytical devices have been proposed and marketed specifically to enable field-based material identification. Technologies reliant on mass, near- and mid-infrared, and Raman spectroscopies are available today, and other platforms are imminent. These systems tend to perform material recognition based on an on-board library of material signatures. While figures of merit for traditional quantitative analytical sensors are broadly established (e.g., SNR, selectivity, sensitivity, limit of detection/decision), measures of performance for material identification systems have not been systematically discussed. In this paper we present an approach to performance characterization similar in spirit to ROC curves, but including elements of precision-recall curves and specialized for the intended-use of material identification systems. Important experimental considerations are discussed, including study design, sources of bias, uncertainty estimation, and cross-validation and the approach as a whole is illustrated using a commercially available handheld Raman material identification system.

Brown, Christopher D.; Green, Robert L.

2006-10-01

171

Digital image processing for system identification  

Microsoft Academic Search

Emerging digital image processing techniques are utilized to demonstrate their potential applications in earthquake engineering, particularly in the area of system identification. In this respect, the objectives of this research are to demonstrate the underlying principle that permits nonlinear system identification, non-intrusively and remotely, with the aid of CCD camera and, for the purpose of the proof-of-concept, to apply the

Masanobu Shinozuka; HungChi Chung; Jianwen Liang

2000-01-01

172

An eYFP reporter gene for the yeast two-hybrid system.  

PubMed

The yeast two-hybrid system is a powerful tool for detecting binary protein interactions, widely used in large-scale interactome mapping. We modified two yeast strains commonly used in yeast two-hybrid experiments by integrating into their genomes a new reporter gene encoding the enhanced yellow fluorescent protein eYFP. The suitability of this reporter gene for interaction screening was evaluated by fluorescence microscopy and fluorescence-activated cell sorting analysis. The gene shows good potential as a two-hybrid reporter gene for detecting strong interactions. Gal4 transcriptional activation gives rise to sufficient fluorescence for detection with a flow cytometer, but the eYFP reporter is not sensitive enough for detecting weak or moderate interactions. This study highlights the advantages of a fluorescent reporter gene in yeast two-hybrid screening. PMID:23385445

Damon, Coralie; Boxus, Mathieu; Twizere, Jean-Claude; Portetelle, Daniel; Vandenbol, Micheline

2013-02-01

173

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

174

Metabolism related toxicity of diclofenac in yeast as model system  

Microsoft Academic Search

Diclofenac is a widely used drug that can cause serious hepatotoxicity, which has been linked to metabolism by cytochrome P450s (P450). To investigate the role of oxidative metabolites in diclofenac toxicity, a model for P450-related toxicity was set up in Saccharomyces cerevisiae. We expressed a drug-metabolizing mutant of cytochrome P450 BM3 (BM3 M11) in yeast. Importantly, BM3 M11 yielded similar

Jolanda S. van Leeuwen; Galvin Vredenburg; Sanja Dragovic; T. F. Jennifer Tjong; J. Chris Vos; Nico P. E. Vermeulen

2011-01-01

175

Metabolism related toxicity of diclofenac in yeast as model system.  

PubMed

Diclofenac is a widely used drug that can cause serious hepatotoxicity, which has been linked to metabolism by cytochrome P450s (P450). To investigate the role of oxidative metabolites in diclofenac toxicity, a model for P450-related toxicity was set up in Saccharomyces cerevisiae. We expressed a drug-metabolizing mutant of cytochrome P450 BM3 (BM3 M11) in yeast. Importantly, BM3 M11 yielded similar oxidative metabolite profiles of diclofenac as human P450s. It was found that yeast strains expressing BM3 M11 grew significantly slower when exposed to diclofenac than strains without BM3 M11. Furthermore, the amount of reactive oxygen species (ROS) after incubation with diclofenac was higher in strains expressing BM3 M11 than in strains without this enzyme, confirming that P450 activity increases diclofenac toxicity. Interestingly, 4'- and 5-hydroxydiclofenac had no effect on cell growth or ROS formation in cells expressing BM3 M11, although hydroxydiclofenac-derived quinone imines were identified in these strains by detection of their glutathione conjugates. This suggests that 4'- and 5-hydroxydiclofenac, as well as their quinone imines, are not involved in toxicity in yeast. Rather, the P450-related toxicity of diclofenac is caused by primary metabolites such as arene oxides resulting in hydroxydiclofenac or radical species formed during decarboxylation. PMID:21111035

van Leeuwen, Jolanda S; Vredenburg, Galvin; Dragovic, Sanja; Tjong, T F Jennifer; Vos, J Chris; Vermeulen, Nico P E

2011-02-01

176

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

177

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast.  

PubMed

Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement. PMID:21873232

Libkind, Diego; Hittinger, Chris Todd; Valério, Elisabete; Gonçalves, Carla; Dover, Jim; Johnston, Mark; Gonçalves, Paula; Sampaio, José Paulo

2011-08-30

178

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

179

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

180

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

181

Rapid identification of mRNA processing defects with a novel single-cell yeast reporter.  

PubMed

It has become increasingly evident that gene expression processes in eukaryotes involve communication and coordination between many complex, independent macromolecular machines. To query these processes and to explore the potential relationships between them in the budding yeast Saccharomyces cerevisiae, we designed a versatile reporter using multicolor high-throughput flow cytometry. Due to its design, this single reporter exhibits a distinctive signature for many defects in gene expression including transcription, histone modification, pre-mRNA splicing, mRNA export, nonsense-mediated decay, and mRNA degradation. Analysis of the reporter in 4967 nonessential yeast genes revealed striking phenotypic overlaps between chromatin remodeling, histone modification, and pre-mRNA splicing. Additionally, we developed a copper-inducible reporter, with which we demonstrate that 5-fluorouracil mimics the mRNA decay phenotype of cells lacking the 3'-5' exonuclease Rrp6p. Our reporter is capable of performing high-throughput, rapid, and large-scale screens to identify and characterize genetic and chemical perturbations of the major eukaryotic gene expression processes. PMID:24671766

Sorenson, Matthew R; Stevens, Scott W

2014-05-01

182

On Markov parameters in system identification  

NASA Technical Reports Server (NTRS)

A detailed discussion of Markov parameters in system identification is given. Different forms of input-output representation of linear discrete-time systems are reviewed and discussed. Interpretation of sampled response data as Markov parameters is presented. Relations between the state-space model and particular linear difference models via the Markov parameters are formulated. A generalization of Markov parameters to observer and Kalman filter Markov parameters for system identification is explained. These extended Markov parameters play an important role in providing not only a state-space realization, but also an observer/Kalman filter for the system of interest.

Phan, Minh; Juang, Jer-Nan; Longman, Richard W.

1991-01-01

183

Subcritical flutter testing and system identification  

NASA Technical Reports Server (NTRS)

Treatment is given of system response evaluation, especially in application to subcritical flight and wind tunnel flutter testing of aircraft. An evaluation is made of various existing techniques, in conjuction with a companion survey which reports theoretical and analog experiments made to study the identification of system response characteristics. Various input excitations are considered, and new techniques for analyzing response are explored, particularly in reference to the prevalent practical case where unwanted input noise is present, such as caused by gusts or wind tunnel turbulence. Further developments are also made of system parameter identification techniques.

Houbolt, J. C.

1974-01-01

184

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

185

Identification of proteins associated with the yeast mitochondrial RNA polymerase by tandem affinity purification  

PubMed Central

The abundance of mitochondrial (mt) transcripts varies under different conditions, and is thought to depend upon rates of transcription initiation, transcription termination/attenuation and RNA processing/degradation. The requirement to maintain the balance between RNA synthesis and processing may involve coordination between these processes; however, little is known about factors that regulate the activity of mtRNA polymerase (mtRNAP). Recent attempts to identify mtRNAP–protein interactions in yeast by means of a generalized tandem affinity purification (TAP) protocol were not successful, most likely because they involved a C-terminal mtRNAP–TAP fusion (which is incompatible with mtRNAP function) and because of the use of whole-cell solubilization protocols that did not preserve the integrity of mt protein complexes. Based upon the structure of T7 RNAP (to which mtRNAPs show high sequence similarity), we identified positions in yeast mtRNAP that allow insertion of a small affinity tag, confirmed the mature N-terminus, constructed a functional N-terminal TAP–mtRNAP fusion, pulled down associated proteins, and identified them by LC–MS–MS. Among the proteins found in the pull-down were a DEAD-box protein (Mss116p) and an RNA-binding protein (Pet127p). Previous genetic experiments suggested a role for these proteins in linking transcription and RNA degradation, in that a defect in the mt degradadosome could be suppressed by overexpression of either of these proteins or, independently, by mutations in either mtRNAP or its initiation factor Mtf1p. Further, we found that Mss116p inhibits transcription by mtRNAP in vitro in a steady-state reaction. Our results support the hypothesis that Mss116p and Pet127p are involved in modulation of mtRNAP activity. Copyright © 2009 John Wiley & Sons, Ltd.

Markov, Dmitriy A; Savkina, Maria; Anikin, Michael; Del Campo, Mark; Ecker, Karen; Lambowitz, Alan M; De Gnore, Jon P; McAllister, William T

2009-01-01

186

Feedback identification of continuous microbial growth systems  

Microsoft Academic Search

The fundamental problem of dynamic modeling of continuous culture systems for process control and optimization is addressed. Forcing a system to bifurcation via feedback control is a very promising method for model discrimination and identification. Dynamic information is obtained by using feedback control to intentionally destabilize a steady state. Using this technique, the dynamic behavior of the chemostat as predicted

D. G. ONeill; G. Lyberatos

1986-01-01

187

Repeated fed-batch rapid fermentation using yeast cells and activated carbon extraction system  

SciTech Connect

The application of a repeated fed-batch rapid ethanol fermentation employing immobilized yeast cells accompanied by an activated carbon extraction system has been investigated in an attempt to increase product yield. Immobilized and free yeast cells were used to effect ethanol fermentations in a simplified nitrogen-free medium containing only glucose and mineral salts. Repeatedly, fermentation broth with a high ethanol concentration (80 to 100 g/L) was extracted using activated carbon beads (BACM) and the resulting broth of low ethanol content (< 50 g/L) was recycled back for further fermentations. The maximum ethanol productivity achieved in this system was 25 g/L/h. 7 figures, 1 table.

Lee, S.S.; Wang, H.Y.

1982-01-01

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

Microsoft Academic Search

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

Guo-Lei Zhou; Yasumasa Miyazaki; T. Nakagawa; Katsunori Tanaka; Kazuo Shishido; H. Matsuda; Makoto Kawamukai

1998-01-01

190

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

191

Genetic Algorithms Based Parameter Identification of Yeast Fed-Batch Cultivation  

Microsoft Academic Search

\\u000a Different kinds of genetic algorithms have been investigated for a parameter identification of a fermentation process. Altogether\\u000a eight realizations of genetic algorithms have been presented - four of simple genetic algorithms and four of multi-population\\u000a ones. Each of them is characterized with a different sequence of implementation of main genetic operators, namely selection,\\u000a crossover and mutation. A comparison of considered

Maria Angelova; Stoyan Tzonkov; Tania Pencheva

2010-01-01

192

Rapid identification of yeasts from positive blood culture bottles by pyrosequencing  

Microsoft Academic Search

We have developed a rapid protocol for the identification of Candida species from positive blood cultures by combining a simple method for nucleic acid extraction and preparation using microbial\\u000a storage cardboards with polymerase chain reaction (PCR) and pyrosequencing of a small region of the 18 S rRNA gene. The protocol\\u000a is robust and easy to implement and can be performed in

I. Quiles-Melero; J. García-Rodriguez; M. P. Romero-Gómez; P. Gómez-Sánchez; J. Mingorance

2011-01-01

193

Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis  

PubMed Central

Identification of the underlying molecular mechanisms for a derived phenotype by adaptive evolution is difficult. Here, we performed a systems-level inquiry into the metabolic changes occurring in the yeast Saccharomyces cerevisiae as a result of its adaptive evolution to increase its specific growth rate on galactose and related these changes to the acquired phenotypic properties. Three evolved mutants (62A, 62B, and 62C) with higher specific growth rates and faster specific galactose uptake were isolated. The evolved mutants were compared with a reference strain and two engineered strains, SO16 and PGM2, which also showed higher galactose uptake rate in previous studies. The profile of intermediates in galactose metabolism was similar in evolved and engineered mutants, whereas reserve carbohydrates metabolism was specifically elevated in the evolved mutants and one evolved strain showed changes in ergosterol biosynthesis. Mutations were identified in proteins involved in the global carbon sensing Ras/PKA pathway, which is known to regulate the reserve carbohydrates metabolism. We evaluated one of the identified mutations, RAS2Tyr112, and this mutation resulted in an increased specific growth rate on galactose. These results show that adaptive evolution results in the utilization of unpredicted routes to accommodate increased galactose flux in contrast to rationally engineered strains. Our study demonstrates that adaptive evolution represents a valuable alternative to rational design in bioengineering of improved strains and, that through systems biology, it is possible to identify mutations in evolved strain that can serve as unforeseen metabolic engineering targets for improving microbial strains for production of biofuels and chemicals.

Hong, Kuk-Ki; Vongsangnak, Wanwipa; Vemuri, Goutham N.; Nielsen, Jens

2011-01-01

194

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

195

A practical approach to rotorcraft systems identification  

NASA Technical Reports Server (NTRS)

A standard for rotorcraft system identification is proposed to facilitate the exchange of data and technology within the industry. This integrated approach utilizes simulations to validate methodology and flight data to validate simulations. A new technique allowing results obtained from separate maneuvers to be systematically combined is also presented and shown to be a fundamental tool in providing a practical approach to rotorcraft identification. The proposed methodology is evaluated using data generated by nonlinear blade-element simulation of the Rotor Systems Research Aircraft.

Du Val, R. W.; Wang, J. C.; Demiroz, M. Y.

1984-01-01

196

Identification of an endoplasmic reticulum membrane protein interacting with DNA polymerase beta by a yeast two-hybrid screen.  

PubMed

Base excision repair (BER) is a key pathway for maintaining genomic stability. A key enzyme in the BER pathway is DNA polymerase beta (polbeta). It has been shown that more than 11% of breast, bladder, esophageal, colon, and gastric cancer samples studied so far exhibit polbeta mutation. A truncated form of polbeta, polbetadelta (exon 11 deletion), identified in a colon tumour sample, exhibited dominant negative activity. Using this polbetadelta as bait, we screened a HeLa cDNA library for any interacting protein(s) in the yeast two-hybrid (Y2H) system. Polbetadelta was cloned into a pGBKT7 vector (pGBKT7-polbetadelta). pGBKT7-polbetadelta was transformed into the yeast strain AH109. Then the cDNA library was co-transformed into AH109/pGBKT7-polbetadelta and screened by the selection procedure. The yeast-purified plasmids were transformed into Escherichia coli. Plasmid DNA was isolated from the colonies, purified, digested with Sma I and Sal I, and the fragments were sequenced. Four positive clones were obtained. Out of these, three proteins were already known to interact with polbeta (XRCC1, MGC5306, and AP endonuclease 1). The only member previously not known to interact with polbeta was phosphatidylinositol glycosylase type S (PIGS). PIGS is a 64-kDa membrane protein, encoded in chromosome 17. The PIGS protein interacts also with wild-type polbeta which was confirmed by co-immunoprecipitation and Western blot analysis. The role of the newly identified protein in the dominant negative function of the variant form of polbeta remains to be seen. PMID:24772827

Panda, Kakali; Khanra, Kalyani; Bhattacharyya, Nandan

2014-01-01

197

Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics  

PubMed Central

Background Chitosan oligosaccharide (COS), a deacetylated derivative of chitin, is an abundant, and renewable natural polymer. COS has higher antimicrobial properties than chitosan and is presumed to act by disrupting/permeabilizing the cell membranes of bacteria, yeast and fungi. COS is relatively non-toxic to mammals. By identifying the molecular and genetic targets of COS, we hope to gain a better understanding of the antifungal mode of action of COS. Results Three different chemogenomic fitness assays, haploinsufficiency (HIP), homozygous deletion (HOP), and multicopy suppression (MSP) profiling were combined with a transcriptomic analysis to gain insight in to the mode of action and mechanisms of resistance to chitosan oligosaccharides. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified are involved in processes such as RNA biology (transcription, translation and regulatory mechanisms), membrane functions (e.g. signalling, transport and targeting), membrane structural components, cell division, and proteasome processes. The transcriptomes of control wild type and 5 suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the Ras signal transduction pathway. Down-regulated transcripts included those encoding protein folding components and respiratory chain proteins. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and pre-treatment with these well characterized environmental stressors provided little or any resistance to COS. Conclusions Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to Amphotericin B, Fluconazole and Terbinafine as the wild type cells and that when COS and Fluconazole are used in combination they act in a synergistic fashion. The gene targets of COS identified in this study indicate that COS’s mechanism of action is different from other commonly studied fungicides that target membranes, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens.

2012-01-01

198

40 CFR 72.33 - Identification of dispatch system.  

Code of Federal Regulations, 2010 CFR

... false Identification of dispatch system. 72.33 Section...Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED...72.33 Identification of dispatch system. (a) Every Phase...shall be treated as part of a dispatch system for purposes...

2009-07-01

199

40 CFR 72.33 - Identification of dispatch system.  

Code of Federal Regulations, 2010 CFR

... false Identification of dispatch system. 72.33 Section...Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED...72.33 Identification of dispatch system. (a) Every Phase...shall be treated as part of a dispatch system for purposes...

2010-07-01

200

Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast  

PubMed Central

Genetic robustness refers to a compensatory mechanism for buffering deleterious mutations or environmental variations. Gene duplication has been shown to provide such functional backups. However, the overall contribution of duplication-based buffering for genetic robustness is rather small. In this study, we investigated whether transcriptional compensation also exists among genes that share similar functions without sequence homology. A set of nonhomologous synthetic-lethal gene pairs was assessed by using a coexpression network, protein-protein interactions, and other types of genetic interactions in yeast. Our results are notably different from those of previous studies on buffering paralogs. The low expression similarity and the conditional coexpression alone do not play roles in identifying the functionally compensatory genes. Additional properties such as synthetic-lethal interaction, the ratio of shared common interacting partners, and the degree of coregulation were, at least in part, necessary to extract functional compensatory genes. Our network-based approach is applicable to select several well-documented cases of compensatory gene pairs and a set of new pairs. The results suggest that transcriptional reprogramming plays a limited role in functional compensation among nonhomologous genes. Our study aids in understanding the mechanism and features of functional compensation more in detail.

Peng, Chien-Hua; Lin, Shu-Hsi; Peng, Shih-Chi; Lyu, Ping-Chiang; Arita, Masanori; Tang, Chuan-Yi

2012-01-01

201

Identification of a New Class of Negative Regulators Affecting Sporulation-Specific Gene Expression in Yeast  

PubMed Central

We characterized two yeast loci, MDS3 and PMD1, that negatively regulate sporulation. Initiation of sporulation is mediated by the meiotic activator IME1, which relies on MCK1 for maximal expression. We isolated the MDS3-1 allele (encoding a truncated form of Mds3p) as a suppressor that restores IME1 expression in mck1 mutants. mds3 null mutations confer similar suppression phenotypes as MDS3-1, indicating that Mds3p is a negative regulator of sporulation and the MDS3-1 allele confers a dominant-negative phenotype. PMD1 is predicted to encode a protein sharing significant similarity with Mds3p. mds3 pmd1 double mutants are better suppressors of mck1 than is either single mutant, indicating that Mds3p and Pmd1p function synergistically. Northern blot analysis revealed that suppression is due to increased IME1 transcript accumulation. The roles of Mds3p and Pmd1p are not restricted to the MCK1 pathway because mds3 pmd1 mutations also suppress IME1 expression defects associated with MCK1-independent sporulation mutants. Furthermore, mds3 pmd1 mutants express significant levels of IME1 even in vegetative cells and this unscheduled expression results in premature sporulation. These phenotypes and interactions with RAS2-Val19 suggest that unscheduled derepression of IME1 is probably due to a defect in recognition of nutritional status.

Benni, M. L.; Neigeborn, L.

1997-01-01

202

Identification and Dissection of a Complex DNA Repair Sensitivity Phenotype in Baker's Yeast  

PubMed Central

Complex traits typically involve the contribution of multiple gene variants. In this study, we took advantage of a high-density genotyping analysis of the BY (S288c) and RM strains of Saccharomyces cerevisiae and of 123 derived spore progeny to identify the genetic loci that underlie a complex DNA repair sensitivity phenotype. This was accomplished by screening hybrid yeast progeny for sensitivity to a variety of DNA damaging agents. Both the BY and RM strains are resistant to the ultraviolet light–mimetic agent 4-nitroquinoline 1-oxide (4-NQO); however, hybrid progeny from a BY×RM cross displayed varying sensitivities to the drug. We mapped a major quantitative trait locus (QTL), RAD5, and identified the exact polymorphism within this locus responsible for 4-NQO sensitivity. By using a backcrossing strategy along with array-assisted bulk segregant analysis, we identified one other locus, MKT1, and a QTL on Chromosome VII that also link to the hybrid 4-NQO–sensitive phenotype but confer more minor effects. This work suggests an additive model for sensitivity to 4-NQO and provides a strategy for mapping both major and minor QTL that confer background-specific phenotypes. It also provides tools for understanding the effect of genetic background on sensitivity to genotoxic agents.

Demogines, Ann; Smith, Erin; Kruglyak, Leonid; Alani, Eric

2008-01-01

203

Identification and purification of a protein that binds DNA cooperatively with the yeast SWI5 protein.  

PubMed Central

The Saccharomyces cerevisiae SWI5 gene encodes a zinc finger protein required for the expression of the HO gene. A protein fusion between glutathione S-transferase and SWI5 was expressed in Escherichia coli and purified. The GST-SWI5 fusion protein formed only a low-affinity complex in vitro with the HO promoter, which was inhibited by low concentrations of nonspecific DNA. This result was surprising, since genetic evidence demonstrated that SWI5 functions at the HO promoter via this site in vivo. A yeast factor, GRF10 (also known as PHO2 and BAS2), that promoted high-affinity binding of SWI5 in the presence of a large excess of nonspecific carrier DNA was purified. Final purification of the 83-kDa GRF10 protein was achieved by cooperative interaction-based DNA affinity chromatography. In vitro binding studies demonstrated that SWI5 and GRF10 bind DNA cooperatively. Methylation interference and missing-nucleoside studies demonstrated that the two proteins bind at adjacent sites, with each protein making unique DNA contacts. SWI5 and GRF10 interactions were not detected in the absence of DNA. The role of cooperative DNA binding in determining promoter specificity of eukaryotic transcription factors is discussed. Images

Brazas, R M; Stillman, D J

1993-01-01

204

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

205

Continuous-Time Bilinear System Identification  

NASA Technical Reports Server (NTRS)

The objective of this paper is to describe a new method for identification of a continuous-time multi-input and multi-output bilinear system. The approach is to make judicious use of the linear-model properties of the bilinear system when subjected to a constant input. Two steps are required in the identification process. The first step is to use a set of pulse responses resulting from a constant input of one sample period to identify the state matrix, the output matrix, and the direct transmission matrix. The second step is to use another set of pulse responses with the same constant input over multiple sample periods to identify the input matrix and the coefficient matrices associated with the coupling terms between the state and the inputs. Numerical examples are given to illustrate the concept and the computational algorithm for the identification method.

Juang, Jer-Nan

2003-01-01

206

Identification of MicroRNA-Like RNAs in Mycelial and Yeast Phases of the Thermal Dimorphic Fungus Penicillium marneffei  

PubMed Central

Background Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in China and Southeast Asia. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less well studied and their potential roles in fungal dimorphism were largely unknown. Based on P. marneffei genome sequence, we hypothesize that miRNA-like RNAs (milRNAs) may be expressed in the dimorphic fungus. Methodology/Principal Findings We attempted to identify milRNAs in P. marneffei in both mycelial and yeast phase using high-throughput sequencing technology. Small RNAs were more abundantly expressed in mycelial than yeast phase. Sequence analysis revealed 24 potential milRNA candidates, including 17 candidates in mycelial and seven in yeast phase. Two genes, dcl-1 and dcl-2, encoding putative Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were identified in P. marneffei. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp., suggesting the co-evolution of dcl-2 among the thermal dimorphic fungi. Moreover, dcl-2 demonstrated higher mRNA expression levels in mycelial than yeast phase by 7 folds (P<0.001). Northern blot analysis confirmed the expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase. Using dcl-1KO, dcl-2KO, dclDKO and qde-2KO deletion mutants, we showed that the biogenesis of both milRNAs were dependent on dcl-2 but not dcl-1 or qde-2. The mRNA expression levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1KD, supporting regulatory function of milRNAs. Conclusions/Significance Our findings provided the first evidence for differential expression of milRNAs in different growth phases of thermal dimorphic fungi and shed light on the evolution of fungal proteins involved in milRNA biogenesis and possible role of post-transcriptional control in governing thermal dimorphism.

Wong, Annette Y. P.; Yeung, Julian M. Y.; Bao, Jessie; Zhang, Na; Lok, Si; Woo, Patrick C. Y.; Yuen, Kwok-Yung

2013-01-01

207

Use of the VITEK 2 system to identify and test the antifungal susceptibility of clinically relevant yeast species.  

PubMed

Eleven quality control isolates (Candida albicans ATCC 64548, C. tropicalis ATCC 200956, C. glabrata ATCC 90030, C. lusitaniae ATCC 200951, C. parapsilosis ATCC 22019, C. krusei ATCC 6258, C. dubliniensis ATCC 6330, Saccharomyces cerevisiae ATCC 9763, Cryptococcus neoformans ATCC 90012, C. gattii FIOCRUZ-CPF 60, and Trichosporon mucoides ATCC 204094) and 32 bloodstream isolates, including C. albicans, C. tropicalis, C. parapsilosis, C. glabrata, C. krusei, C. guilliermondii, C. pelliculosa (Pichia anomala), C. haemulonii, C. lusitaniae, and C. kefyr were identified at the species level by the VITEK 2 system. A set of clinical isolates (32 total) were used as challenge strains to evaluate the ability of the VITEK 2 system to determine the antifungal susceptibility of yeasts compared with the CLSI and EUCAST BMD reference standards. The VITEK 2 system correctly identified 100% of the challenge strains. The identification of yeast species and the evaluation of their susceptibility profiles were performed in an automated manner by the VITEK 2 system after approximately 15 h of growth for most species of Candida. The VITEK 2 system ensures that each test is performed in a standardized manner and provides quantitative MIC results that are reproducible and accurate when compared with the BMD reference methods. This system was able to determine the MICs of amphotericin B, flucytosine, voriconazole, and fluconazole in 15 h or less for the most common clinically relevant Candida species. In addition, the VITEK 2 system could reliably identify resistance to flucytosine, voriconazole, and fluconazole and exhibits excellent quantitative and qualitative agreement with the CLSI or EUCAST broth microdilution reference methods. PMID:24688520

Melhem, M S C; Bertoletti, A; Lucca, H R L; Silva, R B O; Meneghin, F A; Szeszs, M W

2013-12-01

208

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

2013-09-01

209

A New System for Comparative Functional Genomics of Saccharomyces Yeasts  

PubMed Central

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.

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.; Llinas, Manuel; Botstein, David; Troyanskaya, Olga G.; Dunham, Maitreya J.

2013-01-01

210

Extracellular enzyme production and phylogenetic distribution of yeasts in wastewater treatment systems.  

PubMed

The abilities of yeasts to produce different extracellular enzymes and their distribution characteristics were studied in municipal, inosine fermentation, papermaking, antibiotic fermentation, and printing and dyeing wastewater treatment systems. The results indicated that of the 257 yeasts, 16, 14, 55, and 11 produced lipase, protease, manganese dependant peroxidase (MnP), and lignin peroxidase (LiP), respectively. They were distributed in 12 identified and four unidentified genera, in which Candida rugosa (AA-M17) and an unidentified Saccharomycetales (AA-Y5), Pseudozyma sp. (PH-M15), Candida sp. (MO-Y11), and Trichosporon montevideense (MO-M16) were shown to have the highest activity of lipase, protease, Mnp, and LiP, respectively. No yeast had amylase, cellulose, phytase, or laccase activity. Although only 60 isolates produced ligninolytic enzymes, 249 of the 257 yeasts could decolorize different dyes through the mechanism of biodegradation (222 isolates) or bio-sorption. The types of extracellular enzymes that the yeasts produced were significantly shaped by the types of wastewater treated. PMID:23261999

Yang, Qingxiang; Zhang, Hao; Li, Xueling; Wang, Zhe; Xu, Ying; Ren, Siwei; Chen, Xuanyu; Xu, Yuanyuan; Hao, Hongxin; Wang, Hailei

2013-02-01

211

Automatic Fruits Identification System Using Hybrid Technique  

Microsoft Academic Search

In this work, a combination of artificial neural network (ANN), Fourier descriptors (FD) and spatial domain analysis (SDA) has been proposed for the development of an au- tomatic fruits identification and sorting system. Fruits images are captured using digital camera inclined at different angles to the horizontal. Segmentation is used for the classification of the preprocessed images into two non-overlapping

A. M. Aibinu; M. J. E. Salami; A. A. Shafie; N. Hazali; N. Termidzi

2011-01-01

212

System Identification with Reaction-Mass Devices.  

National Technical Information Service (NTIS)

Reaction-mass devices are to be used in a dual role: first for the purpose of system identification, and second for the purpose of vibration suppression. Unlike ground-based shakers, reaction-mass devices have a position constraint which must be maintaine...

R. Quan

1995-01-01

213

Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon  

PubMed Central

The yeast long terminal repeat (LTR) retrotransposon Ty1, like retroviruses, encodes a terminally redundant RNA, which is packaged into virus-like particles (VLPs) and is converted to a DNA copy by the process of reverse transcription. Mutations predicted to interfere with the priming events during reverse transcription and hence inhibit replication are known to dramatically decrease transposition of Ty1. However, additional cis-acting sequences responsible for Ty1 replication and RNA dimerization and packaging have remained elusive. Here we describe a modular mini-Ty1 element encoding the minimal sequence that can be retrotransposed by the Ty1 proteins, supplied in trans by a helper construct. Using a mutagenic screening strategy, we recovered transposition-deficient modular mini-Ty1-HIS3 elements with mutations in sequences required in cis for Ty1 replication and integration. Two distinct clusters of mutations mapped near the 5?-end of the Ty1 RNA. The clusters define a GAGGAGA sequence at the extreme 5?-end of the Ty1 transcript and a complementary downstream UCUCCUC sequence, 264 nt into the RNA. Disruption of the reverse complementarity of these two sequences decreased transposition and restoration of complementarity rescued transposition to wild-type levels. Ty1 cDNA was reduced in cells expressing RNAs with mutations in either of these short sequences, despite nearly normal levels of Ty1 RNA and VLPs. Our results suggest that the intramolecular interaction between the 5?-GAGGAGA and UCUCCUC sequences stabilizes an RNA structure required for efficient initiation of reverse transcription.

BOLTON, ERIC C.; COOMBES, CANDICE; EBY, YOLANDA; CARDELL, MATTIAS; BOEKE, JEF D.

2005-01-01

214

Identification of novel proteins associated with yeast snR30 small nucleolar RNA  

PubMed Central

H/ACA small nucleolar RNPs (snoRNPs) that guide pseudouridylation reactions are comprised of one small nucleolar RNA (snoRNA) and four common proteins (Cbf5, Gar1, Nhp2 and Nop10). Unlike other H/ACA snoRNPs, snR30 is essential for the early processing reactions that lead to the production of 18S ribosomal RNA in the yeast Saccharomyces cerevisiae. To determine whether snR30 RNP contains specific proteins that contribute to its unique functional properties, we devised an affinity purification strategy using TAP-tagged Gar1 and an RNA aptamer inserted in snR30 snoRNA to selectively purify the RNP. Northern blotting and pCp labeling experiments showed that S1-tagged snR30 snoRNA can be selectively purified with streptavidin beads. Protein analysis revealed that aptamer-tagged snR30 RNA was associated with the four H/ACA proteins and a number of additional proteins: Nop6, ribosomal proteins S9 and S18 and histones H2B and H4. Using antibodies raised against Nop6 we show that endogenous Nop6 localizes to the nucleolus and that it cosediments with snR30 snoRNA in sucrose density gradients. We demonstrate through primer extension experiments that snR30 snoRNA is required for cleavages at site A0, A1 and A2, and that the absence of Nop6 decreases the efficiency of cleavage at site A2. Finally, electron microscopy analyses of chromatin spreads from cells depleted of snR30 snoRNA show that it is required for SSU processome assembly.

Lemay, Vincent; Hossain, Ahmed; Osheim, Yvonne N.; Beyer, Ann L.; Dragon, Francois

2011-01-01

215

System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap.  

PubMed

Yeast remains an important model for systems biology and for evaluating proteomics strategies. In-depth shotgun proteomics studies have reached nearly comprehensive coverage, and rapid, targeted approaches have been developed for this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns and gradients coupled to a linear ion trap Orbitrap instrument had an unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell Proteomics 10, 10.1074/mcp.M110.003699). Here we couple an ultra high pressure liquid chromatography system to a novel bench top Orbitrap mass spectrometer (Q Exactive) with the goal of nearly complete, rapid, and robust analysis of the yeast proteome. Single runs of filter-aided sample preparation (FASP)-prepared and LysC-digested yeast cell lysates identified an average of 3923 proteins. Combined analysis of six single runs improved these values to more than 4000 identified proteins/run, close to the total number of proteins expressed under standard conditions, with median sequence coverage of 23%. Because of the absence of fractionation steps, only minuscule amounts of sample are required. Thus the yeast model proteome can now largely be covered within a few hours of measurement time and at high sensitivity. Median coverage of proteins in Kyoto Encyclopedia of Genes and Genomes pathways with at least 10 members was 88%, and pathways not covered were not expected to be active under the conditions used. To study perturbations of the yeast proteome, we developed an external, heavy lysine-labeled SILAC yeast standard representing different proteome states. This spike-in standard was employed to measure the heat shock response of the yeast proteome. Bioinformatic analysis of the heat shock response revealed that translation-related functions were down-regulated prominently, including nucleolar processes. Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities. PMID:22021278

Nagaraj, Nagarjuna; Kulak, Nils Alexander; Cox, Juergen; Neuhauser, Nadin; Mayr, Korbinian; Hoerning, Ole; Vorm, Ole; Mann, Matthias

2012-03-01

216

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

2013-01-01

217

Identification of the Transcription Factor Znc1p, which Regulates the Yeast-to-Hypha Transition in the Dimorphic Yeast Yarrowia lipolytica  

PubMed Central

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.

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

2013-01-01

218

An efficient automatic firearm identification system  

NASA Astrophysics Data System (ADS)

Automatic firearm identification system (AFIS) is highly demanded in forensic ballistics to replace the traditional approach which uses comparison microscope and is relatively complex and time consuming. Thus, several AFIS have been developed for commercial and testing purposes. However, those AFIS are still unable to overcome some of the drawbacks of the traditional firearm identification approach. The goal of this study is to introduce another efficient and effective AFIS. A total of 747 firing pin impression images captured from five different pistols of same make and model are used to evaluate the proposed AFIS. It was demonstrated that the proposed AFIS is capable of producing firearm identification accuracy rate of over 95.0% with an execution time of less than 0.35 seconds per image.

Chuan, Zun Liang; Liong, Choong-Yeun; Jemain, Abdul Aziz; Ghani, Nor Azura Md.

2014-06-01

219

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

2013-11-01

220

Evaluation of API microtube GT system for detection of germ tube production by clinically significant yeasts.  

PubMed Central

A total of 152 fresh consecutive yeast isolates were tested for their ability to produce germ tubes by the API GT system (Analytab products, Plainview, N.Y.) and by a conventional method. The API system was found to be less sensitive than the conventional method. The costs per test by the API system and the conventional method were $0.76 and $0.39, respectively.

Philip, A; Tsui, A; O'Brien, J E

1983-01-01

221

Experimental Verification of a Number of Structural System Identification Algorithms.  

National Technical Information Service (NTIS)

The investigation examines the application of four system identification techniques to problems of earthquake engineering. A number of techniques for structural system identification has been developed which successfully identify properties of linearized ...

H. Gavin M. Shinozuka R. G. Ghanem

1991-01-01

222

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

223

Structural system identification: Structural dynamics model validation  

SciTech Connect

Structural system identification is concerned with the development of systematic procedures and tools for developing predictive analytical models based on a physical structure`s dynamic response characteristics. It is a multidisciplinary process that involves the ability (1) to define high fidelity physics-based analysis models, (2) to acquire accurate test-derived information for physical specimens using diagnostic experiments, (3) to validate the numerical simulation model by reconciling differences that inevitably exist between the analysis model and the experimental data, and (4) to quantify uncertainties in the final system models and subsequent numerical simulations. The goal of this project was to develop structural system identification techniques and software suitable for both research and production applications in code and model validation.

Red-Horse, J.R.

1997-04-01

224

Efficiency of yeast in enhancement of the oxidative defense system in salt-stressed flax seedlings.  

PubMed

The combined effects of yeast (1 ppm) and salinity on germination, seedling growth, metabolite accumulation and antioxidant defense system of flax (Linum usitatissimum) seeds grown at 100, 200 and 300 mM NaCl were studied. In this investigation, the germination was completely inhibited at 300 mM NaCl. Moreover, salinity induced marked increases in lipid peroxidation product (MDA), soluble carbohydrates as well as the reduced glutathione which were concomitant with sharp decrease in total phenols and ascorbic acid contents in 12-day-old flax seedlings. Furthermore, NaCl treatments increased the activities of some antioxidant enzymes (superoxide dismutase; SOD, peroxidase; POX and polyphenol oxidase; PPO). On the other hand, yeast treatments under salinity stress restored the membrane integrity and improved seedling growth. The results suggested that yeast treatments mitigated salinity stress via accumulation of some osmoprotectants such as free amino acids particularly proline which associated with elevating the defense system in terms of ascorbic acid, glutathione and total phenol contents. Yeast treatments also stimulated the activities of some antioxidant enzymes, preventing membrane peroxidation resulting in high capacity for germination and improved seedling growth under sever salt stress. PMID:23567836

Emam, M M

2013-03-01

225

A program for identification of linear systems  

NASA Technical Reports Server (NTRS)

A program has been written for the identification of parameters in certain linear systems. These systems appear in biomedical problems, particularly in compartmental models of pharmacokinetics. The method presented here assumes that some of the state variables are regularly modified by jump conditions. This simulates administration of drugs following some prescribed drug regime. Parameters are identified by a least-square fit of the linear differential system to a set of experimental observations. The method is especially suited when the interval of observation of the system is very long.

Buell, J.; Kalaba, R.; Ruspini, E.; Yakush, A.

1971-01-01

226

Microbial identification system for Space Station Freedom  

NASA Technical Reports Server (NTRS)

The Environmental Health System (EHS) and Health Maintenance Facility (HMF) on Space Station Freedom will require a comprehensive microbiology capability. This requirement entails the development of an automated system to perform microbial identifications on isolates from a variety of environmental and clinical sources and, when required, to perform antimicrobial sensitivity testing. The unit currently undergoing development and testing is the Automated Microbiology System II (AMS II) built by Vitek Systems, Inc. The AMS II has successfully completed 12 months of laboratory testing and evaluation for compatibility with microgravity operation. The AMS II is a promising technology for use on Space Station Freedom.

Brown, Harlan D.; Scarlett, Janie B.; Skweres, Joyce A.; Fortune, Russell L.; Staples, John L.; Pierson, Duane L.

1989-01-01

227

Identification of phosphorylation sites on the yeast ribonucleotide reductase inhibitor Sml1.  

PubMed

Sml1 is a small protein in Saccharomyces cerevisiae which inhibits the activity of ribonucleotide reductase (RNR). RNR catalyzes the rate-limiting step of de novo dNTP synthesis. Sml1 is a downstream effector of the Mec1/Rad53 cell cycle checkpoint pathway. The phosphorylation by Dun1 kinase during S phase or in response to DNA damage leads to diminished levels of Sml1. Removal of Sml1 increases the population of active RNR, which raises cellular dNTP levels. In this study using mass spectrometry and site-directed mutagenesis, we have identified the region of Sml1 phosphorylation to be between residues 52 and 64 containing the sequence GSSASASASSLEM. This is the first identification of a phosphorylation sequence of a Dun1 biological substrate. This sequence is quite different from the consensus Dun1 phosphorylation sequence reported previously from peptide library studies. The specific phosphoserines were identified to be Ser(56), Ser(58), and Ser(60) by chemical modification of these residues to S-ethylcysteines followed by collision activated dissociation. To investigate further Sml1 phosphorylation, we constructed the single mutants S56A, S58A, S60A, and the triple mutant S56A/S58A/S60A and compared their degrees of phosphorylation with that of wild type Sml1. We observed a 90% decrease in the relative phosphorylation of S60A compared with that of wild type, a 25% decrease in S58A, and little or no decrease in the S56A mutant. There was no observed phosphate incorporation in the triple mutant, suggesting that Ser(56), Ser(58), and Ser(60) in Sml1 are the sites of phosphorylation. Further mutagenesis studies reveal that Dun1 kinase requires an acidic residue at the +3 position, and there is cooperativity between the phosphorylation sites. These results show that Dun1 has a unique phosphorylation motif. PMID:14684746

Uchiki, Tomoaki; Dice, Lezlee T; Hettich, Robert L; Dealwis, Chris

2004-03-19

228

Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species.  

PubMed

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. PMID:20668126

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

2010-10-01

229

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

230

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

231

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

232

Identification of dynamic systems, theory and formulation  

NASA Technical Reports Server (NTRS)

The problem of estimating parameters of dynamic systems is addressed in order to present the theoretical basis of system identification and parameter estimation in a manner that is complete and rigorous, yet understandable with minimal prerequisites. Maximum likelihood and related estimators are highlighted. The approach used requires familiarity with calculus, linear algebra, and probability, but does not require knowledge of stochastic processes or functional analysis. The treatment emphasizes unification of the various areas in estimation in dynamic systems is treated as a direct outgrowth of the static system theory. Topics covered include basic concepts and definitions; numerical optimization methods; probability; statistical estimators; estimation in static systems; stochastic processes; state estimation in dynamic systems; output error, filter error, and equation error methods of parameter estimation in dynamic systems, and the accuracy of the estimates.

Maine, R. E.; Iliff, K. W.

1985-01-01

233

System identification of structural acoustic system using the scale correction  

NASA Astrophysics Data System (ADS)

System identification can be a nice tool to make an accurate model of structural acoustic system that can describe the structure-borne noise in a car or an airplane. However, the implementation of the system identification technique to the structural acoustic system is difficult since the system is made of different physical systems. The responses from one system of the hybrid system show different characteristics from those of the others. If we try to identify the system from the responses of different physical systems, we meet a very embarrassing situation. The scales of those signals are so different that the system identification will concentrate on the modelling of the signals with large magnitude. Scale correction process is introduced to adjust the relative magnitude of those signals. When the scale correction is applied, the responses regenerated from the identified system model are similar with the original ones, which means the identified system is correct. This method will be useful for the other hybrid systems such as the structure-control system, structure-soil system and structure-fluid system.

Hwang, Woo Seok; Lee, Doo Ho

2006-02-01

234

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2013 CFR

...HOMELAND SECURITY CIVIL AVIATION SECURITY AIRPORT SECURITY Operations § 1542.211...Temporary identification media. Each airport operator may issue personnel identification...criteria of § 1542.207(d). (c) Airport-approved identification media....

2013-10-01

235

Power system identification toolbox: Phase two progress  

SciTech Connect

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 techniques by evaluating existing software and developing guidelines for best use. Phase Two includes extending current software, developing new analysis algorithms and software, and demonstrating and developing applications. The final phase will focus on reorganizing the software into a modular collection of documented computer programs and developing user manuals with instruction and application guidelines. Phase Two is approximately 50% complete; progress to date and a vision for the final product of the PSI Toolbox are described. The needs of the power industry for specialized system identification methods are particularly acute. The industry is currently pushing to operate transmission systems much closer to theoretical limits by using real-time, large-scale control systems to dictate power flows and maintain dynamic stability. Reliably maintaining stability requires extensive system-dynamic modeling and analysis capability, including measurement-based methods. To serve this need, the BPA has developed specialized system-identification computer codes through in-house efforts and university contract research over the last several years. To make full integrated use of the codes, as well as other techniques, the BPA has commissioned Pacific Northwest Laboratory (PNL) to further develop the codes and techniques into the PSI Toolbox.

Trudnowski, D.J.

1994-08-01

236

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.

237

Structural system identification based on multibranch BPNN  

NASA Astrophysics Data System (ADS)

System identification is especially important for structural health monitoring and vibration control. It is one of the critical factors to control structural vibration with high quality and evaluate whether control method can be applied or not. In this paper, a kind of multi-branch BPNN model is proposed to identify structural dynamic system. In this model, the primary factors that affect structure's dynamic response, namely structure state variables and seismic inputs, are separately treated as the branches of the model, which is expected to enhance prediction precision. The aim of identification is to make the trained model be able to accurately predict structure's future dynamic response. When the model is established, it can be trained with collected dynamic response and seismic wave data. The vibration law of the structure is deposited in the weights of the trained multi-branch BPNN model. Then the model can be used to predict structure's future dynamic response. In this paper, a numerical example is given. The analytic result turns out that the proposed identification model can accurately predict structure's future dynamic response after being trained.

Li, Hongnan; Yang, Hao; Li, Dongsheng

2004-07-01

238

A surface display yeast two-hybrid screening system for high-throughput protein interactome mapping  

Microsoft Academic Search

Despite the wide acceptance of yeast two-hybrid (Y2H) system for protein–protein interaction analysis and discovery, conventional Y2H assays are not well suited for high-throughput screening of the protein interaction network (“interactome”) on a genomic scale due to several limitations, including labor-intensive agar plating and colony selection methods associated with the use of nutrient selection markers, complicated reporter analysis methods associated

Jun Chen; Jianhong Zhou; Claire K. Sanders; John P. Nolan; Hong Cai

2009-01-01

239

Kinetics of enzymatic lysis and disruption of yeast cells: 1. Evaluation of two lytic systems with different properties  

SciTech Connect

Many microorganisms produce enzymes which lyse the walls of yeasts, fungi, and bacteria. The proportions of different enzyme activities present in the lytic system, their action patterns, synergism, and dependence on inhibitors, constitute the activity profile of the lytic system. Taken together, the activity profile and process conditions for lysis determine the reaction rate and the distribution of products from lysis of any given type of cells. Kinetics of glucan hydrolysis, proteolysis, and lysis of brewer's yeast were compared for two extracellular yeast-lytic enzyme systems with different properties. The enzyme sources used were filtered culture broths from Cytophaga sp. NC1B 9497 grown in batch culture and from Oerskovia xanthineolytica LL-G109, grown under carbon limitation in continuous culture. Rate and extent of cell hydrolysis, and the accumulation of soluble proteins, peptides, and carbohydrates from the lysed yeast cells, are discussed in terms of the activity profiles and potential applications of the two enzyme systems. (Refs. 26).

Hunter, J.B.; Asenjo, J.A.

1987-09-01

240

Automated roof identification systems and methods  

US Patent & Trademark Office Database

Automatic roof identification systems and methods are described. Example embodiments include a roof estimation system configured to automatically detect a roof in a target image of a building having a roof. In one embodiment, automatically detecting a roof in a target image includes training one or more artificial intelligence systems to identify likely roof sections of an image. The artificial intelligence systems are trained on historical image data or an operator-specified region of interest within the target image. Then, a likely outline of the roof in the target image can be determined based on the trained artificial intelligence systems. The likely roof outline can be used to generate a roof estimate report. This abstract is provided to comply with rules requiring an abstract, and it is submitted with the intention that it will not be used to interpret or limit the scope or meaning of the claims.

2014-05-20

241

Identification of genes preferentially expressed in the pathogenic yeast phase of Paracoccidioides brasiliensis , using suppression subtraction hybridization and differential macroarray analysis  

Microsoft Academic Search

Paracoccidioides brasiliensis, a thermodimorphic fungus, is the causative agent of paracoccidioidomycosis (PCM), the most prevalent systemic mycosis in Latin America. Pathogenicity appears to be intimately related to the dimorphic transition from the hyphal to the yeast form, which is induced by a shift from environmental temperature to the temperature of the mammalian host. Little information is available on the P.

E. R. Marques; M. E. S. Ferreira; R. D. Drummond; J. M. Felix; M. Menossi; M. Savoldi; L. R. Travassos; R. Puccia; W. L. Batista; K. C. Carvalho; M. H. S. Goldman; G. H. Goldman

2004-01-01

242

Identification of the region in yeast S-II that defines species specificity in its interaction with RNA polymerase II.  

PubMed

Yeast S-II was found to stimulate yeast RNA polymerase II only and not mouse RNA polymerase II. To identify the molecular region of S-II that defines species specificity, we constructed six hybrid S-II molecules consisting of three regions from yeast and/or Ehrlich cell S-II and examined their activity in terms of RNA polymerase II specificity and suppression of 6-azauracil sensitivity in the yeast S-II null mutant. We found that the region 132-270 (amino acid positions) of yeast S-II is indispensable for specific interaction with yeast RNA polymerase II in vitro and for suppression of 6-azauracil sensitivity in vivo. The corresponding region of Ehrlich cell S-II, the region 132-262, was also shown to be essential for its interaction with mouse RNA polymerase II. This region is known to be less conserved than the N- and C-terminal regions in the S-II family suggesting that it is important in the interaction with transcription machinery proteins in a tissue and/or species-specific manner. PMID:9334234

Shimoaraiso, M; Nakanishi, T; Kubo, T; Natori, S

1997-10-17

243

Automated Firearms Identification System (AFIDS), phase 1  

NASA Technical Reports Server (NTRS)

Items critical to the future development of an automated firearms identification system (AFIDS) have been examined, with the following specific results: (1) Types of objective data, that can be utilized to help establish a more factual basis for determining identity and nonidentity between pairs of fired bullets, have been identified. (2) A simulation study has indicated that randomly produced lines, similar in nature to the individual striations on a fired bullet, can be modeled and that random sequences, when compared to each other, have predictable relationships. (3) A schematic diagram of the general concept for AFIDS has been developed and individual elements of this system have been briefly tested for feasibility. Future implementation of such a proposed system will depend on such factors as speed, utility, projected total cost and user requirements for growth. The success of the proposed system, when operational, would depend heavily on existing firearms examiners.

Blackwell, R. J.; Framan, E. P.

1974-01-01

244

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

245

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology  

PubMed Central

Genomic data now allow the large-scale manual or semi-automated reconstruction of metabolic networks. A network reconstruction represents a highly curated organism-specific knowledge base. A few genome-scale network reconstructions have appeared for metabolism in the baker’s yeast Saccharomyces cerevisiae. These alternative network reconstructions differ in scope and content, and further have used different terminologies to describe the same chemical entities, thus making comparisons between them difficult. The formulation of a ‘community consensus’ network that collects and formalizes the ‘community knowledge’ of yeast metabolism is thus highly desirable. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. Special emphasis is laid on referencing molecules to persistent databases or using database-independent forms such as SMILES or InChI strings, since this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language, and we describe the manner in which it can be maintained as a community resource. It should serve as a common denominator for system biology studies of yeast. Similar strategies will be of benefit to communities studying genome-scale metabolic networks of other organisms.

Herrgard, Markus J.; Swainston, Neil; Dobson, Paul; Dunn, Warwick B.; Arga, K. Yalcin; Arvas, Mikko; Bluthgen, Nils; Borger, Simon; Costenoble, Roeland; Heinemann, Matthias; Hucka, Michael; Le Novere, Nicolas; Li, Peter; Liebermeister, Wolfram; Mo, Monica L.; Oliveira, Ana Paula; Petranovic, Dina; Pettifer, Stephen; Simeonidis, Evangelos; Smallbone, Kieran; Spasic, Irena; Weichart, Dieter; Brent, Roger; Broomhead, David S.; Westerhoff, Hans V.; K?rdar, Betul; Penttila, Merja; Klipp, Edda; Palsson, Bernhard ?.; Sauer, Uwe; Oliver, Stephen G.; Mendes, Pedro; Nielsen, Jens; Kell, Douglas B.

2014-01-01

246

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

247

Rapid identification of Prototheca species by the API 20C system.  

PubMed Central

The conventional auxanographic method of testing for the assimilation of carbohydrates and alcohols by the various species of Prototheca requires at least 2 weeks of incubation at 25 to 30 degrees C before definitive results are obtained. Even though Prototheca spp., in culture as well as in fixed tissues, can be identified more rapidly by fluorescent-antibody techniques in which species-specific reagents are used, such diagnostic facilities and reagents are not available in most diagnostic laboratories. The API 20C clinical yeast identification system, a commercially available ready-to-use micromethod, was found to permit the definitive identification of P. stagnora, P. wickerhamii, and P. zopfii within 4 days. Images

Padhye, A A; Baker, J G; D'Amato, R F

1979-01-01

248

Autonomous Frequency-Domain System-Identification Program  

NASA Technical Reports Server (NTRS)

Autonomous Frequency Domain Identification (AU-FREDI) computer program implements system of methods, algorithms, and software developed for identification of parameters of mathematical models of dynamics of flexible structures and characterization, by use of system transfer functions, of such models, dynamics, and structures regarded as systems. Software considered collection of routines modified and reassembled to suit system-identification and control experiments on large flexible structures.

Yam, Yeung; Mettler, Edward; Bayard, David S.; Hadaegh, Fred Y.; Milman, Mark H.; Scheid, Robert E.

1993-01-01

249

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

250

Parameter identification for nonlinear aerodynamic systems  

NASA Technical Reports Server (NTRS)

This final technical report covers a three and one-half year period preceding February 28, 1993 during which support was provided under NASA Grant NAG-1-1065. Following a general description of the system identification problem and a brief survey of methods to attack it, the basic ideas behind the approach taken in this research effort are presented. The results obtained are described with reference to the published work, including the five semiannual progress reports previously submitted and two interim technical reports.

Pearson, Allan E.

1993-01-01

251

Networked Dynamic Systems: Identification, Controllability, and Randomness  

NASA Astrophysics Data System (ADS)

The presented dissertation aims to develop a graph-centric framework for the analysis and synthesis of networked dynamic systems (NDS) consisting of multiple dynamic units that interact via an interconnection topology. We examined three categories of network problems, namely, identification, controllability, and randomness. In network identification, as a subclass of inverse problems, we made an explicit relation between the input-output behavior of an NDS and the underlying interacting network. In network controllability, we provided structural and algebraic insights into features of the network that enable external signal(s) to control the state of the nodes in the network for certain classes of interconnections, namely, path, circulant, and Cartesian networks. We also examined the relation between network controllability and the symmetry structure of the graph. Motivated by the analysis results for the controllability and observability of deterministic networks, a natural question is whether randomness in the network layer or in the layer of inputs and outputs generically leads to favorable system theoretic properties. In this direction, we examined system theoretic properties of random networks including controllability, observability, and performance of optimal feedback controllers and estimators. We explored some of the ramifications of such an analysis framework in opinion dynamics over social networks and sensor networks in estimating the real-time position of a Seaglider from experimental data.

Nabi-Abdolyousefi, Marzieh

252

MIMO system identification using frequency response data  

NASA Technical Reports Server (NTRS)

A solution to the problem of obtaining a multi-input, multi-output statespace model of a system from its individual input/output frequency responses is presented. The Residue Identification Algorithm (RID) identifies the system poles from a transfer function model of the determinant of the frequency response data matrix. Next, the residue matrices of the modes are computed guaranteeing that each input/output frequency response is fitted in the least squares sense. Finally, a realization of the system is computed. Results of the application of RID to experimental frequency responses of a large space structure ground test facility are presented and compared to those obtained via the Eigensystem Realization Algorithm.

Medina, Enrique A.; Irwin, R. D.; Mitchell, Jerrel R.; Bukley, Angelia P.

1992-01-01

253

A Cloning Method for Caspase Substrates that Uses the Yeast Two-Hybrid System: Cloning of the Antiapoptotic Gene Gelsolin  

Microsoft Academic Search

Caspase-mediated proteolysis is a critical and central element of the apoptotic process; therefore, it is important to identify the downstream molecular targets of caspases. We established a method for cloning the genes of caspase substrates by two major modifications of the yeast two-hybrid system: (i) both large and small subunits of active caspases were expressed in yeast under ADH1 promoters

Shinji Kamada; Hajime Kusano; Hisakazu Fujita; Makoto Ohtsu; Richard Chikara Koya; Noboru Kuzumaki; Yoshihide Tsujimoto

1998-01-01

254

System Identification of a Vortex Lattice Aerodynamic Model  

NASA Technical Reports Server (NTRS)

The state-space presentation of an aerodynamic vortex model is considered from a classical and system identification perspective. Using an aerodynamic vortex model as a numerical simulator of a wing tunnel experiment, both full state and limited state data or measurements are considered. Two possible approaches for system identification are presented and modal controllability and observability are also considered. The theory then is applied to the system identification of a flow over an aerodynamic delta wing and typical results are presented.

Juang, Jer-Nan; Kholodar, Denis; Dowell, Earl H.

2001-01-01

255

System Identification of X-33 Neural Network  

NASA Technical Reports Server (NTRS)

Modern flight control research has improved spacecraft survivability as its goal. To this end we need to have a failure detection system on board. In case the spacecraft is performing imperfectly, reconfiguration of control is needed. For that purpose we need to have parameter identification of spacecraft dynamics. Parameter identification of a system is called system identification. We treat the system as a black box which receives some inputs that lead to some outputs. The question is: what kind of parameters for a particular black box can correlate the observed inputs and outputs? Can these parameters help us to predict the outputs for a new given set of inputs? This is the basic problem of system identification. The X33 was supposed to have the onboard capability of evaluating the current performance and if needed to take the corrective measures to adapt to desired performance. The X33 is comprised of both rocket and aircraft vehicle design characteristics and requires, in general, analytical methods for evaluating its flight performance. Its flight consists of four phases: ascent, transition, entry and TAEM (Terminal Area Energy Management). It spends about 200 seconds in ascent phase, reaching an altitude of about 180,000 feet and a speed of about 10 to 15 Mach. During the transition phase which lasts only about 30 seconds, its altitude may increase to about 190,000 feet but its speed is reduced to about 9 Mach. At the beginning of this phase, the Main Engine is Cut Off (MECO) and the control is reconfigured with the help of aerosurfaces (four elevons, two flaps and two rudders) and reaction control system (RCS). The entry phase brings down the altitude of X33 to about 90,000 feet and its speed to about Mach 3. It spends about 250 seconds in this phase. Main engine is still cut off and the vehicle is controlled by complex maneuvers of aerosurfaces. The last phase TAEM lasts for about 450 seconds and the altitude and speed, both are reduced to zero. The present attempt, as a start, focuses only on the entry phase. Since the main engine remains cut off in this phase, there is no thrust acting on the system. This considerably simplifies the equations of motion. We introduce another simplification by assuming the system to be linear after some non-linearities are removed analytically from our consideration. Under these assumptions, the problem could be solved by Classical Statistics by employing the least sum of squares approach. Instead we chose to use the Neural Network method. This method has many advantages. It is modern, more efficient, can be adapted to work even when the assumptions are diluted. In fact, Neural Networks try to model the human brain and are capable of pattern recognition.

Aggarwal, Shiv

2003-01-01

256

Fractional System Identification: An Approach Using Continuous Order-Distributions  

NASA Technical Reports Server (NTRS)

This paper discusses the identification of fractional- and integer-order systems using the concept of continuous order-distribution. Based on the ability to define systems using continuous order-distributions, it is shown that frequency domain system identification can be performed using least squares techniques after discretizing the order-distribution.

Hartley, Tom T.; Lorenzo, Carl F.

1999-01-01

257

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

258

Heat Capacity Identification Method Using MT System  

Microsoft Academic Search

This paper proposes a heat capacity identification method for cooking household appliances. Cooking household appliances select a cooking flow according to a cooking object capacity, hence the heat capacity identification is a very important function. However, a conventional heat capacity identification method has been based on one variable using ``if-then rules'', hence it gives a low accuracy. This paper proposes

Arata Suzuki; Kenji Sugimoto

2007-01-01

259

Heat capacity identification via Mahalanobis Taguchi System  

Microsoft Academic Search

This paper proposes a heat capacity identification method for cooking household appliances. In such appliances, a cooking flow is selected according to its cooking object capacity, hence identification of the heat capacity is a very important function. However, a conventional heat capacity identification method has been based on one variable using ldquoif-then rulesrdquo, thereby giving inaccurate results. This paper proposes

Arata Suzuki; Kenji Sugimoto

2008-01-01

260

Probing Signal Design for Power System Identification  

SciTech Connect

This paper investigates the design of effective input signals for low-level probing of power systems. In 2005, 2006, and 2008 the Western Electricity Coordinating Council (WECC) conducted four large-scale system wide tests of the western interconnected power system where probing signals were injected by modulating the control signal at the Celilo end of the Pacific DC intertie. A major objective of these tests is the accurate estimation of the inter-area electromechanical modes. A key aspect of any such test is the design of an effective probing signal that leads to measured outputs rich in information about the modes. This paper specifically studies low-level probing signal design for power-system identification. The paper describes the design methodology and the advantages of this new probing signal which was successfully applied during these tests. This probing input is a multi-sine signal with its frequency content focused in the range of the inter-area modes. The period of the signal is over two minutes providing high-frequency resolution. Up to 15 cycles of the signal are injected resulting in a processing gain of 15. The resulting system response is studied in the time and frequency domains. Because of the new probing signal characteristics, these results show significant improvement in the output SNR compared to previous tests.

Pierre, John W.; Zhou, Ning; Tuffner, Francis K.; Hauer, John F.; Trudnowski, Daniel J.; Mittelstadt, William

2010-05-31

261

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

262

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

263

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

264

Yeast expression of the Tuber borchii fruiting body specific protein, TBF-1: identification of a noncanonical signal peptide.  

PubMed

The TBF-1 is an 11.9-kDa fruiting body specific protein of the Ascomycetes hypogeous fungus Tuber borchii Vittad. found in aqueous extract and the hyphal cell wall. The tbf-1 gene codes a 12-amino acid N-terminal stretch not present in mature protein. This sequence does not match with any homologous signal sequences stored in data banks. To investigate the role of the N-terminus in TBF-1 localization, cDNA was expressed in Saccharomyces cerevisiae under the control of the 3-phosphoglycerate kinase promoter. Like Tuber, yeast also produces and secretes TBF-1 and the foreign protein binds with the cell wall. A signalless mutant protein was constructed; this DeltaTBF-1 was expressed but not exported by yeast. The secretion of TBF-1 was also suppressed using the sec18(ts) yeast mutant strain grown at nonpermissive temperature as host. Thus we demonstrated that the N-terminal 12-amino acid stretch is a noncanonical signal peptide that leads the TBF-1 toward the classical secretory pathway in yeast. PMID:17581140

Palma, Francesco; Cerigini, Emanuela; Stocchi, Vilberto

2007-07-01

265

Reverse yeast two-hybrid system to identify mammalian nuclear receptor residues that interact with ligands and/or antagonists.  

PubMed

As a critical regulator of drug metabolism and inflammation, Pregnane X Receptor (PXR), plays an important role in disease pathophysiology linking metabolism and inflammation (e.g. hepatic steatosis)(1,2). There has been much progress in the identification of agonist ligands for PXR, however, there are limited descriptions of drug-like antagonists and their binding sites on PXR(3,4,5). A critical barrier has been the inability to efficiently purify full-length protein for structural studies with antagonists despite the fact that PXR was cloned and characterized in 1998. Our laboratory developed a novel high throughput yeast based two-hybrid assay to define an antagonist, ketoconazole's, binding residues on PXR(6). Our method involves creating mutational libraries that would rescue the effect of single mutations on the AF-2 surface of PXR expected to interact with ketoconazole. Rescue or "gain-of-function" second mutations can be made such that conclusions regarding the genetic interaction of ketoconazole and the surface residue(s) on PXR are feasible. Thus, we developed a high throughput two-hybrid yeast screen of PXR mutants interacting with its coactivator, SRC-1. Using this approach, in which the yeast was modified to accommodate the study of the antifungal drug, ketoconazole, we could demonstrate specific mutations on PXR enriched in clones unable to bind to ketoconazole. By reverse logic, we conclude that the original residues are direct interaction residues with ketoconazole. This assay represents a novel, tractable genetic assay to screen for antagonist binding sites on nuclear receptor surfaces. This assay could be applied to any drug regardless of its cytotoxic potential to yeast as well as to cellular protein(s) that cannot be studied using standard structural biology or proteomic based methods. Potential pitfalls include interpretation of data (complementary methods useful), reliance on single Y2H method, expertise in handling yeast or performing yeast two-hybrid assays, and assay optimization. PMID:24300333

Li, Hao; Dou, Wei; Padikkala, Emil; Mani, Sridhar

2013-01-01

266

Benefit-Cost Analysis of the National Animal Identification System.  

National Technical Information Service (NTIS)

The purpose of this study was to conduct a benefit-cost analysis of the United States National Animal Identification System (NAIS). The NAIS is a voluntary federal animal identification system operated by the Animal and Plant Health Inspection Service (AP...

2009-01-01

267

Frequency response based identification of fractional order dynamical systems  

Microsoft Academic Search

In the paper a comparison of different optimization methods to identification of fractional order dynamical systems is presented. The fractional models of the examples of physical systems - ultracapacitors - are established. Then different real frequency responses data from a laboratory setup of the processes are collected and the comparison of identification methods based on Least Squares and Total Least

Andrzej Dzielinski; Grzegorz Sarwas; Dominik Sierociuk; Tomas Skovranek; Ivo Petras

2011-01-01

268

The Anti-spoofing Study of Vein Identification System  

Microsoft Academic Search

The vein identification systems identify a certain person by acquiring the local infrared image of hand (dorsa, palm and finger) and extracting vein pattern. The vein identification systems are widely used in security and surveillance field, but most of them ignore the liveness detection requirement or only check the temperature to prevent spoofing. After studying the spoofing method for vein

Bin Qin; Jian-fei Pan; Guang-zhong Cao; Ge-guo Du

2009-01-01

269

Algorithms for System Identification and Source Location.  

NASA Astrophysics Data System (ADS)

This thesis deals with several topics in least squares estimation and applications to source location. It begins with a derivation of a mapping between Wiener theory and Kalman filtering for nonstationary autoregressive moving average (ARMO) processes. Applying time domain analysis, connections are found between time-varying state space realizations and input-output impulse response by matrix fraction description (MFD). Using these connections, the whitening filters are derived by the two approaches, and the Kalman gain is expressed in terms of Wiener theory. Next, fast estimation algorithms are derived in a unified way as special cases of the Conjugate Direction Method. The fast algorithms included are the block Levinson, fast recursive least squares, ladder (or lattice) and fast Cholesky algorithms. The results give a novel derivation and interpretation for all these methods, which are efficient alternatives to available recursive system identification algorithms. Multivariable identification algorithms are usually designed only for left MFD models. In this work, recursive multivariable identification algorithms are derived for right MFD models with diagonal denominator matrices. The algorithms are of prediction error and model reference type. Convergence analysis results obtained by the Ordinary Differential Equation (ODE) method are presented along with simulations. Sources of energy can be located by estimating time differences of arrival (TDOA's) of waves between the receivers. A new method for TDOA estimation is proposed for multiple unknown ARMA sources and additive correlated receiver noise. The method is based on a formula that uses only the receiver cross-spectra and the source poles. Two algorithms are suggested that allow tradeoffs between computational complexity and accuracy. A new time delay model is derived and used to show the applicability of the methods for non -integer TDOA's. Results from simulations illustrate the performance of the algorithms. The last chapter analyzes the response of exact least squares predictors for enhancement of sinusoids with additive colored noise. Using the matrix inversion lemma and the Christoffel-Darboux formula, the frequency response and amplitude gain of the sinusoids are expressed as functions of the signal and noise characteristics. The results generalize the available white noise case.

Nehorai, Arye

270

Lightweight autonomous chemical identification system (LACIS)  

NASA Astrophysics Data System (ADS)

Smiths Detection and Intelligent Optical Systems have developed prototypes for the Lightweight Autonomous Chemical Identification System (LACIS) for the US Department of Homeland Security. LACIS is to be a handheld detection system for Chemical Warfare Agents (CWAs) and Toxic Industrial Chemicals (TICs). LACIS is designed to have a low limit of detection and rapid response time for use by emergency responders and could allow determination of areas having dangerous concentration levels and if protective garments will be required. Procedures for protection of responders from hazardous materials incidents require the use of protective equipment until such time as the hazard can be assessed. Such accurate analysis can accelerate operations and increase effectiveness. LACIS is to be an improved point detector employing novel CBRNE detection modalities that includes a militaryproven ruggedized ion mobility spectrometer (IMS) with an array of electro-resistive sensors to extend the range of chemical threats detected in a single device. It uses a novel sensor data fusion and threat classification architecture to interpret the independent sensor responses and provide robust detection at low levels in complex backgrounds with minimal false alarms. The performance of LACIS prototypes have been characterized in independent third party laboratory tests at the Battelle Memorial Institute (BMI, Columbus, OH) and indoor and outdoor field tests at the Nevada National Security Site (NNSS). LACIS prototypes will be entering operational assessment by key government emergency response groups to determine its capabilities versus requirements.

Lozos, George; Lin, Hai; Burch, Timothy

2012-05-01

271

Application of a wide-range yeast vector (CoMed(TM)) system to recombinant protein production in dimorphic Arxula adeninivorans, methylotrophic Hansenula polymorpha and other yeasts  

PubMed Central

Background Yeasts provide attractive expression platforms in combining ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. However, early restriction to a single yeast platform can result in costly and time-consuming failures. It is therefore advisable to assess several selected systems in parallel for the capability to produce a particular protein in desired amounts and quality. A suitable vector must contain a targeting sequence, a promoter element and a selection marker that function in all selected organisms. These criteria are fulfilled by a wide-range integrative yeast expression vector (CoMed™) system based on A. adeninivorans- and H. polymorpha-derived elements that can be introduced in a modular way. Results The vector system and a selection of modular elements for vector design are presented. Individual single vector constructs were used to transform a range of yeast species. Various successful examples are described. A vector with a combination of an rDNA sequence for genomic targeting, the E. coli-derived hph gene for selection and the A. adeninivorans-derived TEF1 promoter for expression control of a GFP (green fluorescent protein) gene was employed in a first example to transform eight different species including Hansenula polymorpha, Arxula adeninivorans and others. In a second example, a vector for the secretion of IL-6 was constructed, now using an A. adeninivorans-derived LEU2 gene for selection of recombinants in a range of auxotrophic hosts. In this example, differences in precursor processing were observed: only in A. adeninivorans processing of a MF?1/IL-6 fusion was performed in a faithful way. Conclusion rDNA targeting provides a tool to co-integrate up to 3 different expression plasmids by a single transformation step. Thus, a versatile system is at hand that allows a comparative assessment of newly introduced metabolic pathways in several organisms or a comparative co-expression of bottleneck genes in cases where production or secretion of a certain product is impaired.

Steinborn, Gerhard; Boer, Erik; Scholz, Anja; Tag, Kristina; Kunze, Gotthard; Gellissen, Gerd

2006-01-01

272

A system identification model for adaptive nonlinear control  

NASA Technical Reports Server (NTRS)

A system identification model that combines generalized-spline function approximation with a nonlinear control system is described. The complete control system contains three main elements: a nonlinear-inverse-dynamic control law that depends on a comprehensive model of the plant, a state estimator whose outputs drive the control law, and a function approximation scheme that models the system dynamics. The system-identification task, which combines an extended Kalman filter with a function approximator modeled as an artificial neural network, is considered. The results of an application of the identification techniques to a nonlinear transport aircraft model are presented.

Linse, Dennis J.; Stengel, Robert F.

1991-01-01

273

Identification of PLP2 and RAB5C as novel TPD52 binding partners through yeast two-hybrid screening  

PubMed Central

Tumor protein D52 (TPD52) is overexpressed in different cancers, but its molecular functions are poorly defined. A large, low-stringency yeast two-hybrid screen using full-length TPD52 bait identified known partners (TPD52, TPD52L1, TPD52L2, MAL2) and four other preys that reproducibly bound TPD52 and TPD52L1 baits (PLP2, RAB5C, GOLGA5, YIF1A). PLP2 and RAB5 interactions with TPD52 were confirmed in pull down assays, with interaction domain mapping experiments indicating that both proteins interact with a novel binding region of TPD52. This study provides insights into TPD52 functions, and ways to maximise the efficiency of lowstringency yeast two-hybrid screens.

Shahheydari, Hamideh; Frost, Sarah; Smith, Brian J.; Groblewski, Guy E.; Chen, Yuyan; Byrne, Jennifer A.

2014-01-01

274

Identification of PLP2 and RAB5C as novel TPD52 binding partners through yeast two-hybrid screening.  

PubMed

Tumor protein D52 (TPD52) is overexpressed in different cancers, but its molecular functions are poorly defined. A large, low-stringency yeast two-hybrid screen using full-length TPD52 bait identified known partners (TPD52, TPD52L1, TPD52L2, MAL2) and four other preys that reproducibly bound TPD52 and TPD52L1 baits (PLP2, RAB5C, GOLGA5, YIF1A). PLP2 and RAB5 interactions with TPD52 were confirmed in pull down assays, with interaction domain mapping experiments indicating that both proteins interact with a novel binding region of TPD52. This study provides insights into TPD52 functions, and ways to maximise the efficiency of low-stringency yeast two-hybrid screens. PMID:24604726

Shahheydari, Hamideh; Frost, Sarah; Smith, Brian J; Groblewski, Guy E; Chen, Yuyan; Byrne, Jennifer A

2014-07-01

275

The yeast two-hybrid system detects interactions between Bacillus subtilis sigmaB regulators.  

PubMed

SigmaB, the general stress response sigma factor of Bacillus subtilis, is regulated by the products of seven genes (rsbR, S, T, U, V, W, and X) with which it is cotranscribed. Biochemical techniques previously revealed physical associations among RsbW, RsbV, and sigmaB but failed to detect interactions of RsbR, S, T, U, or X with each other or RsbV, RsbW, or sigmaB. Using the yeast two-hybrid system, we have now obtained evidence for such interactions. The yeast reporter system was activated when RsbS was paired with either RsbR or RsbT, RsbR was paired with RsbT, and RsbV was paired with either RsbU or RsbW. In addition, RsbW2 and RsbR2 dimer formation was detected. RsbX failed to show interactions with itself or any of the other sigB operon products. PMID:8955331

Voelker, U; Voelker, A; Haldenwang, W G

1996-12-01

276

78 FR 6732 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...  

Federal Register 2010, 2011, 2012, 2013

...Vessel Identification System, and Boating Accident Report Database AGENCY: Coast Guard, DHS. ACTION: Rule; information collection...Vessel Identification System, and Boating Accident Report Database rule became effective on April 27, 2012. Under the...

2013-01-31

277

Rapid identification of wine yeast species based on RFLP analysis of the ribosomal internal transcribed spacer (ITS) region  

Microsoft Academic Search

In this study, we identified a total of 33 wine yeast species and strains using the restriction patterns generated from the\\u000a region spanning the internal transcribed spacers (ITS 1 and 2) and the 5.8S rRNA gene. Polymerase chain reaction (PCR) products\\u000a of this rDNA region showed a high length variation for the different species. The size of the PCR products

José Manuel Guillamón; Josepa Sabaté; Eladio Barrio; Josep Cano; Amparo Querol

1998-01-01

278

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

279

Identification of Residues in Fission Yeast and Human P34(cdc2) Required for S-M Checkpoint Control  

PubMed Central

In fission yeast, regulation of p34(cdc2) plays an important role in the checkpoint coupling mitosis to completion of DNA replication. The cdc2 mutations cdc2-3w (C67Y) and cdc2-4w (C67F) abolish checkpoint control without seriously affecting normal cell proliferation. However the molecular basis of this phenotype is not known. To better understand the role of p34(cdc2) in checkpoint control, we have screened for more mutations in Schizosaccharomyces pombe cdc2 with this phenotype. We have isolated cdc2-3w and cdc2-4w, as well as three new cdc2 alleles: cdc2-6w (N66I), cdc2-7w (E8V) and cdc2-8w (K9E). The altered residues map to two different regions on opposite faces of the protein, suggesting that the interaction between p34(cdc2) and components of the checkpoint pathway may be complex. In contrast to cdc2-3w and cdc2-4w, the new mutations alter residues that are conserved between the fission yeast cdc2(+) and other cdks, including the human CDC2 protein. Expression of the equivalent human CDC2 mutants in fission yeast abolishes checkpoint control, suggesting that these residues could be involved in checkpoint-dependent regulation of other eukaryotic cdks.

Basi, G.; Enoch, T.

1996-01-01

280

Saccharomyces cerivisiae as a model system for kidney disease: what can yeast tell us about renal function?  

PubMed Central

Ion channels, solute transporters, aquaporins, and factors required for signal transduction are vital for kidney function. Because mutations in these proteins or in associated regulatory factors can lead to disease, an investigation into their biogenesis, activities, and interplay with other proteins is essential. To this end, the yeast, Saccharomyces cerevisiae, represents a powerful experimental system. Proteins expressed in yeast include the following: 1) ion channels, including the epithelial sodium channel, members of the inward rectifying potassium channel family, and cystic fibrosis transmembrane conductance regulator; 2) plasma membrane transporters, such as the Na+-K+-ATPase, the Na+-phosphate cotransporter, and the Na+-H+ ATPase; 3) aquaporins 1–4; and 4) proteins such as serum/glucocorticoid-induced kinase 1, phosphoinositide-dependent kinase 1, Rh glycoprotein kidney, and trehalase. The variety of proteins expressed and studied emphasizes the versatility of yeast, and, because of the many available tools in this organism, results can be obtained rapidly and economically. In most cases, data gathered using yeast have been substantiated in higher cell types. These attributes validate yeast as a model system to explore renal physiology and suggest that research initiated using this system may lead to novel therapeutics.

Kolb, Alexander R.; Buck, Teresa M.

2011-01-01

281

Using Multi-Instance Hierarchical Clustering Learning System to Predict Yeast Gene Function  

PubMed Central

Time-course gene expression datasets, which record continuous biological processes of genes, have recently been used to predict gene function. However, only few positive genes can be obtained from annotation databases, such as gene ontology (GO). To obtain more useful information and effectively predict gene function, gene annotations are clustered together to form a learnable and effective learning system. In this paper, we propose a novel multi-instance hierarchical clustering (MIHC) method to establish a learning system by clustering GO and compare this method with other learning system establishment methods. Multi-label support vector machine classifier and multi-label K-nearest neighbor classifier are used to verify these methods in four yeast time-course gene expression datasets. The MIHC method shows good performance, which serves as a guide to annotators or refines the annotation in detail.

Liao, Bo; Li, Yun; Jiang, Yan; Cai, Lijun

2014-01-01

282

A yeast cell-based system for screening Candida glabrata multidrug resistance reversal agents and selection of loss-of-function pdr1 mutants.  

PubMed

In the pathogenic yeast Candida glabrata, multidrug resistance is associated with the overexpression of drug efflux pumps caused by gain-of-function mutations in the CgPDR1 gene. CgPdr1p transcription factor, which activates the expression of several drug efflux transporter genes, is considered to be a promising target for compounds sensitizing the multidrug-resistant yeast cells. Here, we describe a cell-based screening system for detecting the inhibitory activity of compounds interfering with the CgPdr1p function in a heterologous genetic background of the hypersensitive Saccharomyces cerevisiae mutant strain. The screening is based on the ability to abrogate the growth defect of cells suffering from the galactose-induced and CgPdr1p-driven overexpression of a dominant lethal pma1(D378N) allele placed under the control of the ScPDR5 promoter. The system allows rapid identification of multidrug resistance reversal agents inhibiting the CgPdr1p activity or loss-of-function Cgpdr1 mutations, and is amenable to high-throughput screening on solid or liquid media. PMID:21129149

Goffa, Eduard; Bialkova, Alexandra; Batova, Monika; Dzugasova, Vladimira; Subik, Julius

2011-03-01

283

33 CFR 401.20 - Automatic Identification System.  

Code of Federal Regulations, 2010 CFR

...Radio Communication Equipment and SystemsâAISâPart 2: Class A Shipborne...Shipborne Automatic Identification System (AIS), NAV 48/18, 6...Guards' maritime Differential Global Positioning System radiobeacon services; or...

2009-07-01

284

Systolic Array Structure for On-Line System Identification.  

National Technical Information Service (NTIS)

In this study, we present an algorithm for system identification for systolic array implementation. With this schema, discrete samples of input and output data of a system with uncertain characteristics are used to determine the parameters of its model. T...

M. Tune

1988-01-01

285

30 CFR 75.1715 - Identification check system.  

Code of Federal Regulations, 2013 CFR

...STANDARDS-UNDERGROUND COAL MINES Miscellaneous § 75.1715 Identification check system. [Statutory Provisions] Each operator of a coal mine shall establish a check-in and check-out system which will...

2013-07-01

286

A Biometric Identification System Based on Eigenpalm and Eigenfinger Features  

Microsoft Academic Search

This paper presents a multimodal biometric identification system based on the features of the human hand. We describe a new biometric approach to personal identification using eigenfinger and eigenpalm features, with fusion applied at the matching-score level.The identification processcanbe divided intothe following phases: capturingthe image;preprocessing; extractingand normalizing the palm and strip-like finger subimages; extracting the eigenpalm and eigenfinger features based

Slobodan Ribaric; Ivan Fratric

2005-01-01

287

Nonlinear filtering and system identification algorithms for autonomous systems  

NASA Astrophysics Data System (ADS)

Autonomy is a key technology for future high-performance and remote operation applications. In essence, autonomy will extend automatic control to broader operating conditions, through more highly uncertain environments, and to a greater tolerance for system faults. An important component for achieving autonomy is accurate and timely information regarding the condition of the system. This information could be used at various levels of autonomy. For example, updated models of the system dynamics could be used to adapt low-level system control. This information could also be used at higher levels to decide whether a system is capable of completing a task. The work presented here involves the investigation of system identification and nonlinear filtering algorithms that are compatible with the general goals of autonomous control. Application to both flexible structures and high performance aircraft is considered. Combining existing identification algorithms in a two-step approach for application to flexible structures is considered. A batch subspace identification algorithm is used in combination with a recursive filtering algorithm to provide a method of generating and updating a linear model for a flexible structure. This method is demonstrated on data collected from a two-link flexible arm. Aircraft state and parameter estimation is also considered. A previously introduced nonlinear filtering algorithm called the Unscented Kalman Filter (UKF) is developed and investigated for two different approaches to the problem. First, the UKF is used to estimate the nonlinear state along with the aerodynamic force and moment environment. Second, the UKF is developed for the more traditional problem of identifying the stability and control derivatives of an aircraft's aerodynamic model.

Brunke, Shelby Scott

2001-07-01

288

Whole Pichia pastoris Yeast Expressing Measles Virus Nucleoprotein as a Production and Delivery System to Multimerize Plasmodium Antigens  

PubMed Central

Yeasts are largely used as bioreactors for vaccine production. Usually, antigens are produced in yeast then purified and mixed with adjuvants before immunization. However, the purification costs and the safety concerns recently raised by the use of new adjuvants argue for alternative strategies. To this end, the use of whole yeast as both production and delivery system appears attractive. Here, we evaluated Pichia pastoris yeast as an alternative vaccine production and delivery system for the circumsporozoite protein (CS) of Plasmodium, the etiologic agent of malaria. The CS protein from Plasmodium berghei (Pb) was selected given the availability of the stringent C57Bl/6 mouse model of infection by Pb sporozoites, allowing the evaluation of vaccine efficacy in vivo. PbCS was multimerized by fusion to the measles virus (MV) nucleoprotein (N) known to auto-assemble in yeast in large-size ribonucleoprotein rods (RNPs). Expressed in P. pastoris, the N-PbCS protein generated highly multimeric and heterogenic RNPs bearing PbCS on their surface. Electron microscopy and immunofluorescence analyses revealed the shape of these RNPs and their localization in peripheral cytoplasmic inclusions. Subcutaneous immunization of C57Bl/6 mice with heat-inactivated whole P. pastoris expressing N-PbCS RNPs provided significant reduction of parasitemia after intradermal challenge with a high dose of parasites. Thus, in the absence of accessory adjuvants, a very low amount of PbCS expressed in whole yeast significantly decreased clinical damages associated with Pb infection in a highly stringent challenge model, providing a proof of concept of the intrinsic adjuvancy of this vaccine strategy. In addition to PbCS multimerization, the N protein contributed by itself to parasitemia delay and long-term mice survival. In the future, mixtures of whole recombinant yeasts expressing relevant Plasmodium antigens would provide a multivalent formulation applicable for antigen combination screening and possibly for large-scale production, distribution and delivery of a malaria vaccine in developing countries.

Jacob, Daria; Ruffie, Claude; Dubois, Myriam; Combredet, Chantal; Amino, Rogerio; Formaglio, Pauline; Gorgette, Olivier; Pehau-Arnaudet, Gerard; Guery, Charline; Puijalon, Odile; Barale, Jean-Christophe; Menard, Robert; Tangy, Frederic; Sala, Monica

2014-01-01

289

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

290

Rapid, Facile Detection of Heterodimer Partners for Target Human G-Protein-Coupled Receptors Using a Modified Split-Ubiquitin Membrane Yeast Two-Hybrid System  

PubMed Central

Potentially immeasurable heterodimer combinations of human G-protein-coupled receptors (GPCRs) result in a great deal of physiological diversity and provide a new opportunity for drug discovery. However, due to the existence of numerous combinations, the sets of GPCR dimers are almost entirely unknown and thus their dominant roles are still poorly understood. Thus, the identification of GPCR dimer pairs has been a major challenge. Here, we established a specialized method to screen potential heterodimer partners of human GPCRs based on the split-ubiquitin membrane yeast two-hybrid system. We demonstrate that the mitogen-activated protein kinase (MAPK) signal-independent method can detect ligand-induced conformational changes and rapidly identify heterodimer partners for target GPCRs. Our data present the abilities to apply for the intermolecular mapping of interactions among GPCRs and to uncover potential GPCR targets for the development of new therapeutic agents.

Nakamura, Yasuyuki; Ishii, Jun; Kondo, Akihiko

2013-01-01

291

Systems biology of monovalent cation homeostasis in yeast: the translucent contribution.  

PubMed

Maintenance of monovalent cation homeostasis (mainly K(+) and Na(+)) is vital for cell survival, and cation toxicity is at the basis of a myriad of relevant phenomena, such as salt stress in crops and diverse human diseases. Full understanding of the importance of monovalent cations in the biology of the cell can only be achieved from a systemic perspective. Translucent is a multinational project developed within the context of the SysMO (System Biology of Microorganisms) initiative and focussed in the study of cation homeostasis using the well-known yeast Saccharomyces cerevisiae as a model. The present review summarize how the combination of biochemical, genetic, genomic and computational approaches has boosted our knowledge in this field, providing the basis for a more comprehensive and coherent vision of the role of monovalent cations in the biology of the cell. PMID:24797924

Ariño, Joaquín; Aydar, Ebru; Drulhe, Samuel; Ganser, Daniel; Jorrín, Jesús; Kahm, Matthias; Krause, Falko; Petrezsélyová, Silvia; Yenush, Lynne; Zimmermannová, Olga; van Heusden, G Paul H; Kschischo, Maik; Ludwig, Jost; Palmer, Chris; Ramos, José; Sychrová, Hana

2014-01-01

292

Development of a System for the Identification of Oil Spills.  

National Technical Information Service (NTIS)

It has been possible to coordinate the work with oil identification systems within Denmark, Finland, Norway and Sweden. The purpose of the project ''Identification of oil spills at sea'' was to fulfil some basic needs: to harmonize the work of the partici...

R. G. Lichtenthaler P. E. Paus I. Andersen H. Guthenberg T. Haegh

1981-01-01

293

Fusing language identification systems using performance confidence indexes  

Microsoft Academic Search

In the field of automatic language identification, several, mostly-empirical, arithmetic fusion operations are currently done to make a consensus decision from a set of acoustics-based identification systems whose estimated performance is taken into account by means of weighting techniques. The paper presents how to apply the discriminant factor analysis method formally to compute and use weighting performance confidence indexes at

Jorge Gutiérrez; Jean-Luc Rouas; Régine André-Obrecht

2004-01-01

294

The Green Card Protocol: An Identification Protocol for Decentralized Systems  

Microsoft Academic Search

The correct identification of the various entities connected to a network is the first and most important step on top of which it is possible to create the chain of trust needed, for example, for authorization and encryption purposes. Unfortunately in fully decentralized systems, typical, for example, of peer-to-peer scenarios, such identification results extremely difficult, mainly for the lack of

Stefano Campadello

2006-01-01

295

Identification and control of dynamical systems using neural networks  

Microsoft Academic Search

It is demonstrated that neural networks can be used effectively for the identification and control of nonlinear dynamical systems. The emphasis is on models for both identification and control. Static and dynamic backpropagation methods for the adjustment of parameters are discussed. In the models that are introduced, multilayer and recurrent networks are interconnected in novel configurations, and hence there is

KUMPATI S. NARENDRA; KANNAN PARTHASARATHY

1990-01-01

296

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

297

System Identification without Lennart Ljung: what would have been different?  

Microsoft Academic Search

This chapter presents a personal view on the development of identification theory in the control community, starting from the year 1965. We show how two landmark papers, (Ho and Kalman, 1965) and (Åström and Bohlin, 1965), gave birth to two main streams of research that have dominated the development of system identification over the last fourty years. The Ho-Kalman paper

Michel Gevers

298

Identification of auxotrophic mutants of the yeast Kluyveromyces marxianus by non-homologous end joining-mediated integrative transformation with genes from Saccharomyces cerevisiae.  

PubMed

The isolation and application of auxotrophic mutants for gene manipulations, such as genetic transformation, mating selection and tetrad analysis, form the basis of yeast genetics. For the development of these genetic methods in the thermotolerant fermentative yeast Kluyveromyces marxianus, we isolated a series of auxotrophic mutants with defects in amino acid or nucleic acid metabolism. To identify the mutated genes, linear DNA fragments of nutrient biosynthetic pathway genes were amplified from Saccharomyces cerevisiae chromosomal DNA and used to directly transform the K. marxianus auxotrophic mutants by random integration into chromosomes through non-homologous end joining (NHEJ). The appearance of transformant colonies indicated that the specific S. cerevisiae gene complemented the K. marxianus mutant. Using this interspecific complementation approach with linear PCR-amplified DNA, we identified auxotrophic mutations of ADE2, ADE5,7, ADE6, HIS2, HIS3, HIS4, HIS5, HIS6, HIS7, LYS1, LYS2, LYS4, LYS9, LEU1, LEU2, MET2, MET6, MET17, TRP3, TRP4 and TRP5 without the labour-intensive requirement of plasmid construction. Mating, sporulation and tetrad analysis techniques for K. marxianus were also established. With the identified auxotrophic mutant strains and S. cerevisiae genes as selective markers, NHEJ-mediated integrative transformation with PCR-amplified DNA is an attractive system for facilitating genetic analyses in the yeast K. marxianus. PMID:24150815

Yarimizu, Tohru; Nonklang, Sanom; Nakamura, Junpei; Tokuda, Shuya; Nakagawa, Takaaki; Lorreungsil, Sasithorn; Sutthikhumpha, Surasit; Pukahuta, Charida; Kitagawa, Takao; Nakamura, Mikiko; Cha-Aim, Kamonchai; Limtong, Savitree; Hoshida, Hisashi; Akada, Rinji

2013-12-01

299

Functional expression of human PP2Ac in yeast permits the identification of novel C-terminal and dominant-negative mutant forms.  

PubMed

The protein phosphatase 2A (PP2A) holoenzyme is structurally conserved among eukaryotes. This reflects a conservation of function in vivo because the human catalytic subunit (PP2Ac) functionally replaced the endogenous PP2Ac of Saccharomyces cerevisiae and bound the yeast regulatory PR65/A subunit (Tpd3p) forming a dimer. Yeast was employed as a novel system for mutagenesis and functional analysis of human PP2Ac, revealing that the invariant C-terminal leucine residue, a site of regulatory methylation, is apparently dispensable for protein function. However, truncated forms of human PP2Ac lacking larger portions of the C terminus exerted a dominant interfering effect, as did several mutant forms containing a substitution mutation. Computer modeling of PP2Ac structure revealed that interfering amino acid substitutions clustered to the active site, and consistently, the PP2Ac-L199P mutant protein was catalytically impaired despite binding Tpd3p. Thus, interfering forms of PP2Ac titrate regulatory subunits and/or substrates into non-productive complexes and will serve as useful tools for studying PP2A function in mammalian cells. The transgenic approach employed here, involving a simple screen for interfering mutants, may be applicable generally to the analysis of structure-function relationships within protein phosphatases and other conserved proteins and demonstrates further the utility of yeast for analyzing gene function. PMID:10446173

Evans, D R; Myles, T; Hofsteenge, J; Hemmings, B A

1999-08-20

300

Neural system prediction and identification challenge  

PubMed Central

Can we infer the function of a biological neural network (BNN) if we know the connectivity and activity of all its constituent neurons?This question is at the core of neuroscience and, accordingly, various methods have been developed to record the activity and connectivity of as many neurons as possible. Surprisingly, there is no theoretical or computational demonstration that neuronal activity and connectivity are indeed sufficient to infer the function of a BNN. Therefore, we pose the Neural Systems Identification and Prediction Challenge (nuSPIC). We provide the connectivity and activity of all neurons and invite participants (1) to infer the functions implemented (hard-wired) in spiking neural networks (SNNs) by stimulating and recording the activity of neurons and, (2) to implement predefined mathematical/biological functions using SNNs. The nuSPICs can be accessed via a web-interface to the NEST simulator and the user is not required to know any specific programming language. Furthermore, the nuSPICs can be used as a teaching tool. Finally, nuSPICs use the crowd-sourcing model to address scientific issues. With this computational approach we aim to identify which functions can be inferred by systematic recordings of neuronal activity and connectivity. In addition, nuSPICs will help the design and application of new experimental paradigms based on the structure of the SNN and the presumed function which is to be discovered.

Vlachos, Ioannis; Zaytsev, Yury V.; Spreizer, Sebastian; Aertsen, Ad; Kumar, Arvind

2013-01-01

301

Development of Graphical User Interface for a System Identification Support Device  

NASA Astrophysics Data System (ADS)

This paper describes an interface for a system identification device on which system identification theory is implemented. A basic system identification procedure includes following steps; 1) collecting I/O data, 2) preprocessing the I/O data, 3) executing identification algorithm and constructing a model, and 4) validating the estimated model. System identification produces different results depend on various identification conditions. This results in a diversity of system identification. On the other hand, the diversity makes system identification problems more complex. The system identification device supports the user, in particular beginners, who execute above processes. The device utilizes MATLAB as a main processing software with a GUI in order to deal with the system identification processes visually. The system identification device is one of the most desireble ways to standardize system identification operations.

Takanashi, Hiroyuki; Adachi, Shuichi

302

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

303

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

304

Automated frequency domain system identification of a large space structure  

NASA Technical Reports Server (NTRS)

This paper presents the development and experimental results of an automated on-orbit system identification method for large flexible spacecraft that yields estimated quantities to support on-line design and tuning of robust high performance control systems. The procedure consists of applying an input to the plant, obtaining an output, and then conducting nonparametric identification to yield the spectral estimate of the system transfer function. A parametric model is determined by curve fitting the spectral estimate to a rational transfer function. The identification method has been demonstrated experimentally on the Large Spacecraft Control Laboratory in JPL.

Yam, Y.; Bayard, D. S.; Hadaegh, F. Y.; Mettler, E.; Milman, M. H.

1989-01-01

305

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

306

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

307

Identification of the genes affecting the regulation of riboflavin synthesis in the flavinogenic yeast Pichia guilliermondii using insertion mutagenesis  

PubMed Central

Pichia guilliermondii is a representative of a group of so-called flavinogenic yeast species that overproduce riboflavin (vitamin B2) in response to iron limitation. Using insertion mutagenesis, we isolated P. guilliermondii mutants overproducing riboflavin. Analysis of nucleotide sequence of recombination sites revealed that insertion cassettes integrated into the genome disrupting P. guilliermondii genes similar to the VMA1 gene of Ashbya gossypii and Saccharomyces cerevisiae and FES1 and FRA1 genes of S. cerevisiae. The constructed P. guilliermondii ?vma1–17 mutant possessed five- to sevenfold elevated riboflavin production and twofold decreased iron cell content as compared with the parental strain. Pichia guilliermondii ?fra1–45 mutant accumulated 1.8–2.2-fold more iron in the cells and produced five- to sevenfold more riboflavin as compared with the parental strain. Both ?vma1–17 and ?fes1–77 knockout strains could not grow at 37 °C in contrast to the wild-type strain and the ?fra1–45 mutant. Increased riboflavin production by the wild-type strain was observed at 37 °C. Although the ?fes1–77 mutant did not overproduce riboflavin, it showed partial complementation when crossed with previously isolated P. guilliermondii riboflavin-overproducing mutant rib80–22. Complementation analysis revealed that ?vma1–17 and ?fra1–45 mutants are distinct from previously reported riboflavin-producing mutants hit1-1, rib80-22 and rib81-31 of this yeast.

Boretsky, Yuriy R.; Pynyaha, Yuriy V.; Boretsky, Volodymyr Y.; Fedorovych, Dariya V.; Fayura, Lyubov R.; Protchenko, Olha; Philpott, Caroline C.; Sibirny, Andriy A.

2012-01-01

308

Identification of a putative alpha-glucan synthase essential for cell wall construction and morphogenesis in fission yeast  

PubMed Central

The cell wall protects fungi against lysis and determines their cell shape. Alpha-glucan is a major carbohydrate component of the fungal cell wall, but its function is unknown and its synthase has remained elusive. Here, we describe a fission yeast gene, ags1+, which encodes a putative alpha-glucan synthase. In contrast to the structure of other carbohydrate polymer synthases, the predicted Ags1 protein consists of two probable catalytic domains for alpha-glucan assembly, namely an intracellular domain for alpha-glucan synthesis and an extracellular domain speculated to cross-link or remodel alpha-glucan. In addition, the predicted Ags1 protein contains a multipass transmembrane domain that might contribute to transport of alpha-glucan across the membrane. Loss of Ags1p function in a temperature-sensitive mutant results in cell lysis, whereas mutant cells grown at the semipermissive temperature contain decreased levels of cell wall alpha-glucan and fail to maintain rod shapes, causing rounding of the cells. These findings demonstrate that alpha-glucan is essential for fission yeast morphogenesis.

Hochstenbach, Frans; Klis, Frans M.; van den Ende, Herman; van Donselaar, Elly; Peters, Peter J.; Klausner, Richard D.

1998-01-01

309

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

2008-06-01

310

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

311

Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray HybridizationD?  

PubMed Central

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: ? factor arrest, elutriation, and arrest of a cdc15 temperature-sensitive mutant. Using periodicity and correlation algorithms, we identified 800 genes that meet an objective minimum criterion for cell cycle regulation. In separate experiments, designed to examine the effects of inducing either the G1 cyclin Cln3p or the B-type cyclin Clb2p, we found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins. Furthermore, we analyzed our set of cell cycle–regulated genes for known and new promoter elements and show that several known elements (or variations thereof) contain information predictive of cell cycle regulation. A full description and complete data sets are available at http://cellcycle-www.stanford.edu

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

1998-01-01

312

Identification of revertants for the cystic fibrosis delta F508 mutation using STE6-CFTR chimeras in yeast.  

PubMed

Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis; the most common mutation is deletion of phenylalanine at position 508 (delta F508). We constructed STE6-CFTR chimeras with portions of the first nucleotide-binding domain (NBD1) of the yeast STE6 a-factor transporter replaced by portions of CFTR NBD1. The chimeras were functional in yeast, but mating efficiency decreased when delta F508 was introduced into NBD1. We isolated two delta F508 revertant mutations (R553M and R553Q) that restored mating; both were located within the CFTR NBD1 sequence. Introduction of these revertant mutations into human CFTR partially corrected the processing and Cl- channel gating defects caused by the delta F508 mutation. These results suggest that the NBD1s of CFTR and STE6 share a similar structure and function and that, in CFTR, the regions containing F508 and R553 interact. They also indicate that the abnormal conformation produced by delta F508 can be partially corrected by additional alterations in the protein. PMID:7682896

Teem, J L; Berger, H A; Ostedgaard, L S; Rich, D P; Tsui, L C; Welsh, M J

1993-04-23

313

Yeast central nervous system infection in a critically ill patient: a case report  

PubMed Central

Introduction Invasive fungal infections are alarmingly common in intensive care unit patients; invasive fungal infections are associated with increased morbidity and mortality. Risk factors are the increased use of indwelling central venous catheters, the use of broad spectrum antibiotics, parenteral nutrition, renal replacement therapy and immunosuppression. Diagnosis of these infections might be complicated, requiring tissue cultures. In addition, therapy of invasive fungal infections might be difficult, given the rising resistance of fungi to antifungal agents. Case presentation We describe the case of a 28-year-old Greek man with yeast central nervous system infection. Conclusions Difficult-to-treat fungal infections may complicate the clinical course of critically ill patients and render their prognosis unfavorable. This report presents a case that was rare and difficult to treat, along with a thorough review of the investigation and treatment of these kinds of fungal infections in critically ill patients.

2014-01-01

314

A Microfluidic System for Studying Ageing and Dynamic Single-Cell Responses in Budding Yeast  

PubMed Central

Recognition of the importance of cell-to-cell variability in cellular decision-making and a growing interest in stochastic modeling of cellular processes has led to an increased demand for high density, reproducible, single-cell measurements in time-varying surroundings. We present ALCATRAS (A Long-term Culturing And TRApping System), a microfluidic device that can quantitatively monitor up to 1000 cells of budding yeast in a well-defined and controlled environment. Daughter cells are removed by fluid flow to avoid crowding allowing experiments to run for over 60 hours, and the extracellular media may be changed repeatedly and in seconds. We illustrate use of the device by measuring ageing through replicative life span curves, following the dynamics of the cell cycle, and examining history-dependent behaviour in the general stress response.

Bakker, Elco; Smith, Stewart; Swain, Peter S.

2014-01-01

315

Evaluation of a lysis-centrifugation system for recovery of yeasts and filamentous fungi from blood.  

PubMed Central

A lysis-centrifugation system (Isolator; E. I. du Pont de Nemours & Co., Inc., Wilmington, Del.) was compared with a biphasic brain heart infusion (BHI) medium in a prospective study of 5,125 fungal blood cultures. The Isolator recovered 90.3% of the positive cultures, compared with 63.4% recovered by the biphasic BHI medium. Overall, the detection of fungemia was increased 36.6% by the Isolator. Mean recovery times for yeasts were 2.12 and 4.90 days for the Isolator and BHI bottles, respectively. Cultures of Histoplasma capsulatum required 8.0 and 24.14 days for recovery by the Isolator and BHI bottles, respectively. The Isolator provided a more rapid and sensitive means of detecting organisms associated with fungemia.

Bille, J; Stockman, L; Roberts, G D; Horstmeier, C D; Ilstrup, D M

1983-01-01

316

Distinct Signaling Roles of Ceramide Species in Yeast Revealed Through Systematic Perturbation and Systems Biology Analyses  

PubMed Central

Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule participating in cellular regulatory events and having implications for disease. A challenge in deciphering ceramide signaling emanates from the myriad of ceramide species that exist and the possibility that many of them may have distinct functions. Here, 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 find that during heat stress distinct metabolic mechanisms control the abundance of different groups of ceramide species. Additionally, distinct groups of ceramide species regulated different sets of functionally related genes, indicating that specific sub-groups of lipids participated in different regulatory pathways. These results indicate a previously unrecognized complexity and versatility of lipid-mediated cell regulation.

Montefusco, David J.; Chen, Lujia; Matmati, Nabil; Lu, Songjian; Newcomb, Benjamin; Cooper, Gregory F.; Hannun, Yusuf A.; Lu, Xinghua

2014-01-01

317

A strategy for increasing an in vivo flux by genetic manipulations. The tryptophan system of yeast.  

PubMed Central

Decreases in enzyme activity often have little effect on the flux carried by the pathway. Similarly, up-modulation of single genes, and hence of the dependent enzyme concentrations, is frequently found to be ineffective in increasing the flux in the pathway in which the enzyme occurs. This insensitivity to enzyme variation is demonstrated experimentally for five separate enzymes in the tryptophan synthesis system of yeast, first by down-modulation of the gene dose and secondly by increasing the dose using multi-copy vectors. Such a lack of response is discussed in terms of the concepts of metabolic control analysis. When these five enzymes, however, were simultaneously increased by a multi-copy vector carrying all five genes, a substantial elevation of the flux to tryptophan was observed. These findings revealed a new phenomenon, namely the more than additive effects on the flux of simultaneous elevations of several enzyme activities.

Niederberger, P; Prasad, R; Miozzari, G; Kacser, H

1992-01-01

318

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

Microsoft Academic Search

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

JULIAN KONIG; CHRISTIAN JULIUS; SEBASTIAN BAUMANN; MATTHIAS HOMANN; H. ULRICH GORINGER; MICHAEL FELDBRUGGE

2007-01-01

319

Frequency weighted system identification and linear quadratic controller design  

NASA Technical Reports Server (NTRS)

Application of filters for frequency weighting of Markov parameters (pulse response functions) is described in relation to system/observer identification. The time domain identification approach recovers a model which has a pulse response weighted according to frequency. The identified model is composed of the original system and filters. The augmented system is in a form which can be used directly for frequency weighted linear quadratic controller design. Data from either single or multiple experiments can be used to recover the Markov parameters. Measured acceleration signals from a truss structure are used for system identification and the model obtained is used for frequency weighted controller design. The procedure makes the identification and controler design complementary problems.

Horta, Lucas G.; Phan, Minh; Juang, Jer-Nan; Longman, Richard W.; Sulla, Jeffrey L.

1991-01-01

320

Los Alamos Scientific Laboratory Electronic Vehicle Identification System.  

National Technical Information Service (NTIS)

A three-digit electronic identification system is described. Digits may be decimal (1000 combinations) or hexidecimal (8192 combinations). Battery-powered transponders are interrogated with a lower-power (1 W) radio signal. Line-of-sight interrogations up...

J. A. Landt R. E. Bobbett A. R. Koelle P. H. Salazar

1980-01-01

321

Some after-dinner reflections on system identification  

NASA Technical Reports Server (NTRS)

The growth of the field of system identification is discussed along with changes in methodology which have taken place in recent years. The similarity between pattern recognition and system identification is pointed out, involving the modelling in the latter and the feature selection problem in the former. It is stated that once a model is formulated, including the disturbances and measurement errors, the parameter finding can be formulated as a statistical estimation problem. The various techniques and their application are discussed.

Balakrishnan, A. V.

1974-01-01

322

Digital image processing for non-linear system identification  

Microsoft Academic Search

Emerging digital image processing techniques demonstrate their potential applications in engineering mechanics, particularly in the area of system identification involving non-linear characteristics of mechanical and structural systems. The objective of this study is to demonstrate the proof-of-concept that the techniques permit the identification non-intrusively and remotely. First, the efficacy of the digital image processing method is shown by identifying the

H.-C. Chung; J. Liang; S. Kushiyama; M. Shinozuka

2004-01-01

323

Identification of regioisomers and enantiomers of triacylglycerols in different yeasts using reversed- and chiral-phase LC-MS.  

PubMed

LC with atmospheric pressure chemical ionization (ACPI) MS with RP and chiral phase was used for separation of triacylglycerols (TAGs) from yeasts of the genera Candida, Kluyveromyces, Rhodotorula, Saccharomyces, Torulospora, Trichosporon, and Yarrowia. Chiral LC-APCI-MS is based on using two columns in series packed with a 3,5-dimethylphenyl carbamate modified ?-cyclodextrin chiral phase. All regioisomers and enantiomers of TAGs containing one to five double bonds were separated. Molecular species of TAGs, i.e. regioisomers and enantiomers, were identified and quantified by MS/MS. Among the 94 identified TAGs, the most abundant were triolein, oleopalmitoleoolein, and dipalmitoleoolein. In strains producing palmitoleic acid in amounts >25% of total fatty acids (FAs), this acid, or unsaturated FA is bound in sn-1. In strains containing palmitoleic acid at 10-25% total FAs this acid is mainly bound in sn-3, saturated FA being bound in sn-1. Strains containing <10% palmitoleic acid form preferentially symmetrical TAGs. PMID:23963893

Rezanka, Tomáš; Kolouchová, Irena; Cejková, Alena; Cajthaml, Tomáš; Sigler, Karel

2013-10-01

324

Identification of a protein that binds to the Ho endonuclease recognition sequence at the yeast mating type locus.  

PubMed Central

Mating type switching in Saccharomyces cerevisiae initiates when Ho endonuclease makes a site-specific double-stranded break at MAT, the yeast mating type locus. To identify other proteins involved in this process, we examined whether extracts prepared from ho- mutants contain additional factors that bind near the recognition sequence for Ho. Using an electrophoretic mobility shift assay, we isolated a chromatographic fraction that contains an activity, named YZbp, which binds to two sequences flanking the recognition sequence at MATalpha and to one sequence overlapping it at MATa. MAT plasmids carrying mutations in the YZbp recognition sequence are cleaved by purified Ho at wild-type efficiencies in an in vitro assay. These same plasmids, however, are not cleaved by Ho inside cells, demonstrating that YZbp acts as a positive activator of in vivo cleavage. YZbp is present in all cell types, even those not undergoing mating type switching, suggesting that it has additional cellular functions.

Wang, R; Jin, Y; Norris, D

1997-01-01

325

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

326

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

327

Identification of active magnetic bearing system with a flexible rotor  

NASA Astrophysics Data System (ADS)

Active magnetic bearings (AMBs) are widely applied in high-speed rotating machinery, especially in special environments. In designing and adjusting an AMB system, the mathematical model of the system plays an important role. Identification is a useful method to obtain the models of AMB systems. This paper concentrates on identification method for an AMB system with a flexible rotor. Based on the theoretical system model and the measured frequency-response model, the proposed method estimates the unknown parameters and establishes the transfer function matrix model of the AMB system. According to the theoretical model, this paper decomposes the identification procedure into a few steps and the model is sequentially reduced by these steps. In this procedure, the submodels are identified separately and finally combined together. The proposed method is validated by experiments on three AMB systems.

Sun, Zhe; He, Ying; Zhao, Jingjing; Shi, Zhengang; Zhao, Lei; Yu, Suyuan

2014-12-01

328

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.

329

Identification of Oil Spills at Sea: Development of a System for the Identification of Oil Spills.  

National Technical Information Service (NTIS)

A system for the identification of oil spilled at sea is proposed. The system includes oil sampling procedures and analytical methods. Hydrocarbon compounds are studied by UV or UV-fluorescence-spectroscopy, LRGC, HRGC and IR-spectroscopy; the contents of...

R. G. Lichtenthaler P. E. Paus

1982-01-01

330

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

331

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

332

Parameter identification for nonlinear aerodynamic systems  

NASA Technical Reports Server (NTRS)

Continuing work on frequency analysis for transfer function identification is discussed. A new study was initiated into a 'weighted' least squares algorithm within the context of the Fourier modulating function approach. The first phase of applying these techniques to the F-18 flight data is nearing completion, and these results are summarized.

Pearson, Allan E.

1992-01-01

333

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

334

Model Identification of Risk Management System  

Microsoft Academic Search

It is important issue for the study of method of the project risk assessment. The quantitative method is used to resolve construction project risk assessment in this paper. Firstly, the study of project risk management and risk assessment is made a review. Secondly, the project risk management systematic framework is constructed, which include five purchases: risk identification, risk assessment, risk

Liu Ren-hui; Zhai Feng-yong

2008-01-01

335

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

336

System identification methods for aircraft flight control development and validation  

NASA Technical Reports Server (NTRS)

System-identification methods compose a mathematical model, or series of models, from measurements of inputs and outputs of dynamic systems. The extracted models allow the characterization of the response of the overall aircraft or component subsystem behavior, such as actuators and on-board signal processing algorithms. This paper discusses the use of frequency-domain system-identification methods for the development and integration of aircraft flight-control systems. The extraction and analysis of models of varying complexity from nonparametric frequency-responses to transfer-functions and high-order state-space representations is illustrated using the Comprehensive Identification from FrEquency Responses (CIFER) system-identification facility. Results are presented for test data of numerous flight and simulation programs at the Ames Research Center including rotorcraft, fixed-wing aircraft, advanced short takeoff and vertical landing (ASTOVL), vertical/short takeoff and landing (V/STOL), tiltrotor aircraft, and rotor experiments in the wind tunnel. Excellent system characterization and dynamic response prediction is achieved for this wide class of systems. Examples illustrate the role of system-identification technology in providing an integrated flow of dynamic response data around the entire life-cycle of aircraft development from initial specifications, through simulation and bench testing, and into flight-test optimization.

Tischler, Mark B.

1995-01-01

337

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

338

A portable air jet actuator device for mechanical system identification.  

PubMed

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 Coanda? 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. PMID:21456788

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

2011-03-01

339

RFLP analysis of the ribosomal internal transcribed spacers and the 5.8S rRNA gene region of the genus Saccharomyces: a fast method for species identification and the differentiation of flor yeasts.  

PubMed

The PCR amplification and subsequent restriction analysis of the region spanning the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene was applied to the identification of yeasts belonging to the genus Saccharomyces. This methodology has previously been used for the identification of some species of this genus, but in the present work, this application was extended to the identification of new accepted Saccharomyces species (S. kunashirensis, S. martiniae, S. rosinii, S. spencerorum, and S. transvaalensis), as well as to the differentiation of an interesting group of Saccharomyces cerevisiae strains, known as flor yeasts, which are responsible for ageing sherry wine. Among the species of the Saccharomyces sensu lato complex, the high diversity observed, either in the length of the amplified region (ranged between 700 and 875 bp) or in their restriction patterns allows the unequivocal identification of these species. With respect to the four sibling species of the Saccharomyces sensu stricto complex, only two of them, S. bayanus and S. pastorianus, cannot be differentiated according to their restriction patterns, which is in accordance with the hybrid origin (S. bayanus x S. cerevisiae) of S. pastorianus. The flor S. cerevisiae strains exhibited restriction patterns different from those typical of the species S. cerevisiae. These differences can easily be used to differentiate this interesting group of strains. We demonstrate that the specific patterns exhibited by flor yeasts are due to the presence of a 24-bp deletion located in the ITS 1 region and that this could have originated as a consequence of a slipped-strand mispairing during replication or be due to an unequal crossing-over. A subsequent restriction analysis of this region from more than 150 flor strains indicated that this deletion is fixed in flor yeast populations. PMID:11016699

Fernádez-Espinar, M T; Esteve-Zarzoso, B; Querol, A; Barrio, E

2000-07-01

340

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

341

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

342

Identification of a New Sea Urchin Ets Protein, SpEts4, by Yeast One-Hybrid Screening with the Hatching Enzyme Promoter  

PubMed Central

We report the use of a yeast one-hybrid system to isolate a transcriptional regulator of the sea urchin embryo hatching enzyme gene, SpHE. This gene is asymmetrically expressed along the animal-vegetal axis of sea urchin embryos under the cell-autonomous control of maternal regulatory activities and therefore provides an excellent entry point for understanding the mechanism that establishes animal-vegetal developmental polarity. To search for transcriptional regulators, we used a fragment of the SpHE promoter containing several individual elements instead of the conventional bait that contains a multimerized cis element. This screen yielded a number of positive clones that encode a new member of the Ets family, named SpEts4. This protein contains transcriptional activation activity, since expression of reporter genes in yeast does not depend on the presence of the yeast GAL4 activation domain. Sequences in the N-terminal region of SpEts4 mediate the activation activity, as shown by deletion or domain-swapping experiments. The newly identified DNA binding protein binds with a high degree of specificity to a SpHE promoter Ets element and forms a complex with a mobility identical to that obtained with 9-h sea urchin embryo nuclear extracts. SpEts4 positively regulates SpHE transcription, since mutation of the SpEts4 site in SpHE promoter transgenes reduces promoter activity in vivo while SpEts4 mRNA coinjection increases its output. As expected for a positive SpHE transcriptional regulator, the timing of SpEts4 gene expression precedes the transient expression of SpHE in the very early sea urchin blastula.

Wei, Zheng; Angerer, Robert C.; Angerer, Lynne M.

1999-01-01

343

Data security in a ship detection and Identification System  

Microsoft Academic Search

The use and access of space-based and terrestrial assets for maritime surveillance has developed rapidly in the recent decades. These developments have implications for civil, commercial and military stakeholders and are used by both advanced and developing countries. There are many sensors and systems applicable to the maritime domain such as Vessel Monitoring Systems (VMS), Automatic Identification System (AIS), airborne

Bustanul Arifin; Edward Ross; Yuval Brodsky

2011-01-01

344

Expert system for nuclide identification in gamma spectrum analysis  

Microsoft Academic Search

An expert system coupled with the gamma spectrum analysis system SAMPO has been developed for automating the qualitative identification of radionuclides as well as for determinating the quantitative parameters of the spectrum components. The program is written in C-language and runs in various environments ranging from PC's to UNIX workstations. The expert system utilizes a complete gamma library with over

P. A. Aarnio; J. J. Ala-Heikkilae; T. T. Hakulinen; J. T. Routti

1994-01-01

345

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

346

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

347

Identification and typing of Malassezia yeasts using amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD) and denaturing gradient gel electrophoresis (DGGE).  

PubMed

Three molecular tools, amplified fragment length polymorphism (AFLP), denaturing gradient gel electrophoresis (DGGE) and random amplified polymorphic DNA (RAPD) analysis, were explored for their usefulness to identify isolates of Malassezia yeasts. All seven species could be separated by AFLP and DGGE. Using AFLP, four genotypes could be distinguished within M. furfur. AFLP genotype 4 contained only isolates from deep human sources, and ca. 80% of these isolates were from patients with systemic disease. Most of the systemic isolates belonged to a single RAPD genotype. This suggests that systemic conditions strongly select for a particular genotype. Although the clinical use of DGGE may be limited due to technical demands, it remains a powerful tool for the analysis of complex clinical samples. PMID:12702352

Theelen, B; Silvestri, M; Guého, E; van Belkum, A; Boekhout, T

2001-07-01

348

Identification of nonlinear hysteretic systems by artificial neural network  

NASA Astrophysics Data System (ADS)

An identification method is developed for nonlinear hysteretic systems by use of artificial neural network in the paper. Employing the Bouc-Wen differential model widely used for memory-type nonlinear hysteretic systems, the approach sets up a Bouc-Wen model-based neural network. The weights of the designed specifically network correspond to the Bouc-Wen model parameters and are thus physical ones. Taking advantage of powerful function approximation capability of neural network, the nonlinear hysteretic systems can be identified with the proposed approach by network training. The identification scheme is validated by a simulated case and thereafter applied to modeling of a wire cable vibration isolation experimental system. The results show that the presented identification method can identify the nonlinear hysteretic systems with high accuracy.

Xie, S. L.; Zhang, Y. H.; Chen, C. H.; Zhang, X. N.

2013-01-01

349

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

350

A system designed for black-spot's automatic identification  

Microsoft Academic Search

An automatic identification system for the OLED's black-spot detection was designed in this paper. Complete approaches based on machine vision technology are proposed to get the sub-pixel location of black-spots. In this method, feature area is recognized based on the identification of spots' edge characteristics. The method of circle fitting is used to get positions of the spots' center. The

Li-Gui Feng; Chen-Wen Bin

2010-01-01

351

System Identification of Small-Size Unmanned Helicopter Dynamics  

Microsoft Academic Search

Abstmcf: Flight testing of a fully-instrumented model-scale unmanned helicopter (Yamaha R-SO with loft. diameter rotor) was conducted for the purpose of dynamic model identification. This paper describes the application of CIFER' system identification techniques, which have been developed for full size helicopters, to this aircraft. An accurate, high-bandwidth, linear state-space model was derived for the hover condition. The model structure

Bernard Mettler; Mark B. Tischler; Takeo Kanade

352

A Clustering Technique for the Identification of Piecewise Affine Systems  

Microsoft Academic Search

We propose a new technique for the identification of discrete-time hybrid systems in the Piece-Wise Affine (PWA) form. This problem can be formulated as the reconstruction of a possibly discontinuous PWA map with a multi-dimensional domain. In order to achieve our goal, we provide an algorithm that exploits the combined use of clustering, linear identification, and pattern recognition techniques. This

Giancarlo Ferrari-trecate; Marco Muselli; Diego Liberati; Manfred Morari

2001-01-01

353

A Clustering Technique for the Identification of Piecewise Affine systems  

Microsoft Academic Search

We propose a new technique for the identification of discrete-time hybrid systems in the Piece-Wise Affine (PWA) form. The\\u000a identification cation algorithm proposed in [10] is first considered and then improved under various aspects. Measures of confidence on the samples are introduced and exploited\\u000a in order to improve the performance of both the clustering algorithm used for classifying the data

Giancarlo Ferrari-Trecate; Marco Muselli; Diego Liberati; Manfred Morari

354

SESAM: A Biometric Person Identification System Using Sensor Fusion  

Microsoft Academic Search

Abstract In the present paper we describe the person authentication system SESAM. Person identification and verification still is a very difficult task. Using one biometric feature, i.e. the photograph or the sound of the voice, leads to good results, but there is no reliable way,to verify the classification. In order to reach robust identification and verification we are combining,three different

Ulrich Dieckmann; P. Plankensteiner; Ralf Schamburger; Bernhard Fröba; Sebastian Meller

1997-01-01

355

Identification of human protein interaction domains using an ORFeome-based yeast two-hybrid fragment library.  

PubMed

Physical interactions between proteins are essential for biological processes. Hence, there have been major efforts to elucidate the complete networks of protein-protein interactions, or "interactomes", of various organisms. Detailed descriptions of protein interaction networks should include information on the discrete domains that mediate these interactions, yet most large-scale efforts model interactions between whole proteins only. We previously developed a yeast two-hybrid-based strategy to systematically map interaction domains and generated a domain-based interactome network for 750 proteins involved in C. elegans early embryonic development. Here, we expand the concept of Y2H-based interaction domain mapping to the genome-wide level. We generated a human fragment library by randomly fragmenting the full-length open reading frames (ORFs) present in the human ORFeome collection. Screens using several proteins required for cell division or polarity establishment as baits demonstrate the ability to accurately identify interaction domains for human proteins using this approach, while the experimental quality of the Y2H data was independently verified in coaffinity purification assays. The library generation strategy can easily be adapted to generate libraries from full-length ORF collections of other organisms. PMID:23718855

Waaijers, Selma; Koorman, Thijs; Kerver, Jana; Boxem, Mike

2013-07-01

356

Recursive and optimal multi-level algorithms for the identification of stochastic systems applications to bipeds control and identification  

Microsoft Academic Search

We present a generalisation of doubly stochastic processes intelligent agents processing based hidden Markov models to non linear stochastic identification and control of dynamic systems with state representation. This stochastic approach is applied to the control and identification of a humanoid robot. This stochastic generalisation has two aspects: First, the hidden Markov models application to control and identification of non

A. Khoukhi

2001-01-01

357

Identification of Glycolytic Enzyme Polypeptides on the Two-Dimensional Protein Map of Saccharomyces cerevisiae and Application to the Study of Some Wine Yeasts  

PubMed Central

Using a modification of the basic two-dimensional polyacrylamide gel electrophoresis technique, the polypeptides of the protein map of Saccharomyces cerevisiae involved in glycolysis were investigated. This study resulted in a reassignment of two of the seven glycolytic enzyme polypeptides previously identified (Ludwig et al., Mol. Cell. Biol. 2:117-126, 1982), those corresponding to phosphoglycerate kinase and to alcohol dehydrogenase. It also resulted in the identification of two additional glycolytic polypeptides, the enolase B monomer and the glyceraldehyde phosphate dehydrogenase B monomer. The glycolytic enzymes polypeptides so identified were investigated in 5 laboratory strains (all S. cerevisiae) and in 11 commerical strains used for wine making (S. cerevisiae and Saccharomyces bayanus). It appeared highly significant that a particular electrophoretic variant of the glyceraldehyde phosphate dehydrogenase B monomer was found only in the wine yeasts. Furthermore, it was strongly suggested that S. cerevisiae and S. bayanus strains are distinguishible on the basis of a different electrophoretic migration of the enolase B monomer. Images

Brousse, Michel; Bataille, Nelly; Boucherie, Helian

1985-01-01

358

Strategy for detecting cellular transcripts promoted by human endogenous long terminal repeats: identification of a novel gene (CDC4L) with homology to yeast CDC4.  

PubMed

Several families of repetitive sequences related to integrated retroviruses have been identified in the human genome. The largest of these families, the RTVL-H family, has close to 1000 members in addition to a similar number of solitary long terminal repeats (LTRs) dispersed on all chromosomes. Previous work has shown that the expression of genomic RTVL-H elements is driven by their LTRs and that some LTRs can promote expression of a reporter gene. These observations suggest that some endogenous RTVL-HLTRs may naturally regulate the transcription of adjacent cellular genes or that rearrangements involving these elements may cause aberrant gene expression. To investigate this possibility, we have used a differential screening strategy to identify chimeric cDNA clones derived from LTR-promoted transcripts. Here we report the identification and analysis of four such clones isolated from an NTera2D1 (teratocarcinoma) cDNA library. Two of the clones, AF-1 and AF-2, contain termination codons in all reading frames. Another clone, AF-4, contains LTR sequences linked in the genome to a CpG island. The fourth clone, AF-3, contains an 862-bp open reading frame representing part of a novel gene (CDC4L) with homology to the yeast cell division cycle gene CDC4. These findings indicate that RTVL-H elements may be involved in the regulation of diverse cellular transcripts in human cells. PMID:1505956

Feuchter, A E; Freeman, J D; Mager, D L

1992-08-01

359

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

360

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

361

System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes  

PubMed Central

One of the most obvious phenotypes of a cell is its metabolic activity, which is defined by the fluxes in the metabolic network. Although experimental methods to determine intracellular fluxes are well established, only a limited number of fluxes can be resolved. Especially in eukaryotes such as yeast, compartmentalization and the existence of many parallel routes render exact flux analysis impossible using current methods. To gain more insight into the metabolic operation of S. cerevisiae we developed a new computational approach where we characterize the flux solution space by determining elementary flux modes (EFMs) that are subsequently classified as thermodynamically feasible or infeasible on the basis of experimental metabolome data. This allows us to provably rule out the contribution of certain EFMs to the in vivo flux distribution. From the 71 million EFMs in a medium size metabolic network of S. cerevisiae, we classified 54% as thermodynamically feasible. By comparing the thermodynamically feasible and infeasible EFMs, we could identify reaction combinations that span the cytosol and mitochondrion and, as a system, cannot operate under the investigated glucose batch conditions. Besides conclusions on single reactions, we found that thermodynamic constraints prevent the import of redox cofactor equivalents into the mitochondrion due to limits on compartmental cofactor concentrations. Our novel approach of incorporating quantitative metabolite concentrations into the analysis of the space of all stoichiometrically feasible flux distributions allows generating new insights into the system-level operation of the intracellular fluxes without making assumptions on metabolic objectives of the cell.

Jol, Stefan J.; Kummel, Anne; Terzer, Marco; Stelling, Jorg; Heinemann, Matthias

2012-01-01

362

Classification of Yeasts of the Genus Malassezia by Sequencing of the ITS and D1\\/D2 Regions of DNA  

Microsoft Academic Search

\\u000a Yeasts of the genus Malassezia are known commensals of human beings and warm-blooded animals. Currently, they are considered emergent pathogen yeasts and\\u000a have been described as causative agents of systemic opportunistic infections. An accurate identification of Malassezia spp. is of relevance to determine the role each species plays in the development of cutaneous and systemic infections. The\\u000a taxonomy of Malassezia

Lidia Pérez-Pérez; Manuel Pereiro; Jaime Toribio

363

Digital system identification and its application to digital flight control  

NASA Technical Reports Server (NTRS)

On-line system identification of linear discrete systems for implementation in a digital adaptive flight controller is considered by the conventional extended Kalman filter and a decoupling process in which the linear state estimation problem and the linear parameter identification problem are each treated separately and alternately. Input requirements for parameter identifiability are established using the standard conditions of observability for a time variant system. Experimental results for simulated linearized lateral aircraft motion are included along with the effect of different initialization and updating procedures for the priming trajectory used by the filter.

Kotob, S.; Kaufman, H.

1974-01-01

364

Simple Methods to Detect Triacylglycerol Biosynthesis in a Yeast-Based Recombinant System  

Microsoft Academic Search

Standard methods to quantify the activity of triacylglycerol (TAG) synthesizing enzymes DGAT and PDAT (TAG-SE) require a sensitive\\u000a but rather arduous laboratory assay based on radio-labeled substrates. Here we describe two straightforward methods to detect\\u000a TAG production in baker’s yeast Saccharomyces cerevisiae. First we demonstrate that a quadruple knockout yeast strain deficient in storage lipids has a reduced growth rate

Rodrigo M. P. Siloto; Martin Truksa; Xiaohua He; Thomas McKeon; Randall J. Weselake

2009-01-01

365

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

366

Model abstraction results using state-space system identifications  

Microsoft Academic Search

In this paper we report on state-space system identification approaches to dynamic behavioral abstraction of military simulation models. Two stochastic simulation models were identified under a variety of scenarios. The `Attrition Simulation' is a model of two opposing forces with multiple weapon system types. The `Mission Simulation' is a model of a squadron of aircraft performing battlefield air interdiction. Four

Douglas A. Popken

2000-01-01

367

Ideogram identification in a realtime traffic sign recognition system  

Microsoft Academic Search

A robust system for the automatic detection of traffic signs has been developed at the Image Recognition Laboratory of the University of Koblenz. This traffic sign recognition (TSR) system was originally designed to localize traffic signs and to recognize their classes, e.g. prohibition signs, danger signs, beacons, etc. The exact identification of traffic signs is added. Traffic signs are identified

Lutz Priese; Raimund Lakmann; Volker Rehrmann

1995-01-01

368

Identification of Critical Points in the Quality Management System  

Microsoft Academic Search

Creating a quality management system can help organizations and other stakeholders in satisfying customer needs and expectations. Moreover, a well-implemented quality management ensures the organization a capable structure to make continuous improvement actions. Thus, after the evaluation of the quality management system elements, the identification of critical points is a very important element. There are several ways of assessing and

Tünde SZABÓ

2011-01-01

369

Faulted Branch Identification on Power Distribution Systems Under Noisy Environment  

Microsoft Academic Search

Faulted branch identification is extremely important for power distribution systems operation and restoration. Also, noisy environments are common in substations, where the relays are normally installed. In this paper a novel formulation that estimates the faulted section of an unbalanced power distribu- tion system considering a noisy environment is presented. The method uses travelling waves and autocorrelation theory, and was

Karen Rezende; Adalberto Shuck Jr; Arturo Suman Bretas

370

[Screening of new binding partners of CIKS with yeast two-hybrid system].  

PubMed

The NF-kappaB transcription factor plays important regulatory roles in inflammation, apoptosis, immune and stress responses. IkappaB kinase (IKK) composed of two catalytic subunits and a regulator subunit, acts as a key component of NF-kappaB activation pathway through phosphorylation of IkappaB, the inhibitor of NF-kappaB. CIKS (connection to IKK and SAPK), a newly identified cellular protein, is involved in NF-kappaB and JNK activation. Although it has been known that CIKS interacts with IKK complex, and activates both IKK and SAPK when overexpressed; the underling mechanisms are poorly understood. To better understand the physiological roles of CIKS, we have screened human HeLa MATCHMAKER cDNA library for new binding partners of CIKS by using the yeast two-hybrid system with truncated CIKS (151-574) as the bait. The yeast strain AH109 was sequentially transformed with the bait plasmid and the library. The transformants were screened on SD(-Leu/-Trp/-His/-Ade/ + X-alpha-gal)selective plates. Positive clones were restreaked on SD(-Leu/-Trp / + X-alpha-gal)plates three times to allow loss of some of the AD/library plasmids while maintaining selective pressure on both the DNA-BD and AD vectors. After 3 screenings on SD(-Leu/-Trp / + X-alpha-gal), the positive clones were further verified on SD(-Leu/-Trp/-His/-Ade/ + X-alpha-gal) plates. The inserts in AD/library plasmids were amplified by PCR and PCR products were characterized by Hae III digestion to eliminate the duplicates. After screening in selective plates, the positive AD/library plasmids were rescued via transformation of E. coli HB101 and the interactions of CIKS (151-574) with positive AD/library plasmids were further assessed by yeast two-hybrid analysis. Finally, the DNA sequences of the positive AD/library plasmids were determined and BLAST analysis against the databases was performed. The BLAST results indicate that the inserts in the positive plasmids encode RIKEN cDNA 473340F03, PLAC8, CD27BP (Siva-1), CDC5L, SnRNP smB, and DVL2. CDC5L is a key component of the multi-protein complex essential for the formation of pre-mRNA splicing product and is not required for spliceosome assembly. A role for CDC5L in the cell division cycle has been precious suggested as its overexpression of this protein in mammalian cells leads to a shortening G2 phase of the cell cycle, and a negative-dominant mutant of CDC5L lacking the N-terminal activation domain delays the G2 phase cell's entry into the mitosis. It has been reported that SnRNP smB participates in pre-mRNA splicing and CD27BP (Siva-1) binds to and inhibits BCL-XL-mediated protection against UV radiation-induced apoptosis and regulates T cell homeostasis. The functions of RIKEN cDNA 473340F03, PLAC8 and DVL2 are unknown. It has been suggested that CIKS functions as a critical component for cross-talk between NF-kappaB and JNK signaling pathways. IKK subunits, which have been demonstrated to interact with CIKS, were not shown up in this experiment. We speculate that the truncated CIKS (151-574) bait may not contain the binding domain that mediates the interaction of IKK subunits with CIKS. Taken together, the above results suggest that CIKS may play a role in cell regulation through interacting with various cellular proteins. Further investigations are required to characterize these interactions. PMID:15966320

Huang, Guo-Jin; Zhang, Zhi-Qing; Yao, Li-Hong; Chen, Ai-Jun; Xu, Chun-Xiao

2003-03-01

371

The use of Fenton's system in the yeast industry wastewater treatment.  

PubMed

The paper presents the results of the research conducted with the use of hydrogen peroxide and iron (II) sulfate or chloride in the chemical pretreatment of Saccharomyces cerevisae yeast industry wastewater. It was found that the use of Fenton's system permitted a high reduction of sugar-like substances and total decolorizing of non-sugar compounds. The level of COD reduction depended on the amount and mutual proportions of COD:Fe(II):H2O2, as well as a type of the applied salt Fe(II). For iron concentrations: 1000-4000 mg l(-1) with molar excess [H2O2]:[Fe(II)] - 2-14:1 and reaction pH - 3.1-3.4, very high reproducibility of results and the COD reduction exceeding 75% were obtained. For this range of the reagent concentrations, the distribution of COD reduction values correlated with the equation: COD = - Ax4 + Bx3 - Cx2 + Dx - E (where: x = [H2O2]:[Fe(II)]). Additional neutralization with the use of lime milk made the secondary reduction of CODr(CaO) value possible, which resulted in the reduction of the total CODT above 90%. The method enabled us to consider the possibility of the preliminary chemical elimination of the wastewater load, which might increase the effectiveness of working wastewater treatment plants, especially in cases of continuous and occasional overloads above the level assumed by the project. PMID:15747596

Zak, S

2005-01-01

372

Mapping Yeast Transcriptional Networks  

PubMed Central

The term “transcriptional network” refers to the mechanism(s) that underlies coordinated expression of genes, typically involving transcription factors (TFs) binding to the promoters of multiple genes, and individual genes controlled by multiple TFs. A multitude of studies in the last two decades have aimed to map and characterize transcriptional networks in the yeast Saccharomyces cerevisiae. We review the methodologies and accomplishments of these studies, as well as challenges we now face. For most yeast TFs, data have been collected on their sequence preferences, in vivo promoter occupancy, and gene expression profiles in deletion mutants. These systematic studies have led to the identification of new regulators of numerous cellular functions and shed light on the overall organization of yeast gene regulation. However, many yeast TFs appear to be inactive under standard laboratory growth conditions, and many of the available data were collected using techniques that have since been improved. Perhaps as a consequence, comprehensive and accurate mapping among TF sequence preferences, promoter binding, and gene expression remains an open challenge. We propose that the time is ripe for renewed systematic efforts toward a complete mapping of yeast transcriptional regulatory mechanisms.

Hughes, Timothy R.; de Boer, Carl G.

2013-01-01

373

Exploring Protein Interactions on a Minimal Type II Polyketide Synthase Using a Yeast Two-Hybrid System  

Microsoft Academic Search

Summary Interactions between proteins that form the 'minimal' type II polyketide synthase in the doxorubicin producing biosynthetic pathway from Streptomyces peucetius were investi- gated using a yeast two-hybrid system (Y2H). Proteins that function as the so called 'chain length factor' (DpsB) and putative transacylase (DpsD) were found to interact with the ketosynthase subunit (DpsA), which can also interact with itself.

Gaetano Castaldo; John Crosby; Paul F. Long

2005-01-01

374

Interactions Among Members of the Bcl2 Protein Family Analyzed with a Yeast Two-Hybrid System  

Microsoft Academic Search

Interactions of the Bcl-2 protein with itself and other members of the Bcl-2 family, including Bcl-X-L, Bcl-X-S, Mcl-1, and Bax, were explored with a yeast two-hybrid system. Fusion proteins were created by linking Bcl-2 family proteins to a LexA DNA-binding domain or a B42 trans-activation domain. Protein-protein interactions were examined by expression of these fusion proteins in Saccharomyces cerevisiae having

Takaaki Sato; Motoi Hanada; Sharon Bodrug; Shinji Irie; Natsuko Iwama; Lawrence H. Boise; Craig B. Thompson; Erica Golemis; Linda Fong; Hong-Gang Wang; John C. Reed

1994-01-01

375

Identification of Regions Involved in Substrate Binding and Dimer Stabilization within the Central Domains of Yeast Hsp40 Sis1  

PubMed Central

Protein folding, refolding and degradation are essential for cellular life and are regulated by protein homeostatic processes such those that involve the molecular chaperone DnaK/Hsp70 and its co-chaperone DnaJ. Hsp70 action is initiated when proteins from the DnaJ family bind an unfolded protein for delivery purposes. In eukaryotes, the DnaJ family can be divided into two main groups, Type I and Type II, represented by yeast cytosolic Ydj1 and Sis1, respectively. Although sharing some unique features both members of the DnaJ family, Ydj1 and Sis1 are structurally and functionally distinct as deemed by previous studies, including the observation that their central domains carry the structural and functional information even in switched chimeras. In this study, we combined several biophysical tools for evaluating the stability of Sis1 and mutants that had the central domains (named Gly/Met rich domain and C-terminal Domain I) deleted or switched to those of Ydj1 to gain insight into the role of these regions in the structure and function of Sis1. The mutants retained some functions similar to full length wild-type Sis1, however they were defective in others. We found that: 1) Sis1 unfolds in at least two steps as follows: folded dimer to partially folded monomer and then to an unfolded monomer. 2) The Gly/Met rich domain had intrinsically disordered characteristics and its deletion had no effect on the conformational stability of the protein. 3) The deletion of the C-terminal Domain I perturbed the stability of the dimer. 4) Exchanging the central domains perturbed the conformational stability of the protein. Altogether, our results suggest the existence of two similar subdomains in the C-terminal domain of DnaJ that could be important for stabilizing each other in order to maintain a folded substrate-binding site as well as the dimeric state of the protein.

Borges, Julio C.; Seraphim, Thiago V.; Mokry, David Z.; Almeida, Fabio C. L.; Cyr, Douglas M.; Ramos, Carlos H. I.

2012-01-01

376

Microfiltration of recombinant yeast cells using a rotating disk dynamic filtration system.  

PubMed

To develop a highly efficient cell harvest step under time constraint, a novel rotating disk dynamic filtration system was studied on the laboratory scale (0.147-ft.(2) nylon membrane) for concentrating recombinant yeast cells containing an intracellular product. The existing cross-flow microfiltration method yielded pseudo-steady state flux values below 25 LMH (L/m(2). h) even at low membrane loadings (10 L/ft.(2)). By creating high shear rates (up to 120,000(-1)) on the membrane surface using a rotating solid disk, this dynamic filter has demonstrated dramatically improved performance, presumably due to minimal cake buildup and reduced membrane fouling. Among the many factors investigated, disk rotating speed, which determines shear rates and flow patterns, was found to be the most important adjustable parameter. Our experimental results have shown that the flux increases with disk rotating speed, increases with transmembrane pressure at higher cell concentrations, and can be sustained at high levels under constant flux mode. At a certain membrane loading level, there was a critical speed below which it behaved similarly to a flat sheet system with equivalent shear. Average flux greater than 200 LMH has been demonstrated at 37-L/ft.(2) loading at maximum speed to complete sixfold concentration and 15-volume diafiltration for less than 100 min. An order of magnitude improvement over the crossflow microfiltration control was projected for large scale production. This superior performance, however, would be achieved at the expense of additional power input and heat dissipation, especially when cell concentration reaches above 80 g dry cell weight (DCW)/L. Although a positive linear relationship between power input and dynamic flux at a certain concentration factor has been established, high cell density associated with high viscosity impacted adversely on effective average shear rates and, eventually, severe membrane fouling, rather than cake formation, would limit the performance of this novel system. PMID:18623499

Lee, S S; Burt, A; Russotti, G; Buckland, B

1995-11-20

377

A novel yeast system for in vivo selection of recognition sequences: defining an optimal c-Myb-responsive element  

PubMed Central

Yeast (Saccharomyces cerevisiae) has proved to be a highly valuable tool in a range of screening methods. We present in this work the design and use of a novel yeast effector–reporter system for selection of sequences recognised by DNA-binding proteins in vivo. A dual HIS3–lacZ reporter under the control of a single randomised response element facilitates both positive growth selection of binding sequences and subsequent quantification of the strength of the selected sequence. A galactose-inducible effector allows discrimination between reporter activation caused by the protein under study and activation due to endogenous factors. The system mimics the physiological gene dosage relationship between transcription factor and target genes in vivo by using a low copy effector plasmid and a high copy reporter plasmid, favouring sequence selectivity. The utility of the novel yeast screening system was demonstrated by using it to refine the definition of an optimal recognition element for the c-Myb transcription factor (MRE). We present screening data supporting an extended MRE consensus closely mimicking known strong response elements and where a sequence of 11 nt influences activity. Novel features include a more strict sequence requirement in the second half-site of the MRE where a T-rich sequence is preferred in vivo.

Berge, Tone; Bergholtz, Stine L.; Andersson, Kristin Brevik; Gabrielsen, Odd S.

2001-01-01

378

Evaluation of the Sensititre system for identification of Enterobacteriaceae.  

PubMed Central

The Sensititre identification system (Seward Laboratory/GIBCO Laboratories) consists of a microplate containing a pattern of 24 biochemicals repeated four times together with an automatic inoculation device and a microcomputer-assisted data interpretation component. A total of 1,415 isolates of Enterobacteriaceae plus 6 isolates of other glucose-fermenting gram-negative bacilli were tested in three hospital laboratories in parallel with API 20E (Analytab Products). Discrepancies were resolved by conventional biochemical testing. Sensititre yielded correct identifications at the species level with 94.6% of the isolates and at the genus level with an additional 1.9%. API 20E yielded correct species identification with 91.1% and genus only identification with an additional 6.7% of the isolates. For the routine identification of clinical Enterobacteriaceae isolates, the Sensititre system compares favorably with API 20E and offers clinical laboratories the economy of a microtiter plate system as well as the benefit of a microcomputer capable of other microbiological and data management applications. Images

Staneck, J L; Vincelette, J; Lamothe, F; Polk, E A

1983-01-01

379

A network identity authentication system based on Fingerprint identification technology  

NASA Astrophysics Data System (ADS)

Fingerprint verification is one of the most reliable personal identification methods. However, most of the automatic fingerprint identification system (AFIS) is not run via Internet/Intranet environment to meet today's increasing Electric commerce requirements. This paper describes the design and implementation of the archetype system of identity authentication based on fingerprint biometrics technology, and the system can run via Internet environment. And in our system the COM and ASP technology are used to integrate Fingerprint technology with Web database technology, The Fingerprint image preprocessing algorithms are programmed into COM, which deployed on the internet information server. The system's design and structure are proposed, and the key points are discussed. The prototype system of identity authentication based on Fingerprint have been successfully tested and evaluated on our university's distant education applications in an internet environment.

Xia, Hong-Bin; Xu, Wen-Bo; Liu, Yuan

2005-11-01

380

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

381

Biometric identification system based on keyboard filtering  

Microsoft Academic Search

We have revised several authentication systems based on biometric technology to resume advantages and disadvantages. Because pure hardware biometric systems of user authentication have low rate on results over computational and economic cost, alternate biometric methods of low computational cost based on software development, are also being evaluated. We have developed a first prototype of a software system to elicitate

Òscar Coltell; J. M. Badfa; Guillermo Torres

1999-01-01

382

On neural networks in identification and control of dynamic systems  

NASA Technical Reports Server (NTRS)

This paper presents a discussion of the applicability of neural networks in the identification and control of dynamic systems. Emphasis is placed on the understanding of how the neural networks handle linear systems and how the new approach is related to conventional system identification and control methods. Extensions of the approach to nonlinear systems are then made. The paper explains the fundamental concepts of neural networks in their simplest terms. Among the topics discussed are feed forward and recurrent networks in relation to the standard state-space and observer models, linear and nonlinear auto-regressive models, linear, predictors, one-step ahead control, and model reference adaptive control for linear and nonlinear systems. Numerical examples are presented to illustrate the application of these important concepts.

Phan, Minh; Juang, Jer-Nan; Hyland, David C.

1993-01-01

383

Identification of finite dimensional models of infinite dimensional dynamical systems  

Microsoft Academic Search

The identification of finite dimensional discrete-time models of deterministic linear and nonlinear infinite dimensional systems from pointwise observations is investigated. The input and output observations are used to construct finite dimensional approximations of the solution and the forcing function which are expanded in terms of a finite element basis. An algorithm to determine a minimal basis to approximate the data

Daniel Coca; Stephen A. Billings

2002-01-01

384

Using ECG as a measure in biometric identification systems  

Microsoft Academic Search

Over the last few years, there has been a number of publications suggesting the use of Electrocardiogram (ECG) as a biometric measure. Motivated by the level of sustainability to attacks the ECG provides, it can be combined in a multi-modal biometric identification system or, when the permanence and collectability issues are not an issue and the false positive margin problem

Babak Nasri; Mouhcine Guennoun; Khalil El-Khatib

2009-01-01

385

Expert system for nuclide identification in gamma spectrum analysis  

Microsoft Academic Search

Gamma spectrum analysis is a standard tool in many fields today. Often the task is to find out the exact composition and concentrations of radionuclides in a measured spectrum. A full manual identification of a complex spectrum requires considerable expertise on the part of the laboratory personnel and takes usually several hours.An expert system coupled with the gamma spectrum analysis

P. A. Aarnio; J. J. Ala-Heikkilä; T. T. Hakulinen; J. T. Routti

1995-01-01

386

PULSE SHAPE DISCRIMINATION FOR THE NUCLEAR MATERIALS IDENTIFICATION SYSTEM (NMIS)  

Microsoft Academic Search

Preliminary results from efforts to implement on-line, fast pulse shape discrimination (PSD) methods in the Nuclear Materials Identification System (NMIS) are discussed. Previous NMIS implementations used fast plastic scintillation detectors that did not allow discrimination of neutrons and gamma rays. Time coincidence signatures acquired by NMIS thus included contributions from both neutrons and gamma rays. It has been shown that

J. S. Neal; W. L. Bryan; C. L. Britton; J. D. Edwards; S. A. Pozzi; J. T. Mihalczo

387

System identification of a bridge with lead–rubber bearings  

Microsoft Academic Search

This study develops an identification algorithm to investigate the dynamic properties of a base-isolated highway bridge equipped with lead–rubber bearings. A linear model is used for the substructure while a bilinear hysteretic model is chosen for the bearing system. The nonlinear hysteresis in the latter is characterized through a backbone curve. Application of Masing criterion enables the multivalue restoring force

R. Y. Tan; M. C. Huang

2000-01-01

388

Large Plastic Scintillation Detectors for the Nuclear Materials Identification System  

Microsoft Academic Search

Future measurements with the Nuclear Materials Identification System require large, on the order of one meter by one meter, detectors for increased sensitivity. As the container to be interrogated or the distance gets larger, increased detector size is required for increased sensitivity. Large liquid and fast plastic scintillation detectors are being designed to meet experiment requirements. Large scintillation detectors present

J. S. Neal; J. T. Mihalczo; M. T. Hiatt; J. D. Edwards

2004-01-01

389

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

390

Methods of Identification of Nonlinear Mechanical Vibrating Systems  

Microsoft Academic Search

Methods for determination of the dynamic characteristics and parameters of mechanical vibrating systems by processing experimental data on controlled vibrations are presented. These methods are intended for construction of mathematical models of objects to be identified and classed as parametric and nonparametric methods. The quadrature formulas of the nonparametric-identification method are derived by inverting the integral parameters of approximate analytical

N. P. Plakhtienko

2000-01-01

391

Identification of uncertain nonlinear systems for robust fuzzy control.  

PubMed

In this paper, we consider fuzzy identification of uncertain nonlinear systems in Takagi-Sugeno (T-S) form for the purpose of robust fuzzy control design. The uncertain nonlinear system is represented using a fuzzy function having constant matrices and time varying uncertain matrices that describe the nominal model and the uncertainty in the nonlinear system respectively. The suggested method is based on linear programming approach and it comprises the identification of the nominal model and the bounds of the uncertain matrices and then expressing the uncertain matrices into uncertain norm bounded matrices accompanied by constant matrices. It has been observed that our method yields less conservative results than the other existing method proposed by Skrjanc et al. (2005). With the obtained fuzzy model, we showed the robust stability condition which provides a basis for different robust fuzzy control design. Finally, different simulation examples are presented for identification and control of uncertain nonlinear systems to illustrate the utility of our proposed identification method for robust fuzzy control. PMID:19683234

Senthilkumar, D; Mahanta, Chitralekha

2010-01-01

392

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

2010-12-01

393

Hybrid System Modeling and Event Identification  

Microsoft Academic Search

. Hybrid control systems contain two distinct types of systems,continuous state and discrete-state, that interact with each other. Their studyis essential in designing sequential supervisory controllers for continuousstatesystems, and it is central in designing control systems with high degreeof autonomy.After an introduction to intelligent autonomous control and its relation tohybrid control, models for the plant, controller, and interface are introduced.The

Panos J. Antsaklis; Michael D. Lemmon; James A. Stiver

1993-01-01

394

Screening of hepatocyte proteins binding with the middle surface protein of the hepatitis B virus by the yeast two?hybrid system.  

PubMed

The effect of the middle hepatitis B virus surface protein (MHBs) remains to be elucidated. To investigate the biological function of the MHBs protein, the present study performed yeast two?hybrid screening to search for proteins that interact with the MHBs protein in hepatocytes. The bait plasmid expressing the MHBs protein was constructed by cloning the gene of the MHBs protein into pGBKT7, then the recombinant plasmid DNA was transformed into AH109 yeast (a type). The transformed yeast AH109 was mated with yeast Y187 (? type) containing the liver cDNA library plasmid in 2X yeast peptone dextrose adenine (YPDA) medium. The mated diploid yeast was plated on quadruple dropout medium (SD/?Trp?Leu?His?Ade) containing X???gal for selection and screening. Following extracting and sequencing of the plasmids from positive (blue) colonies, the sequence analysis was conducted and analyzed by bioinformatics methods. Two colonies were selected and sequenced. Among them, one was the human DNA sequence from the clone RP11?490D19 on chromosome 9 and the other was homo sapiens 12 BAC RP11?180M15 (Roswell Park Cancer Institute Human BAC Library). The yeast two?hybrid system is an effective method for identifying hepatocyte proteins that interact with MHBs. The MHBs protein binds with different proteins suggesting that it has multiple functions in vivo. PMID:24676405

Li, Zhiqun; Linghu, Enqiang; Cheng, Jun

2014-06-01

395

Gene engineering in yeast for biodegradation: Immunological cross-reactivity among cytochrome p-450 system proteins of saccharomyces cerevisiae and candida tropicalis  

SciTech Connect

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 yeast, Saccharomyces cerevisiae, and an n-alkane utilizing yeast, Candida tropicalis ATCC750 are examined. Standard methods were used to purify cytochrome P-450 and NADPH-cytochrome c (P-450) reductase proteins from cells cultured by semi-anaerobic glucose fermentation (S. cerevisiae, C. tropicalis) and by growth on tetradecane (C. tropicalis). Polyvalent antisera prepared in rabbits to some of these proteins were used in tests of immunological relatedness among the purified proteins using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and nitrocellulose filter immunoblots. The results provide evidence for gene relationships which should prove useful in gene isolation and subsequent engineering of P-450 enzyme systems in yeast.

Loper, J.C.; Chen, C.; Dey, C.R.

1993-01-01

396

Identification of a mechanical vibration system  

NASA Technical Reports Server (NTRS)

The actual values of the parameters of a precision instrument assembly vibration system are determined according to experimental amplitude-frequency characteristics. The assembly is considered as a complex mechanical vibrating system, consisting of elements with concentrated and distributed parameters. A calculation procedure was compiled.

Korablev, S. S.; Filatov, Y. Y.; Shapin, V. I.

1973-01-01

397

Molecular cloning of amphioxus uncoupling protein and assessment of its uncoupling activity using a yeast heterologous expression system  

SciTech Connect

Research highlights: {yields} Invertebrates, for example amphioxus, do express uncoupling proteins. {yields} Both the sequence and the uncoupling activity of amphioxus UCP resemble UCP2. {yields} UCP1 is the only UCP that can form dimer on yeast mitochondria. -- Abstract: The present study describes the molecular cloning of a novel cDNA fragment from amphioxus (Branchiostoma belcheri) encoding a 343-amino acid protein that is highly homologous to human uncoupling proteins (UCP), this protein is therefore named amphioxus UCP. This amphioxus UCP shares more homology with and is phylogenetically more related to mammalian UCP2 as compared with UCP1. To further assess the functional similarity of amphioxus UCP to mammalian UCP1 and -2, the amphioxus UCP, rat UCP1, and human UCP2 were separately expressed in Saccharomyces cerevisiae, and the recombinant yeast mitochondria were isolated and assayed for the state 4 respiration rate and proton leak, using pYES2 empty vector as the control. UCP1 increased the state 4 respiration rate by 2.8-fold, and the uncoupling activity was strongly inhibited by GDP, while UCP2 and amphioxus UCP only increased the state 4 respiration rate by 1.5-fold and 1.7-fold in a GDP-insensitive manner, moreover, the proton leak kinetics of amphioxus UCP was very similar to UCP2, but much different from UCP1. In conclusion, the amphioxus UCP has a mild, unregulated uncoupling activity in the yeast system, which resembles mammalian UCP2, but not UCP1.

Chen, Kun [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China)] [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China); Sun, Guoxun [Department of Hematology, Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001 (China)] [Department of Hematology, Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001 (China); Lv, Zhiyuan; Wang, Chen [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China)] [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China); Jiang, Xueyuan, E-mail: xueyuanjiang@yahoo.com.cn [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China)] [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China); Li, Donghai, E-mail: lidonghai@gmail.com [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China)] [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China); Zhang, Chenyu, E-mail: cyzhang@nju.edu.cn [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China)] [Jiangsu Diabetes Research Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu (China)

2010-10-01

398

A protein interaction map of soybean mosaic virus strain G7H based on the yeast two-hybrid system.  

PubMed

A protein interaction map of Soybean mosaic virus (SMV) strain G7H was generated by the yeast two-hybrid system. Clones encoding the genes P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa, NIb, and CP were fused downstream of the GAL4 binding domain (GAL4-BD) and of the GAL4 activation domain (GAL4-AD). The GAL4-BD and GAL4-AD fusion derivatives of each gene were co-transformed into yeast and transformants in which interaction took place were identified on selective media. Interacting fusion proteins were extracted from the yeast cells, run on SDS-PAGE gels and finally checked by Western blotting with GAL4 polyclonal antibodies. Strong interactions were detected between the pairs CP/CP, HC-Pro/HC-Pro, NIa/NIa, and CP/HC-Pro. Relatively weak but significant interaction was detected between VPg and NIa. Although not all of the protein-protein interactions previously reported in other potyviruses were detected, the interactions revealed here were, in general, similar to those reported previously. PMID:15359133

Kang, Sung-Hwan; Lim, Won-Seok; Kim, Kook-Hyung

2004-08-31

399

Xplor 2--an optimized transformation/expression system for recombinant protein production in the yeast Arxula adeninivorans.  

PubMed

Combining ease of genetic manipulation and fermentation with the ability to secrete and to glycosylate proteins in the basic eukaryotic manner, Arxula adeninivorans provides an attractive expression platform. Based on a redesign of the basic vector, a new Arxula vector system, Xplor 2, for heterologous gene expression was established, which allows (1) the construction of expression plasmids for supertransformation of A. adeninivorans strains secreting target proteins of biotechnological interest and (2) the integration of small vector cassettes consisting of yeast DNA sequences only. For this purpose, a set of modules including the ATRP1m selection-marker module, expression modules for constitutive expression of the genes phyK (Klebsiella-derived phytase) and IFNalpha2a (human interferon alpha), the HARS (Hansenula polymorpha autonomous replication sequence) for autonomous replication and the chaperone module AHSB4 promoter -HpCNE1 gene (calnexin) -PHO5 terminator to improve secretion efficiency were constructed and integrated in various combinations in the basic vector Xplor 2. After removal of the complete Escherichia coli-based plasmid parts (resistance marker, ColE1 ori and f1(-) origin), the remaining yeast-based linear vector fragment with or without rDNA targeting sequences were transformed as yeast rDNA integrative expression cassettes and yeast integrative expression cassettes (YICs), respectively, and the resulting strains were tested for their capacity to secrete PhyK or IFNalpha2a. Maximal expression levels were consistently obtained using YICs for transformation irrespective of whether or not they carry HARS and/or calnexin modules. It is recommended that at least 50 such transformants be analyzed to ensure selection of the best transformants. PMID:19672589

Böer, Erik; Piontek, Michael; Kunze, Gotthard

2009-09-01

400

Los Alamos Scientific Laboratory electronic vehicle identification system  

SciTech Connect

A three-digit electronic identification system is described. Digits may be decimal (1000 combinations) or hexidecimal (8192 combinations). Battery-powered transponders are interrogated with a lower-power (1 W) radio signal. Line-of-sight interrogations up to 33 m (100 ft) are possible. Successful interrogations up to 7 m (20 ft) are possible for concealed transponders (that is, in the engine compartment). Vehicles moving at high rates of speed can be interrogated. This system provides data in a computer-compatible RS232 format. The system can be used for other applications with little or no modification. A similar system is in present use for identification and temperature monitoring of livestock. No unforeseen problems exist for expanding the coding scheme to identify larger numbers of objects.

Landt, J.A.; Bobbett, R.E.; Koelle, A.R.; Salazar, P.H.

1980-01-01

401

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

402

Evaluation of the acetaldehyde production and degradation potential of 26 enological Saccharomyces and non- Saccharomyces yeast strains in a resting cell model system  

Microsoft Academic Search

Acetaldehyde is relevant for wine aroma, wine color, and microbiological stability. Yeast are known to play a crucial role\\u000a in production and utilization of acetaldehyde during fermentations but comparative quantitative data are scarce. This research\\u000a evaluated the acetaldehyde metabolism of 26 yeast strains, including commercial Saccharomyces and non-Saccharomyces, in a reproducible resting cell model system. Acetaldehyde kinetics and peak values

Erhu Li; Ramón Mira de Orduña

403

Biosorption of Basic Violet 5BN and Basic Green by waste brewery’s yeast from single and multicomponent systems  

Microsoft Academic Search

Background and aim  The biosorption of Basic Violet 5BN (BV) and Basic Green (BG) by waste brewery’s yeast (WBY) from single and binary systems\\u000a was investigated.\\u000a \\u000a \\u000a \\u000a \\u000a Results and discussion  For the single system, the adsorption of both dyes is pH-dependent and the optimum value is 5.0. At a lower initial concentration,\\u000a the kinetic data agree well with both pseudo-first-order and pseudo-second-order models,

Yunhai Wu; Li Jiang; YaJun Wen; JianXin Zhou; Shixun Feng

404

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

405

Neurodynamical Systems for Cognition and Target Identification.  

National Technical Information Service (NTIS)

Our study of cognitive automated target recognition based on the neural paradigm for information processing reveals that inclusion of bifurcation and synchronicity (phase-locking) in network dynamics can markedly improve the performance of ATR systems. Th...

N. H. Farhat

1994-01-01

406

78 FR 58785 - Unique Device Identification System  

Federal Register 2010, 2011, 2012, 2013

...Healthcare Common Procedural Coding System Level II code; indications that a device is mercury free, Di(2- ethylhexyl)phthalate free, and thimerosal free; information on recalls, storage and handling conditions, hazardous warnings,...

2013-09-24

407

Real-Time Person Identification System for Intelligent Digital TV  

Microsoft Academic Search

Intelligent digital TV (iDTV) is an enhanced digital TV that can automatically provide user-personalized services for each audience. For the user-personalized services, the iDTV should recognize audiences in real-time. Thus, in this paper, we define a novel structure of the iDTV and propose a real-time person identification system embedded in the iDTV. The proposed system consists of three phases: preprocessing

Min-Cheol Hwang; Le Thanh Ha; Seung-Kyun Kim; Sung-Jea Ko

2007-01-01

408

Non-parametric identification of non-linear oscillating systems  

Microsoft Academic Search

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

M. Peifer; J. Timmer; H. U. Voss

2003-01-01

409

Non-linear system identification using neural networks  

Microsoft Academic Search

Multi-layered neural networks offer an exciting alternative for modelling complex non-linear systems. This paper investigates the identification of discrete-time nonlinear systems using neural networks with a single hidden layer. New parameter estimation algorithms are derived for the neural network model based on a prediction error formulation and the application to both simulated and real data is included to demonstrate the

S. CHEN; S. A. BILLINGS; P. M. GRANT

1990-01-01

410

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

...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)...

2014-04-01

411

Bright Fluorescence Monitoring System Utilizing Zoanthus sp. Green Fluorescent Protein (ZsGreen) for Human G-Protein-Coupled Receptor Signaling in Microbial Yeast Cells  

PubMed Central

G-protein-coupled receptors (GPCRs) are currently the most important pharmaceutical targets for drug discovery because they regulate a wide variety of physiological processes. Consequently, simple and convenient detection systems for ligands that regulate the function of GPCR have attracted attention as powerful tools for new drug development. We previously developed a yeast-based fluorescence reporter ligand detection system using flow cytometry. However, using this conventional detection system, fluorescence from a cell expressing GFP and responding to a ligand is weak, making detection of these cells by fluorescence microscopy difficult. We here report improvements to the conventional yeast fluorescence reporter assay system resulting in the development of a new highly-sensitive fluorescence reporter assay system with extremely bright fluorescence and high signal-to-noise (S/N) ratio. This new system allowed the easy detection of GPCR signaling in yeast using fluorescence microscopy. Somatostatin receptor and neurotensin receptor (implicated in Alzheimer’s disease and Parkinson’s disease, respectively) were chosen as human GPCR(s). The facile detection of binding to these receptors by cognate peptide ligands was demonstrated. In addition, we established a highly sensitive ligand detection system using yeast cell surface display technology that is applicable to peptide screening, and demonstrate that the display of various peptide analogs of neurotensin can activate signaling through the neurotensin receptor in yeast cells. Our system could be useful for identifying lead peptides with agonistic activity towards targeted human GPCR(s).

Nakamur