These are representative sample records from Science.gov related to your search topic.
For comprehensive and current results, perform a real-time search at Science.gov.
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

Collaborative evaluation of the Abbott yeast identification system.  

PubMed Central

The Abbott yeast identification system (Abbott Laboratories, Diagnostics Division, Irving, Tex.) is a 24-h, instrumental method for identifying medically important yeasts, based on matrix analysis of 19 biochemical reactions and the germ tube test. The system was evaluated in two clinical laboratories by using 179 coded isolates, which included a high percentage of the less frequently encountered species. Based upon results with these coded isolates and from previously obtained laboratory data, the system software was adjusted and accuracy of the yeast identification system was further evaluated with 378 isolates from clinical sources. Of the 378 clinical yeast isolates tested, 364 (96%) were correctly identified with the Abbott system. Isolates were deliberately selected so that germ tube-positive isolates made up less than 10% of the clinical isolates tested. PMID:6381526

Cooper, B H; Prowant, S; Alexander, B; Brunson, D H

1984-01-01

3

A Bipartite Recombinant Yeast System for the Identification of Subtype-Selective Estrogen Receptor Ligands  

Microsoft Academic Search

Since the estrogen receptor ? (ER?) and ? (ER?) are thought to mediate different biological effects, there is intense interest\\u000a in designing or screening subtype-selective ER ligands. Here, we constructed a biosensor identified as bipartite recombinant\\u000a yeast system (BRYS) to screen and evaluate subtype-selective ER ligands. Uniform design and immunoblotting was used to determine\\u000a an optimal dose of copper which

Kaiwei Liang; Liuqing Yang; Zhimin Xiao; Jian Huang

2009-01-01

4

[A comparative study between the Vitek YBC and Microscan Walk Away RYID automated systems with conventional phenotypic methods for the identification of yeasts of clinical interest].  

PubMed

The aim of this study was to compare the identification of clin- ically relevant yeasts by the Vitek YBC and Microscan Walk Away RYID automated methods with conventional phenotypic methods. One hundred and ninety three yeast strains isolated from clinical samples and five controls strains were used. All the yeasts were identified by the automated methods previously mentioned and conventional phenotypic methods such as carbohydrate assimilation, visualization of microscopic morphology on corn meal agar and the use of chromogenic agar. Variables were assessed by 2 x 2 contingency tables, McNemar's Chi square, the Kappa index, and concordance values were calculated, as well as major and minor errors for the automated methods. Yeasts were divided into two groups: (1) frequent isolation and (2) rare isolation. The Vitek YBC and Microscan Walk Away RYID systems were concordant in 88.4 and 85.9% respectively, when compared to conventional phenotypic methods. Although both automated systems can be used for yeasts identification, the presence of major and minor errors indicates the possibility of misidentifications; therefore, the operator of this equipment must use in parallel, phenotypic tests such as visualization of microscopic morphology on corn meal agar and chromogenic agar, especially against infrequently isolated yeasts. Automated systems are a valuable tool; however, the expertise and judgment of the microbiologist are an important strength to ensure the quality of the results. PMID:25558750

Ferrara, Giuseppe; Mercedes Panizol, Maria; Mazzone, Marja; Delia Pequeneze, Maria; Reviakina, Vera

2014-12-01

5

Rapid methods for identification of yeasts.  

PubMed Central

Opportunistic infections by yeasts have been implicated as one of the major causes of complications in the compromised patient. Rapid recognition and identification of these yeasts is essential for patient management, but conventional liquid medium methods for completing identification tests are cumbersome and time consuming. Rapid tests have been devised based on modifications of methods commonly used in bacteriology. These rapid methods included tests for carbohydrate and nitrate assimilation, fermentation, and urease production. These were compared with several current methods for accuracy of results, for time to final identification, and for economy of time and reagents. In addition, the usual tests for pseudogerm tube formation, for production of hyphae or pseudohyphae, and for growth temperatures were included. The rapid tests achieved 96% or better accuracy compared with expected results, and 46 species of yeasts were identified in 1 to 2 days compared with the 10 to 14 days required by conventional liquid culture methods. Images PMID:1241586

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

1975-01-01

6

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. PMID:9227858

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

1997-01-01

7

Identification of yeast cell cycle transcription factors using dynamic system model  

Microsoft Academic Search

To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs) that regulate the expression of cell cycle-regulated genes. We developed a method to identify cell cycle TFs in yeast by integrating current ChIP-chip, mutant, transcription factor binding site (TFBS), and cell cycle gene expression data. We identified 17 cell cycle TFs, 12 of

Wei-Sheng Wu

2010-01-01

8

Identification of proteins that interact with a protein of interest: Applications of the yeast two-hybrid system  

Microsoft Academic Search

The yeast two-hybrid system is a molecular genetic test for protein interaction. Here we describe a step by step procedure to screen for proteins that interact with a protein of interest using the two-hybrid system. This process includes, construction and testing of the bait plasmid, screening a plasmid library for interacting fusion proteins, elimination of false positives and deletion analysis

R. Daniel Gietz; Barbara Triggs-Raine; Anne Robbins; Kevin C. Graham; Robin A. Woods

1997-01-01

9

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 Central

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

2014-01-01

10

Multicenter evaluation of the new VITEK 2 advanced colorimetric yeast identification card.  

PubMed

The performance of the new VITEK 2 Advanced Colorimetry yeast identification (YST) card for use with the VITEK 2 system (bioMérieux, Inc., Hazelwood, MO) was compared to that of the API 20C AUX (API) system (bioMérieux SA, Marcy-l'Etoile, France) in a multicenter evaluation. A total of 12 quality control, 64 challenge, and 623 clinical yeast isolates were used in the study. Comparisons of species identification, platform reliability, and substrate reproducibility were made between YST and API, with API considered the reference standard. Quality control testing to assess system and substrate reproducibility matched expected results >/=95% of the time. The YST card correctly identified 100% of the challenge strains, which covered the species range of the manufacturer's performance claims. Using clinical isolates, the YST card correctly identified 98.5%, with 1.0% of isolates incorrectly identified and 0.5% unidentified. Among clinical isolates, the YST card generated fewer low-discrimination results (18.9%) than did API (30.0%). The time to identification with YST was 18 h, compared to 48 to 72 h with API. The colorimetric YST card used with the VITEK 2 provides a highly automated, objective yeast identification method with excellent performance and reproducibility. We found this system useful for timely and accurate identification of significant yeast species in the clinical microbiology laboratory. PMID:17267631

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

2007-04-01

11

Microfermentation Test For Identification Of Yeast  

NASA Technical Reports Server (NTRS)

Microfermentation test developed as supplementary method for use in identifying yeasts, especially in clinical and environmental studies. In comparison with traditional fermentation tests, simpler and easier, and requiries less equipment, material, and laboratory space. Results obtained in days instead of weeks.

Pierson, D. L.; Mishra, S. K.; Molina, Thomas C.

1995-01-01

12

Molecular and phenotypic identification of the yeast pathogen Candida dubliniensis  

Microsoft Academic Search

Candida dubliniensis is an emerging yeast pathogen generally misclassified as Candida albicans by standard diagnostic procedures. This study examined the efficiency of molecular identification, based on a discriminative PCR test, in a prospective study on the prevalence of C. dubliniensis among 103 oropharyngeal isolates from HIV-infected individuals or transplant recipients, and 30 vaginal isolates. All of the isolates had been

Oliver Kurzai; Hans-Christian Korting; Dag Harmsen; Wilfried Bautsch; Michael Molitor; Matthias Frosch; Fritz A. Mühlschlegel

2000-01-01

13

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. PMID:23467187

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

2013-01-01

14

[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

15

The yeast expression system for recombinant glycosyltransferases  

Microsoft Academic Search

Glycosyltransferases are increasingly being used for in vitro synthesis of oligosaccharides. Since these enzymes are difficult to purify from natural sources, expression systems for soluble forms of the recombinant enzymes have been developed. This review focuses on the current state of development of yeast expression systems. Two yeast species have mainly been used, i.e. Saccharomyces cerevisiae and Pichia pastoris. Safety

Martine Malissard; Steffen Zeng; Eric G. Berger

1999-01-01

16

Yeast identification in floral nectar of Mimulus aurantiacus (Invited)  

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

17

Production of serpins using yeast expression systems  

Microsoft Academic Search

Serpins occupy a unique niche in the field of biology. As more of them are discovered, the need to produce sufficient quantities of each to aid experimental and therapeutic research increases. Yeast expression systems are well suited for the production of recombinant serpins. The genetics of many yeast species is well understood and readily manipulated to induce the targeted over-production

Philip A. Pemberton; Phillip I. Bird

2004-01-01

18

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

PubMed Central

Background The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species. Methods A total number of 270 yeast strains including 169 Candida albicans, 33 C. tropicalis, 24 C. glabrata, 18 C. parapsilosis, 12 C. krusei, 5 Trichosporon spp., 4 C. kefyr, 2 C. lusitaniae, 1 Saccharomyces cerevisiae and 1 Geotrichum candidum were included. The strains were first identified by germ tube test, morphological characteristics on cornmeal tween 80 agar and Vitek 32 and API 20 C AUX systems. In parallel, they were also streaked onto CHROMagar Candida and bismuth sulphite glucose glycine yeast agar plates. The results were read according to the color, morphology of the colonies and the existance of halo around them after 48 hours of incubation at 37°C. Results The sensitivity and specificity values for C. albicans strains were found to be 99.4, 100% for CHROMagar Candida and 87.0, 75.2% for BiGGY agar, respectively. The sensitivity of CHROMagar Candida to identify C. tropicalis, C. glabrata and C. krusei ranged between 90.9 and 100% while the specificity was 100%. The sensitivity rates for BiGGY agar were 66.6 and 100% while the specificity values were found to be 95.4 and 100% for C. tropicalis and C. krusei, respectively. Conclusions It can be concluded that the use of CHROMagar Candida is an easy and reliable method for the presumptive identification of most commonly isolated Candida species especially C. albicans, C. tropicalis and C. krusei. The lower sensitivity and specificity of BiGGY agar to identify commonly isolated Candida species potentially limits the clinical usefulness of this agar. PMID:14613587

Yücesoy, Mine; Marol, Serhat

2003-01-01

19

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

PubMed

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

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

2012-01-01

20

Coenzyme Q systems in ascomycetous black yeasts  

Microsoft Academic Search

72 Strains belonging to 44 species of ascomycetous black yeasts were analyzed for their coenzyme Q systems. Prevalent were Q-10 and dihydrogenated Q-10 systems. Members of the Dothidealean suborder Dothideineae have Q-10 (H2), while those belonging to the suborder Pseudosphaeriineae mostly have Q-10. The anamorph genus Exophiala Carmichael and the teleomorph genus Capronia Sacc. seem to be heterogenous.

Y. Yamada; Kazue Sugihara; G. W. Eijk; H. J. Roeijmans; G. S. Hoog

1989-01-01

21

`Calling Cards' method for high-throughput identification of targets of yeast DNA-binding proteins  

E-print Network

`Calling Cards' method for high-throughput identification of targets of yeast DNA-binding proteins--a `calling card'--that provides a record of that protein's visit to that region of the genome. The calling card is the yeast Ty5 retrotransposon, whose integrase interacts with the Sir4 protein. If Sir4

Mitra, Rob

22

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

Microsoft Academic Search

A molecular approach is used for the identification of yeast isolated from table olives. Our results validate those obtained in the past by the classical biochemical methodology. Yeast were isolated from both aerobically and anaerobically processed black table olives and also from canned seasoned green table olives. Molecular identification methodology used included restriction pattern analysis of both PCR-amplified 5.8S rRNA

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

2006-01-01

23

DETECTION, IDENTIFICATION AND ENUMERATION METHODS FOR SPOILAGE YEASTS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Microbiological spoilage of foods and beverages is caused by a wide variety of bacteria, molds and yeasts. Yeast growth is favored by low pH, generally 5.5 or lower, and by the presence of sugars, organic acids and other easily metabolized carbon sources. Yeast spoilage is often manifested by grow...

24

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

PubMed

This manuscript describes the effect of a glucosamine complex and its different constituents on the metabolism of yeast cells. Indeed, the yeast model biosystem offers important advantages in the understanding of basic cellular and molecular processes. For example, the possibility to differentiate aerobic and anaerobic metabolism allows the measurement of glycolysis and mitochondria importance in the control of energetic metabolism and stress-responsive. Yeast growth and division can be controlled efficiently and effectively by adjusting environmental conditions that mimic some aspect of those experienced by chondrocytes in an osteoarthritic milieu, such as low oxygen and nutriment availabilities, high oxidative stress, etc. The glucosamine complex or some of its components (glucosamine sulphate, MSM, Ribes nigrum and silicon) enhanced cellular proliferation and CO(2) production of yeast cells cultured under severe conditions. In addition, it allows a larger output of protons from the cells into the medium. Glucosamine complex supplementation also boosted cellular resistance to stresses such as heat shock, H(2)O(2)-induced peroxidation and ethanol. The beneficial effects of the complex were primarily due to R. nigrum and to glucosamine sulphate components. The protective effect of the glucosamine complex can be explained by an increase of cellular energy level through intensification of mitochondrial functionality and intracellular machinery (anaerobic glycolysis). An additional effect on protein kinase activation is not unlikely. PMID:18662850

Dillemans, Monique; Appelboom, Thierry; Van Nedervelde, Laurence

2008-11-01

25

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

26

Research paper Rapid identification of CD4+ T-cell epitopes using yeast displaying  

E-print Network

Research paper Rapid identification of CD4+ T-cell epitopes using yeast displaying pathogen 2008 Accepted 13 March 2008 Available online 14 April 2008 Identification of CD4+ T-cell epitopes, and autoantigens. Here we report a facile, accurate, and high-throughput method for CD4+ T-cell epitope

Zhao, Huimin

27

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). PMID:23678071

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

2013-01-01

28

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. PMID:24048537

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

29

Comparative analysis of Gram's stain, PNA-FISH and Sepsityper with MALDI-TOF MS for the identification of yeast direct from positive blood cultures.  

PubMed

Fungaemia diagnosis could be improved by reducing the time to identification of yeast from blood cultures. This study aimed to evaluate three rapid methods for the identification of yeast direct from blood cultures; Gram's stain analysis, the AdvanDX Peptide Nucleic Acid in Situ Hybridisation Yeast Traffic Light system (PNA-FISH YTL) and Bruker Sepsityper alongside matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-TOF MS). Fifty blood cultures spiked with a known single yeast strain were analysed by blinded operators experienced in each method. Identifications were compared with MALDI-TOF MS CHROMagar Candida culture and ITS rRNA sequence-based identifications. On first attempt, success rates of 96% (48/50) and 76% (36/50) were achieved using PNA-FISH YTL and Gram's stain respectively. MALDI-TOF MS demonstrated a success rate of 56% (28/50) when applying manufacturer's species log score thresholds and 76% (38/50) using in-house parameters, including lowering the species log score threshold to >1.5. In conclusion, PNA-FISH YTL demonstrated a high success rate successfully identifying yeast commonly encountered in fungaemia. Sepsityper(™) with MALDI-TOF MS was accurate but increased sensitivity is required. Due to the misidentification of commonly encountered yeast Gram's stain analysis demonstrated limited utility in this setting. PMID:24862948

Gorton, Rebecca L; Ramnarain, P; Barker, K; Stone, N; Rattenbury, S; McHugh, T D; Kibbler, C C

2014-10-01

30

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

PubMed Central

Computer-based Fourier-transform infrared spectroscopy (FT-IR) was used to identify food-borne, predominantly fermentative yeasts. Dried yeast suspensions provided the films suitable for FT-IR measurement. Informative windows in the spectrum were selected and combined to achieve optimal results. A reference spectrum library was assembled, based on 332 defined yeast strains from international yeast collections and our own isolates. All strains were identified with conventional methods using physiological and morphological characteristics. In order to assess identification quality, another 722 unknown yeast isolates not included in the reference spectrum library were identified both by classical methods and by comparison of their FT-IR spectra with those of the reference spectrum library. Ninety-seven and one-half percent of these isolates were identified correctly by FT-IR. Easy handling, rapid identification within 24 h when starting from a single colony, and a high differentiation capacity thus render FT-IR technology clearly superior to other routine methods for the identification of yeasts. PMID:9603836

Kümmerle, Michael; Scherer, Siegfried; Seiler, Herbert

1998-01-01

31

Implant identification system.  

PubMed

Osseointegrated oral implantology has become a widespread option of dental care. A universal system of implant identification is required to enable dentists, patients and participating third parties to accurately identify a particular implant and historically record and follow its bio-clinical status. A simple system, based on the existing FDI two-digit tooth identification system is presented. PMID:10858743

Colgan, P J

1999-04-01

32

Identification of Yeasts From the Suwannee River Florida Estuary1  

PubMed Central

The yeast flora of the Suwannee River estuary in Florida has been studied. The predominant genera were Candida and Rhodotorula; however, the yeast most frequently isolated was Cryptococcus laurentii. Nine ascosporogenous species were isolated, with Hansenula saturnus predominating. The salinity range of the sediments was 0.4 to 20.6%; in the estuary water, 0.07 to 0.25%; and in the open Gulf of Mexico, 18 to 20%. Images PMID:16349995

Lazarus, C. R.; Koburger, J. A.

1974-01-01

33

Mitochondrial Telomeres as Molecular Markers for Identification of the Opportunistic Yeast Pathogen Candida parapsilosis  

PubMed Central

Recent studies have demonstrated that a large number of organisms carry linear mitochondrial DNA molecules possessing specialized telomeric structures at their ends. Based on this specific structural feature of linear mitochondrial genomes, we have developed an approach for identification of the opportunistic yeast pathogen Candida parapsilosis. The strategy for identification of C. parapsilosis strains is based on PCR amplification of specific DNA sequences derived from the mitochondrial telomere region. This assay is complemented by immunodetection of a protein component of mitochondrial telomeres. The results demonstrate that mitochondrial telomeres represent specific molecular markers with potential applications in yeast diagnostics and taxonomy. PMID:11923346

Nosek, Jozef; Tomáška, L'ubomír; Ry?ovská, Adriana; Fukuhara, Hiroshi

2002-01-01

34

Comparison and optimization of two MALDI-TOF MS platforms for the identification of medically relevant yeast species.  

PubMed

The rapid identification of yeast is essential for the optimization of antifungal therapy. The objective of our study was to evaluate two matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platforms, the bioMérieux VITEK MS (IVD Knowledgebase v.2.0) and Bruker Biotyper (software version 3.1), for the rapid identification of medically relevant yeast. One hundred and seventeen isolates, representing six genera and 18 species, were analyzed using multiple direct smear methods to optimize identification. Sequence analysis was the gold standard for comparison. Isolates were analyzed with VITEK MS using the direct smear method +/- a 25 % formic acid on-plate extraction. For Biotyper, isolates were analyzed using direct smear without formic acid, and with 25 % and 100 % formic acid on-plate extractions. When all methods were included, VITEK MS correctly identified 113 (96.6 %) isolates after 24 h with one misidentification, and Biotyper correctly identified 77 (65.8 %) isolates using a threshold of ?2.0 with no misidentifications. Using a revised threshold of ?1.7, Biotyper correctly identified 103 (88.0 %) isolates, with 3 (2.6 %) misidentifications. For both platforms, the number of identifications was significantly increased using a formic acid overlay (VITEK MS, p?identification (p?yeast identification on both MS platforms, and more isolates are identified using the VITEK MS system (p?

Pence, M A; McElvania TeKippe, E; Wallace, M A; Burnham, C-A D

2014-10-01

35

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data  

E-print Network

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Abstract Mounting evidence shows that many protein complexes are conserved in evolution. Here we use combines protein interaction data, that are available for each of the two species, and orthology

Shamir, Ron

36

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. PMID:16517841

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

2006-01-01

37

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 PMID:3937494

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

1985-01-01

38

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. PMID:24822114

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

2014-01-01

39

Identification of yeast and human 5-aminoimidazole-4-carboxamide-1-?-d-ribofuranoside (AICAr) transporters.  

PubMed

5-Aminoimidazole-4-carboxamide-1-?-d-ribofuranoside (AICAr) is the precursor of the active monophosphate form (AICAR), a small molecule with potent anti-proliferative and low energy mimetic properties. The molecular bases for AICAR toxicity at the cellular level are poorly understood. Here, we report the isolation and characterization of several yeast AICAr-hypersensitive mutants. Identification of the cognate genes allowed us to establish that thiamine transporters Thi7 and Thi72 can efficiently take up AICAr under conditions where they are overexpressed. We establish that, under standard growth conditions, Nrt1, the nicotinamide riboside carrier, is the major AICAr transporter in yeast. A study of AICAR accumulation in human cells revealed substantial disparities among cell lines and confirmed that AICAr enters cells via purine nucleoside transporters. Together, our results point to significant differences between yeast and human cells for both AICAr uptake and AICAR accumulation. PMID:24778186

Ceschin, Johanna; Saint-Marc, Christelle; Laporte, Jean; Labriet, Adrien; Philippe, Chloé; Moenner, Michel; Daignan-Fornier, Bertrand; Pinson, Benoît

2014-06-13

40

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

PubMed

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

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

2010-06-30

41

Systematic identification of cell size regulators in budding yeast  

PubMed Central

Cell size is determined by a complex interplay between growth and division, involving multiple cellular pathways. To identify systematically processes affecting size control in G1 in budding yeast, we imaged and analyzed the cell cycle of millions of individual cells representing 591 mutants implicated in size control. Quantitative metric distinguished mutants affecting the mechanism of size control from the majority of mutants that have a perturbed size due to indirect effects modulating cell growth. Overall, we identified 17 negative and dozens positive size control regulators, with the negative regulators forming a small network centered on elements of mitotic exit network. Some elements of the translation machinery affected size control with a notable distinction between the deletions of parts of small and large ribosomal subunit: parts of small ribosomal subunit tended to regulate size control, while parts of the large subunit affected cell growth. Analysis of small cells revealed additional size control mechanism that functions in G2/M, complementing the primary size control in G1. Our study provides new insights about size control mechanisms in budding yeast. PMID:25411401

Soifer, Ilya; Barkai, Naama

2014-01-01

42

Robust identification of stabilizable systems  

Microsoft Academic Search

For stabilizable systems for which a stabilizing controller is known approximately, the authors consider system identification in the graph, gap and chordal metrics using robust H? identification of the closed-loop transfer function. Error bounds are derived showing that robust convergence is guaranteed. Two notions of robust identification of stable systems are compared, and an alternative identification technique, based on smoothing,

J. R. Partington; P. M. Makila

1991-01-01

43

A Combined Yeast\\/Bacteria Two-hybrid System  

Microsoft Academic Search

Two-hybrid screening is a standard method used to iden- tify and characterize protein-protein interactions and has become an integral component of many proteomic inves- tigations. The two-hybrid system was initially developed using yeast as a host organism. However, bacterial two- hybrid systems have also become common laboratory tools and are preferred in some circumstances, although yeast and bacterial two-hybrid systems

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

44

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

45

Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests  

PubMed Central

The recent availability of whole-genome scale data sets that investigate complementary and diverse aspects of transcriptional regulation has spawned an increased need for new and effective computational approaches to analyze and integrate these large scale assays. Here, we propose a novel algorithm, based on random forest methodology, to relate gene expression (as derived from expression microarrays) to sequence features residing in gene promoters (as derived from DNA motif data) and transcription factor binding to gene promoters (as derived from tiling microarrays). We extend the random forest approach to model a multivariate response as represented, for example, by time-course gene expression measures. An analysis of the multivariate random forest output reveals complex regulatory networks, which consist of cohesive, condition-dependent regulatory cliques. Each regulatory clique features homogeneous gene expression profiles and common motifs or synergistic motif groups. We apply our method to several yeast physiological processes: cell cycle, sporulation, and various stress conditions. Our technique displays excellent performance with regard to identifying known regulatory motifs, including high order interactions. In addition, we present evidence of the existence of an alternative MCB-binding pathway, which we confirm using data from two independent cell cycle studies and two other physioloigical processes. Finally, we have uncovered elaborate transcription regulation refinement mechanisms involving PAC and mRRPE motifs that govern essential rRNA processing. These include intriguing instances of differing motif dosages and differing combinatorial motif control that promote regulatory specificity in rRNA metabolism under differing physiological processes. PMID:19543377

Xiao, Yuanyuan; Segal, Mark R.

2009-01-01

46

Identification and functional reconstitution of the yeast peroxisomal adenine nucleotide transporter  

PubMed Central

The requirement for small molecule transport systems across the peroxisomal membrane has previously been postulated, but not directly proven. Here we report the identification and functional reconstitution of Ant1p (Ypr128cp), a peroxisomal transporter in the yeast Saccharomyces cerevisiae, which has the characteristic sequence features of the mitochondrial carrier family. Ant1p was found to be an integral protein of the peroxisomal membrane and expression of ANT1 was oleic acid inducible. Targeting of Ant1p to peroxisomes was dependent on Pex3p and Pex19p, two peroxins specifically required for peroxisomal membrane protein insertion. Ant1p was essential for growth on medium-chain fatty acids as the sole carbon source. Upon reconstitution of the overexpressed and purified protein into liposomes, specific transport of adenine nucleotides could be demonstrated. Remarkably, both the substrate and inhibitor specificity differed from those of the mitochondrial ADP/ATP transporter. The physiological role of Ant1p in S.cerevisiae is probably to transport cytoplasmic ATP into the peroxisomal lumen in exchange for AMP generated in the activation of fatty acids. PMID:11566870

Palmieri, Luigi; Rottensteiner, Hanspeter; Girzalsky, Wolfgang; Scarcia, Pasquale; Palmieri, Ferdinando; Erdmann, Ralf

2001-01-01

47

The application of whole-cell protein electrophoresis for the classification and identification of basidiomycetous yeast species.  

PubMed

The relationships among 65 basidiomycetous yeast strains were determined by one-dimensional electrophoresis of SDS-solubilized whole-cell proteins. Protein profiles were compared by the Pearson product moment correlation coefficient (r). The strains investigated represented species from the genera Cystofilobasidium, Filobasidium, Filobasidiella, Kondoa, Leucosporidium, Mrakia and Rhodosporidium. Except for the genus Mrakia, all species constituted separate protein electrophoretic clusters. The species of the genus Mrakia (M. frigida, M. gelida, M. nivalis and M. stokesii) show highly similar protein patterns, suggesting that these four species may be synonymous. Strains of two varieties of Filobasidiella neoformans, F. neoformans var. neoformans and F. neoformans var. bacillispora, could not be differentiated by protein electrophoresis. For the delineation of the protein electrophoretic clusters of the yeasts studied, literature data relying on other criteria, such as DNA base composition, carbon source utilization patterns, enzymatic protein electrophoregrams, ubiquinone systems, DNA-DNA homology and rRNA sequence data were used. It was demonstrated that a database of SDS-protein patterns provides a valuable tool for the identification of yeasts. PMID:1575470

Vancanneyt, M; Van Lerberge, E; Berny, J F; Hennebert, G L; Kersters, K

1992-01-01

48

Immobilized yeast bioreactor systems for continuous beer fermentation  

PubMed

Two different types of immobilized yeast bioreactors were examined for continuous fermentation of high-gravity worts. One of these is a fluidized bed reactor (FBR) that employs porous glass beads for yeast immobilization. The second system is a loop reactor containing a porous silicon carbide cartridge (SCCR) for immobilizing the yeast cells. Although there was some residual fermentable sugar in the SCCR system product, nearly complete attenuation of the wort sugars was achieved in either of the systems when operated as a two-stage process. Fermentation could be completed in these systems in only half the time required for a conventional batch process. Both the systems showed similar kinetics of extract consumption, and therefore similar volumetric productivity. As compared to the batch fermentation, total fusel alcohols were lower; total esters, while variable, were generally higher. The yeast biomass production was similar to that in a conventional fermentation process. As would be expected in an accelerated fermentation system, the levels of vicinal diketones (VDKs) were higher. To remove the VDKs, the young beer was heat-treated to convert the VDK precursors and processed through a packed bed immobilized yeast bioreactor for VDK assimilation. The finished product from the FBR system was found to be quite acceptable from a flavor perspective, albeit different from the product from a conventional batch process. Significantly shortened fermentation times demonstrate the feasibility of this technology for beer production. PMID:9933520

Tata; Bower; Bromberg; Duncombe; Fehring; Lau; Ryder; Stassi

1999-01-01

49

High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories.  

PubMed

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. PMID:20053859

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

2010-03-01

50

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. PMID:20053859

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

2010-01-01

51

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

PubMed Central

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

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

2013-01-01

52

Identification of predominant yeasts associated with artisan Mexican cocoa fermentations using culture-dependent and culture-independent approaches.  

PubMed

The process of cocoa fermentation is a very important step for the generation or aromatic compounds, which are attributable to the metabolism of the microorganisms involved. There are some reports about this process and the identification of microorganisms; however, there are no reports identifying the yeasts involved in a Mexican cocoa fermentation process using molecular biology techniques, including restricted fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE). The aim of this study was to identify the main yeast species associated with Mexican cocoa fermentations employing culture-dependent and -independent techniques achieving two samplings with a 1 year time difference at the same site. Isolation of the microorganisms was performed in situ. Molecular identification of yeast isolates was achieved by RFLP analysis and rDNA sequencing. Total DNA from the microorganisms on the cocoa beans was utilized for the DGGE analysis. Bands from the DGGE gels were excised and sequenced. Nineteen isolated yeasts were identified (al specie level), three of which had never before been associated with cocoa fermentations worldwide. The detected predominant yeast varied from one technique to another. Hanseniaspora sp. resulted dominant in DGGE however Saccharomyces cerevisiae was the principal isolated species. In conclusion, the culture-dependent and -independent techniques complement each other showing differences in the main yeasts involved in spontaneous cocoa fermentation, probably due to the physiological states of the viable but non culturable yeasts. Furthermore important differences between the species detected in the two samplings were detected. PMID:25566818

Arana-Sánchez, A; Segura-García, L E; Kirchmayr, M; Orozco-Ávila, I; Lugo-Cervantes, E; Gschaedler-Mathis, A

2015-02-01

53

Performance of optimized McRAPD in identification of 9 yeast species frequently isolated from patient samples: potential for automation  

PubMed Central

Background Rapid, easy, economical and accurate species identification of yeasts isolated from clinical samples remains an important challenge for routine microbiological laboratories, because susceptibility to antifungal agents, probability to develop resistance and ability to cause disease vary in different species. To overcome the drawbacks of the currently available techniques we have recently proposed an innovative approach to yeast species identification based on RAPD genotyping and termed McRAPD (Melting curve of RAPD). Here we have evaluated its performance on a broader spectrum of clinically relevant yeast species and also examined the potential of automated and semi-automated interpretation of McRAPD data for yeast species identification. Results A simple fully automated algorithm based on normalized melting data identified 80% of the isolates correctly. When this algorithm was supplemented by semi-automated matching of decisive peaks in first derivative plots, 87% of the isolates were identified correctly. However, a computer-aided visual matching of derivative plots showed the best performance with average 98.3% of the accurately identified isolates, almost matching the 99.4% performance of traditional RAPD fingerprinting. Conclusion Since McRAPD technique omits gel electrophoresis and can be performed in a rapid, economical and convenient way, we believe that it can find its place in routine identification of medically important yeasts in advanced diagnostic laboratories that are able to adopt this technique. It can also serve as a broad-range high-throughput technique for epidemiological surveillance. PMID:19903328

2009-01-01

54

Identification of genes whose expressions are enhanced or reduced in baker's yeast during fed-batch culture process using molasses medium by DNA microarray analysis.  

PubMed

Genes whose expression levels are enhanced or reduced during the cultivation process that uses cane molasses in baker's yeast production were identified in this study. The results showed that baker's yeast grown in molasses medium had higher fermentation ability and stress tolerance compared with baker's yeast grown in synthetic medium. Molasses apparently provided not only sugar as a carbon source but also provided functional components that enhanced or reduced expression of genes involved in fermentation ability and stress tolerance. To identify the genes whose expression is enhanced or reduced during cultivation in molasses medium, DNA microarray analysis was then used to compare the gene expression profile of cells grown in molasses with that of cells grown in synthetic medium. To simulate the commercial baker's yeast production process, cells were cultivated using a fed-batch culture system. In molasses medium, genes involved in the synthesis or uptake of vitamins (e.g., biotin, pyridoxine and thiamine) showed enhanced expression, suggesting that vitamin concentrations in molasses medium were lower than those in synthetic medium. Genes involved in formate dehydrogenase and maltose assimilation showed enhanced expression in molasses medium. In contrast, genes involved in iron utilization (e.g., siderophore, iron transporter and ferroxidase) showed enhanced expression in synthetic medium, suggesting that iron starvation occurred. The genes involved in the metabolism of amino acids also showed enhanced expression in synthetic medium. This identification of genes provides information that will help improve the baker's yeast production process. PMID:15925003

Shima, Jun; Kuwazaki, Seigo; Tanaka, Fumiko; Watanabe, Hajime; Yamamoto, Hideki; Nakajima, Ryoichi; Tokashiki, Tadaaki; Tamura, Hiromi

2005-06-25

55

Performance and Cost Analysis of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Routine Identification of Yeast?  

PubMed Central

Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ?1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory. PMID:21270234

Dhiman, Neelam; Hall, Leslie; Wohlfiel, Sherri L.; Buckwalter, Seanne P.; Wengenack, Nancy L.

2011-01-01

56

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. PMID:12864730

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

2003-01-01

57

Immobilized yeast cell systems for continuous fermentation applications.  

PubMed

In several yeast-related industries, continuous fermentation systems offer important economical advantages in comparison with traditional systems. Fermentation rates are significantly improved, especially when continuous fermentation is combined with cell immobilization techniques to increase the yeast concentration in the fermentor. Hence the technique holds a great promise for the efficient production of fermented beverages, such as beer, wine and cider as well as bio-ethanol. However, there are some important pitfalls, and few industrial-scale continuous systems have been implemented. Here, we first review the various cell immobilization techniques and reactor setups. Then, the impact of immobilization on cell physiology and fermentation performance is discussed. In a last part, we focus on the practical use of continuous fermentation and cell immobilization systems for beer production. PMID:16937245

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

2006-10-01

58

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

59

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. PMID:23516407

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

2013-01-01

60

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

Microsoft Academic Search

Four sourdoughs (A to D) were produced under practical conditions, using a starter obtained from a mixture of three commercially available sourdough starters and baker's yeast. The doughs were continuously propa- gated until the composition of the microbiota remained stable. A fungi-specific PCR-denaturing gradient gel electrophoresis (DGGE) system was established to monitor the development of the yeast biota. The analysis

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

2003-01-01

61

Dietary Yeasts Reduce Inflammation in Central Nerve System via Microflora  

PubMed Central

Objectives The intestinal microflora affects the pathogenesis of several autoimmune diseases by influencing immune system function. Some bacteria, such as lactic acid bacteria, have been reported to have beneficial effects on immune function. However, little is known about the effects of yeasts. Here, we aimed to investigate the effects of various dietary yeasts contained in fermented foods on experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), and to elucidate the mechanisms underlying these effects. Methods The effects of eight yeasts selected from 18 types of yeasts contained in fermented foods were examined using an EAE model. Of these, Candida kefyr was investigated by analyzing the intestinal microflora and its effects on intestinal and systemic immune states. Results Administration of C. kefyr ameliorated the severity of EAE. Reduced numbers of Th17 cells, suppressed interleukin (IL)-6 production by intestinal explants, and increased Tregs and CD103-positive regulatory dendritic cells in mesenteric lymph nodes (MLNs) were observed. Analysis of 16s-rDNA from feces of C. kefyr-treated mice demonstrated increased Lactobacillales and decreased Bacteroides compared to control flora. Transfer of intestinal microbiota also resulted in decreased Bacteroides and ameliorated symptoms of EAE. Thus, oral administration of C. kefyr ameliorated EAE by altering the microflora, accompanied by increased Tregs and CD103-positive regulatory dendritic cells in MLNs and decreased Th17 cells in the intestinal lamina propria. Interpretation Oral ingestion of C. kefyr may have beneficial effects on MS by modifying microflora. In addition, our findings also suggested the potential health benefits of dietary yeasts. PMID:25642435

Takata, Kazushiro; Tomita, Takayuki; Okuno, Tatsusada; Kinoshita, Makoto; Koda, Toru; Honorat, Josephe A; Takei, Masaya; Hagihara, Kouichiro; Sugimoto, Tomoyuki; Mochizuki, Hideki; Sakoda, Saburo; Nakatsuji, Yuji

2015-01-01

62

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

63

Construction of a GAL1-regulated yeast cDNA expression library and its application to the identification of genes whose overexpression causes lethality in yeast.  

PubMed

We have constructed a galactose-inducible expression library by cloning yeast cDNAs unidirectionally under control of the GAL1 promoter in a centromeric shuttle vector. Eleven independent libraries were made each with an average size of about 1 x 10(6) clones, about 50 times larger than the reported mRNA population in a yeast cell. From this library, LEU2 and HIS3 cDNAs were recovered at a frequency of about 1 in 10(4) and in 12 out of 13 cases these were expressed in a galactose-dependent manner. Sequence analysis of leu2 and his3 complementing cDNAs indicates that they contain all the coding sequence and much of the 5' untranslated region. To test the utility of the library for the identification of genes whose overexpression confers a specific phenotype, we screened 25,000 yeast transformants for lethality on galactose. Among 15 clones that showed galactose inducible lethality were cDNAs encoding structural proteins, including ACT1 (actin), TUB2 (beta-tubulin) and ABP1 (actin-binding protein 1), and genes in signal transduction pathways, including TPK1 (a cAMP-dependent protein kinase) and GLC7 (type 1 protein phosphatase). cDNAs overexpressing NHPB (nonhistone protein B) and NSR1 (nuclear sequence recognition protein) were also found to be lethal. Among these, ACT1 was isolated four times, and NSR1 three times. The useful features of this library for cDNA cloning in yeast by complementation, and for the identification of genes whose over-expression confers specific phenotypes, are discussed. PMID:1468625

Liu, H; Krizek, J; Bretscher, A

1992-11-01

64

Identification of a putative RNA helicase (HRH1), a human homolog of yeast Prp22.  

PubMed

In the budding yeast Saccharomyces cerevisiae, a number of PRP genes known to be involved in pre-mRNA processing have been genetically identified and cloned. Three PRP genes (PRP2, PRP16, and PRP22) were shown to encode putative RNA helicases of the family of proteins with DEAH boxes. However, any such splicing factor containing the helicase motifs in vertebrates has not been identified. To identify human homologs of this family, we designed PCR primers corresponding to the highly conserved region of the DEAH box protein family and successfully amplified five cDNA fragments, using HeLa poly(A)+ RNA as a substrate. One fragment, designated HRH1 (human RNA helicase 1), is highly homologous to Prp22, which was previously shown to be involved in the release of spliced mRNAs from the spliceosomes. Expression of HRH1 in a S. cerevisiae prp22 mutant can partially rescue its temperature-sensitive phenotype. These results strongly suggest that HRH1 is a functional human homolog of the yeast Prp22 protein. Interestingly, HRH1 but not Prp22 contains an arginine- and serine-rich domain (RS domain) which is characteristic of some splicing factors, such as members of the SR protein family. We could show that HRH1 can interact in vitro and in the yeast two-hybrid system with members of the SR protein family through its RS domain. We speculate that HRH1 might be targeted to the spliceosome through this interaction. PMID:7935475

Ono, Y; Ohno, M; Shimura, Y

1994-11-01

65

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

66

Running title: Yeasts from refrigerated commercial shell eggs Identification of yeasts isolated from commercial shell eggs stored at refrigerated temperatures  

Technology Transfer Automated Retrieval System (TEKTRAN)

Yeasts and molds can grow on or in eggs, causing spoilage. Washed and unwashed eggs (treatments) were collected aseptically on three separate days (replications) from a commercial processing facility and stored for 10 weeks at 4ºC. Ten eggs from each treatment were sampled weekly (110 eggs/treatme...

67

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

68

Persistent identification of time-varying systems  

Microsoft Academic Search

Identification of time-varying systems, especially slowly time-varying systems, is of importance in the development of a comprehensive theory of adaptation. The persistent identification measures employed in this paper capture a main characterization in such identification problems, namely, one input signal must be used for identification of all possible observation windows. This paper establishes several essential features in persistent identification problems

Le Yi Wang

1997-01-01

69

Rapid Molecular Identification of Pathogenic Yeasts by Pyrosequencing Analysis of 35 Nucleotides of Internal Transcribed Spacer 2 ?  

PubMed Central

Rapid identification of yeast species isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. Here, we have evaluated the utility of pyrosequencing analysis of a portion of the internal transcribed spacer 2 region (ITS2) for identification of pathogenic yeasts. A total of 477 clinical isolates encompassing 43 different fungal species were subjected to pyrosequencing analysis in a strictly blinded study. The molecular identifications produced by pyrosequencing were compared with those obtained using conventional biochemical tests (AUXACOLOR2) and following PCR amplification and sequencing of the D1-D2 portion of the nuclear 28S large rRNA gene. More than 98% (469/477) of isolates encompassing 40 of the 43 fungal species tested were correctly identified by pyrosequencing of only 35 bp of ITS2. Moreover, BLAST searches of the public synchronized databases with the ITS2 pyrosequencing signature sequences revealed that there was only minimal sequence redundancy in the ITS2 under analysis. In all cases, the pyrosequencing signature sequences were unique to the yeast species (or species complex) under investigation. Finally, when pyrosequencing was combined with the Whatman FTA paper technology for the rapid extraction of fungal genomic DNA, molecular identification could be accomplished within 6 h from the time of starting from pure cultures. PMID:20702674

Borman, Andrew M.; Linton, Christopher J.; Oliver, Debra; Palmer, Michael D.; Szekely, Adrien; Johnson, Elizabeth M.

2010-01-01

70

Influence of the farming system on the epiphytic yeasts and yeast-like fungi colonizing grape berries during the ripening process.  

PubMed

Grape berries are colonized by a wide array of epiphytic microorganisms such as yeast and filamentous fungi. This microbiota plays a major role in crop health and also interferes with the winemaking process. In this study, culture-dependent and -independent methods were used to investigate the dynamics and diversity of the yeast and yeast-like microorganisms on the grape berry surface during maturation and the influence of cropping systems in this microflora. The results showed a significant impact of both the farming system and the maturity stage on the epiphytic yeast and yeast-like community. A quantitative approach based on counting cultivable populations indicated an increase in the yeast and yeast-like population during the grape ripening process, reaching a maximum when the berries became overripe. The cultivable yeast and yeast-like population also varied significantly depending on the farming system. Microorganism counts were significantly higher for organically- than conventionally-farmed grapes. The yeast and yeast-like community structures were analysed by culture independent methods, using CE-SSCP. The results revealed changes in the genetic structure of the yeast and yeast-like community throughout the ripening process, as well as the impact of the farming system. Copper-based fungicide treatments were revealed as the main factor responsible for the differences in microbial population densities between samples of different farming systems. The results showed a negative correlation between copper levels and yeast and yeast-like populations, providing evidence that copper inhibited this epiphytic community. Taken together, our results showed that shifts in the microbial community were related to changes in the composition of the grape-berry surface, particularly sugar exudation and the occurrence of copper residues from pesticide treatments. PMID:24603471

Martins, Guilherme; Vallance, Jessica; Mercier, Anne; Albertin, Warren; Stamatopoulos, Panagiotis; Rey, Patrice; Lonvaud, Aline; Masneuf-Pomarède, Isabelle

2014-05-01

71

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. PMID:12008673

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

72

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

73

Identification and characterization of yeast isolated from the elaboration of seasoned green table olives  

Microsoft Academic Search

The purpose of this study was to investigate the yeast population during the processing of green table olives. In the fresh olives, yeast were found at concentrations of around 3.0logcfu\\/g, with Cryptococcus spp. being predominant. In the brine, the yeast concentrations were greater than 4.9logcfu\\/ml, with Pichia anomala, Kluyveromyces marxianus, and Saccharomyces cerevisiae being the predominant species. Unlike the yeast

Alejandro Hernández; Alberto Martín; Emilio Aranda; Francisco Pérez-Nevado; María G. Córdoba

2007-01-01

74

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%. PMID:23913433

Thornton, Mark A.; Thornton, Roy J.

2013-01-01

75

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. PMID:21246036

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

76

A yeast pheromone-based inter-species communication system.  

PubMed

We report on a pheromone-based inter-species communication system, allowing for a controlled cell-cell communication between the two species Saccharomyces cerevisiae and Schizosaccharomyces pombe as a proof of principle. It exploits the mating response pathways of the two yeast species employing the pheromones, ?- or P-factor, as signaling molecules. The authentic and chimeric pheromone-encoding genes were engineered to code for the P-factor in S. cerevisiae and the ?-factor in S. pombe. Upon transformation of the respective constructs, cells were enabled to express the mating pheromone of the opposite species. The supernatant of cultures of S. pombe cells expressing ?-factor were able to induce a G1 arrest in the cell cycle, a change in morphology to the typical shmoo effect and expression driven by the pheromone-responsive FIG1 promoter in S. cerevisiae. The supernatant of cultures of S. cerevisiae cells expressing P-factor similarly induced cell cycle arrest in G1, an alteration in morphology typical for mating as well as the activation of the pheromone-responsive promoters of the rep1 and sxa2 genes in a pheromone-hypersensitive reporter strain of S. pombe. Apparently, both heterologous pheromones were correctly processed and secreted in an active form by the cells of the other species. Our data clearly show that the species-specific pheromone systems of yeast species can be exploited for a controlled inter-species communication. PMID:25331280

Hennig, Stefan; Clemens, André; Rödel, Gerhard; Ostermann, Kai

2015-02-01

77

Identification of Human Proteins Functionally Conserved with the Yeast Putative Adaptors ADA2 and GCN5  

Microsoft Academic Search

Transcriptional adaptor proteins are required for full function of higher eukaryotic acidic activators in the yeastSaccharomyces cerevisiae, suggesting that this pathway of activation is evolutionarily conserved. Consis- tent 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 yeastandhumanproteins,perhapsmoresignificantisconservationofkeysequencefeatureswithotherknown

REYES CANDAU; PAUL A. MOORE; LIAN WANG; NICKOLAI BARLEV; CAROL Y. YING; CRAIG A. ROSEN; ANDSHELLEY L. BERGER

78

Roles for the Two-hybrid System in Exploration of the Yeast Protein Interactome  

Microsoft Academic Search

Comprehensive analysis of protein-protein interactions is a challenging endeavor of functional proteomics and has been best explored in the budding yeast. The yeast pro- tein interactome analysis was achieved first by using the yeast two-hybrid system in a proteome-wide scale and next by large-scale mass spectrometric analysis of affin- ity-purified protein complexes. While these interaction data have led to a

Takashi Ito; Kazuhisa Ota; Hiroyuki Kubota; Yoshihiro Yamaguchi; Tomoko Chiba; Kazumi Sakuraba; Mikio Yoshida

2002-01-01

79

RAPID IDENTFICATION OF ASCOMYCETOUS YEASTS FROM CLINICAL SPECIMENS BY A MOLECULAR-BASED FLOW CYTOMETRY METHOD AND COMPARISION WITH IDENTIFICATIONS FROM PHENOTYPIC ASSAYS  

Technology Transfer Automated Retrieval System (TEKTRAN)

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. LSU rRNA D1/D2 gene sequence analysis was also performed and served as the reference for correct strain identif...

80

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. PMID:24903109

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

2014-01-01

81

Random amplified polymorphic DNA and restriction enzyme analysis of PCR amplified rDNA in taxonomy: two identification techniques for food-borne yeasts.  

PubMed

The random amplified polymorphic DNA (RAPD) assay and the restriction enzyme analysis of PCR amplified rDNA are compared for the identification of the common spoilage yeasts Zygosaccharomyces bailii, Z. rouxii, Saccharomyces cerevisiae, Candida valida and C. lipolytica. Both techniques proved to be adequate tools for yeast identification. Since the RAPD does provide less stable patterns than restriction enzyme analysis of PCR amplified rDNA, and a large amount of data had to be compared without data reduction, Principal Component Analysis (PCA) was applied successfully for clustering the RAPD patterns. The success of PCA is highly influenced by the primer used in RAPD and the amount of reference samples. A large amount of reference samples improves the performance of clustering in PCA. The primer of choice was shown to be important with respect to the discriminatory power of the RAPD method. Some primers used enabled discrimination on the subspecies level. The results collected with both typing methods justify the conclusion that the present typing system can be applied for taxonomical purposes. PMID:8567491

Baleiras Couto, M M; Vogels, J T; Hofstra, H; Huis in't Veld, J H; van der Vossen, J M

1995-11-01

82

IDENTIFICATION OF YEASTS ISOLATED FROM COMMERCIAL SHELL EGGS STORED AT REFRIGERATED TEMPERATURES  

Technology Transfer Automated Retrieval System (TEKTRAN)

Yeasts and molds, which are able to withstand harsh environmental stresses, can grow on or in eggs and cause spoilage. Egg meats readily absorb off odors, including those caused by yeast or mold growth, so their presence on eggs may constitute a quality concern. Washed and unwashed eggs (treatment...

83

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

Microsoft Academic Search

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

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

84

Automated drug identification system  

NASA Technical Reports Server (NTRS)

System speeds up analysis of blood and urine and is capable of identifying 100 commonly abused drugs. System includes computer that controls entire analytical process by ordering various steps in specific sequences. Computer processes data output and has readout of identified drugs.

Campen, C. F., Jr.

1974-01-01

85

Projectile Identification System  

Microsoft Academic Search

The U.S. Army plans for the needs of future warfare to retain its technological superiority. Future Combat Systems (FCS) is a major effort designed to meet this need. FCS includes multiple automated fire weapons. On current systems, a human typically enters information about each projectile loaded. This is a slow process, placing the soldier and the weapon in danger. Cybernet

Glenn J. Beach; Charles J. Cohen; Gary Moody; Martha Henry

2003-01-01

86

Sparse LMS for system identification  

Microsoft Academic Search

We propose a new approach to adaptive system identification w hen the system model is sparse. The approach applies the ?1 relaxation, common in compressive sensing, to improve the performance of LMS-type adaptive methods. This results in two new algorithms, the Zero-Attracting LMS (ZA-LMS) and the Reweighted Zero- Attracting LMS (RZA-LMS). The ZA-LMS is derived via combin- ing a ?1

Yilun Chen; Yuantao Gu; Alfred O. Hero III

2009-01-01

87

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. PMID:24939186

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

2014-01-01

88

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

89

The BESIII muon identification system  

NASA Astrophysics Data System (ADS)

The muon identification system of BESIII experiment at the IHEP is described. The muon counter (MUC) is composed of resistive plate chambers (RPCs) working in self-quenching streamer mode with the gas mixture Ar/C 2F 4H 2/C 4H 10=50/42/8. The design, the construction, the mass production and the quality control result of the detectors are described in detail. The paper also presents the performance of the bare RPCs and the superlayer modules with cosmic rays. Finally, the subsystems of MUC, including the RPC superlayer modules, the gas systems, the HV and LV system and the readout electronic system, are also presented.

Zhang, Jiawen; Qian, Sen; Chen, Jin; Du, Zhizhen; Han, Jifeng; Li, Rubo; Liu, Jichen; Liang, Hao; Mao, Yajun; Ma, Liehua; Wang, Yifang; Xie, Yigang; Xie, Yuguang; Zhang, Qingmin; Zhao, Jianbing; Zhao, T.; Zhou, Yongzhao

2010-03-01

90

Structural Aspects of System Identification  

NASA Technical Reports Server (NTRS)

The problem of identifying linear dynamical systems is studied by considering structural and deterministic properties of linear systems that have an impact on stochastic identification algorithms. In particular considered is parametrization of linear systems so that there is a unique solution and all systems in appropriate class can be represented. It is assumed that a parametrization of system matrices has been established from a priori knowledge of the system, and the question is considered of when the unknown parameters of this system can be identified from input/output observations. It is assumed that the transfer function can be asymptotically identified, and the conditions are derived for the local, global and partial identifiability of the parametrization. Then it is shown that, with the right formulation, identifiability in the presence of feedback can be treated in the same way. Similarly the identifiability of parametrizations of systems driven by unobserved white noise is considered using the results from the theory of spectral factorization.

Glover, Keith

1973-01-01

91

Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system.  

PubMed

The budding yeast Saccharomyces cerevisiae is a powerful model organism for studying fundamental aspects of eukaryotic cell biology. This Primer article presents a brief historical perspective on the emergence of this organism as a premier experimental system over the course of the past century. An overview of the central features of the S. cerevisiae genome, including the nature of its genetic elements and general organization, is also provided. Some of the most common experimental tools and resources available to yeast geneticists are presented in a way designed to engage and challenge undergraduate and graduate students eager to learn more about the experimental amenability of budding yeast. Finally, a discussion of several major discoveries derived from yeast studies highlights the far-reaching impact that the yeast system has had and will continue to have on our understanding of a variety of cellular processes relevant to all eukaryotes, including humans. PMID:24807111

Duina, Andrea A; Miller, Mary E; Keeney, Jill B

2014-05-01

92

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

Microsoft Academic Search

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

M. Gerard Waters; Giinter Blobel

1986-01-01

93

Use of yeast as a system to study amyloid toxicity.  

PubMed

The formation of amyloid-like fibrils is a hallmark of several neurodegenerative diseases. How the assembly of amyloid-like fibrils contributes to cell death is a major unresolved question in the field. The budding yeast Saccharomyces cerevisiae is a powerful model organism to study basic mechanisms for how cellular pathways regulate amyloid assembly and proteotoxicity. For example, studies of the amyloidogenic yeast prion [RNQ(+)] have revealed novel roles by which molecular chaperones protect cells from the accumulation of cytotoxic protein species. In budding yeast there are a variety of cellular assays that can be employed to analyze the assembly of amyloid-like aggregates and mechanistically dissect how cellular pathways influence proteotoxicity. In this review, we describe several assays that are routinely used to investigate aggregation and toxicity of the [RNQ(+)] prion in yeast. PMID:21115125

Summers, Daniel W; Cyr, Douglas M

2011-03-01

94

ISL Person Identification Systems in the CLEAR 2007 Evaluations  

Microsoft Academic Search

In this paper, we present ISL person identification systems in the CLEAR 2007 evaluations. The identification systems consist of a face recogni- tion system, a speaker identification system and a multi-modal identification system that combines the individual systems. The experimental results show that the face recognition system outperforms the speaker identification system significantly on the short duration test segments. They

Hazim Kemal Ekenel; Qin Jin; Mika Fischer; Rainer Stiefelhagen

2007-01-01

95

Continuous beer fermentation using immobilized yeast cell bioreactor systems.  

PubMed

Traditional beer fermentation and maturation processes use open fermentation and lager tanks. Although these vessels had previously been considered indispensable, during the past decades they were in many breweries replaced by large production units (cylindroconical tanks). These have proved to be successful, both providing operating advantages and ensuring the quality of the final beer. Another promising contemporary technology, namely, continuous beer fermentation using immobilized brewing yeast, by contrast, has found only a limited number of industrial applications. Continuous fermentation systems based on immobilized cell technology, albeit initially successful, were condemned to failure for several reasons. These include engineering problems (excess biomass and problems with CO(2) removal, optimization of operating conditions, clogging and channeling of the reactor), unbalanced beer flavor (altered cell physiology, cell aging), and unrealized cost advantages (carrier price, complex and unstable operation). However, recent development in reactor design and understanding of immobilized cell physiology, together with application of novel carrier materials, could provide a new stimulus to both research and application of this promising technology. PMID:15932239

Brányik, Tomás; Vicente, António A; Dostálek, Pavel; Teixeira, José A

2005-01-01

96

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

Microsoft Academic Search

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

Qingxiang Yang; Min Yang; Shujun Zhang; Wenzhou Lv

2005-01-01

97

Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast  

PubMed Central

Every protein has a biosynthetic cost to the cell based on the synthesis of its constituent amino acids. In order to optimise growth and reproduction, natural selection is expected, where possible, to favour the use of proteins whose constituents are cheaper to produce, as reduced biosynthetic cost may confer a fitness advantage to the organism. Quantifying the cost of amino acid biosynthesis presents challenges, since energetic requirements may change across different cellular and environmental conditions. We developed a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models and investigated the effects of the cost of amino acid synthesis on Saccharomyces cerevisiae gene expression and protein evolution. First, we used our two new and six previously reported measures of amino acid cost in conjunction with codon usage bias, tRNA gene number and atomic composition to identify which of these factors best predict transcript and protein levels. Second, we compared amino acid cost with rates of amino acid substitution across four species in the genus Saccharomyces. Regardless of which cost measure is used, amino acid biosynthetic cost is weakly associated with transcript and protein levels. In contrast, we find that biosynthetic cost and amino acid substitution rates show a negative correlation, but for only a subset of cost measures. In the economy of the yeast cell, we find that the cost of amino acid synthesis plays a limited role in shaping transcript and protein expression levels compared to that of translational optimisation. Biosynthetic cost does, however, appear to affect rates of amino acid evolution in Saccharomyces, suggesting that expensive amino acids may only be used when they have specific structural or functional roles in protein sequences. However, as there appears to be no single currency to compute the cost of amino acid synthesis across all cellular and environmental conditions, we conclude that a systems approach is necessary to unravel the full effects of amino acid biosynthetic cost in complex biological systems. PMID:20808905

Barton, Michael D.; Delneri, Daniela; Oliver, Stephen G.; Rattray, Magnus; Bergman, Casey M.

2010-01-01

98

Identification and population dynamics of yeasts in sourdough fermentation processes by PCR-denaturing gradient gel electrophoresis.  

PubMed

Four sourdoughs (A to D) were produced under practical conditions, using a starter obtained from a mixture of three commercially available sourdough starters and baker's yeast. The doughs were continuously propagated until the composition of the microbiota remained stable. A fungi-specific PCR-denaturing gradient gel electrophoresis (DGGE) system was established to monitor the development of the yeast biota. The analysis of the starter mixture revealed the presence of Candida humilis, Debaryomyces hansenii, Saccharomyces cerevisiae, and Saccharomyces uvarum. In sourdough A (traditional process with rye flour), C. humilis dominated under the prevailing fermentation conditions. In rye flour sourdoughs B and C, fermented at 30 and 40 degrees C, respectively, S. cerevisiae became predominant in sourdough B, whereas in sourdough C the yeast counts decreased within a few propagation steps below the detection limit. In sourdough D, which corresponded to sourdough C in temperature but was produced with rye bran, Candida krusei became dominant. Isolates identified as C. humilis and S. cerevisiae were shown by randomly amplified polymorphic DNA-PCR analysis to originate from the commercial starters and the baker's yeast, respectively. The yeast species isolated from the sourdoughs were also detected by PCR-DGGE. However, in the gel, additional bands were visible. Because sequencing of these PCR fragments from the gel failed, cloning experiments with 28S rRNA amplicons obtained from rye flour were performed, which revealed Cladosporium sp., Saccharomyces servazii, S. uvarum, an unculturable ascomycete, Dekkera bruxellensis, Epicoccum nigrum, and S. cerevisiae. The last four species were also detected in sourdoughs A, B, and C. PMID:14660398

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

2003-12-01

99

Isolation and identification of killer yeasts from Agave sap (aguamiel) and pulque  

Microsoft Academic Search

Wild killer yeasts have been identified as inhibitory to strains used as starters in the production of alcoholic beverages such as beer and wine; therefore, killer or killer-resistant strains have been sought for use in alcoholic fermentations. In the current paper a total of 16 strains belonging to six species were isolated. From two samples of Agave sap (aguamiel) the

A. R. Estrada-Godina; A. E. Cruz-Guerrero; P. Lappe; M. Ulloa; M. García-Garibay; L. Gómez-Ruiz

2001-01-01

100

Identification of the reactive cysteine residues in yeast dipeptidyl peptidase III.  

PubMed

Dipeptidyl peptidases III (DPPs III) form a distinct metallopeptidase family characterized by the unique HEXXGH motif. High susceptibility to inactivation by organomercurials suggests the presence of a reactive cysteine residue(s) in, or close to, their active site. Yeast DPP III contains five Cys, none of which is absolutely conserved within the family. In order to identify reactive residue(s), site-directed mutagenesis on yeast His(6)-tagged DPP III was employed to substitute specifically all five cysteine residues to serine. The variant enzymes thus obtained were enzymatically active and showed an overall structure not greatly affected by the mutations as judged by circular dichroism. Analysis by native and SDS-PAGE under non-reducing conditions revealed the existence of a monomeric and dimeric form in all DPP III proteins except in the C130S, implying that dimerization of yeast DPP III is mediated by the surface-exposed cysteine 130. The investigation of the effect of thiol reagent 4,4'-dithiodipyridine (DTDP) on all five Cys to Ser single protein variants showed that Cys639 and Cys518 are more reactive than the remainder. Only the C639S mutant protein displayed the remarkable resistance against p-hydroxy-mercuribenzoate (pHMB) indicating that modification of Cys639 is responsible for the fast inactivation of yeast DPP III by this sulfhydryl reagent. PMID:19825391

Jajcanin-Jozi?, Nina; Deller, Sigrid; Pavkov, Tea; Macheroux, Peter; Abrami?, Marija

2010-01-01

101

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2013 CFR

...Transportation Other Regulations Relating to Transportation (Continued) TRANSPORTATION SECURITY ADMINISTRATION, DEPARTMENT OF HOMELAND SECURITY CIVIL AVIATION SECURITY AIRPORT SECURITY Operations § 1542.211 Identification systems....

2013-10-01

102

49 CFR 1542.211 - Identification systems.  

...Transportation Other Regulations Relating to Transportation (Continued) TRANSPORTATION SECURITY ADMINISTRATION, DEPARTMENT OF HOMELAND SECURITY CIVIL AVIATION SECURITY AIRPORT SECURITY Operations § 1542.211 Identification systems....

2014-10-01

103

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2012 CFR

...Transportation Other Regulations Relating to Transportation (Continued) TRANSPORTATION SECURITY ADMINISTRATION, DEPARTMENT OF HOMELAND SECURITY CIVIL AVIATION SECURITY AIRPORT SECURITY Operations § 1542.211 Identification systems....

2012-10-01

104

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

PubMed Central

Protein modification by methylation is important in cellular function. We show here that the Saccharomyces cerevisiae YBR261C/TAE1 gene encodes an N-terminal protein methyltransferase catalyzing the modification of two ribosomal protein substrates, Rpl12ab and Rps25a/Rps25b. The YBR261C/Tae1 protein is conserved across eukaryotes; all of these proteins share sequence similarity with known seven beta strand class I methyltransferases. Wild type yeast cytosol and mouse heart cytosol catalyze the methylation of a synthetic peptide (PPKQQLSKY) that contains the first eight amino acids of the processed N-terminus of Rps25a/Rps25b. However, no methylation of this peptide is seen in yeast cytosol from a ?YBR261C/tae1 deletion strain. Yeast YBR261C/TAE1 and the human ortholog METTL11A genes were expressed as fusion proteins in Escherichia coli and were shown to be capable of stoichiometrically dimethylating the N-terminus of the synthetic peptide. Furthermore, the YBR261C/Tae1 and METTL11A recombinant proteins methylate variants of the synthetic peptide containing N-terminal alanine and serine residues. However, methyltransferase activity is largely abolished when the proline residue in position 2 or the lysine residue in position 3 is substituted. Thus, the methyltransferases described here specifically recognize the N-terminal X-Pro-Lys sequence motif and we suggest designating the yeast enzyme Ntm1 and the human enzyme NTMT1. These enzymes may account for nearly all previously described eukaryotic protein N-terminal methylation reactions. A number of other yeast and humans proteins also share the recognition motif and may be similarly modified. We conclude that protein X-Pro-Lys N-terminal methylation reactions catalyzed by the enzymes described here may be widespread in nature. PMID:20481588

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

2010-01-01

105

Aircraft System Identification Using Artificial Neural Networks  

E-print Network

Aircraft System Identification Using Artificial Neural Networks Kenton Kirkpatrick , Jim May Jr linear system identification for aircraft using artificial neural net- works. The output of a linear aircraft system consists of linear combinations of state and control inputs. Determining linear models

Valasek, John

106

Efficient Synthesis of a 72-kDa Mitochondrial Polypeptide Using the Yeast Ty Expression System  

Microsoft Academic Search

Using the Ty system from yeast we report the efficient expression of a heterologous eukaryotic gene encoding a 72 kDa mitochondrial polypeptide. The pFM2IIBglII expression vector was initially modified for this purpose by inserting the factor Xaprotease cleavage site. TheTyAgene, which encodes the structural component of the yeast virus-like particles (VLPs), and the eukaryoticyst1 gene, encoding a 72 kDa mitochondrial

Stefanie Pöggeler; Christian Schwerk; Ute Kämper; Ulrich Kück

1996-01-01

107

Direct identification of clinically relevant bacterial and yeast microcolonies and macrocolonies on solid culture media by Raman spectroscopy.  

PubMed

Decreasing turnaround time is a paramount objective in clinical diagnosis. We evaluated the discrimination power of Raman spectroscopy when analyzing colonies from 80 strains belonging to nine bacterial and one yeast species directly on solid culture medium after 24-h (macrocolonies) and 6-h (microcolonies) incubation. This approach, that minimizes sample preparation and culture time, would allow resuming culture after identification to perform downstream antibiotic susceptibility testing. Correct identification rates measured for macrocolonies and microcolonies reached 94.1% and 91.5%, respectively, in a leave-one-strain-out cross-validation mode without any correction for possible medium interference. Large spectral differences were observed between macrocolonies and microcolonies, that were attributed to true biological differences. Our results, conducted on a very diversified panel of species and strains, were obtained by using simple and robust sample preparation and preprocessing procedures, while still confirming published results obtained by using more complex elaborated protocols. Instrumentation is simplified by the use of 532-nm laser excitation yielding a Raman signal in the visible range. It is, to our knowledge, the first side-by-side full classification study of microorganisms in the exponential and stationary phases confirming the excellent performance of Raman spectroscopy for early species-level identification of microorganisms directly from an agar culture. PMID:24522809

Espagnon, Isabelle; Ostrovskii, Denis; Mathey, Raphaël; Dupoy, Mathieu; Joly, Pierre L; Novelli-Rousseau, Armelle; Pinston, Frédéric; Gal, Olivier; Mallard, Frédéric; Leroux, Denis F

2014-02-01

108

Yeast mitochondrial F1F0-ATP synthase exists as a dimer: identification of three dimer-specific subunits.  

PubMed Central

Using the technique of blue native gel electrophoresis, the oligomeric state of the yeast mitochondrial F1F0-ATP synthase was analysed. Solubilization of mitochondrial membranes with low detergent to protein ratios led to the identification of the dimeric state of the ATP synthase. Analysis of the subunit composition of the dimer, in comparison with the monomer, revealed the presence of three additional small proteins. These dimer-specific subunits of the ATP synthase were identified as the recently described subunit e/Tim11 (Su e/Tim11), the putative subunit g homolog (Su g) and a new component termed subunit k (Su k). Although, as shown here, these three proteins are not required for the formation of enzymatically active ATP synthase, Su e/Tim11 and Su g are essential for the formation of the dimeric state. Su e/Tim11 appears to play a central role in this dimerization process. The dimer-specific subunits are associated with the membrane bound F0-sector. The F0-sector may thereby be involved in the dimerization of two monomeric F1F0-ATP synthase complexes. We speculate that the F1F0-ATP synthase of yeast, like the other complexes of oxidative phosphorylation, form supracomplexes to optimize transduction of energy and to enhance the stability of the complex in the membrane. PMID:9857174

Arnold, I; Pfeiffer, K; Neupert, W; Stuart, R A; Schägger, H

1998-01-01

109

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

PubMed Central

We characterized the ability of a yeast to cleave the aromatic structure of the dioxin-like compound dibenzofuran. The yeast strain was isolated from a dioxin-contaminated soil sample and identified as Trichosporon mucoides. During incubation of glucose-pregrown cells with dibenzofuran, six major metabolites were detected by high-performance liquid chromatography. The formation of four different monohydroxylated dibenzofurans was proven by comparison of analytical data (gas chromatography-mass spectrometry) with that for authentic standards. Further oxidation produced 2,3-dihydroxydibenzofuran and its ring cleavage product 2-(1-carboxy methylidene)-2,3-dihydrobenzo[b]furanylidene glycolic acid, which were characterized by mass spectrometry and 1H nuclear magnetic resonance spectroscopy. These two metabolites are derived from 2-hydroxydibenzofuran and 3-hydroxydibenzofuran, as shown by incubation experiments using these monohydroxylated dibenzofurans as substrates. PMID:9603837

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

1998-01-01

110

Isolation and characterization of a dibenzofuran-degrading yeast: identification of oxidation and ring cleavage products.  

PubMed

We characterized the ability of a yeast to cleave the aromatic structure of the dioxin-like compound dibenzofuran. The yeast strain was isolated from a dioxin-contaminated soil sample and identified as Trichosporon mucoides. During incubation of glucose-pregrown cells with dibenzofuran, six major metabolites were detected by high-performance liquid chromatography. The formation of four different monohydroxylated dibenzofurans was proven by comparison of analytical data (gas chromatography-mass spectrometry) with that for authentic standards. Further oxidation produced 2, 3-dihydroxydibenzofuran and its ring cleavage product 2-(1-carboxy methylidene)-2,3-dihydrobenzo[b]furanylidene glycolic acid, which were characterized by mass spectrometry and 1H nuclear magnetic resonance spectroscopy. These two metabolites are derived from 2-hydroxydibenzofuran and 3-hydroxydibenzofuran, as shown by incubation experiments using these monohydroxylated dibenzofurans as substrates. PMID:9603837

Hammer, E; Krowas, D; Schäfer, A; Specht, M; Francke, W; Schauer, F

1998-06-01

111

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

SciTech Connect

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

Holmes, R.L.

1982-04-01

112

Identification and Cloning of Two Novel Allergens from the Lipophilic Yeast, Malassezia furfur  

Microsoft Academic Search

Two novel allergens, designated Mal f 2 and Mal f 3 according to the WHO\\/IUIS Allergen Nomenclature Subcommittee recommendation, were isolated from the lipophilic yeastMalassezia furfurcell extracts and the genes coding for those were cloned. Mal f 2 and Mal f 3 had apparent molecular weights of 21 kDa and 20 kDa, respectively, on SDS–PAGE under reducing conditions. The identified

Hiroshi Yasueda; Takashi Hashida-Okado; Akemi Saito; Katsuhisa Uchida; Masanobu Kuroda; Yoshimi Onishi; Kazuo Takahashi; Hideyo Yamaguchi; Kazutoh Takesako; Kazuo Akiyama

1998-01-01

113

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

Microsoft Academic Search

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

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

2003-01-01

114

Misidentification of clinical yeast isolates by using the updated Vitek Yeast Biochemical Card.  

PubMed Central

The Vitek Yeast Biochemical Card (YBC) is widely used as a rapid identification (RI) (within 48 h) system for clinical yeast isolates. We compared the RI results obtained by the YBC technique with matched results obtained with the API 20C system. The RI of germ tube-negative yeasts isolated from 222 clinical specimens was performed with the YBC system, and the results were compared with those of standard identifications obtained by using the API 20C system and morphology, with additional biochemical reactions performed as required. Commonly isolated yeasts (Candida albicans [n = 29], Candida tropicalis [n = 40], Torulopsis [Candida] glabrata [n = 28], Candida parapsilosis [n = 12], and Cryptococcus neoformans [n = 14]) were generally well identified (115 of 123 [93%] identified correctly, with only C. albicans, C. tropicalis, and C. neoformans mis- or unidentified more than once). The RI of less commonly isolated yeasts included in the YBC database, however, was less successful (54 of 99 [55%] correct). The YBC card failed to identify 42% (10 of 24) of Candida krusei isolates, 80% (4 of 5) of Candida lambica isolates, 88% (7 of 8) of Trichosporon beigelii isolates, and 83% (10 of 12) of Cryptococcus isolates (non-C. neoformans species). For most identification failures (79%; 42 of 53) there was no identification by the end of 48 h; the other identification failures (21%; 11 of 53) gave definite but incorrect identifications. Of eight rare clinical yeast isolates not included in the Vitek database, six were correctly, not identified, while two (25%) were falsely assigned a definite RI (one Hansenula fabianii isolate was identified as Rhodotorula glutinis, and one Hansenula isolate [non-Hansenula anomala] was identified as Hansenula anomala). While the Vitek YBC rapidly and adequately identifies common yeast isolates, it fails in the RI of more unusual organisms. PMID:7883873

Dooley, D P; Beckius, M L; Jeffrey, B S

1994-01-01

115

Misidentification of clinical yeast isolates by using the updated Vitek Yeast Biochemical Card.  

PubMed

The Vitek Yeast Biochemical Card (YBC) is widely used as a rapid identification (RI) (within 48 h) system for clinical yeast isolates. We compared the RI results obtained by the YBC technique with matched results obtained with the API 20C system. The RI of germ tube-negative yeasts isolated from 222 clinical specimens was performed with the YBC system, and the results were compared with those of standard identifications obtained by using the API 20C system and morphology, with additional biochemical reactions performed as required. Commonly isolated yeasts (Candida albicans [n = 29], Candida tropicalis [n = 40], Torulopsis [Candida] glabrata [n = 28], Candida parapsilosis [n = 12], and Cryptococcus neoformans [n = 14]) were generally well identified (115 of 123 [93%] identified correctly, with only C. albicans, C. tropicalis, and C. neoformans mis- or unidentified more than once). The RI of less commonly isolated yeasts included in the YBC database, however, was less successful (54 of 99 [55%] correct). The YBC card failed to identify 42% (10 of 24) of Candida krusei isolates, 80% (4 of 5) of Candida lambica isolates, 88% (7 of 8) of Trichosporon beigelii isolates, and 83% (10 of 12) of Cryptococcus isolates (non-C. neoformans species). For most identification failures (79%; 42 of 53) there was no identification by the end of 48 h; the other identification failures (21%; 11 of 53) gave definite but incorrect identifications. Of eight rare clinical yeast isolates not included in the Vitek database, six were correctly, not identified, while two (25%) were falsely assigned a definite RI (one Hansenula fabianii isolate was identified as Rhodotorula glutinis, and one Hansenula isolate [non-Hansenula anomala] was identified as Hansenula anomala). While the Vitek YBC rapidly and adequately identifies common yeast isolates, it fails in the RI of more unusual organisms. PMID:7883873

Dooley, D P; Beckius, M L; Jeffrey, B S

1994-12-01

116

System identification for passive linear quantum systems  

E-print Network

System identification is a key enabling component for the implementation of quantum technologies, including quantum control. In this paper, we consider the class of passive linear input-output systems, and investigate several basic questions: (1) which parameters can be identified? (2) Given sufficient input-output data, how do we reconstruct system parameters? (3) How can we optimize the estimation precision by preparing appropriate input states and performing measurements on the output? We show that minimal systems can be identified up to a unitary transformation on the modes, and systems satisfying a Hamiltonian connectivity condition called "infecting" are completely identifiable. We propose a frequency domain design based on a Fisher information criterion, for optimizing the estimation precision for coherent input state. As a consequence of the unitarity of the transfer function, we show that the Heisenberg limit with respect to the input energy can be achieved using non-classical input states.

Madalin Guta; Naoki Yamamoto

2014-08-27

117

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

PubMed

A gene from Saccharomyces cerevisiae has been mapped, cloned, sequenced and shown to encode a catalytic subunit of an N-terminal acetyltransferase. Regions of this gene, NAT1, and the chloramphenicol acetyltransferase genes of bacteria have limited but significant homology. A nat1 null mutant is viable but exhibits a variety of phenotypes, including reduced acetyltransferase activity, derepression of a silent mating type locus (HML) and failure to enter G0. All these phenotypes are identical to those of a previously characterized mutant, ard1. NAT1 and ARD1 are distinct genes that encode proteins with no obvious similarity. Concomitant overexpression of both NAT1 and ARD1 in yeast causes a 20-fold increase in acetyltransferase activity in vitro, whereas overexpression of either NAT1 or ARD1 alone does not raise activity over basal levels. A functional iso-1-cytochrome c protein, which is N-terminally acetylated in a NAT1 strain, is not acetylated in an isogenic nat1 mutant. At least 20 other yeast proteins, including histone H2B, are not N-terminally acetylated in either nat1 or ard1 mutants. These results suggest that NAT1 and ARD1 proteins function together to catalyze the N-terminal acetylation of a subset of yeast proteins. PMID:2551674

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

1989-07-01

118

Identification of Cell Cycle-regulated Genes in Fission YeastD?  

PubMed Central

Cell cycle progression is both regulated and accompanied by periodic changes in the expression levels of a large number of genes. To investigate cell cycle-regulated transcriptional programs in the fission yeast Schizosaccharomyces pombe, we developed a whole-genome oligonucleotide-based DNA microarray. Microarray analysis of both wild-type and cdc25 mutant cell cultures was performed to identify transcripts whose levels oscillated during the cell cycle. Using an unsupervised algorithm, we identified 747 genes that met the criteria for cell cycle-regulated expression. Peaks of gene expression were found to be distributed throughout the entire cell cycle. Furthermore, we found that four promoter motifs exhibited strong association with cell cycle phase-specific expression. Examination of the regulation of MCB motif-containing genes through the perturbation of DNA synthesis control/MCB-binding factor (DSC/MBF)-mediated transcription in arrested synchronous cdc10 mutant cell cultures revealed a subset of functional targets of the DSC/MBF transcription factor complex, as well as certain gene promoter requirements. Finally, we compared our data with those for the budding yeast Saccharomyces cerevisiae and found ?140 genes that are cell cycle regulated in both yeasts, suggesting that these genes may play an evolutionarily conserved role in regulation of cell cycle-specific processes. Our complete data sets are available at http://giscompute.gis.a-star.edu.sg/~gisljh/CDC. PMID:15616197

Peng, Xu; Karuturi, R. Krishna Murthy; Miller, Lance D.; Lin, Kui; Jia, Yonghui; Kondu, Pinar; Wang, Long; Wong, Lim-Soon; Liu, Edison T.; Balasubramanian, Mohan K.; Liu, Jianhua

2005-01-01

119

Identification of Fractional-Order Dynamical Systems  

Microsoft Academic Search

This contribution deals with identification of fractional-order dynamical systems. We consider systems whose mathematical description is a three-member differential equation in which the orders of derivatives can be real numbers. We give a discretization method and a numerical solution of differential equations of this type. An experimental method of identification is given which is based on evaluation of transfer characteristics.

L. Dorcak; V. Lesko; I. Kostial

2002-01-01

120

System identification for robust control design  

SciTech Connect

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

Dohner, J.L.

1995-04-01

121

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

122

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

123

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

PubMed Central

Telomeres are the nucleoprotein complexes at eukaryotic chromosomal ends. Telomeric DNA is synthesized by the ribonucleoprotein telomerase, which comprises a telomerase reverse transcriptase (TERT) and a telomerase RNA (TER). TER contains a template for telomeric DNA synthesis. Filamentous fungi possess extremely short and tightly regulated telomeres. Although TERT is well conserved between most organisms, TER is highly divergent and thus difficult to identify. In order to identify the TER sequence, we used the unusually long telomeric repeat sequence of Aspergillus oryzae together with reverse-transcription-PCR and identified a transcribed sequence that contains the potential template within a region predicted to be single stranded. We report the discovery of TERs from twelve other related filamentous fungi using comparative genomic analysis. These TERs exhibited strong conservation with the vertebrate template sequence, and two of these potentially use the identical template as humans. We demonstrate the existence of important processing elements required for the maturation of yeast TERs such as an Sm site, a 5? splice site and a branch point, within the newly identified TER sequences. RNA folding programs applied to the TER sequences show the presence of secondary structures necessary for telomerase activity, such as a yeast-like template boundary, pseudoknot, and a vertebrate-like three-way junction. These telomerase RNAs identified from filamentous fungi display conserved structural elements from both yeast and vertebrate TERs. These findings not only provide insights into the structure and evolution of a complex RNA but also provide molecular tools to further study telomere dynamics in filamentous fungi. PMID:23555591

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

2013-01-01

124

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. PMID:23524242

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

2013-01-01

125

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

PubMed

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

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

2011-01-01

126

Biochemical, cellular and molecular identification of DNA polymerase ? in yeast mitochondria.  

PubMed

DNA replication occurs in various compartments of eukaryotic cells such as the nuclei, mitochondria and chloroplasts, the latter of which is used in plants and algae. Replication appears to be simpler in the mitochondria than in the nucleus where multiple DNA polymerases, which are key enzymes for DNA synthesis, have been characterized. In mammals, only one mitochondrial DNA polymerase (pol ?) has been described to date. However, in the mitochondria of the yeast Saccharomyces cerevisiae, we have found and characterized a second DNA polymerase. To identify this enzyme, several biochemical approaches such as proteinase K treatment of sucrose gradient purified mitochondria, analysis of mitoplasts, electron microscopy and the use of mitochondrial and cytoplasmic markers for immunoblotting demonstrated that this second DNA polymerase is neither a nuclear or cytoplasmic contaminant nor a proteolytic product of pol ?. An improved purification procedure and the use of mass spectrometry allowed us to identify this enzyme as DNA polymerase ?. Moreover, tagging DNA polymerase ? with a fluorescent probe demonstrated that this enzyme is localized both in the nucleus and in the organelles of intact yeast cells. The presence of two replicative DNA polymerases may shed new light on the mtDNA replication process in S. cerevisiae. PMID:23160073

Lasserre, Jean-Paul; Plissonneau, Jacqueline; Velours, Christophe; Bonneu, Marc; Litvak, Simon; Laquel, Patricia; Castroviejo, Michel

2013-04-01

127

Identification and characterization of endo-?-N-acetylglucosaminidase from methylotrophic yeast Ogataea minuta.  

PubMed

In four yeast strains, Ogataea minuta, Candida parapolymorpha, Pichia anomala and Zygosaccharomyces rouxii, we identified endo-?-N-acetylglucosaminidase (ENGase) homologous sequences by database searches; in each of the four species, a corresponding enzyme activity was also confirmed in crude cell extract obtained from each strain. The O. minuta ENGase (Endo-Om)-encoding gene was directly amplified from O. minuta genomic DNA and sequenced. The Endo-Om-encoding gene contained a 2319-bp open-reading frame; the deduced amino acid sequence indicated that the putative protein belonged to glycoside hydrolase family 85. The gene was introduced into O. minuta, and the recombinant Endo-Om was overexpressed and purified. When the enzyme assay was performed using an agalacto-biantennary oligosaccharide as a substrate, Endo-Om exhibited both hydrolysis and transglycosylation activities. Endo-Om exhibited hydrolytic activity for high-mannose, hybrid, biantennary and (2,6)-branched triantennary N-linked oligosaccharides, but not for tetraantennary, (2,4)-branched triantennary, bisecting N-acetylglucosamine structure and core-fucosylated biantennary N-linked oligosaccharides. Endo-Om also was able to hydrolyze N-glycans attached to RNase B and human transferrin under both denaturing and nondenaturing conditions. Thus, the present study reports the detection and characterization of a novel yeast ENGase. PMID:23436287

Murakami, Satoshi; Takaoka, Yuki; Ashida, Hisashi; Yamamoto, Kenji; Narimatsu, Hisashi; Chiba, Yasunori

2013-06-01

128

Adaptive sparse system identification using wavelets  

Microsoft Academic Search

This paper proposes the use of wavelets for the identification of an unknown sparse system whose impulse response (IR) is rich in spectral content. The superior time localization property of wavelets allows for the identification and subsequent adaptation of only the nonzero IR regions, resulting in lower complexity and faster convergence speed. An added advantage of using wavelets is their

K. C. Ho; Shannon D. Blunt

2002-01-01

129

Characterisation of Mammalian GLUT Glucose Transporters in a Heterologous Yeast Expression System  

Microsoft Academic Search

We have developed a new heterologous expression system for mammalian glucose transporters. The system is based on a Saccharomyces cerevisiae strain completely deleted for all its endogenous hexose transporters and unable to take up and to grow on hexoses. To target the heterologous glucose transporters into the yeast plasma membrane in a fully active form, additional mutations had to be

Roman Wieczorke; Silke Dlugai; Stefanie Krampe; Eckhard Boles

2003-01-01

130

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

Microsoft Academic Search

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

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

2008-01-01

131

Identification and Control of Mechanical Systems  

NASA Astrophysics Data System (ADS)

The control of vibrating systems is a significant issue in the design of aircraft, spacecraft, bridges, and high-rise buildings. This book discusses the control of vibrating systems, integrating structural dynamics, vibration analysis, modern control, and system identification. By integrating these subjects engineers will need only one book, rather than several texts or courses, to solve vibration control problems. The authors cover key developments in aerospace control and identification theory, including virtual passive control, observer and state-space identification, and data-based controller synthesis. They address many practical issues and applications, and show examples of how various methods are applied to real systems. Some methods show the close integration of system identification and control theory from the state-space perspective, rather than from the traditional input-output model perspective of adaptive control. This text will be useful for advanced undergraduate and beginning graduate students in aerospace, mechanical, and civil engineering, as well as for practicing engineers.

Juang, Jer-Nan; Phan, Minh Q.

2001-08-01

132

Identification of medically relevant species of arthroconidial yeasts by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry.  

PubMed

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was used for an extensive identification study of arthroconidial yeasts, using 85 reference strains from the CBS-KNAW yeast collection and 134 clinical isolates collected from medical centers in Qatar, Greece, and Romania. The test set included 72 strains of ascomycetous yeasts (Galactomyces, Geotrichum, Saprochaete, and Magnusiomyces spp.) and 147 strains of basidiomycetous yeasts (Trichosporon and Guehomyces spp.). With minimal preparation time, MALDI-TOF MS proved to be an excellent diagnostic tool that provided reliable identification of most (98%) of the tested strains to the species level, with good discriminatory power. The majority of strains were correctly identified at the species level with good scores (>2.0) and seven of the tested strains with log score values between 1.7 and 2.0. The MALDI-TOF MS results obtained were consistent with validated internal transcribed spacer (ITS) and/or large subunit (LSU) ribosomal DNA sequencing results. Expanding the mass spectrum database by increasing the number of reference strains for closely related species, including those of nonclinical origin, should enhance the usefulness of MALDI-TOF MS-based diagnostic analysis of these arthroconidial fungi in medical and other laboratories. PMID:23678074

Kolecka, Anna; Khayhan, Kantarawee; Groenewald, Marizeth; Theelen, Bart; Arabatzis, Michael; Velegraki, Aristea; Kostrzewa, Markus; Mares, Mihai; Taj-Aldeen, Saad J; Boekhout, Teun

2013-08-01

133

Identification of Medically Relevant Species of Arthroconidial Yeasts 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) was used for an extensive identification study of arthroconidial yeasts, using 85 reference strains from the CBS-KNAW yeast collection and 134 clinical isolates collected from medical centers in Qatar, Greece, and Romania. The test set included 72 strains of ascomycetous yeasts (Galactomyces, Geotrichum, Saprochaete, and Magnusiomyces spp.) and 147 strains of basidiomycetous yeasts (Trichosporon and Guehomyces spp.). With minimal preparation time, MALDI-TOF MS proved to be an excellent diagnostic tool that provided reliable identification of most (98%) of the tested strains to the species level, with good discriminatory power. The majority of strains were correctly identified at the species level with good scores (>2.0) and seven of the tested strains with log score values between 1.7 and 2.0. The MALDI-TOF MS results obtained were consistent with validated internal transcribed spacer (ITS) and/or large subunit (LSU) ribosomal DNA sequencing results. Expanding the mass spectrum database by increasing the number of reference strains for closely related species, including those of nonclinical origin, should enhance the usefulness of MALDI-TOF MS-based diagnostic analysis of these arthroconidial fungi in medical and other laboratories. PMID:23678074

Kolecka, Anna; Khayhan, Kantarawee; Groenewald, Marizeth; Theelen, Bart; Arabatzis, Michael; Velegraki, Aristea; Kostrzewa, Markus; Mares, Mihai; Taj-Aldeen, Saad J.

2013-01-01

134

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

PubMed Central

Black yeast members of the Herpotrichiellaceae present a complex ecological behavior: They are often isolated from rather extreme environments polluted with aromatic hydrocarbons, while they are also regularly involved in human opportunistic infections. A selective technique to promote the in vitro growth of herpotrichiellaceous fungi was applied to investigate their ecophysiology. Samples from natural ecological niches and man-made environments that might contain black yeasts were enriched on an inert solid support at low humidity and under a controlled atmosphere rich in volatile aromatic hydrocarbons. Benzene, toluene, and xylene were provided separately as the sole carbon and energy source via the gas phase. The assayed isolation protocol was highly specific toward mesophilic Exophiala species (70 strains of this genus out of 71 isolates). Those were obtained predominantly from creosote-treated railway ties (53 strains), but isolates were also found on wild berries (11 strains) and in guano-rich soil samples (six strains). Most of the isolates were obtained on toluene (43 strains), but enrichments on xylene and benzene also yielded herpotrichiellaceous fungi (17 and 10 isolates, respectively). Based upon morphological characterizations and DNA sequences of the full internal transcriber spacers (ITS) and the 8.5S rRNA genes, the majority of the obtained isolates were affiliated to the recently described species Exophiala xenobiotica (32 strains) and Exophiala bergeri (nine strains). Members of two other phylogenetic groups (24 and two strains, respectively) somewhat related to E. bergeri were also found, and a last group (three strains) corresponded to an undescribed Exophiala species. PMID:20333373

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

2010-01-01

135

Identification of Information in Decision Systems  

E-print Network

Extending unique identification to non-physical objects (data, information, decisions, knowledge) is a challenging problem in systems engineering. The tools and technologies available for naming physical objects may soon ...

Datta, Shoumen

2007-01-01

136

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

137

Identification of Multi-Input Biological Systems  

Microsoft Academic Search

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

Panos Z. Marmarelis; Ken-Ichi Naka

1974-01-01

138

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

PubMed Central

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, MSC; Bertoletti, A; Lucca, HRL; Silva, RBO; Meneghin, FA; Szeszs, MW

2013-01-01

139

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

140

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. PMID:22727066

2012-01-01

141

Antibody engineering: Comparison of bacterial, yeast, insect and mammalian expression systems  

Microsoft Academic Search

Engineered antibody molecules, and their fragments, are being increasingly exploited as scientific and clinical tools. However, one factor that can limit the applicability of this technology is the ability to express large amounts of active protein. In this review we describe the relative advantages and disadvantages of bacterial, yeast, insect and mammalian expression systems, and discuss some of the problems

R Verma; E Boleti; A. J. T George

1998-01-01

142

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. PMID:9383076

Benni, M. L.; Neigeborn, L.

1997-01-01

143

Identification of silencer binding proteins from yeast: possible roles in SIR control and DNA replication  

PubMed Central

The `silent' yeast mating-type loci (HML and HMR) are repressed by sequences (HMLE and HMRE) located over 1 kb from their promoters which have properties opposite those of enhancers, and are called `silencers'. Both silencers contain autonomously replicating sequences (ARS). Silencer activity requires four trans-acting genes called SIR (silent information regulator). We have identified two DNA binding factors, SBF-B and SBF-E, which bind to known regulatory elements at HMRE. SBF-B binds to a region involved in both the silencer and ARS functions of HMRE, but does not bind to HMLE. This factor also binds to the unlinked ARS1 element. SBF-E recognizes a sequence found at both silencers. These results suggest that the two silencers may be composed of different combinations of regulatory elements at least one of which is common to both. Neither factor appears to be a SIR gene product. Hence the SIR proteins may not directly interact with the silencer control sites. ImagesFig. 2.Fig. 3.Fig. 4.Fig. 5.Fig. 6.Fig. 7. PMID:15981337

Shore, David; Stillman, David J.; Brand, Andrea H.; Nasmyth, Kim A.

1987-01-01

144

Identification of functional connections between calmodulin and the yeast actin cytoskeleton.  

PubMed Central

One of four intragenic complementing groups of temperature-sensitive yeast calmodulin mutations, cmd1A, results in a characteristic functional defect in actin organization. We report here that among the complementing mutations, a representative cmd1A mutation (cmd1-226: F92A) is synthetically lethal with a mutation in MYO2 that encodes a class V unconventional myosin with calmodulin-binding domains. Gel overlay assay shows that a mutant calmodulin with the F92A alteration has severely reduced binding affinity to a GST-Myo2p fusion protein. Random replacement and site-directed mutagenesis at position 92 of calmodulin indicate that hydrophobic and aromatic residues are allowed at this position, suggesting an importance of hydrophobic interaction between calmodulin and Myo2p. To analyze other components involved in actin organization through calmodulin, we isolated and characterized mutations that show synthetic lethal interaction with cmd1-226; these "cax" mutants fell into five complementation groups. Interestingly, all the mutations themselves affect actin organization. Unlike cax2, cax3, cax4, and cax5 mutations, cax1 shows allele-specific synthetic lethality with the cmd1A allele. CAX1 is identical to ANP1/GEM3/MCD2, which is involved in protein glycosylation. CAX4 is identical to the ORF YGR036c, and CAX5 is identical to MNN10/SLC2/BED1. We discuss possible roles for Cax proteins in the regulation of the actin cytoskeleton. PMID:9725829

Sekiya-Kawasaki, M; Botstein, D; Ohya, Y

1998-01-01

145

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

146

Identification of a Novel Type of Spacer Element Required for Imprinting in Fission Yeast  

PubMed Central

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

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

2011-01-01

147

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

PubMed

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

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

2011-03-01

148

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

PubMed

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

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

2002-04-01

149

Global Identification of New Substrates for the Yeast Endoribonuclease, RNase Mitochondrial RNA Processing (MRP)*  

PubMed Central

RNase mitochondrial RNA processing (MRP) is an essential, evolutionarily conserved endoribonuclease composed of 10 different protein subunits and a single RNA. RNase MRP has established roles in multiple pathways including ribosome biogenesis, cell cycle regulation, and mitochondrial DNA replication. Although each of these functions is important to cell growth, additional functions may exist given the essential nature of the complex. To identify novel RNase MRP substrates, we utilized RNA immunoprecipitation and microarray chip analysis to identify RNA that physically associates with RNase MRP. We identified several new potential substrates for RNase MRP including a cell cycle-regulated transcript, CTS1; the yeast homolog of the mammalian p27Kip1, SIC1; and the U2 RNA component of the spliceosome. In addition, we found RNase MRP to be involved in the regulation of the Ty1 transposon RNA. These results reinforce and broaden the role of RNase MRP in cell cycle regulation and help to identify new roles of this endoribonuclease. PMID:22977255

Aulds, Jason; Wierzbicki, Sara; McNairn, Adrian; Schmitt, Mark E.

2012-01-01

150

RAPD analysis: a rapid technique for differentiation of spoilage yeasts.  

PubMed

Techniques for the identification of the spoilage yeasts Saccharomyces cerevisiae and members of the Zygosaccharomyces genus from food and beverages sources were evaluated. The use of identification systems based on physiological characteristics resulted often in incomplete identification or misidentification. Also the cellular fatty acid analysis failed on differentiating species within the Zygosaccharomyces genus. However, the Random Amplified Polymorphic DNA (RAPD) assay, using selected 10-mer oligonucleotides, allowed discrimination between all species tested. For this RAPD assay, a simple and reproducible method of DNA isolation from spoilage yeast cells is described. PMID:7703018

Baleiras Couto, M M; van der Vossen, J M; Hofstra, H; Huis in 't Veld, J H

1994-12-01

151

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. PMID:23826133

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

2013-01-01

152

Identification and Control of Mechanical Systems  

Microsoft Academic Search

The control of vibrating systems is a significant issue in the design of aircraft, spacecraft, bridges, and high-rise buildings. This book discusses the control of vibrating systems, integrating structural dynamics, vibration analysis, modern control, and system identification. By integrating these subjects engineers will need only one book, rather than several texts or courses, to solve vibration control problems. The authors

Jer-Nan Juang; Minh Q. Phan

2001-01-01

153

System identification and control using genetic algorithms  

Microsoft Academic Search

It is shown how genetic algorithms can be applied for system identification of both continuous and discrete time systems. It is shown that they are effective in both domains and are able to directly identify physical parameters or poles and zeros. This can be useful because changing one physical parameter might affect every parameter of a system transfer function. The

Kristinn Kristinsson; Guy A. Dumont

1992-01-01

154

Nonlinear system identification on a combine harvester  

Microsoft Academic Search

The traction system of a combine harvester contains considerable nonlinearities. The objective of this paper is to derive a model of the propulsion which can then be used for regulator design. First the nonlinearities are quantified by analyzing the output of the system excited by a multisine. Standard linear system identification techniques (such as ARX and ARMAX) are then compared

Tom Coen; Johan Paduart; Jan Anthonis; Johan Schoukens; Josse De Baerdemaeker

2006-01-01

155

Identification of a 45-kDa protein at the protein import site of the yeast mitochondrial inner membrane.  

PubMed Central

Import of proteins into mitochondria involves the cooperation of protein translocation systems in the outer and inner membranes. We have identified a 45-kDa protein at the protein import site of the yeast mitochondrial inner membrane. This 45-kDa protein could be crosslinked to a partly translocated precursor, which cannot be imported across the inner membrane when the matrix is depleted of ATP. In addition, an antibody against this protein strongly inhibited protein import into right-side-out inner-membrane vesicles. The 45-kDa protein accounts for only 0.1% of mitochondrial protein and appears peripherally attached to the outer face of the inner membrane. The properties of this protein suggest that it is a component of the protein import system of the mitochondrial inner membrane. Images PMID:1465421

Scherer, P E; Manning-Krieg, U C; Jenö, P; Schatz, G; Horst, M

1992-01-01

156

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

Technology Transfer Automated Retrieval System (TEKTRAN)

A three-plasmid yeast expression system utilizing the portable small ubiquitin-like modifier (SUMO) vector set combined with the efficient endogenous yeast protease Ulp1 was developed for production of large amounts of soluble functional protein in Saccharomyces cerevisiae. Each vector has a differ...

157

Potassium uptake system Trk2 is crucial for yeast cell viability during anhydrobiosis.  

PubMed

Yeasts grow at very different potassium concentrations, adapting their intracellular cation levels to changes in the external environment. Potassium homeostasis is maintained with the help of several transporters mediating the uptake and efflux of potassium with various affinities and mechanisms. In the model yeast Saccharomyces cerevisiae, two uptake systems, Trk1 and Trk2, are responsible for the accumulation of a relatively high intracellular potassium content (200-300 mM) and the efflux of surplus potassium is mediated by the Tok1 channel and active exporters Ena ATPase and Nha1 cation/proton antiporter. Using a series of deletion mutants, we studied the role of individual potassium transporters in yeast cell resistance to dehydration. The Trk2 transporter (whose role in S. cerevisiae physiology was not clear) is important for cell viability in the stationary phase of growth and, moreover, it plays a crucial role in the yeast survival of dehydration/rehydration treatments. Mutants lacking the TRK2 gene accumulated significantly lower amounts of potassium ions in the stationary culture growth phase, and these lower amounts correlated with decreased resistance to dehydration/rehydration stress. Our results showed Trk2 to be the major potassium uptake system in stationary cells, and potassium content to be a crucial parameter for desiccation survival. PMID:24267958

Borovikova, Diana; Herynkova, Pavla; Rapoport, Alexander; Sychrova, Hana

2014-01-01

158

System identification in the repetition domain  

NASA Technical Reports Server (NTRS)

Procedures for system identification using realization theory in conjunction with learning control ideas are developed. The Markov parameters of the system are identified by combining data from repeated experiments. Three approaches are discussed for identification of as many Markov parameters as sample points in the experiment. Making use of all the parameters, realization theory is then employed to determine the system order and to obtain a minimal order representation. The first two approaches are non-recursive, which in the case of noise-free data yields a one step solution. The third approach uses a recursive formulation rendered from adaptive control but modified for successive experiments. A simple example shows the numerical convergence of the identified parameters as a function of the number of experiments. The procedure presented herein is an extension of the existing Eigensystem Realization Algorithm (ERA), which has been successfully applied for system identification of large structures.

Juang, Jer-Nan; Horta, Lucas G.; Longman, Richard W.

1990-01-01

159

Gaussian process based recursive system identification  

NASA Astrophysics Data System (ADS)

This paper is concerned with the problem of recursive system identification using nonparametric Gaussian process model. Non-linear stochastic system in consideration is affine in control and given in the input-output form. The use of recursive Gaussian process algorithm for non-linear system identification is proposed to alleviate the computational burden of full Gaussian process. The problem of an online hyper-parameter estimation is handled using proposed ad-hoc procedure. The approach to system identification using recursive Gaussian process is compared with full Gaussian process in terms of model error and uncertainty as well as computational demands. Using Monte Carlo simulations it is shown, that the use of recursive Gaussian process with an ad-hoc learning procedure offers converging estimates of hyper-parameters and constant computational demands.

Prüher, Jakub; Šimandl, Miroslav

2014-12-01

160

Choosing Between Yeast and Bacterial Expression Systems: Yield Dependent  

NASA Technical Reports Server (NTRS)

Green fluorescent protein (GFP) is a naturally occurring fluorescent protein isolated from the jellyfish Aequorea victoria. The intrinsic fluorescence of the protein is due to a chromophore located in the center of the molecule. Its usefulness has been established as a marker for gene expression and localization of gene products. GFP has recently been utilized as a model protein for crystallization studies at NASA/MSFC, both in earth-based and in microgravity experiments. Because large quantities of purified protein were needed, the cDNA of GFP was cloned into the Pichia pastoris pPICZ(alpha) C strain, with very little protein secreted into the media. Microscopic analysis prior to harvest showed gigantic green fluorescent yeast, but upon harvesting most protein was degraded. Trial fermentations of GFP cloned into pPICZ A for intracellular expression provided unsatisfactory yield. GFP cloned into E, coli was overexpressed at greater than 150 mg/liter, with purification yields at greater than 100mg/liter.

Miller, Rebecca S.; Malone, Christine C.; Moore, Blake P.; Burk, Melissa; Crawford, Lisa; Karr, Laurel J.; Curreri, Peter A. (Technical Monitor)

2002-01-01

161

GENE ENGINEERING IN YEAST FOR BIODEGRADATION: IMMUNOLOGICAL CROSS-REACTIVITY AMONG CYTOCHROME P-450 SYSTEM PROTEINS OF SACCHAROMYCES CEREVISIAE AND CANDIDA TROPICALIS  

EPA Science Inventory

Yeasts are eukaryotic microorganisms whose cytochrome P-450 monoxygenase systems may be amenable to genetic engineering for the hydroxylation and detoxication of polychlorinated aromatic hydrocarbons. e are examining the molecular genetic properties of strains of bakers yeast, Sa...

162

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

163

A Modified MuDPIT Separation Identified 4,488 Proteins in a System Wide Analysis of Quiescence in Yeast  

PubMed Central

A modified multidimensional protein identification technology (MudPIT) separation was coupled to an LTQ Orbitrap Velos mass spectrometer and used to rapidly identify the near complete yeast proteome from a whole cell tryptic digest. This modified on-line two dimensional liquid chromatography separation consists of 39 strong cation exchange steps followed by a short 18.5 min reversed-phase (RP) gradient. A total of 4,269 protein identifications were made from 4,189 distinguishable protein families from yeast during log phase growth. The “Micro” MudPIT separation performed as well as a standard MudPIT separation in 40% less gradient time. The majority of the yeast proteome can now be routinely covered in less than a days’ time with high reproducibility and sensitivity. The newly devised separation method was used to detect changes in protein expression during cellular quiescence in yeast. An enrichment in the GO annotations ‘oxidation reduction’, ‘catabolic processing’ and ‘cellular response to oxidative stress’ was seen in the quiescent cellular fraction, consistent with their long lived stress resistant phenotypes. Heterogeneity was observed in the stationary phase fraction with a less dense cell population showing reductions in KEGG pathway categories of ‘Ribosome’ and ‘Proteasome’, further defining the complex nature of yeast populations present during stationary phase growth. In total 4,488 distinguishable protein families were identified in all cellular conditions tested. PMID:23540446

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

2013-01-01

164

Molecular comparisons for identification of food spoilage yeasts and prediction of species that may develop in different food products  

Technology Transfer Automated Retrieval System (TEKTRAN)

Spoilage of foods and beverages by yeasts is often characterized by objectionable odors, appearance, taste, texture or build-up of gas in packaging containers, resulting in loss of the product. Seldom is human health compromised by products spoiled by yeasts even though some spoilage is caused by sp...

165

Transformation system for prototrophic industrial yeasts using the AUR1 gene as a dominant selection marker.  

PubMed

We show a new transformation system for prototrophic yeast strains including those of Saccharomyces cerevisiae, Kluyveromyces lactis, K. marxianus, and Candida glabrata. This system is composed of an antibiotic, aureobasidin A (AbA), and its resistance gene AUR1-C as a selection marker. Southern analysis of genomic DNAs of the transformants indicated that the copy number of the plasmid increased from one to more than four, depending on the concentration of AbA used for selection of the transformants. The AUR1-C gene was also effective as a selection marker for gene disruption, and was able to disrupt both copies of the gene on homologous chromosomes of diploid cells by a single round of transformation. This system has a broad application in the transformation and gene disruption of prototrophic strains of a variety of yeast species. PMID:9541018

Hashida-Okado, T; Ogawa, A; Kato, I; Takesako, K

1998-03-20

166

System Identification through Model Composition and Stochastic Search  

Microsoft Academic Search

System identification methodologies are useful for identifying characteristics of structural systems using measurement data. However, incorrect systems might be identified when many combinations of system characteristics result in the same predicted responses at measured locations. The reliability of identification is affected by a number of factors that most previous work has overlooked. This paper presents a system identification methodology that

Y. Robert-Nicoud; B. Raphael; I. F. C. Smith

2005-01-01

167

Linear system identification using proper orthogonal decomposition  

Microsoft Academic Search

A least-square-based method to identify the system matrices of linear dynamical systems is proposed. The primary focus is on the identification of a reduced-order model of the system operating in the mid-frequency range of vibration. Proper orthogonal decomposition (POD) is used for the model reduction. Such reduced-order model circumvents the limitations of traditional modal analysis which, although well-adapted in the

Mohammad Khalil; Sondipon Adhikari; Abhijit Sarkar

2007-01-01

168

Identification of Wild Yeast Strains and Analysis of Their ?-Glucan and Glutathione Levels for Use in Makgeolli Brewing.  

PubMed

Makgeolli, also known as Takju, is a non-filtered traditional Korean alcoholic beverage that contains various floating matter, including yeast cells, which contributes to its high physiological functionality. In the present study, we assessed the levels of ?-glucan and glutathione in various yeast strains isolated from traditional Korean Nuruk and selected a ?-glucan- and glutathione-rich yeast strain to add value to Makgeolli by enhancing its physiological functionality through increased levels of these compounds. Yeast ?-glucan levels ranged from 6.26% to 32.69% (dry basis) and were strongly species-dependent. Dried Saccharomyces cerevisiae isolated from Nuruk contained 25.53 µg/mg glutathione, 0.70 µg/mg oxidized glutathione, and 11.69 µg/g and 47.85 µg/g spermidine and L-ornithine monohydrochloride, respectively. To produce functional Makgeolli, a ?-glucan- and glutathione-rich yeast strain was selected in a screening analysis. Makgeolli fermented with the selected yeast strain contained higher ?-glucan and glutathione levels than commercial Makgeolli. Using the selected yeast strain to produce Makgeolli with high ?-glucan and glutathione content may enable the production of functional Makgeolli. PMID:25606008

Kang, Sun Hee; Kim, Hye Ryun; Kim, Jae Ho; Ahn, Byung Hak; Kim, Tae Wan; Lee, Jang-Eun

2014-12-01

169

Identification of Wild Yeast Strains and Analysis of Their ?-Glucan and Glutathione Levels for Use in Makgeolli Brewing  

PubMed Central

Makgeolli, also known as Takju, is a non-filtered traditional Korean alcoholic beverage that contains various floating matter, including yeast cells, which contributes to its high physiological functionality. In the present study, we assessed the levels of ?-glucan and glutathione in various yeast strains isolated from traditional Korean Nuruk and selected a ?-glucan- and glutathione-rich yeast strain to add value to Makgeolli by enhancing its physiological functionality through increased levels of these compounds. Yeast ?-glucan levels ranged from 6.26% to 32.69% (dry basis) and were strongly species-dependent. Dried Saccharomyces cerevisiae isolated from Nuruk contained 25.53 µg/mg glutathione, 0.70 µg/mg oxidized glutathione, and 11.69 µg/g and 47.85 µg/g spermidine and L-ornithine monohydrochloride, respectively. To produce functional Makgeolli, a ?-glucan- and glutathione-rich yeast strain was selected in a screening analysis. Makgeolli fermented with the selected yeast strain contained higher ?-glucan and glutathione levels than commercial Makgeolli. Using the selected yeast strain to produce Makgeolli with high ?-glucan and glutathione content may enable the production of functional Makgeolli. PMID:25606008

Kang, Sun Hee; Kim, Hye Ryun; Kim, Jae Ho; Ahn, Byung Hak; Kim, Tae Wan

2014-01-01

170

Associations of UBE2I with RAD52, UBL1, p53, and RAD51 Proteins in a Yeast Two-Hybrid System  

Microsoft Academic Search

The yeast RAD52-dependent pathway is involved in DNA recombination and double-strand break repair. Yeast ubiquitin-conjugating enzyme UBC9 participates in S- and M-phase cyclin degradation and mitotic control. Using the human RAD52 protein as the “bait” in a yeast two-hybrid system, we have identified a human homolog of yeast UBC9, designated UBE2I, that interacts with RAD52, RAD51, p53, and a ubiquitin-like

Zhiyuan Shen; Paige E. Pardington-Purtymun; Jarmon C. Comeaux; Robert K. Moyzis; David J. Chen

1996-01-01

171

Production of ?-linolenic acid using a novel heterologous expression system in the oleaginous yeast Lipomyces kononenkoae  

Microsoft Academic Search

A novel expression system was established in the oleaginous yeast, Lipomyces kononenkoae. The expression vector pLK-rhPHG of L. kononenkoae was constructed and using the hygromycin phosphotransferase gene and green fluorescent protein gene as reporter genes. A\\u000a delta 6-fatty acid desaturase gene (D6DM) from Cunninghamella echinulata MIAN6 was then expressed in this strain. The recombinant strain accumulated about 1.2% ?-linolenic acid

Ping Wang; Xia Wan; Yinbo Zhang; Mulan Jiang

172

Construction and application of a yeast expression system for thymosin ?1  

Microsoft Academic Search

We want to construct a yeast expression system for thymosin ?1 (T?1) to make the orally administered T?1 preparation possible. The whole T?1 DNA fragment was obtained by PCR. After being digested with restriction enzymes, it was cloned into pYES2 vector. Sequencing was performed to identify the recombinant. The sequence of T?1 in recombinant coincided with the original one reported

CHEN FENG; CHEN XIANG-MING; CHEN ZHI; JIANG HAN-LIANG; PAN XIAO-PING; HU ZHONG-RONG; LIU RONG-HUA; CHEN XIAO-MING

173

Optical disk uses in criminal identification systems  

NASA Astrophysics Data System (ADS)

A significant advancement in law enforcement tools has been made possible by the rapid and innovative development of electronic imaging for criminal identification systems. In particular, development of optical disks capable of high-capacity and random-access storage has provided a unique marriage of application and technology. Fast random access to any record, non-destructive reading of stored images, electronic sorting and transmission of images and an accepted legal basis for evidence are a few of the advantages derived from optical disk technology. This paper discusses the application of optical disk technology to both Automated Fingerprint Identification Systems (AFIS) and Automated Mugshot Retrieval Systems (AMRS). The following topics are addressed in light of AFIS and AMRS user requirements and system capabilities: Write once vs. rewritable, gray level and storage requirements, multi-volume library systems, data organization and capacity trends.

Sypherd, Allen D.

1990-08-01

174

State Identification in Nonlinear Systems  

SciTech Connect

A state estimation method based on finding a system state that causes a model to match a set of system measurements is regularized by requiring that sudden changes in system state be avoided. The required optimization is accomplished by a pattern search algorithm. The method does not require derivative information or linearization of the model. Is has been applied to a 10 dimensional model of a fast reactor system.

Holloway, James Paul [Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI 48109-2104 (United States)

2005-02-06

175

Improved system identification with Renormalization Group.  

PubMed

This paper proposes an improved system identification method with Renormalization Group. Renormalization Group is applied to a fine data set to obtain a coarse data set. The least squares algorithm is performed on the coarse data set. The theoretical analysis under certain conditions shows that the parameter estimation error could be reduced. The proposed method is illustrated with examples. PMID:24444706

Wang, Qing-Guo; Yu, Chao; Zhang, Yong

2014-09-01

176

Zigbee Wireless Vehicular Identification and Authentication System  

Microsoft Academic Search

We propose a Zigbee technology based wireless vehicle identification and driver authentication system consisting of a central database of authorized vehicles, Zigbee RF Vehicle tags, RF tag Reader and RF tag Writer. Zigbee is based on IEEE 802.15.4 standard for Wireless Personal Area Networks (WPANs) that is being used in many commercial and research applications today where it has become

S. D. Dissanayake; P. P. C. Karunasekara; D. D. Lakmanaarachchi; A. Rathnayaka; A. T. L. Samarasinghe

2008-01-01

177

IDENTIFICATION OF FLUID SYSTEMS USING GENETIC PROGRAMMING  

E-print Network

], for engineering design [3]. This paper illustrates the effectiveness of the genetic programming paradigmIDENTIFICATION OF FLUID SYSTEMS USING GENETIC PROGRAMMING Andrew H. Watson and Ian C. Parmee Plymouth Engineering Design Centre, University of Plymouth, PL4 8AA, UK email: awatson

Fernandez, Thomas

178

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

Microsoft Academic Search

A three-plasmid yeast expression system utilizing the portable small ubiquitin-like modifier (SUMO) vector set combined with the efficient endogenous yeast protease Ulp1 was developed for production of large amounts of soluble functional protein in Saccharomyces cerevisiae. Each vector has a different selectable marker (URA, TRP, or LEU), and the system provides high expression levels of three different proteins simultaneously. This

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

2009-01-01

179

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

PubMed

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

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

2007-01-01

180

Fanconi anemia protein complex: mapping protein interactions in the yeast 2- and 3-hybrid systems.  

PubMed

Fanconi anemia (FA) is an autosomal recessive syndrome characterized by progressive bone marrow failure and cancer predisposition. Eight FA complementation groups have been identified. The FANCA, FANCC, FANCE, FANCF, and FANCG proteins form a nuclear complex required for the monoubiquination of the FANCD2 protein. To investigate the architecture of the FA protein complex, the yeast 2-hybrid system was used to map contact points of the FANCA/FANCG, FANCC/FANCE, and FANCF/FANCG interactions. FANCG was shown to interact with both the amino-terminus of FANCA and the carboxyl-terminal region of FANCF. A FANCG mutant truncated at the carboxyl-terminus retained the ability to interact with FANCA. The interaction between FANCG and FANCF was ablated by a Leu71Pro mutant of FANCG. A central region of FANCE was sufficient for FANCC binding. A Leu554Pro mutant of FANCC failed to interact with FANCE. To further examine complex assembly, the yeast 3-hybrid system was used to investigate the ability of FANCG to act as a molecular bridge in mediating interaction between other FA proteins. FANCG was able to mediate interaction between FANCA and FANCF, as well as between monomers of FANCA. Direct interaction between FANCE and FANCD2 was also demonstrated in the yeast 2-hybrid system. This interaction involving an amino-terminal region of FANCD2 may provide a link between the FA protein complex and its downstream targets. PMID:12649160

Gordon, Susan M; Buchwald, Manuel

2003-07-01

181

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

182

Identification and Quantitation of Phosphorus Metabolites in Yeast Neutral pH Extracts by Nuclear Magnetic Resonance Spectroscopy  

Microsoft Academic Search

31P NMR spectroscopy offers a possibility to obtain a survey of all low-molecular-weight phosphorylated compounds in yeast. The yeast cells have been extracted using chloroform into a neutral aqueous phase. The use of high fields and the neutral pH extracts, which are suitable for NMR analysis, results in well-resolved 31P NMR spectra. Two-dimensional NMR experiments, such as proton-detected heteronuclear single

Anita Teleman; Peter Richard; Mervi Toivari; Merja Penttilä

1999-01-01

183

Model Identification and Validation for a Heating System using MATLAB System Identification Toolbox  

NASA Astrophysics Data System (ADS)

This paper proposed a systematic approach to select a mathematical model for an industrial heating system by adopting system identification techniques with the aim of fulfilling the design requirement for the controller. The model identification process will begin by collecting real measurement data samples with the aid of MATLAB system identification toolbox. The criteria for selecting the model that could validate model output with actual data will based upon: parametric identification technique, picking the best model structure with low order among ARX, ARMAX and BJ, and then applying model estimation and validation tests. Simulated results have shown that the BJ model has been best in providing good estimation and validation based upon performance criteria such as: final prediction error, loss function, best percentage of model fit, and co-relation analysis of residual for output.

Junaid Rabbani, Muhammad; Hussain, Kashan; khan, Asim-ur-Rehman; Ali, Abdullah

2013-12-01

184

Parameter identification for nonlinear aerodynamic systems  

NASA Technical Reports Server (NTRS)

Parameter identification for nonlinear aerodynamic systems is examined. It is presumed that the underlying model can be arranged into an input/output (I/O) differential operator equation of a generic form. The algorithm estimation is especially efficient since the equation error can be integrated exactly given any I/O pair to obtain an algebraic function of the parameters. The algorithm for parameter identification was extended to the order determination problem for linear differential system. The degeneracy in a least squares estimate caused by feedback was addressed. A method of frequency analysis for determining the transfer function G(j omega) from transient I/O data was formulated using complex valued Fourier based modulating functions in contrast with the trigonometric modulating functions for the parameter estimation problem. A simulation result of applying the algorithm is given under noise-free conditions for a system with a low pass transfer function.

Pearson, Allan E.

1990-01-01

185

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

186

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

187

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

188

NONLINEAR SYSTEM IDENTIFICATION OF A MOORED STRUCTURAL SYSTEM  

Microsoft Academic Search

This paper addresses the practical application of a multiple- input\\/single-output nonlinear system identification technique on ocean structural systems. An ocean structure exhibiting nonlinear behavior due to geometric nonlinearity of mooring line angles and the complexity of hydrodynamic excitations is chosen for this analytical study. Given the input wave characteristics, wave force and the system response, the method identifies the hydrodynamic

S. Narayanan; S. C. S. Yim; P. A. Palo

189

Biodiversity of yeast mycobiota in "sucuk," a traditional Turkish fermented dry sausage: phenotypic and genotypic identification, functional and technological properties.  

PubMed

In this study, yeasts from Turkish fermented sucuks were identified and their functional and technological properties were evaluated. Two hundred fifty-five yeast isolates were obtained from 35 different sucuk samples from different regions of Turkey. The yeast isolates were determined as genotypic using 2 different polymerase chain reaction (PCR) methods (rep-PCR and RAPD-PCR). Functional and technological properties of including proteolytic, lipolytic, and catalase activities, tolerance to NaCl and bile, as well as growing rates at different temperature and pH conditions selected yeast strains were also evaluated. Candida zeylanoides and Debaryomyces hansenii were dominant strains in sucuk samples. All C. zeylanoides and D. hansenii tested could grow at the condition of 15% NaCl and 0.3% bile salt. However, none of the strains were able to grow at 37 °C, even though catalase activity, weak proteolytic and lipolytic activities was still observed. D. hansenii were able to grow only at pH 3, while some of C. zeylanoides could grow at lower pH levels (pH 2). Three and 4 strains of C. zeylanoides showed ?-hemolysis activity and nitrate reduction ability to nitrite, respectively. D. hansenii did not have properties, which are ?-hemolysis, nitrate reduction, or hydrogen sulfide production. Overall, diverse yeast mycobiota present in Turkish fermented sucuk and their functional and technological properties were revealed with this study. PMID:25273925

Ozturk, Ismet; Sagdic, Osman

2014-11-01

190

Eigenvector Algorithm for Blind MA System Identification  

Microsoft Academic Search

We present a novel approach to the blind estimation of a linear time-invariant possibly mixed-phase movingaverage (MA) system (channel) based on second and fourth order statistics of the stationary received signal. Asthe algorithm incorporates the solution of an eigenvector problem, it is termed EVI standing for EigenVectorapproach to blind Identification. One of EVI's main features is its ability to obtain

Bjorn Jelonnek; Dieter Boss; Karl-dirk Kammeyer

1995-01-01

191

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

192

System identification of Drosophila olfactory sensory neurons  

PubMed Central

The lack of a deeper understanding of how olfactory sensory neurons (OSNs) encode odors has hindered the progress in understanding the olfactory signal processing in higher brain centers. Here we employ methods of system identification to investigate the encoding of time-varying odor stimuli and their representation for further processing in the spike domain by Drosophila OSNs. In order to apply system identification techniques, we built a novel low-turbulence odor delivery system that allowed us to deliver airborne stimuli in a precise and reproducible fashion. The system provides a 1% tolerance in stimulus reproducibility and an exact control of odor concentration and concentration gradient on a millisecond time scale. Using this novel setup, we recorded and analyzed the in-vivo response of OSNs to a wide range of time-varying odor waveforms. We report for the first time that across trials the response of OR59b OSNs is very precise and reproducible. Further, we empirically show that the response of an OSN depends not only on the concentration, but also on the rate of change of the odor concentration. Moreover, we demonstrate that a two-dimensional (2D) Encoding Manifold in a concentration-concentration gradient space provides a quantitative description of the neuron’s response. We then use the white noise system identification methodology to construct one-dimensional (1D) and two-dimensional (2D) Linear-Nonlinear-Poisson (LNP) cascade models of the sensory neuron for a fixed mean odor concentration and fixed contrast. We show that in terms of predicting the intensity rate of the spike train, the 2D LNP model performs on par with the 1D LNP model, with a root mean-square error (RMSE) increase of about 5 to 10%. Surprisingly, we find that for a fixed contrast of the white noise odor waveforms, the nonlinear block of each of the two models changes with the mean input concentration. The shape of the nonlinearities of both the 1D and the 2D LNP model appears to be, for a fixed mean of the odor waveform, independent of the stimulus contrast. This suggests that white noise system identification of Or59b OSNs only depends on the first moment of the odor concentration. Finally, by comparing the 2D Encoding Manifold and the 2D LNP model, we demonstrate that the OSN identification results depend on the particular type of the employed test odor waveforms. This suggests an adaptive neural encoding model for Or59b OSNs that changes its nonlinearity in response to the odor concentration waveforms. PMID:20730480

Kim, Anmo J.; Slutskiy, Yevgeniy B.

2013-01-01

193

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

194

Contribution of Yeast Models to Neurodegeneration Research  

PubMed Central

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

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

2012-01-01

195

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

196

Injectable electronic identification, monitoring, and stimulation systems.  

PubMed

Historically, electronic devices such as pacemakers and neuromuscular stimulators have been surgically implanted into animals and humans. A new class of implants made possible by advances in monolithic electronic design and implant packaging is small enough to be implanted by percutaneous injection through large-gauge hypodermic needles and does not require surgical implantation. Among these, commercially available implants, known as radio frequency identification (RFID) tags, are used for livestock, pet, laboratory animal, and endangered-species identification. The RFID tag is a subminiature glass capsule containing a solenoidal coil and an integrated circuit. Acting as the implanted half of a transcutaneous magnetic link, the RFID tag is powered by and communicates with an extracorporeal magnetic reader. The tag transmits a unique identification code that serves the function of identifying the animal. Millions of RFID tags have been sold since the early 1980s. Based on the success of the RFID tags, research laboratories have developed injectable medical implants, known as micromodules. One type of micromodule, the microstimulator, is designed for use in functional-neuromuscular stimulation. Each microstimulator is uniquely addressable and could comprise one channel of a multichannel functional-neuromuscular stimulation system. Using bidirectional telemetry and commands, from a single extracorporeal transmitter, as many as 256 microstimulators could form the hardware basis for a complex functional-neuromuscular stimulation feedback-control system. Uses include stimulation of paralyzed muscle, therapeutic functional-neuromuscular stimulation, and neuromodulatory functions such as laryngeal stimulation and sleep apnea. PMID:11701487

Troyk, P R

1999-01-01

197

Characterization of an extracellular enzyme system produced by Micromonospora chalcea with lytic activity on yeast cells.  

PubMed

Growth of Micromonospora chalcea on a defined medium containing laminarin as the sole carbon source induced the production of an extracellular enzyme system capable of lysing cells of various yeast species. Production of the lytic enzyme system was repressed by glucose. Incubation of sensitive cells with the active component enzymes of the lytic system produced protoplasts in high yield. Analysis of the enzyme composition indicated that beta(1-->3) glucanase and protease were the most prominent hydrolytic activities present in the culture fluids. The system also displayed weak chitinase and beta(1-->6) glucanase activities whilst devoid of mannanase activity. Our observations suggest that the glucan supporting the cell wall framework of susceptible yeast cells is not directly accessible to the purified endo-beta(1-->3) glucanase and that external proteinaceous components prevent breakdown of this polymer in whole cells. We propose that protease acts in synergy with beta(1-->3) glucanase and that the primary action of the former on surface components allows subsequent solubilization of inner glucan leading to lysis. PMID:10849171

Gacto, M; Vicente-Soler, J; Cansado, J; Villa, T G

2000-06-01

198

Identification of a Conserved Motif in the Yeast Golgi GDP-mannose Transporter Required for Binding to Nucleotide Sugar*  

E-print Network

to Nucleotide Sugar* Received for publication, October 5, 2000, and in revised form, November 3, 2000 Published in the Golgi complex are modified by the addition of sugars. In the yeast Saccha- romyces cerevisiae of the Golgi is mediated by the VRG4 gene product, a nucleotide sugar transporter that is a member of a large

Citovsky, Vitaly

199

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

200

Linear system identification using proper orthogonal decomposition  

NASA Astrophysics Data System (ADS)

A least-square-based method to identify the system matrices of linear dynamical systems is proposed. The primary focus is on the identification of a reduced-order model of the system operating in the mid-frequency range of vibration. Proper orthogonal decomposition (POD) is used for the model reduction. Such reduced-order model circumvents the limitations of traditional modal analysis which, although well-adapted in the low-frequency range, is prone to computational and conceptual difficulties in the mid-frequency range. The inverse problem involving the identification of the mass, damping and stiffness matrices is posed in the framework of a linear least-square estimation problem. To achieve this objective, Kronecker algebra is aptly exploited for a concise mathematical formulation to identify these matrix-valued variables. Tikhonov regularisation is used to satisfy the symmetry property of the system matrices. The application of the proposed methodology is demonstrated using an example of multiple degree-of-freedom discrete linear dynamical system. The robustness of the new methodology is investigated using a noise sensitivity study.

Khalil, Mohammad; Adhikari, Sondipon; Sarkar, Abhijit

2007-11-01

201

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

PubMed Central

Evaluation of gene expression in baker's yeast requires the extraction and collection of pure samples of RNA. However, in bread dough this task is difficult due to the complex composition of the system. We found that a liquid model system can be used to analyze the transcriptional response of industrial strains in dough with a high sugar content. The production levels of CO2 and glycerol by two commercial strains in liquid and flour-based doughs were correlated. We extracted total RNA from both a liquid and a flour-based dough. We used Northern blotting to analyze mRNA levels of three stress marker genes, HSP26, GPD1, and ENA1, and 10 genes in different metabolic subcategories. All 13 genes had the same transcriptional profile in both systems. Hence, the model appears to effectively mimic the environment encountered by baker's yeast in high-sugar dough. The liquid dough can be used to help understand the connections between technological traits and biological functions and to facilitate studies of gene expression under commercially important, but experimentally intractable, conditions. PMID:15746311

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

2005-01-01

202

Yeast killer toxins and dimorphism.  

PubMed Central

The differential action of four selected yeast killer toxins on the mycelial and yeast forms of four isolates of the dimorphic fungus Sporothrix schenckii was comparatively evaluated. The results confirmed that the yeast killer phenomenon is present among hyphomycetes and yeasts and that both morphological forms of S. schenckii are susceptible to the action of the same yeast killer toxin. Quantitative differences in the response to the killer action of the mycelial and yeast forms in individual strains were also observed. To avoid retroconversion of the dimorphic forms, we used a modification of the conventional killer system. Images PMID:2754015

Polonelli, L; Conti, S; Campani, L; Morace, G; Fanti, F

1989-01-01

203

ISL Person Identification Systems in the CLEAR Evaluations  

Microsoft Academic Search

In this paper, we presented three person identification systems that we have developed for the CLEAR evaluations. Two of the\\u000a developed identification systems are based on single modalities- audio and video, whereas the third system uses both of these\\u000a modalities. The visual identification system analyzes the face images of the individuals to determine the identity of the\\u000a person. It processes

Hazim Kemal Ekenel; Qin Jin

2006-01-01

204

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

205

Identification of Delta Operator System Using Neural Network  

NASA Astrophysics Data System (ADS)

This paper proposes application of neural network in identification of dynamical system modelled with delta operator. The advantage of using delta operator such as greater numerical robustness in computation compared to shift operator is considered. Model for identification is implemented into realizable neural network structure using the inverse delta operator. Simulation example is presented to demonstrate that the proposed identification scheme works very well.

Ghosh, S. K.; Sarkar, P.

2014-08-01

206

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

PubMed Central

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

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

2008-01-01

207

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

Microsoft Academic Search

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

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

2008-01-01

208

The application of whole-cell protein electrophoresis for the classification and identification of basidiomycetous yeast species  

Microsoft Academic Search

The relationships among 65 basidiomycetous yeast strains were determined by one-dimensional electrophoresis of SDS-solubilized whole-cell proteins. Protein profiles were compared by the Pearson product moment correlation coefficient (r). The strains investigated represented species from the generaCystofilobasidium, Filobasidium, Filobasidiella, Kondoa, Leucosporidium, Mrakia andRhodosporidium. Except for the genusMrakia, all species constituted separate protein electrophoretic clusters. The species of the genusMrakia (M. frigida,

Marc Vancanneyt; Eddy Van Lerberge; Jean-Francois Berny; Gregoire L. Hennebert; Karel Kersters

1992-01-01

209

Effects of distillation system and yeast strain on the aroma profile of Albariño (Vitis vinifera L.) grape pomace spirits.  

PubMed

Orujo is a traditional alcoholic beverage produced in Galicia (northwest Spain) from distillation of grape pomace, a byproduct of the winemaking industry. In this study, the effect of the distillation system (copper charentais alembic versus packed column) and the yeast strain (native yeast L1 versus commercial yeast L2) on the chemical and sensory characteristics of orujo obtained from Albariño (Vitis vinifera L.) grape pomace has been analyzed. Principal component analysis, with two components explaining 74% of the variance, is able to clearly differentiate the distillates according to distillation system and yeast strain. Principal component 1, mainly defined by C6-C12 esters, isoamyl octanoate, and methanol, differentiates L1 from L2 distillates. In turn, principal component 2, mainly defined by linear alcohols, linalool, and 1-hexenol, differentiates alembic from packed column distillates. In addition, an aroma descriptive test reveals that the distillate obtained with a packed column from a pomace fermented with L1 presented the highest positive general impression, which is associated with the highest fruity and smallest solvent aroma scores. Moreover, chemical analysis shows that use of a packed column increases average ethanol recovery by 12%, increases the concentration of C6-C12 esters by 25%, and reduces the concentration of higher alcohols by 21%. In turn, L2 yeast obtained lower scores in the alembic distillates aroma profile. In addition, with L1, 9% higher ethanol yields were achieved, and L2 distillates contained 34%-40% more methanol than L1 distillates. PMID:25307564

Arrieta-Garay, Y; Blanco, P; López-Vázquez, C; Rodríguez-Bencomo, J J; Pérez-Correa, J R; López, F; Orriols, I

2014-10-29

210

In-silico identification and characterization of organic and inorganic chemical stress responding genes in yeast (Saccharomyces cerevisiae).  

PubMed

To study the life processes of all eukaryotes, yeast (Saccharomyces cerevisiae) is a significant model organism. It is also one of the best models to study the responses of genes at transcriptional level. In a living organism, gene expression is changed by chemical stresses. The genes that give response to chemical stresses will provide good source for the strategies in engineering and formulating mechanisms which are chemical stress resistant in the eukaryotic organisms. The data available through microarray under the chemical stresses like lithium chloride, lactic acid, weak organic acids and tomatidine were studied by using computational tools. Out of 9335 yeast genes, 388 chemical stress responding genes were identified and characterized under different chemical stresses. Some of these are: Enolases 1 and 2, heat shock protein-82, Yeast Elongation Factor 3, Beta Glucanase Protein, Histone H2A1 and Histone H2A2 Proteins, Benign Prostatic Hyperplasia, ras GTPase activating protein, Establishes Silent Chromatin protein, Mei5 Protein, Nondisjunction Protein and Specific Mitogen Activated Protein Kinase. Characterization of these genes was also made on the basis of their molecular functions, biological processes and cellular components. PMID:25111117

Barozai, Muhammad Younas Khan; Bashir, Farrukh; Muzaffar, Shafia; Afzal, Saba; Behlil, Farida; Khan, Muzaffar

2014-10-15

211

Identification of the gene PaEMT1 for biosynthesis of mannosylerythritol lipids in the basidiomycetous yeast Pseudozyma antarctica.  

PubMed

The yeast Pseudozyma antarctica produces a large amount of glycolipid biosurfactants known as mannosylerythritol lipids (MELs), which show not only excellent surface-active properties but also versatile biochemical actions. To investigate the biosynthesis of MELs in the yeast, we recently reported expressed sequence tag (EST) analysis and estimated genes expressing under MEL production conditions. Among the genes, a contiguous sequence of 938 bp, PA_004, showed high sequence identity to the gene emt1, encoding an erythritol/mannose transferase of Ustilago maydis, which is essential for MEL biosynthesis. The predicted translation product of the extended PA_004 containing the two introns and a stop codon was aligned with Emt1 of U. maydis. The predicted amino acid sequence shared high identity (72%) with Emt1 of U. maydis, although the amino-terminal was incomplete. To identify the gene as PaEMT1 encoding an erythritol/mannose transferase of P. antarctica, the gene-disrupted strain was developed by the method for targeted gene disruption, using hygromycin B resistance as the selection marker. The obtained ?PaEMT1 strain failed to produce MELs, while its growth was the same as that of the parental strain. The additional mannosylerythritol into culture allowed ?PaEMT1 strain to form MELs regardless of the carbon source supplied, indicating a defect of the erythritol/mannose transferase activity. Furthermore, we found that MEL formation is associated with the morphology and low-temperature tolerance of the yeast. PMID:20564650

Morita, Tomotake; Ito, Emi; Kitamoto, Hiroko K; Takegawa, Kaoru; Fukuoka, Tokuma; Imura, Tomohiro; Kitamoto, Dai

2010-11-01

212

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

Code of Federal Regulations, 2012 CFR

...281 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Technical Operations § 25...Identification System (ATIS). All satellite uplink transmissions...

2012-10-01

213

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

Code of Federal Regulations, 2013 CFR

...281 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Technical Operations § 25...Identification System (ATIS). All satellite uplink transmissions...

2013-10-01

214

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

Code of Federal Regulations, 2011 CFR

...281 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS Technical Operations § 25...Identification System (ATIS). All satellite uplink transmissions...

2011-10-01

215

System for identification and control of arrival of vehicles  

Microsoft Academic Search

The objective of this project was to develop an identification system for moving vehicles using radio frequency, with the aim of recording the times in which buses belonging to the urban transport system of passengers make their pass by a set of checkpoints located over their routes. The identification system was designed and implemented using XBee ® modules, which allows

Camilo Alexey Suarez Buitrago; Jhon Jairo Ramirez Echeverry

2011-01-01

216

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

217

Introduction to Automatic Data Identification Systems  

NSDL National Science Digital Library

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

Jones, Jeff

2010-02-17

218

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. PMID:17439666

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

219

Nonlinear system identification in offshore structural reliability  

SciTech Connect

Nonlinear forces acting on offshore structures are examined from a system identification perspective. The nonlinearities are induced by ocean waves and may become significant in many situations. They are not necessarily in the form of Morison`s equation. Various wave force models are examined. The force function is either decomposed into a set of base functions or it is expanded in terms of the wave and structural kinematics. The resulting nonlinear system is decomposed into a number of parallel no-memory nonlinear systems, each followed by a finite-memory linear system. A conditioning procedure is applied to decouple these linear sub-systems; a frequency domain technique involving autospectra and cross-spectra is employed to identify the linear transfer functions. The structural properties and those force transfer parameters are determine with the aid of the coherence functions. The method is verified using simulated data. It provides a versatile and noniterative approach for dealing with nonlinear interaction problems encountered in offshore structural analysis and design.

Spanos, P.D. [Rice Univ., Houston, TX (United States); Lu, R. [Hudson Engineering Corporation, Houston, TX (United States)

1995-08-01

220

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

Microsoft Academic Search

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

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

1996-01-01

221

Genetic Characterization of a Mammalian Protein-Protein Interaction Domain by Using a Yeast Reverse Two-Hybrid System  

Microsoft Academic Search

Many biological processes rely upon protein-protein interactions. Hence, detailed analysis of these interactions is critical for their understanding. Due to the complexities involved, genetic approaches are often needed. In yeast and phage, genetic characterizations of protein complexes are possible. However, in multicellular organisms, such characterizations are limited by the lack of powerful selection systems. Herein we describe genetic selections that

Marc Vidal; Pascal Braun; Elbert Chen; Jef D. Boeke; Ed Harlow

1996-01-01

222

High-throughput construction of expression system using yeast Pichia pastoris, and its application to membrane proteins  

Microsoft Academic Search

The well-established method for high-throughput construction of an expression system of the yeast Saccharomyces cerevisiae uses homologous recombination between an expression plasmid and a target gene (with homologous regions of the plasmid on both ends added by PCR). This method has been widely used for membrane proteins using plasmids containing GFP, and has been successfully used to investigate the cellular

Kimihiko Mizutani; Soshi Yoshioka; Yukiko Mizutani; So Iwata; Bunzo Mikami

2011-01-01

223

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. PMID:24950344

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

2014-01-01

224

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. PMID:25026870

2014-01-01

225

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. PMID:1445205

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

1992-01-01

226

Online Identification of Nonlinear Spatiotemporal Systems Using Kernel Learning Approach  

Microsoft Academic Search

The identification of nonlinear spatiotemporal sys- tems is of significance to engineering practice, since it can always provide useful insight into the underlying nonlinear mechanism and physical characteristics under study. In this paper, nonlinear spatiotemporal system models are transformed into a class of multi-input-multi-output (MIMO) partially linear systems (PLSs), and an effective online identification algorithm is therefore proposed by using

Hanwen Ning; Xingjian Jing; Li Cheng

2011-01-01

227

Identification and use of zinc finger transcription factors that increase production of recombinant proteins in yeast and mammalian cells.  

PubMed

Randomized ZFP-TF libraries could induce a specific phenotype without detailed knowledge about the phenotype of interest because, theoretically, the libraries could modulate any gene in the target organism. We have developed a novel method for enhancing the efficiency of recombinant protein production in mammalian and microbial cells using combinatorial libraries of zinc finger protein transcription factors. To this end, we constructed tens of thousands of zinc finger proteins (ZFPs) with distinct DNA-binding specificities and fused these ZFPs to either a transcriptional activation or repression domain to make transcriptional activators or repressors, respectively. Expression vectors that encode these artificial transcription factors were delivered into Saccharomyces cerevisiae or HEK 293 cells along with reporter plasmids that code for human growth hormone (hGH) or SEAP (secreted alkaline phosphatase) (for yeast or HEK, respectively). Expression of the reporter genes was driven by either the cytomegalovirus (CMV) or SV40 virus promoters. After transfection, we screened the cells for increased synthesis of the reporter proteins. From these cells, we then isolated several ZFP-transcription factors (ZFP-TFs) that significantly increased hGH or SEAP synthesis and subjected these regulatory proteins to further characterization. Our results show that randomized ZFP-TF libraries are useful tools for improving the yield of heterologous recombinant protein both in yeast and mammalian cells. PMID:15932240

Park, Kyung-Soon; Seol, Wongi; Yang, Hyo-Young; Lee, Seong-Il; Kim, Sung Keun; Kwon, Ryuk Jun; Kim, Eui-Joong; Roh, Young-Hoon; Seong, Baik Lin; Kim, Jin-Soo

2005-01-01

228

Identification of C18:1-Phytoceramide as the Candidate Lipid Mediator for Hydroxyurea Resistance in Yeast*  

PubMed Central

Recent studies showed that deletion of ISC1, the yeast homologue of the mammalian neutral sphingomyelinase, resulted in an increased sensitivity to hydroxyurea (HU). This raised an intriguing question as to whether sphingolipids are involved in pathways initiated by HU. In this study, we show that HU treatment led to a significant increase in Isc1 activity. Analysis of sphingolipid deletion mutants and pharmacological analysis pointed to a role for ceramide in mediating HU resistance. Lipid analysis revealed that HU induced increases in phytoceramides in WT cells but not in isc1? cells. To probe functions of specific ceramides, we developed an approach to supplement the medium with fatty acids. Oleate (C18:1) was the only fatty acid protecting isc1? cells from HU toxicity in a ceramide-dependent manner. Because phytoceramide activates protein phosphatases in yeast, we evaluated the role of CDC55, the regulatory subunit of ceramide-activated protein phosphatase PP2A. Overexpression of CDC55 overcame the sensitivity to HU in isc1? cells. However, addition of oleate did not protect the isc1?,cdc55? double mutant from HU toxicity. These results demonstrate that HU launches a lipid pathway mediated by a specific sphingolipid, C18:1-phytoceramide, produced by Isc1, which provides protection from HU by modulating Swe1 levels through the PP2A subunit Cdc55. PMID:23620586

Matmati, Nabil; Metelli, Alessandra; Tripathi, Kaushlendra; Yan, Shuqi; Mohanty, Bidyut K.; Hannun, Yusuf A.

2013-01-01

229

Construction of stable laboratory and industrial yeast strains expressing a foreign gene by integrative transformation using a dominant selection system.  

PubMed

An expression cassette of mouse dihydrofolate reductase (Mdhfr) cDNA under control of the yeast cytochrome c promoter was inserted in a yeast plasmid containing the ARS1 sequence. The ARS replicating function was destroyed by BglII treatment prior to yeast transformation. Using this linearized plasmid, genomic transformants could be obtained from either laboratory or industrial strains of bakers' yeast based on direct methotrexate (MTX)-resistance selection. The entire sequence of the linearized plasmid was integrated by homologous recombination at the ARS region of the host chromosome. The results indicate that repetitive and homologous recombination occurs readily in such transformations. The stability of the constructed integrants was more than 99.95% per generation in non-selective medium, and tandem repeats of up to six copies (i.e., about 44 kb) were not changed even after 30 generations in rich medium. Expression in rich medium of cointegrated, human interleukin 2 cDNA under control of the triose phosphate isomerase promoter was shown by Western blot experiments in both laboratory and industrial yeast strains. Furthermore, a comparison of the transcription efficiency of the Mdhfr gene in the chromosome with that in the plasmid revealed that the efficiency was almost proportional to the number of gene copies, irrespective of the location of the transcription unit. These results show that by using the MTX/Mdhfr dominant selection-amplification system one can construct stable recombinant yeast strains suitable for heterologous gene expression in laboratory as well as in industrial fermentation conditions. PMID:3556323

Zhu, J; Contreras, R; Fiers, W

1986-01-01

230

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

231

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

2012-06-01

232

Development of a novel PCR assay for the identification of the black yeast, Exophiala (Wangiella) dermatitidis from adult patients with cystic fibrosis (CF).  

PubMed

Cystic fibrosis (CF) patients may suffer increased morbidity and mortality through colonisation, allergy and invasive infection from fungi. The black yeast, Exophiala dermatitidis (synonym Wangiella dermatitidis) has been found with increasing frequency in sputum specimens of CF patients, with reported isolation rates ranging from 1.1 to 15.7%. At present, no diagnostic PCR exists to aid with the clinical laboratory detection and identification of this organism. A novel species-specific PCR-based assay was developed for the detection of E. dermatitidis, based on employment of rDNA operons and interspacer (ITS) regions between these rDNA operons. Two novel primers, (designated ExdF & ExdR) were designed in silico with the aid of computer-aided alignment software and with the alignment of multiple species of Exophiala, as well as with other commonly described yeasts and filamentous fungi within CF sputum, including Candida, Aspergillus and Scedosporium. An amplicon of approximately 455 bp was generated, spanning the partial ITS1 region - the complete 5.8S rDNA region - partial ITS2 region, employing ExdF (forward primer [16-mer], 5'-CCG CCT ATT CAG GTC C-3' and ExdR (reverse primer [16-mer], 5'-TCT CTC CCA CTC CCG C-3', was employed and optimised on extracted genomic DNA from a well characterised culture of E. dermatitidis, as well as with high quality genomic DNA template from a further 16 unrelated fungi, including Candida albicans, C. dubliniensis, C. parapsilosis, C. glabrata, Scedosporium apiospermum, Penicillium sp., Aspergillus fumigatus, Aspergillus versicolor, Pichia guilliermondii, Rhodotorula sp., Trichosporon sp., Aureobasidium pullulans, Fusarium sp., Mucor hiemalis, Bionectria ochroleuca, Gibberella pulicaris. Results demonstrated that only DNA from E. dermatitidis gave an amplification product of the expected size, whilst none of the other fungi were amplifiable. Subsequent employment of this primer pair detected this yeast from mycological cultures from 2/50 (4%) adult CF patients. These two patients were the only patients who were previously shown to have a cultural history of E. dermatitidis from their sputum. E. dermatitidis is a slow-growing fungus, which usually takes up to two weeks to culture in the microbiology laboratory and therefore is slow to detect conventionally, with the risk of bacterial overgrowth from common co-habiting pan- and multiresistant bacterial pathogens from sputum, namely Pseudomonas aeruginosa and Burkholderia cepacia complex organisms, hence this species-specific PCR assay may help detect this organism from CF sputum more specifically and rapidly. Overall, employment of this novel assay may help in the understanding of the occurrence, aetiology and epidemiology of E. dermatitidis, as an emerging fungal agent in patients with CF. PMID:18571996

Nagano, Yuriko; Elborn, J Stuart; Millar, B Cherie; Goldsmith, Colin E; Rendall, Jackie; Moore, John E

2008-11-01

233

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

PubMed

Pichia guilliermondii is a representative of a group of so-called flavinogenic yeast species that overproduce riboflavin (vitamin B(2)) 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. PMID:21261808

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

2011-05-01

234

Nonlinear system identification based on internal recurrent neural networks.  

PubMed

A novel approach for nonlinear complex system identification based on internal recurrent neural networks (IRNN) is proposed in this paper. The computational complexity of neural identification can be greatly reduced if the whole system is decomposed into several subsystems. This approach employs internal state estimation when no measurements coming from the sensors are available for the system states. A modified backpropagation algorithm is introduced in order to train the IRNN for nonlinear system identification. The performance of the proposed design approach is proven on a car simulator case study. PMID:19496207

Puscasu, Gheorghe; Codres, Bogdan; Stancu, Alexandru; Murariu, Gabriel

2009-04-01

235

Entropy-based separation of yeast cells using a microfluidic system of conjoined spheres  

SciTech Connect

A physical model is derived to create a biological cell separator that is based on controlling the entropy in a microfluidic system having conjoined spherical structures. A one-dimensional simplified model of this three-dimensional problem in terms of the corresponding effects of entropy on the Brownian motion of particles is presented. This dynamic mechanism is based on the Langevin equation from statistical thermodynamics and takes advantage of the characteristics of the Fokker-Planck equation. This mechanism can be applied to manipulate biological particles inside a microfluidic system with identical, conjoined, spherical compartments. This theoretical analysis is verified by performing a rapid and a simple technique for separating yeast cells in these conjoined, spherical microfluidic structures. The experimental results basically match with our theoretical model and we further analyze the parameters which can be used to control this separation mechanism. Both numerical simulations and experimental results show that the motion of the particles depends on the geometrical boundary conditions of the microfluidic system and the initial concentration of the diffusing material. This theoretical model can be implemented in future biophysics devices for the optimized design of passive cell sorters.

Huang, Kai-Jian; Qin, S.-J., E-mail: shuijie.qin@gmail.com; Bai, Zhong-Chen; Zhang, Xin [Guizhou Provincial Key Lab for Photoelectron Technology and Application, Guizhou University, GuiYang 550025 (China); Mai, John D. [Department of Mechanical and Biomedical Engineering, City University of Hong Kong (Hong Kong)

2013-11-21

236

A deceptive pollination system targeting drosophilids through olfactory mimicry of yeast.  

PubMed

In deceptive pollination, insects are bamboozled into performing nonrewarded pollination. A prerequisite for the evolutionary stability in such systems is that the plants manage to generate a perfect sensory impression of a desirable object in the insect nervous system [1]. The study of these plants can provide important insights into sensory preference of their visiting insects. Here, we present the first description of a deceptive pollination system that specifically targets drosophilid flies. We show that the examined plant (Arum palaestinum) accomplishes its deception through olfactory mimicry of fermentation, a strategy that represents a novel pollination syndrome. The lily odor is composed of volatiles characteristic of yeast, and produces in Drosophila melanogaster an antennal detection pattern similar to that elicited by a range of fermentation products. By functional imaging, we show that the lily odors target a specific subset of odorant receptors (ORs), which include the most conserved OR genes in the drosophilid olfactome. Furthermore, seven of eight visiting drosophilid species show a congruent olfactory response pattern to the lily, in spite of comprising species pairs separated by ?40 million years [2], showing that the lily targets a basal function of the fly nose, shared by species with similar ecological preference. PMID:20933425

Stökl, Johannes; Strutz, Antonia; Dafni, Amots; Svatos, Ales; Doubsky, Jan; Knaden, Markus; Sachse, Silke; Hansson, Bill S; Stensmyr, Marcus C

2010-10-26

237

Time-Delay System Identification Using Genetic Algorithm -Part Two  

E-print Network

-site issues, such as the excitation condition, measured data quality, selected identification algorithmTime-Delay System Identification Using Genetic Algorithm - Part Two: FOPDT/SOPDT Model Approximation Zhenyu Yang Glen T. Seested Department of Energy Technology, Aalborg University, Esbjerg Campus

Yang, Zhenyu

238

TRIAGE FRAMEWORK FOR RESOURCE CONSERVATION IN A SPEAKER IDENTIFICATION SYSTEM  

E-print Network

TRIAGE FRAMEWORK FOR RESOURCE CONSERVATION IN A SPEAKER IDENTIFICATION SYSTEM· A. Jairam, E. Singer (prioritizing and discarding) data to conserve resources for a speaker identification (SID) system. Our work and are not necessarily endorsed by the United States Government. ABSTRACT We present a novel framework for triaging

239

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

240

System Identification and Modelling of a High Performance Hydraulic Actuator  

E-print Network

System Identification and Modelling of a High Performance Hydraulic Actuator Benoit Boulet, Laeeque 3480 University Street, Montr5al, Quebec, CANADA H3A 2A7 Abstract Detailed knowledge of actuator with the experimental identification and modelling of the nonlinear dynamics ofa high performance hydraulic actuator

Hayward, Vincent

241

Non-linear system identification in flow-induced vibration  

SciTech Connect

The paper introduces a method of identification of non-linear systems encountered in marine engineering applications. The non-linearity is accounted for by a combination of linear subsystems and known zero-memory non-linear transformations; an equivalent linear multi-input-single-output (MISO) system is developed for the identification problem. The unknown transfer functions of the MISO system are identified by assembling a system of linear equations in the frequency domain. This system is solved by performing the Cholesky decomposition of a related matrix. It is shown that the proposed identification method can be interpreted as a {open_quotes}Gram-Schmidt{close_quotes} type of orthogonal decomposition of the input-output quantities of the equivalent MISO system. A numerical example involving the identification of unknown parameters of flow (ocean wave) induced forces on offshore structures elucidates the applicability of the proposed method.

Spanos, P.D.; Zeldin, B.A. [Rice Univ., Houston, TX (United States); Lu, R. [Hudson Engineering Corp., Houston, TX (United States)

1996-12-31

242

Comparison of the Vitek MS and Bruker Microflex LT MALDI-TOF MS platforms for routine identification of commonly isolated bacteria and yeast in the clinical microbiology laboratory.  

PubMed

This study compared the diagnostic performance of Bruker's Microflex LT and bioMérieux's Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry systems. A total of 477 isolates were tested on both instruments. Discrepant results were resolved by sequencing. Overall, there was no statistically significant difference between the proportion of isolates correctly identified, miscalled or not called by each instrument. Although both systems were good at identifying yeast (66/69 to species level), the confidence level was high only to genus level for 30% of the isolates on the Bruker. Both systems performed with high accuracy when evaluated solely on Food and Drug Administration-approved organisms for each database. A user-based assessment of the 2 instruments revealed an overall preference for the Vitek MS instrument. PMID:25446889

Deak, Eszter; Charlton, Carmen L; Bobenchik, April M; Miller, Shelley A; Pollett, Simon; McHardy, Ian H; Wu, Max T; Garner, Omai B

2015-01-01

243

Some aspects of the identification of continuous vibrating systems  

NASA Technical Reports Server (NTRS)

This paper deals with the identification of systems described by the one-dimensional, second order wave equation. Such equations arise commonly in various areas of mathematical physics, such as, acoustics, elastic wave propagation, and electromagnetic theory. Assuming that suitable measurements are made at only one point in the spatial domain, sufficient conditions for unique identification of the system eigenvalues and system coefficients are presented.

Udwadia, F. E.; Garba, J. A.

1982-01-01

244

UASIS: Universal Automatic SNP Identification System  

PubMed Central

Background SNP (Single Nucleotide Polymorphism), the most common genetic variations between human beings, is believed to be a promising way towards personalized medicine. As more and more research on SNPs are being conducted, non-standard nomenclatures may generate potential problems. The most serious issue is that researchers cannot perform cross referencing among different SNP databases. This will result in more resources and time required to track SNPs. It could be detrimental to the entire academic community. Results UASIS (Universal Automated SNP Identification System) is a web-based server for SNP nomenclature standardization and translation at DNA level. Three utilities are available. They are UASIS Aligner, Universal SNP Name Generator and SNP Name Mapper. UASIS maps SNPs from different databases, including dbSNP, GWAS, HapMap and JSNP etc., into an uniform view efficiently using a proposed universal nomenclature and state-of-art alignment algorithms. UASIS is freely available at http://www.uasis.tk with no requirement of log-in. Conclusions UASIS is a helpful platform for SNP cross referencing and tracking. By providing an informative, unique and unambiguous nomenclature, which utilizes unique position of a SNP, we aim to resolve the ambiguity of SNP nomenclatures currently practised. Our universal nomenclature is a good complement to mainstream SNP notations such as rs# and HGVS guidelines. UASIS acts as a bridge to connect heterogeneous representations of SNPs. PMID:22369494

2011-01-01

245

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. PMID:24018767

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

2013-01-01

246

Development and Validation of an In-House Database for Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry-Based Yeast Identification Using a Fast Protein Extraction Procedure  

PubMed Central

In recent studies evaluating the usefulness of the matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based identification of yeasts for the routine diagnosis of fungal infections, preanalytical sample processing has emerged as a critical step for reliable MALDI-TOF MS outcomes, especially when the Bruker Daltonics Biotyper software was used. In addition, inadequate results often occurred due to discrepancies between the methods used for clinical testing and database construction. Therefore, we created an in-house MALDI-TOF MS library using the spectra from 156 reference and clinical yeast isolates (48 species in 11 genera), which were generated with a fast sample preparation procedure. After a retrospective validation study, our database was evaluated on 4,232 yeasts routinely isolated during a 6-month period and fast prepared for MALDI-TOF MS analysis. Thus, 4,209 (99.5%) of the isolates were successfully identified to the species level (with scores of ?2.0), with 1,676 (39.6%) having scores of >2.3. For the remaining 23 (0.5%) isolates, no reliable identification (with scores of <1.7) was obtained. Interestingly, these isolates were almost always from species uniquely represented or not included in the database. As the MALDI-TOF MS results were, except for 23 isolates, validated without additional phenotypic or molecular tests, our proposed strategy can enhance the rapidity and accuracy of MALDI-TOF MS in identifying medically important yeast species. However, while continuous updating of our database will be necessary to enrich it with more strains/species of new and emerging yeasts, the present in-house MALDI-TOF MS library can be made publicly available for future multicenter studies. PMID:24554755

De Carolis, Elena; Vella, Antonietta; Vaccaro, Luisa; Torelli, Riccardo; Posteraro, Patrizia; Ricciardi, Walter; Posteraro, Brunella

2014-01-01

247

Microscreening toxicity system based on living magnetic yeast and gradient chips.  

PubMed

There is an increasing demand for easy and cost-effective methods to screen the toxicological impact of the growing number of chemical mixtures being generated by industry. Such a screening method has been developed using viable, genetically modified green fluorescent protein (GFP) reporter yeast that was magnetically functionalised and held within a microfluidic device. The GFP reporter yeast was used to detect genotoxicity by monitoring the exposure of the cells to a well-known genotoxic chemical (methyl methane sulfonate, MMS). The cells were magnetised using biocompatible positively charged PAH-stabilised magnetic nanoparticles with diameters around 15 nm. Gradient mixing was utilised to simultaneously expose yeast to a range of concentrations of toxins, and the effective fluorescence emitted from the produced GFP was measured. The magnetically enhanced retention of the yeast cells, with their facile subsequent removal and reloading, allowed for very convenient and rapid toxicity screening of a wide range of chemicals. This is the first report showing magnetic yeast within microfluidic devices in a simple bioassay, with potential applications to other types of fluorescent reporter yeast in toxicological and biomedical research. The microfluidic chip offers a simple and low-cost screening test that can be automated to allow multiple uses (adapted to different cell types) of the device on a wide range of chemicals and concentrations. PMID:20924564

García-Alonso, Javier; Fakhrullin, Rawil F; Paunov, Vesselin N; Shen, Zheng; Hardege, Joerg D; Pamme, Nicole; Haswell, Stephen J; Greenway, Gillian M

2011-05-01

248

Nonlinear stochastic system identification techniques for biological tissues/  

E-print Network

This research develops a device capable of measuring the nonlinear dynamic mechanical properties of human tissue in vivo. The enabling technology is the use of nonlinear stochastic system identification techniques in ...

Chen, Yi, S.M. Massachusetts Institute of Technology

2010-01-01

249

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

250

College students򠰥rceptions of the national animal identification system  

E-print Network

governmentsponsored electronic national identification system for livestock is relatively new, many pros and cons exist regarding increased biosecurity and increased surveillance by the government. While many adult producer groups have expressed their concerns over...

Long, Jeanie Marie

2009-05-15

251

PARAMETER AND SYSTEM IDENTIFICATION FOR FLUID FLOW IN UNDERGROUND RESERVOIRS  

E-print Network

PARAMETER AND SYSTEM IDENTIFICATION FOR FLUID FLOW IN UNDERGROUND RESERVOIRS A.T. Watson Department and simulation of the flow of fluids in underground reservoirs is an essential exercise for planning aspects

Ewing, Richard E.

252

Multi-channel blind system identification for central hemodynamic monitoring  

E-print Network

Multi-channel Blind System Identification (MBSI) is a technique for estimating both an unknown input and unknown channel dynamics from simultaneous output measurements at different channels through which the input signal ...

Zhang, Yi, 1973-

2002-01-01

253

Genetic Analysis of Homomeric Interactions of Human Immunodeficiency Virus Type 1 Integrase Using the Yeast Two-Hybrid System  

Microsoft Academic Search

The retroviral integrase protein (IN) is responsible for catalyzing a concerted integration reaction in which the two termini of linear viral DNA are joined to host DNA. To probe the potential for IN to form protein multimers, we used the yeast two-hybrid system. The coexpression of a GAL4 DNA binding domain-IN fusion and a GAL4 activation domain-IN fusion together resulted

Ganjam V. Kalpana; Stephen P. Goff

1993-01-01

254

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

255

The cellular prion protein (PrP) selectively binds to Bcl2 in the yeast two-hybrid system  

Microsoft Academic Search

Bcl-2 can rescue neurons from death and might, therefore, exert its action by associating with neuron-specific proteins. Using LexA-Bcl-2 as bait, we find that the cellular prion protein (PrP) interacts with Bcl-2, but not Bax, in the yeast two-hybrid system. Since the PrP gene has been implicated in neurodegenerative disorders, this preliminary observation suggests a potential pathogenic mechanism for these

Cornelia Kurschner; James I. Morgan

1995-01-01

256

PICK1: a perinuclear binding protein and substrate for protein kinase C isolated by the yeast two-hybrid system  

Microsoft Academic Search

Abstract. Protein kinase C (PKC) plays a central role in the control of proliferation and differentiation of a wide range of cell types by mediating,the signal trans- duction response to hormones,and growth,factors. Upon activation by diacylglycerol, PKC translocates to different subcellular sites where,it phosphorylates numerous proteins, most of which are unidentified. We used the yeast two-hybrid system to identify pro-

J. Staudinger; J Zhou; R Burgess; Sj Elledge; En Olson

1995-01-01

257

Construction of a yeast expression system with positive selection for gene insertion in the absence of a specific phenotype  

Microsoft Academic Search

A positive-selection system of cloned inserts in Escherichia coli has been devised using a streptomycin-resistant (Smr) gene and streptomycin-dependent (Smd) E. coli. A vector, pHA394, based on the yeast expression vector pAM82 has the Smr gene, which inactivates streptomycin (Sm) and invalidates the streptomycin dependence, resulting in a very low transformation efficiency. Replacement of the Smr gene by the recombinant

Yoshio Hashimoto; Takeyoshi Miki; Masami Mukae; Tadashi Ueda; Taiji Imoto

1998-01-01

258

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

259

Development and application of a DNA microarray-based yeast two-hybrid system  

PubMed Central

The yeast two-hybrid (Y2H) system is the most widely applied methodology for systematic protein–protein interaction (PPI) screening and the generation of comprehensive interaction networks. We developed a novel Y2H interaction screening procedure using DNA microarrays for high-throughput quantitative PPI detection. Applying a global pooling and selection scheme to a large collection of human open reading frames, proof-of-principle Y2H interaction screens were performed for the human neurodegenerative disease proteins huntingtin and ataxin-1. Using systematic controls for unspecific Y2H results and quantitative benchmarking, we identified and scored a large number of known and novel partner proteins for both huntingtin and ataxin-1. Moreover, we show that this parallelized screening procedure and the global inspection of Y2H interaction data are uniquely suited to define specific PPI patterns and their alteration by disease-causing mutations in huntingtin and ataxin-1. This approach takes advantage of the specificity and flexibility of DNA microarrays and of the existence of solid-related statistical methods for the analysis of DNA microarray data, and allows a quantitative approach toward interaction screens in human and in model organisms. PMID:23275563

Suter, Bernhard; Fontaine, Jean-Fred; Yildirimman, Reha; Raskó, Tamás; Schaefer, Martin H.; Rasche, Axel; Porras, Pablo; Vázquez-Álvarez, Blanca M.; Russ, Jenny; Rau, Kirstin; Foulle, Raphaele; Zenkner, Martina; Saar, Kathrin; Herwig, Ralf; Andrade-Navarro, Miguel A.; Wanker, Erich E.

2013-01-01

260

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. PMID:11600718

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

2001-01-01

261

Identification of power system load dynamics using artificial neural networks  

Microsoft Academic Search

Power system loads are important in the planning and operation of an electric power system. Load characteristics can significantly influence the results of synchronous stability and voltage stability studies. This paper presents a methodology for the identification of power system load dynamics using neural networks. Input-output data of a power system dynamic load is used to design a neural network

M. Bostanci; J. Koplowitz; C. W. Taylor

1997-01-01

262

Attack Detection and Identification in Cyber-Physical Systems  

E-print Network

Attack Detection and Identification in Cyber-Physical Systems Fabio Pasqualetti, Florian D¨orfler, and Francesco Bullo Abstract Cyber-physical systems are ubiquitous in power systems, transportation networks for cyber- physical systems, attacks, and monitors; (ii) we characterize fundamental monitoring limitations

Bullo, Francesco

263

Evaluation of risk factors in patients with vulvovaginal candidiasis and the value of chromID Candida agar versus CHROMagar Candida for recovery and presumptive identification of vaginal yeast species.  

PubMed

Vulvovaginal candidiasis (VVC), particularly the recurrent form, remains an intractable problem for clinicians, microbiologists, and patients. It is essential to confirm the clinical diagnosis by mycological methods and avoid empirical therapy. The recovery of yeast in fungal culture, such as on Sabouraud dextrose agar, remains the gold standard for diagnosis. In this investigation, we examined 474 participants, including 122 (25.7%) with acute VVC cases, 249 (52.5%) who had recurrent VVC (RVVC) cases, and 103 (21.7%) healthy controls. We also administered a questionnaire to obtain information on patient lifestyle and medical, gynecological, and sexual history. In addition, we compared the performance of chromID Candida agar (CAN2) to CHROMagar Candida (CAC) and Sabouraud dextrose agar with gentamicin and chloramphenicol (SGC2). The yeasts were identified by conventional methods including the germ tube test, microscopic morphology on cornmeal-Tween 80 agar, and the commercial API 20C AUX system. We detected yeasts in 60 of 122 (49.2%) patients with acute VVC cases, 110 of 249 (44.2%) with RVVC cases, and in 35 of 103 (34%) healthy controls (P = 0.07). A total of 205 samples were found to be positive for fungi (43.2%), of which 176 (85.9%) were monofungal, and 29 (14.1%) were polyfungal. In addition, 198 of these samples (96.6%) were positive on CAN2, 195 (95.1%) on CAC, 189 (92.2%) on SGC2, and 183 (89.3%) samples on all three (P = 0.17). The 234 yeast isolates recovered were C. albicans (n = 118), C. glabrata (n = 82), C. kefyr (n = 11), C. krusei (n = 9), C. lipolytica (n = 3), C. colliculosa (n = 2), C. parapsilosis (n = 2), C. pelliculosa (n = 2), C. tropicalis (n = 2), and other species of Candida (n = 3). Of the 29 polyfungal populations, 28 (96.6%) were detected in CAN2, 25 in (86.2%) CAC, and 25 (86.2%) on both (P = 0.35). Notably, we detected the high predominance of C. albicans+C. glabrata (86.2%) in polyfungal populations. Briefly, the detection of C. albicans after 24 h of incubation was easier on CAN2 (64.4%) than on CAC (25.4%). This study showed that CAN2 is a rapid and reliable medium for immediate identification of C. albicans and for detecting polyfungal populations in vaginal specimens. We observed that the use of antibiotics, intrauterine devices, as well as, perineal laceration, short anovaginal distance (< 3 cm), and genital epilation in common areas are predisposing factors for RVVC (P < 0.001). In addition, we detected that the use of menstrual pad, using an (IUD), and having a history of childbirth increased the risk of both acute and recurrent VVC (P < 0.01), whereas the use of a daily pad and walking daily significantly decreased the risk of both acute and recurrent VVC (P < 0.01). PMID:20608776

Guzel, Ahmet Bari?; Ilkit, Macit; Akar, Tuba; Burgut, Refik; Demir, S Cansun

2011-01-01

264

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

2012-04-01

265

Nonfermentative bacilli: evaluation of three systems for identification.  

PubMed Central

Three systems for the identification of nonfermentative bacilli were evaluated for their rapidity and accuracy of identification of 217 strains. Two of the systems, API 20E (API) and Oxi/Ferm tube (OxiF), are available as kits; the oxidative attack (OA) system is not commerically available. The overall accuracies of the OA, API, and OxiF systems were 91, 69, and 50%, respectively. Identification within 48 h was achieved for 98% of the strains by OA, for 50% by API, and for 18% by OxiF. Most of the organisms that were either misidentified or not identified by API and OxiF were those nonfermentative bacilli which are relatively more fastidious or rarely encountered or both. All three systems accurately identified nonfermentative bacilli commonly isolated at Olive View Medical Center, namely, Pseudomonas aeruginosa, Acinetobacter anitratus, Pseudomonas maltophilia, Acinetobacter lwoffi, saccharolytic flavobacteria (CDC IIb), moraxellae, Pseudomonas fluorescens, and Pseudomonas putida. The OA system identified 100% of the above organisms correctly, API identified 99.4%, and OxiF identified 99.3%. Since these organisms comprise 92% of the total number of nonfermentative bacilli isolated at Olive View Medical Center, we conclude that both API and OxiF may be useful alternatives to conventional methods, based on accuracy of identification alone. These two systems were considered substantially inferior to the OA system when both accuracy and rapidity of identification were taken into account. PMID:389945

Otto, L A; Blachman, U

1979-01-01

266

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

267

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

268

Kinetochore Structure: Pulling Answers from Yeast  

E-print Network

Despite the identification of multiple kinetochore proteins, their structure and organization has remained unclear. New work uses electron microscopy to visualize isolated budding yeast kinetochore particles and reveal the ...

Cheeseman, Iain M.

269

Identification of host proteins interacting with the integrin-like A domain of Toxoplasma gondii micronemal protein MIC2 by yeast-two-hybrid screening.  

PubMed

Background Toxoplasma gondii is an obligate intracellular protozoan, causing the important zoonosis toxoplasmosis. This parasite utilizes a unique form of locomotion called gliding motility to find and invade host cells. The micronemal adhesin MIC2 plays critical roles in these processes by binding to substrates and host cell receptors using its extracellular adhesive domains. Although MIC2 is known to mediate important interactions between parasites and host cells during invasion, the specific host proteins interacting with MIC2 have not been clearly identified. In this study, we used a yeast-two-hybrid system to search for host proteins that interact with MIC2.MethodsDifferent adhesive domains of MIC2 were cloned into the pGBKT7 vector and expressed in fusion with the GAL4 DNA-binding domain as baits. Expression of bait proteins in yeast cells was analyzed by immuno-blotting and their autoactivation was tested via comparison with the pGBKT7 empty vector, which expressed the GAL4 DNA binding-domain only. To identify host proteins interacting with MIC2, a mouse cDNA library cloned into a GAL4 activation-domain expressing vector was screened by yeast-two-hybrid using the integrin-like A domain of MIC2 (residues 74¿270) as bait. After initial screening and exclusion of false positive hits, positive preys were sequenced and analyzed using BLAST analysis and Gene Ontology Classifications.ResultsTwo host proteins that had not previously been reported to interact with T. gondii MIC2 were identified: they are LAMTOR1 (late endosomal/lysosomal adaptor, MAPK and mTOR activator 1) and RNaseH2B (ribonuclease H2 subunit B). Gene Ontology analysis indicated that these two proteins are associated with many cellular processes, such as lysosome maturation, signaling transduction, and RNA catabolism.ConclusionThis study is the first one to report interactions between Toxoplasma gondii MIC2 and two host proteins, LAMTOR1 and RNaseH2B. The data will help us to gain a better understanding of the function of MIC2 and suggest that MIC2 may play roles in modulating host signal transduction and other biological processes in addition to binding host cells. PMID:25423901

Wang, Yifan; Fang, Rui; Yuan, Yuan; Hu, Min; Zhou, Yanqin; Zhao, Junlong

2014-11-26

270

Combined parametric-nonparametric identification of Hammerstein systems  

Microsoft Academic Search

A novel, parametric-nonparametric, methodology for Hammerstein system identification is proposed. Assuming random input and correlated output noise, the parameters of a nonlinear static characteristic and finite impulse-response system dynamics are estimated separately, each in two stages. First, the inner signal is recovered by a nonparametric regression function estimation method (Stage 1) and then system parameters are solved independently by the

Zygmunt Hasiewicz; Grzegorz Mzyk

2004-01-01

271

A modular and hybrid connectionist system for speaker identification.  

PubMed

This paper presents and evaluates a modular/hybrid connectionist system for speaker identification. Modularity has emerged as a powerful technique for reducing the complexity of connectionist systems, and allowing a priori knowledge to be incorporated into their design. Text-independent speaker identification is an inherently complex task where the amount of training data is often limited. It thus provides an ideal domain to test the validity of the modular/hybrid connectionist approach. To achieve such identification, we develop, in this paper, an architecture based upon the cooperation of several connectionist modules, and a Hidden Markov Model module. When tested on a population of 102 speakers extracted from the DARPA-TIMIT database, perfect identification was obtained. PMID:7584887

Bennani, Y

1995-07-01

272

Nitrile Metabolizing Yeasts  

NASA Astrophysics Data System (ADS)

Nitriles and amides are widely distributed in the biotic and abiotic components of our ecosystem. Nitrile form an important group of organic compounds which find their applications in the synthesis of a large number of compounds used as/in pharmaceutical, cosmetics, plastics, dyes, etc>. Nitriles are mainly hydro-lyzed to corresponding amide/acid in organic chemistry. Industrial and agricultural activities have also lead to release of nitriles and amides into the environment and some of them pose threat to human health. Biocatalysis and biotransformations are increasingly replacing chemical routes of synthesis in organic chemistry as a part of ‘green chemistry’. Nitrile metabolizing organisms or enzymes thus has assumed greater significance in all these years to convert nitriles to amides/ acids. The nitrile metabolizing enzymes are widely present in bacteria, fungi and yeasts. Yeasts metabolize nitriles through nitrilase and/or nitrile hydratase and amidase enzymes. Only few yeasts have been reported to possess aldoxime dehydratase. More than sixty nitrile metabolizing yeast strains have been hither to isolated from cyanide treatment bioreactor, fermented foods and soil. Most of the yeasts contain nitrile hydratase-amidase system for metabolizing nitriles. Transformations of nitriles to amides/acids have been carried out with free and immobilized yeast cells. The nitrilases of Torulopsis candida>and Exophiala oligosperma>R1 are enantioselec-tive and regiospecific respectively. Geotrichum>sp. JR1 grows in the presence of 2M acetonitrile and may have potential for application in bioremediation of nitrile contaminated soil/water. The nitrilase of E. oligosperma>R1 being active at low pH (3-6) has shown promise for the hydroxy acids. Immobilized yeast cells hydrolyze some additional nitriles in comparison to free cells. It is expected that more focus in future will be on purification, characterization, cloning, expression and immobilization of nitrile metabolizing enzymes of yeasts.

Bhalla, Tek Chand; Sharma, Monica; Sharma, Nitya Nand

273

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

274

Convenient gram-scale metabolite synthesis by engineered fission yeast strains expressing functional human P450 systems.  

PubMed

The growing need for the characterization of cytochrome P450 (P450) metabolites often necessitates their synthesis up to Gram-scale. This task may in principle be achieved by using various techniques including chemical synthesis, the use of laboratory animals, in vitro P450 systems or microbial biotransformation. However, these approaches are in many instances unfavorable due to low yields, laborious purification, costs of cofactors, or the formation of non-physiologic metabolites. The fission yeast Schizosaccharomyces pombe has previously been shown by others and us to be very well suited for the heterologous expression of human P450s. In this study, we demonstrate whole-cell biotransformation reactions carried out with fission yeast strains that coexpress human cytochrome P450 reductase (CPR) and one of the following P450 isoforms: CYP2B6, CYP2C9, CYP2C19, CYP2D6, or CYP3A4, respectively. These strains could successfully convert their respective standard substrates but showed different responses with respect to incubation pH, the presence of glucose, and temperature, respectively. In addition, the preparative of synthesis of 2.8 g of 4'-hydroxydiclofenac was achieved by whole-cell biotransformation of diclofenac using a CPR-CYP2C9 coexpressing fission yeast strain. PMID:20927605

Dr?gan, C?lin-Aurel; Peters, Frank T; Bour, Pierre; Schwaninger, Andrea E; Schaan, Stefanie M; Neunzig, Ina; Widjaja, Maria; Zapp, Josef; Kraemer, Thomas; Maurer, Hans H; Bureik, Matthias

2011-04-01

275

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

276

Yeast Infections  

MedlinePLUS

Candida is the scientific name for yeast. It is a fungus that lives almost everywhere, including in ... infection that causes white patches in your mouth Candida esophagitis is thrush that spreads to your esophagus, ...

277

Online identification of nonlinear spatiotemporal systems using kernel learning approach.  

PubMed

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

Ning, Hanwen; Jing, Xingjian; Cheng, Li

2011-09-01

278

Growth assays to assess polyglutamine toxicity in yeast.  

PubMed

Protein misfolding is associated with many human diseases, particularly neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. Huntington's disease (HD) is caused by the abnormal expansion of a polyglutamine (polyQ) region within the protein huntingtin. The polyQ-expanded huntingtin protein attains an aberrant conformation (i.e. it misfolds) and causes cellular toxicity. At least eight further neurodegenerative diseases are caused by polyQ-expansions, including the Spinocerebellar Ataxias and Kennedy's disease. The model organism yeast has facilitated significant insights into the cellular and molecular basis of polyQ-toxicity, including the impact of intra- and inter-molecular factors of polyQ-toxicity, and the identification of cellular pathways that are impaired in cells expressing polyQ-expansion proteins. Importantly, many aspects of polyQ-toxicity that were found in yeast were reproduced in other experimental systems and to some extent in samples from HD patients, thus demonstrating the significance of the yeast model for the discovery of basic mechanisms underpinning polyQ-toxicity. A direct and relatively simple way to determine polyQ-toxicity in yeast is to measure growth defects of yeast cells expressing polyQ-expansion proteins. This manuscript describes three complementary experimental approaches to determine polyQ-toxicity in yeast by measuring the growth of yeast cells expressing polyQ-expansion proteins. The first two experimental approaches monitor yeast growth on plates, the third approach monitors the growth of liquid yeast cultures using the BioscreenC instrument. Furthermore, this manuscript describes experimental difficulties that can occur when handling yeast polyQ models and outlines strategies that will help to avoid or minimize these difficulties. The protocols described here can be used to identify and to characterize genetic pathways and small molecules that modulate polyQ-toxicity. Moreover, the described assays may serve as templates for accurate analyses of the toxicity caused by other disease-associated misfolded proteins in yeast models. PMID:22415521

Duennwald, Martin L

2012-01-01

279

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). PMID:24340008

Nakamura, Yasuyuki; Ishii, Jun; Kondo, Akihiko

2013-01-01

280

Assessment of uncoupling activity of uncoupling protein 3 using a yeast heterologous expression system  

Microsoft Academic Search

Uncoupling protein 3L, uncoupling protein 1 and the mitochondrial oxoglutarate carrier were expressed in Saccharomyces cerevisae. Effects on different parameters related to the energy expenditure were studied. Both uncoupling protein 3L and uncoupling protein 1 reduced the growth rate by 49% and 32% and increased the whole yeast O2 consumption by 31% and 19%, respectively. In isolated mitochondria, uncoupling protein

Chen-Yu Zhang; Thilo Hagen; Vamsi K Mootha; Lawrence J Slieker; Bradford B Lowell

1999-01-01

281

Simple method to detect triacylglycerol biosynthesis in a yeast-based recombinant system  

Technology Transfer Automated Retrieval System (TEKTRAN)

Standard methods to quantify the activity of triacylglycerol (TAG) synthesizing enzymes DGAT and PDAT (TAG-SE) require a sensitive but rather arduous laboratory assay based on radio-labeled substrates. Here we describe two straightforward methods to detect TAG production in baker’s yeast Saccharomyc...

282

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

283

Associations of UBE2I with RAD52, UBL1, p53, and RAD51 proteins in a yeast two-hybrid system  

SciTech Connect

The yeast RAD52-dependent pathway is involved in DNA recombination and double-strand break repair. Yeast ubiquitin-conjugating enzyme UBC9 participates in S- and M-phase cyclin degradation and mitotic control. Using the human RAD52 protein as the bait in a yeast two-hybrid system, we have identified a human homolog of yeast UBC9, designated UBE2I, that interacts with RAD52, RAD51, p53, and a ubiquitin-like protein UBL1. These interactions are UBE2I-specific, since another DNA repair-related ubiquitin-conjugating enzyme, RAD6 (UBC2), does not interact with these proteins. The interaction of UBE2I with RAD52 is mediated by RAD52`s self-association region. These results suggest that the RAD52-dependent processes, cell cycle control, p53-mediated pathway(s), and ubiquitination interact through human UBE2I. 22 refs., 3 figs.

Shen, Zhiyuan; Pardington-Purtymun, P.E.; Comeaux, J.C. [Los Alamos National Labs., NM (United States)] [and others] [Los Alamos National Labs., NM (United States); and others

1996-10-15

284

Triage Framework for Resource Conservation in a Speaker Identification System  

Microsoft Academic Search

We present a novel framework for triaging (prioritizing and discarding) data to conserve resources for a speaker identification (SID) system. Our work is motivated by applications that require a SID system to process an overwhelming volume of audio data. We design a triage filter whose goal is to conserve recognizer resources while preserving relevant content. We propose triage methods that

A. Jairam; E. Singer; D. A. Reynolds

2007-01-01

285

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

286

Bounded error identification of systems with time-varying parameters  

Microsoft Academic Search

This note presents a new approach to guaranteed system identification for time-varying parameterized discrete-time systems. A bounded description of noise in the measurement is considered. The main result is an algorithm to compute a set that contains the parameters consistent with the measured output and the given bound of the noise. This set is represented by a zonotope, that is,

J. M. Bravo; T. Alamo; E. F. Camacho

2006-01-01

287

An experimental study of a model reference system identification method  

Microsoft Academic Search

A model reference system identification method based on the hyperstability approach is used to realize an on-line modelling system for an internal combustion engine. The performance of this method, even in the presence of non-linearity and different orders of the plant and model, is found to be satisfactory.

CHANG-CHIEH HANG

1976-01-01

288

Yeast: A Research Organism for Teaching Genetics.  

ERIC Educational Resources Information Center

Explains why laboratory strains of bakers yeast, Saccharomyces cerevisiae, are particularly suited for classroom science activities. Describes the sexual life cycle of yeast and the genetic system with visible mutations. Presents an overview of activities that can be done with yeast and gives a source for teachers to obtain more information. (PR)

Manney, Thomas R.; Manney, Monta L.

1992-01-01

289

Power system dynamic load identification and stability  

Microsoft Academic Search

Proper power system load models are playing more important roles in power system stability analysis in today's stressed power systems. Different load models may cause a large difference in stability analytical results. Measurement based load modeling gives a closer look at the real power system loads and their dynamic characteristics. In this paper, genetic algorithms and evolutionary programming based system

S. Z. Zhu; Z. Y. Dong; K. P. Wong; Z. H. Wang

2000-01-01

290

Development of a transformation and selection system for the glycolipid-producing yeast Candida bombicola.  

PubMed

Sophorolipids are surface-active compounds synthesized by the non-pathogenic yeast Candida bombicola. Over recent decades much effort has been spent to optimize culture conditions in order to improve the yield and production process. As far as we know, however, hardly any attention has been given to the genetics of the producing yeast strain itself and there are no published results available on the genetic engineering of C. bombicola. Nevertheless, this can be a useful tool for the study of the sophorolipid synthesis pathway and open up perspectives for improved production. A first step is the development of a suitable transformation and selection method. This article describes the creation and selection of an uracil auxotrophic C. bombicola mutant, which can be transformed back to prototrophy with the species' own orotidine 5'-phosphate decarboxylase or URA3 gene. Successful transformation was confirmed by a PCR-based method discriminating between the wild-type and mutated URA3 gene. PMID:18327888

Van Bogaert, Inge N A; De Maeseneire, Sofie L; Develter, Dirk; Soetaert, Wim; Vandamme, Erick J

2008-04-01

291

A wide-range integrative yeast expression vector system based on Arxula adeninivorans -derived elements  

Microsoft Academic Search

An Arxula adeninivorans integration vector was applied to a range of alternative yeast species including Saccharomyces cerevisiae, Debaryomyces hansenii, Debaryomyces polymorphus, Hansenula polymorpha and Pichia pastoris. The vector harbours a conserved A. adeninivorans-derived 25S rDNA sequence for targeting, the A. adeninivorans-derived TEF1 promoter for expression control of the reporter sequence, and the Escherichia coli-derived hph gene conferring resistance against hygromycin

Yaroslav Terentiev; Almudena Huarto Pico; Erik Böer; Thomas Wartmann; Jens Klabunde; Uta Breuer; Wolfgang Babel; Manfred Suckow; Gerd Gellissen; Gotthard Kunze

2004-01-01

292

Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range  

E-print Network

Although the proteins comprising many signaling systems are known, less is known about their numbers per cell. Existing measurements often vary by more than 10-fold. Here, we devised improved quantification methods to ...

Thomson, Ty M.

293

Yeast as a model system to screen purine derivatives against human CDK1 and CDK2 kinases.  

PubMed

Cyclin-dependent kinases (Cdk) play crucial roles in cell cycle progression. Aberrant activation of Cdk1 has been observed in a number of primary tumors and Cdk2 is deregulated in various malignancies. The therapeutic value of targeting Cdk1 and Cdk2 has been explored in a number of experimental systems. In the present study, taking advantage of the fact that deletion of the yeast CDC28 gene is functionally complemented by human CDK1 or CDK2, we set up an in vivo screen system to evaluate the inhibitory potency of purine derivatives against these two human Cdks. We constructed three isogenic strains highly sensitive to small molecules and harboring genes CDK1, CDK2 or CDC28, under the control of the CDC28 promoter. In a proof of principle assay, we determined the inhibitory effect of 82 purine derivatives on the growth rate of these strains. Thirty-three of them were revealed to be able to inhibit the Cdk1- or Cdk2-harboring strains but not the Cdc28-harboring strain, suggesting a specific inhibitory effect on human Cdks. Our data demonstrate that the yeast-based assay is an efficient system to identify potential specific inhibitors that should be preferentially selected for further investigation in cultured human cell lines. PMID:25541464

Mayi, Thérèse; Facca, Céline; Anne, Sandrine; Vernis, Laurence; Huang, Meng-Er; Legraverend, Michel; Faye, Gérard

2015-02-10

294

Neural System Identification Garrett B. Stanley, PhD 1  

E-print Network

(Marmarelis and Marmarelis, 1978). Central to the framework of system identification is the idea that complex of neuronal information in a number of studies (Perkel et al., 1967; DeBoer and Kuyper, 1968; Marmarelis and Naka, 1973a; Marmarelis and Naka, 1973b; 1 #12;Brillinger et al., 1976), and has subsequently become

295

Battery status identification of battery management system with asynchronous sampling  

Microsoft Academic Search

Battery management system (BMS) which measures battery status with high accuracy has a critical effect on the performance of power battery and the entire car. To solve the problem of identification precision decreasing for the reason of BMS asynchronous sampling, the original computing method is improved by using gradient adjustment method and based on order 2 RC battery model. A

Qiang Gu; Xiusheng Cheng; Zhonghua Lu; Xi Liu; Yongdao Song

2011-01-01

296

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

297

FORENSIC IDENTIFICATION REPORTING USING AUTOMATIC SPEAKER RECOGNITION SYSTEMS  

E-print Network

FORENSIC IDENTIFICATION REPORTING USING AUTOMATIC SPEAKER RECOGNITION SYSTEMS J. Gonzalez to the bayesian approach for evidence analysis and forensic reporting. This approach, firmly established in other forensic areas as fingerprint, DNA or fiber analysis, suits the needs of both the court and the forensic

Autonoma de Madrid, Universidad

298

A quadratic programming-based method for quantized system identification  

E-print Network

Wang ,1 Qinghua Zhang College of Engineering, Peking University, Beijing, China 100871 (e-mail: liuxianen@pku.edu.cn). College of Engineering, Peking University, Beijing, China 100871 (e-mail: jiandong the identification problem for finite impulse (FIR) systems, usually viewed as a nonlinear estimation problem

Wang, Jiandong

299

Feature Level Fusion of Speech and Face Image Based Person Identification System  

Microsoft Academic Search

Person identification system that used multiple biometric can improve performance than using a single biometric. This paper presents feature level fusion of dual tree complex wavelet transform speech and face image features for person identification system. Results of experiments using a VidTIMIT database presented to show the identification rate of multibiometric system more improved compared with single biometric system.

Y. B. G. Sugiarta; R. Bambang; Hendrawan; Suhardi

2010-01-01

300

Dynamic interaction between Isp45 and mitochondrial hsp70 in the protein import system of the yeast mitochondrial inner membrane.  

PubMed Central

The protein import system of the yeast mitochondrial inner membrane includes at least three membrane proteins that presumably form a transmembrane channel as well as several chaperone proteins that mediate the import and refolding of precursor proteins. We show that one of the membrane proteins, Isp45, spans the mitochondrial inner membrane yet is extracted from this membrane at high pH. Solubilization of mitochondria with a nonionic detergent releases Isp45 as a complex with the chaperones mitochondrial hsp70 (mhsp70) and GrpEp. Both chaperones reversibly dissociate from Isp45 upon addition of ATP or adenosine 5'-[gamma-thio]triphosphate, suggesting that dissociation requires the binding of ATP. Control experiments indicate that the interaction between mhsp70 and Isp45 occurs in the intact mitochondria. We propose that Isp45 lines the inside of a proteinaceous channel across the inner membrane and that it is the membrane anchor for an ATP-driven "import motor" composed of mhsp70 and GrpEp. This arrangement is reminiscent of the protein transport systems of the yeast endoplasmic reticulum and the bacterial plasma membrane. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 PMID:7809127

Kronidou, N G; Oppliger, W; Bolliger, L; Hannavy, K; Glick, B S; Schatz, G; Horst, M

1994-01-01

301

Biosorption of mercury on magnetically modified yeast cells  

Microsoft Academic Search

Brewer's yeast (bottom yeast, Saccharomyces cerevisiae subsp. uvarum) cells were magnetically modified using water based magnetic fluid stabilized perchloric acid. The magnetically modified yeast cells were characterized by scanning electron microscopy (SEM) and electron spin resonance (ESR). Hg2+ biosorption-desorption properties of magnetically modified yeast cells from synthetic solutions were utilized in batch system. The biosorption process was fast; 80% of

Handan Yavuz; Adil Denizli; Hakan Güngüne?; Mirka Safarikova; Ivo Safarik

2006-01-01

302

Copper Biosorption on Magnetically Modified Yeast Cells Under Magnetic Field  

Microsoft Academic Search

Brewer's yeast (bottom yeast, Saccharomyces cerevisiae subsp. uvarum) cells were magnetically modified using water-based magnetic fluid stabilized perchloric acid. The magnetically modified yeast cells were characterized by scanning electron microscopy (SEM). Cu biosorption properties of magnetically modified yeast cells from synthetic solutions were utilized in a continuous magnetic system. The Cu ion-binding capacity decreased drastically with the increase of the

Lokman Uzun; Necdet Sa?lam; Mirka Safarikova; Ivo Safarik; Adil Denizli

2011-01-01

303

Compact Modeling of Nonlinear Analog Circuits Using System Identification via Semidefinite Programming and Incremental Stability Certification  

E-print Network

This paper presents a system identification technique for generating stable compact models of typical analog circuit blocks in radio frequency systems. The identification procedure is based on minimizing the model error ...

Bond, Bradley N.

304

Coherency identification for power system dynamic equivalents  

Microsoft Academic Search

Coherency-based approach to the problem of constructing power system dynamic equivalents has been very successful in applications. The key step in this approach is to identify groups of coherent generators. An analytic study of coherency is conducted. An algebraic characterization of coherency is given. An algorithm, based on the algebraic characterization, to identify coherent groups directly from system data is

F. Wu; NATARAJAN NARASIMHAMURTHI

1983-01-01

305

Improving the Yeast Three-Hybrid System for High-Throughput Target Discovery  

E-print Network

High-throughput screening and rational design can be used to create bioactive compounds with high affinity for selected therapeutic targets. However, a significant challenge in preclinical drug development is the identification ...

Bailey, Kyle

2011-05-27

306

Wavelet Transforms for System Identification in Civil Engineering  

Microsoft Academic Search

The time-frequency character of wavelet transforms allows adaptation of both traditional time and frequency domain system identification approaches to ex- amine nonlinear and non-stationary data. Although chal- lenges did not surface in prior applications concerned with mechanical systems, which are characterized by higher frequency and broader-band signals, the transition to the time-frequency domain for the analysis of civil engineer- ing

T. Kijewski; A. Kareem

2003-01-01

307

Identification of nonlinear biological systems using laguerre expansions of kernels  

Microsoft Academic Search

Identification of nonlinear dynamic systems using the Volterra-Wiener approach requires the estimation of system kernels from\\u000a input-output data. A kernel estimation technique, originally proposed by Wiener (1958) and recently studied by Ogura (1986),\\u000a employs Laguerre expansions of the kernels and estimates the unknown expansion coefficients via time-averaging of covariance\\u000a samples. This paper presents another implementation of the technique which utilizes

Vasilis Z. Marmarelis

1993-01-01

308

Numerical gradient methods for flux identification in a system of conservation laws  

E-print Network

Numerical gradient methods for flux identification in a system of conservation laws Franc¸ois James , Marie Postel Abstract The identification of the flux for a system of conservation laws engineers results. Keywords: hyperbolic systems of conservation laws ­ flux identification ­ discrete

Paris-Sud XI, Université de

309

Asymptotic inference in system identification for the atom maser  

E-print Network

System identification is an integrant part of control theory and plays an increasing role in quantum engineering. In the quantum set-up, system identification is usually equated to process tomography, i.e. estimating a channel by probing it repeatedly with different input states. However for quantum dynamical systems like quantum Markov processes, it is more natural to consider the estimation based on continuous measurements of the output, with a given input which may be stationary. We address this problem using asymptotic statistics tools, for the specific example of estimating the Rabi frequency of an atom maser. We compute the Fisher information of different measurement processes as well as the quantum Fisher information of the atom maser, and establish the local asymptotic normality of these statistical models. The statistical notions can be expressed in terms of spectral properties of certain deformed Markov generators and the connection to large deviations is briefly discussed.

Catalin Catana; Merlijn van Horssen; Madalin Guta

2011-12-09

310

Neural network identification of power system transfer functions  

SciTech Connect

This paper describes an investigation into the use of a multilayered neural network for measuring the transfer function of a power system for use in power system stabilizer (PSS) tuning and assessing PSS damping. The objectives are to quickly and accurately measure the transfer function relating the electric power output to the AVR PSS reference voltage input of a system with the plant operating under normal conditions. In addition, the excitation signal used in the identification procedure is such that it will not adversely affect the terminal voltage or the system frequency. This research emphasized the development of a neural network that is easily trained and robust to changing system conditions. Performance studies of the trained neural network are described. Simulation studies suggest the practical feasibility of the algorithm as a stand-alone identification package and as a portion of a self-tuning algorithm requiring identification in the strategy. The same technique applied to a forward modeling scheme can be used to test the damping contribution from different control strategies.

Gillard, D.M.; Bollinger, K.E. [Univ. of Alberta, Edmonton, Alberta (Canada)] [Univ. of Alberta, Edmonton, Alberta (Canada)

1996-03-01

311

Improving Peptide Identification Using Empirical Scoring Systems  

PubMed Central

Summary Peptides and proteins are routinely identified from peptide fragmentation spectra acquired in a mass spectrometer, analyzed by database search engines. The types of fragments that can be formed are known, and it is also well appreciated that certain fragment types are more common or more informative than others. However, most search engines do not use detailed knowledge of peptide fragmentation, but rather consider a limited range of fragments, giving each an equivalent weighting in their scoring system that decides which results are likely to be correct. This chapter will discuss efforts to make use of information about the frequency of observation of different fragment ion types in order to produce more sophisticated and sensitive scoring systems and will demonstrate how these new scoring systems are particularly powerful for analysis of electron capture or electron transfer dissociation data. PMID:23666726

Chalkley, Robert J.

2015-01-01

312

System Identification for Nonlinear Control Using Neural Networks  

NASA Technical Reports Server (NTRS)

An approach to incorporating artificial neural networks in nonlinear, adaptive control systems is described. The controller contains three principal elements: a nonlinear inverse dynamic control law whose coefficients depend on a comprehensive model of the plant, a neural network that models system dynamics, and a state estimator whose outputs drive the control law and train the neural network. Attention is focused on the system identification task, which combines an extended Kalman filter with generalized spline function approximation. Continual learning is possible during normal operation, without taking the system off line for specialized training. Nonlinear inverse dynamic control requires smooth derivatives as well as function estimates, imposing stringent goals on the approximating technique.

Stengel, Robert F.; Linse, Dennis J.

1990-01-01

313

Generalized Sensitivity Functions in Physiological System Identification  

Microsoft Academic Search

Parameters of physiological models are commonly associated in an input–output experiment with a specific pattern of the system response. This association is often made on an intuitive basis by traditional sensitivity analysis, i.e., by inspecting the variations of model output trajectories with respect to parameter variations. However, this approach provides limited information since, for instance, it ignores correlation among parameters.

Karl Thomaseth; Claudio Cobelli

1999-01-01

314

Set Membership identification of nonlinear systems  

Microsoft Academic Search

In the paper the problem of identifying nonlinear dynamic systems, described in nonlinear regression form, is considered, using !nite an d n oise-corrupted measuremen ts. Most methods inthe literature are based onthe estimationof a model withina !n itely parametrized model class describing the functional form of involved nonlinearities. A key problem in these methods is the proper choice of the

Mario Milanese; Carlo Novara

2004-01-01

315

Communications device identification methods, communications methods, wireless communications readers, wireless communications systems, and articles of manufacture  

DOEpatents

Communications device identification methods, communications methods, wireless communications readers, wireless communications systems, and articles of manufacture are described. In one aspect, a communications device identification method includes providing identification information regarding a group of wireless identification devices within a wireless communications range of a reader, using the provided identification information, selecting one of a plurality of different search procedures for identifying unidentified ones of the wireless identification devices within the wireless communications range, and identifying at least some of the unidentified ones of the wireless identification devices using the selected one of the search procedures.

Steele, Kerry D [Kennewick, WA; Anderson, Gordon A [Benton City, WA; Gilbert, Ronald W [Morgan Hill, CA

2011-02-01

316

System Identification: Time Varying and Nonlinear Methods  

E-print Network

&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, John L. Junkins Committee Members, Aniruddha Datta Jer-Nan Juang Daniele Mortari Othon K. Rediniotis Srinivas R... + + + ? ? ? ? ? ? ? ? ?= ? ? ? ? ? ?? ? ? ? (2.11) and 1 ...k k k kR B AB ?? ?=? ? (2.12) Although the grammians are infinite matrices, usually for a system which is both Controllable and Observable (minimal), the principal full rank components of the corresponding grammians have most...

Majji, Manoranjan

2010-07-14

317

Spacecraft structural system identification by modal test  

NASA Technical Reports Server (NTRS)

A structural parameter estimation procedure using the measured natural frequencies and kinetic energy distribution as observers is proposed. The theoretical derivation of the estimation procedure is described and its constraints and limitations are explained. This procedure is applied to a large complex spacecraft structural system to identify the inertia matrix using modal test results. The inertia matrix is chosen after the stiffness matrix has been updated by the static test results.

Chen, J.-C.; Peretti, L. F.; Garba, J. A.

1984-01-01

318

Evaluation of the peptide nucleic acid fluorescence in situ hybridisation technology for yeast identification directly from positive blood cultures: an Italian experience.  

PubMed

Fungaemia is an increasing nosocomial pathology. The 'gold standard' for detection of fungaemia is blood culture, but it is time-consuming and its sensitivity for early detection is low. On the other hand, yeasts present different antifungal sensitivity patterns to be quickly detected to allow an effective treatment. The aim of this study was to evaluate the diagnostic performances of PNA-FISH to directly identify yeasts from blood cultures and to compare results with those obtained by culture. A total of 176 blood cultures positive for yeasts at direct Gram stain and 24 negative blood cultures as control collected from 15 Italian hospitals, included in a network coordinated by the Medical Mycology Committee, Italian Society of Clinical Microbiology (AMCLI), were examined both by culture and PNA-FISH technology. Sensitivity of the PNA-FISH technique evaluated for five Candida species was 99.3% and specificity, 100%. Distinguishing which yeast is implicated in fungaemia and whether the infection is caused by multiple species are important for the selection of antifungal therapy. The PNA-FISH technique is a very useful approach because the test discriminates between groups of Candida species with different susceptibility pattern, particularly against azoles and echinocandins, with only a 90-minute turn-around time after the Gram-stain reading. PMID:22233292

Farina, Claudio; Perin, Silvana; Andreoni, Stefano; Conte, Marco; Fazii, Paolo; Lombardi, Gianluigi; Manso, Esther; Morazzoni, Cristina; Sanna, Silvana

2012-09-01

319

CONTAGEM DE BOLORES E LEVEDURAS EM FUBÁ E IDENTIFICAÇÃO DE GÊNEROS POTENCIALMENTE TOXIGÊNICOS COUNTING OF MOULDS AND YEASTS IN CORN MEAL AND IDENTIFICATION OF POTENTIALLY TOXIGENIC GENERA  

Microsoft Academic Search

Corn meal is a very popular food that is present in almost every Brazilian home. As well as all the corn-based products, corn meal is likely to be contaminated by moulds and yeasts. Many moulds are potentially mycotoxigenic and therefore they produce toxins that are harmful to human health. The results obtained after the analysis of five brands of corn

R. V. ALHADAS

320

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

Microsoft Academic Search

Three molecular tools, amplified fragment length polymorphism (AFLPTm), 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

Bart Theelen; Massimiliano Silvestri; Eveline Guého; Alex van Belkum; Teun Boekhout

2001-01-01

321

CHARACTERIZATION OF THE ALKANE-INDUCIBLE CYTOCHROME P450 (P450ALK) GENE FROM THE YEAST CANDIDA TROPICALIS: IDENTIFICATION OF A NEW P450 FAMILY  

EPA Science Inventory

The P450alk gene, which is inducible by the assimilation of alkane in Candida tropicalis, was sequenced and characterized. Structural features described in promoter and terminator regions of Saccharomyces yeast genes are present in the P450alk gene and some particular structures ...

322

CHARACTERIZATION OF THE ALKANE-INDUCIBLE CYTOCHROME P450 (P450ALK) GENE FROM THE YEAST CANDIDA TROPICALIS: IDENTIFICATION OF A NEW P450 GENE FAMILY  

EPA Science Inventory

The P450ALK gene, which is inducible by the assimilation of alkane in Candida tropicalis, was sequenced and characterized. tructural features described in promoter and terminator regions of Saccharomyces yeast genes are present in the P450alk gene and some particular structures a...

323

High Expression of Methylotrophic Yeast-Derived Recombinant Human Erythropoietin in a pH-Controlled Batch System  

PubMed Central

To accomplish the worldwide demand for recombinant human erythropoietin (rHuEpo) as a therapeutic, application of cost-efficient expression system of methylotrophic yeast Pichia pastoris (P. pastoris) rather than mammalian cells is indispensable. Herein, a report on high levels secreted-expression of Pichia-derived rHuEpo by batch fermentation in a pH stabilized format is presented. The full length cDNA of rHuEpo was inserted into pPICZ?A vector under control of AOX1 promoter, downstream of the secretion-?-factor and electroporated into P. pastoris strain X33. The highest expression transformant was selected by screening among the colonies surviving high concentration of Zeocin (1.0 mg/ml), followed by comparative small scale expression analysis by ELISA. Stabilization of pH around 6.0 by adding phosphoric acid into the culture media during induction period, improved the yield of expression to 150 mg/l of the media. Single-step Nickel-affinity chromatography was employed for purification of rHuEpo-6xHis to 80% purity. Analyses by SDS-PAGE, Western blot and N-terminal protein sequencing confirmed the authenticity of the 33 kDa expressed rHuEpo with a native N-terminal indicating the proper cleavage of secretion-signal. Results of this study, further confirmed the possibility of employing methylotrophic yeast for scaled up production aims of rHuEpo as a cost-efficient expression system when provided evidence for higher expression yields through application of pH-controlled systems. PMID:23407145

Maleki, Ahmad; Roohvand, Farzin; Tajerzadeh, Hosnieh; Khanahmad, Hossein; Nobari, Maryam B.; Beiruti, Ahmad; Najafabadi, Abdolhossein Rouholamini

2010-01-01

324

A new class of wavelet networks for nonlinear system identification.  

PubMed

A new class of wavelet networks (WNs) is proposed for nonlinear system identification. In the new networks, the model structure for a high-dimensional system is chosen to be a superimposition of a number of functions with fewer variables. By expanding each function using truncated wavelet decompositions, the multivariate nonlinear networks can be converted into linear-in-the-parameter regressions, which can be solved using least-squares type methods. An efficient model term selection approach based upon a forward orthogonal least squares (OLS) algorithm and the error reduction ratio (ERR) is applied to solve the linear-in-the-parameters problem in the present study. The main advantage of the new WN is that it exploits the attractive features of multiscale wavelet decompositions and the capability of traditional neural networks. By adopting the analysis of variance (ANOVA) expansion, WNs can now handle nonlinear identification problems in high dimensions. PMID:16121728

Billings, Stephen A; Wei, Hua-Liang

2005-07-01

325

The Yeast Three-Hybrid System as an Experimental Platform to Identify Proteins Interacting with Small Signaling Molecules in Plant Cells: Potential and Limitations  

PubMed Central

Chemical genetics is a powerful scientific strategy that utilizes small bioactive molecules as experimental tools to unravel biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that can be used to dissect functions of biological systems. Once the bioactivity of a natural or synthetic compound has been critically evaluated the challenge remains to identify its molecular target and mode of action, which usually is a time-consuming and labor-intensive process. To facilitate this task, we decided to implement the yeast three-hybrid (Y3H) technology as a general experimental platform to scan the whole Arabidopsis proteome for targets of small signaling molecules. The Y3H technology is based on the yeast two-hybrid system and allows direct cloning of proteins that interact in vivo with a synthetic hybrid ligand, which comprises the biologically active molecule of interest covalently linked to methotrexate (Mtx). In yeast nucleus the hybrid ligand connects two fusion proteins: the Mtx part binding to dihydrofolate reductase fused to a DNA-binding domain (encoded in the yeast strain), and the bioactive molecule part binding to its potential protein target fused to a DNA-activating domain (encoded on a cDNA expression vector). During cDNA library screening, the formation of this ternary, transcriptional activator complex leads to reporter gene activation in yeast cells, and thereby allows selection of the putative targets of small bioactive molecules of interest. Here we present the strategy and experimental details for construction and application of a Y3H platform, including chemical synthesis of different hybrid ligands, construction of suitable cDNA libraries, the choice of yeast strains, and appropriate screening conditions. Based on the results obtained and the current literature we discuss the perspectives and limitations of the Y3H approach for identifying targets of small bioactive molecules. PMID:22639623

Cottier, Stéphanie; Mönig, Timon; Wang, Zheming; Svoboda, Ji?í; Boland, Wilhelm; Kaiser, Markus; Kombrink, Erich

2011-01-01

326

Wavelet features for failure detection and identification in vibration systems  

Microsoft Academic Search

The result of this effort is an extremely flexible and powerful methodology for failure detection and identification (FDI) in vibrating systems. The essential elements of this methodology are: (1) an off-line set of techniques to identify high-energy, statistically significant features in the continuous wavelet transform (CWT); (2) a CWT-based preprocessor to extract the most useful features from the sensor signal;

James C. Deckert; Alonso E. Rhenals; Robert R. Tenney; Alan S. Willsky

1992-01-01

327

Gunshot identification system by integration of open source consumer electronics  

NASA Astrophysics Data System (ADS)

This work presents a prototype of low-cost gunshots identification system that uses consumer electronics in order to ensure the existence of gunshots and then classify it according to a previously established database. The implementation of this tool in the urban areas is to set records that support the forensics, hence improving law enforcement also on developing countries. An analysis of its effectiveness is presented in comparison with theoretical results obtained with numerical simulations.

López R., Juan Manuel; Marulanda B., Jose Ignacio

2014-05-01

328

Material Outgassing, Identification and Deposition, MOLIDEP System  

NASA Technical Reports Server (NTRS)

The outgassing tests are performed employing a modified vacuum operated Cahn analytical microbalance, identified as the MOLIDEP system. The test measures under high vacuum, the time varying Molecular mass loss of a material sample held at a chosen temperature; it Identifies the outgassing molecular components using an inline SRS 300 amu Residual Gas Analyzer (RGA) and employs a temperature controlled 10 MHz Quartz Crystal Microbalance (QCM) to measure the condensable DEPosits. Both the QCM and the RGA intercept within the conductive passage the outgassing products being evacuated by a turbomolecular pump. The continuous measurements of the mass loss, the rate of loss, the sample temperature, the rate of temperature change, the QCM temperature and the QCM recorded condensable deposits or rate of deposits are saved to an Excel spreadsheet. A separate computer controls the RGA.

Scialdone, John J.; Montoya, Alex F.

2002-01-01

329

Computational requirements for on-orbit identification of space systems  

NASA Technical Reports Server (NTRS)

For the future space systems, on-orbit identification (ID) capability will be required to complement on-orbit control, due to the fact that the dynamics of large space structures, spacecrafts, and antennas will not be known sufficiently from ground modeling and testing. The computational requirements for ID of flexible structures such as the space station (SS) or the large deployable reflectors (LDR) are however, extensive due to the large number of modes, sensors, and actuators. For these systems the ID algorithm operations need not be computed in real-time, only in near real-time, or an appropriate mission time. Consequently the space systems will need advanced processors and efficient parallel processing algorithm design and architectures to implement the identification algorithms in near real-time. The MAX computer currently being developed may handle such computational requirements. The purpose is to specify the on-board computational requirements for dynamic and static identification for large space structures. The computational requirements for six ID algorithms are presented in the context of three examples: the JPL/AFAL ground antenna facility, the space station (SS), and the large deployable reflector (LDR).

Hadaegh, Fred Y.

1988-01-01

330

Interaction Between Yeasts and Zinc  

NASA Astrophysics Data System (ADS)

Zinc is an essential trace element in biological systems. For example, it acts as a cellular membrane stabiliser, plays a critical role in gene expression and genome modification and activates nearly 300 enzymes, including alcohol dehydrogenase. The present chapter will be focused on the influence of zinc on cell physiology of industrial yeast strains of Saccharomyces cerevisiae, with special regard to the uptake and subsequent utilisation of this metal. Zinc uptake by yeast is metabolism-dependent, with most of the available zinc translocated very quickly into the vacuole. At cell division, zinc is distributed from mother to daughter cells and this effectively lowers the individual cellular zinc concentration, which may become zinc depleted at the onset of the fermentation. Zinc influences yeast fermentative performance and examples will be provided relating to brewing and wine fermentations. Industrial yeasts are subjected to several stresses that may impair fermentation performance. Such stresses may also impact on yeast cell zinc homeostasis. This chapter will discuss the practical implications for the correct management of zinc bioavailability for yeast-based biotechnologies aimed at improving yeast growth, viability, fermentation performance and resistance to environmental stresses

Nicola, Raffaele De; Walker, Graeme

331

Computer systems for photo-identification and theodolite tracking of cetaceans.  

E-print Network

??Two separate computer-based systems were evaluated for two different methodological techniques (photo-identification and theodolite tracking) of cetacean research. The photo-identification program, Finscan, was evaluated to… (more)

Gailey, Glenn Andrew

2012-01-01

332

System identification methods for metal rubber devices  

NASA Astrophysics Data System (ADS)

Metal rubber (MR) devices, a new wire mesh material, have been extensively used in recent years due to several unique properties especially in adverse environments. Although many practical studies have been completed, the related theoretical research on metal rubber is still in its infancy. In this paper, a semi-constitutive dynamic model that involves nonlinear elastic stiffness, nonlinear viscous damping and bilinear hysteresis Coulomb damping is adopted to model MR devices. The model is first approximated by representing the bilinear hysteresis damping as Chebyshev polynomials of the first kind and then generalised by taking into account the effects of noises. A very efficient systematic procedure based on the orthogonal least squares (OLS) algorithm, the adjustable prediction error sum of squares (APRESS) criterion and the nonlinear model validity tests is proposed for model structure detection and parameter estimation of MR devices for the first time. The OLS algorithm provides a powerful tool to effectively select the significant model terms step by step, one at a time, by orthogonalising the associated terms and maximising the error reduction ratio, in a forward stepwise manner. The APRESS statistic regularises the OLS algorithm to facilitate the determination of the optimal number of model terms that should be included into the model. And whether the final identified dynamic model is adequate and acceptable is determined by the model validity tests. Because of the orthogonal property of the OLS algorithm, the selection of the dynamic model terms and noise model terms are totally decoupled and the approach also leads to a parsimonious model. Numerical ill-conditioning problems which can arise in the conventional least squares algorithm can be avoided as well. The methods of choosing the sampling interval for nonlinear systems are also incorporated into the approach. Finally by utilising the response of a cylindrical MR specimen, it is shown how the model structure can be detected in a practical application.

Zhang, B.; Lang, Z. Q.; Billings, S. A.; Tomlinson, G. R.; Rongong, J. A.

2013-08-01

333

Yeasts associated with nectarines and their potential for biological control of brown rot.  

PubMed

Resident fruit microflora has been the source of biocontrol agents for the control of postharvest decay of fruits and the active ingredient in commercialized biocontrol products. With the exception of grapes and apples, information on the resident microflora of other fruits is only fragmentary, but greater knowledge in this area can be very helpful in developing biocontrol strategies. We characterized the yeast microflora of nectarines ('Croce del Sud') from the early stages of fruit development until harvest. The fruit samples were collected from trees in an unmanaged orchard. The resident fruit microflora was separated from the occasionally deposited microorganisms by discarding initial fruit washings before the final wash, followed by sonication and plating on NYDA medium. The isolated yeasts were identified by BIOLOG and by sequencing the D1/D2 domain of a large subunit of the rRNA gene and, where available, the ITS sequence. BIOLOG identified 19 and the genetic analysis 23 species of yeasts. Although the identification by these two systems was not always the same, the predominant yeasts were Rhodotorula spp., Sporodiobolus spp., Cryptococcus spp., Pichia spp., Candida spp. and yeast-like Aureobasidium pullulans. Several of the taxa appear to represent new species. The preliminary biocontrol tests against brown rot of nectarine fruit caused by Monilinia fructicola indicates significant decay control potential of some of the identified yeast species, namely Cryptococcus magnus, Cryptococcus sp. nov., Sporidiobolus pararoseus, A. pullulans and Rhodotorula sp. nov. PMID:20225339

Janisiewicz, W J; Kurtzman, C P; Buyer, J S

2010-07-01

334

Characteristics and Efficiency of Glutamine Production by Coupling of a Bacterial Glutamine Synthetase Reaction with the Alcoholic Fermentation System of Baker’s Yeast  

PubMed Central

Glutamine production with bacterial glutamine synthetase (GS) and the sugar-fermenting system of baker’s yeast for ATP regeneration was investigated by determining the product yield obtained with the energy source for ATP regeneration (i.e., glucose) for yeast fermentation. Fructose 1,6-bisphosphate was accumulated temporarily prior to the formation of glutamine in mixtures which consisted of dried yeast cells, GS, their substrate (glucose and glutamate and ammonia), inorganic phosphate, and cofactors. By an increase in the amounts of GS and inorganic phosphate, the amounts of glutamine formed increased to 19 to 54 g/liter, with a yield increase of 69 to 72% based on the energy source (glucose) for ATP regeneration. The analyses of sugar fermentation of the yeast in the glutamine-producing mixtures suggested that the apparent hydrolysis of ATP by a futile cycle(s) at the early stage of glycolysis in the yeast cells reduces the efficiency of ATP utilization. Inorganic phosphate inhibits phosphatase(s) and thus improves glutamine yield. However, the analyses of GS activity in the glutamine-producing mixtures suggested that the higher concentration of inorganic phosphate as well as the limited amount of ATP-ADP caused the low reactivity of GS in the glutamine-producing mixtures. A result suggestive of improved glutamine yield under the conditions with lower concentrations of inorganic phosphate was obtained by using a yeast mutant strain that had low assimilating ability for glycerol and ethanol. In the mutant, the activity of the enzymes involved in gluconeogenesis, especially fructose 1,6-bisphosphatase, was lower than that in the wild-type strain. PMID:9687456

Wakisaka, Shinji; Ohshima, Yoshifumi; Ogawa, Masahiro; Tochikura, Tatsurokuro; Tachiki, Takashi

1998-01-01

335

Use of PCR Coupled with Electrospray Ionization Mass Spectrometry for Rapid Identification of Bacterial and Yeast Bloodstream Pathogens from Blood Culture Bottles ?  

PubMed Central

Sepsis is among the top 10 causes of mortality in the United States. Rapid administration of antibiotics is one of the most important contributors to patient survival, yet only a limited number of methods exist for rapid identification of microbes cultivated from bloodstream infections, which can lead to sepsis. While traditional single-target molecular methods have been shown to greatly improve survival for septic patients by enabling rapid deescalation of broad-spectrum antibiotics, multiplex methods offer even greater possibilities. A novel multiplex method, PCR coupled to electrospray ionization mass spectrometry (PCR/ESI-MS), was used to identify the genus and species of microorganisms found to cause human bloodstream infections. DNA was directly extracted from 234 BacT-Alert blood culture bottles, and results were compared to those obtained by clinical reference standard methods. The study results demonstrated 98.7% and 96.6% concordance at the genus and species levels, respectively. Mixtures of microbes were identified in 29 blood culture bottles, including mixed species of the same genus, as well as mixtures containing Gram-positive and Gram-negative organisms, exemplifying the PCR/ESI-MS capability to identify multiple organisms simultaneously without the need for cultivation. This study demonstrates high analytical accuracy in comparison to routine subculture of blood culture bottles and phenotypic identification of microbes. Without foreknowledge of the microorganisms potentially present, the PCR/ESI-MS methods can deliver accurate results in as little as 5 to 6 h after a positive alarm from the automated blood culture system; however, current batch mode testing limits the method's clinical utility at this time. PMID:21048006

Kaleta, Erin J.; Clark, Andrew E.; Johnson, Desiree R.; Gamage, Dulini C.; Wysocki, Vicki H.; Cherkaoui, Abdessalam; Schrenzel, Jacques; Wolk, Donna M.

2011-01-01

336

Biological tissue identification using a multispectral imaging system  

NASA Astrophysics Data System (ADS)

A multispectral imaging system enabling biological tissue identifying and differentiation is presented. The measurement of ?(?) spectral radiance factor cube for four tissue types (beef muscle, pork muscle, turkey muscle and beef liver) present in the same scene was carried out. Three methods for tissue identification are proposed and their relevance evaluated. The first method correlates the scene spectral radiance factor with tissue database characteristics. This method gives detection rates ranging from 63.5 % to 85 %. The second method correlates the scene spectral radiance factor derivatives with a database of tissue ?(?) derivatives. This method is more efficient than the first one because it gives detection rates ranging from 79 % to 89 % with over-detection rates smaller than 0.2 %. The third method uses the biological tissue spectral signature. It enhances contrast in order to afford tissue differentiation and identification.

Delporte, Céline; Sautrot, Sylvie; Ben Chouikha, Mohamed; Viénot, Françoise; Alquié, Georges

2013-02-01

337

Non-parametric identification of non-linear oscillating systems  

NASA Astrophysics Data System (ADS)

The problem of system identification from a time series of measurements is solved by using non-parametric additive models. Having only few structural information about the system, a non-parametric approach may be more appropriate than a parametric one for which detailed prior knowledge is needed. Based on non-parametric regression, the functions in the additive models are estimated by a penalized least-squares approach using backfitting. The optimal smoothing parameters are determined via generalized cross-validation, making this approach completely adaptive to the data. The procedure is applied to identify the non-linear restoring force of vibrationally excited helical wire rope isolators.

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

2003-11-01

338

A light-inducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast  

PubMed Central

Protein localization plays a central role in cell biology. Although powerful tools exist to assay the spatial and temporal dynamics of proteins in living cells, our ability to control these dynamics has been much more limited. We previously used the phytochrome B– phytochrome-interacting factor light-gated dimerization system to recruit proteins to the plasma membrane, enabling us to control the activation of intracellular signals in mammalian cells. Here we extend this approach to achieve rapid, reversible, and titratable control of protein localization for eight different organelles/positions in budding yeast. By tagging genes at the endogenous locus, we can recruit proteins to or away from their normal sites of action. This system provides a general strategy for dynamically activating or inactivating proteins of interest by controlling their localization and therefore their availability to binding partners and substrates, as we demonstrate for galactose signaling. More importantly, the temporal and spatial precision of the system make it possible to identify when and where a given protein's activity is necessary for function, as we demonstrate for the mitotic cyclin Clb2 in nuclear fission and spindle stabilization. Our light-inducible organelle-targeting system represents a powerful approach for achieving a better understanding of complex biological systems. PMID:23761071

Yang, Xiaojing; Jost, Anna Payne-Tobin; Weiner, Orion D.; Tang, Chao

2013-01-01

339

Nonlinear stochastic system identification of skin using volterra kernels.  

PubMed

Volterra kernel stochastic system identification is a technique that can be used to capture and model nonlinear dynamics in biological systems, including the nonlinear properties of skin during indentation. A high bandwidth and high stroke Lorentz force linear actuator system was developed and used to test the mechanical properties of bulk skin and underlying tissue in vivo using a non-white input force and measuring an output position. These short tests (5 s) were conducted in an indentation configuration normal to the skin surface and in an extension configuration tangent to the skin surface. Volterra kernel solution methods were used including a fast least squares procedure and an orthogonalization solution method. The practical modifications, such as frequency domain filtering, necessary for working with low-pass filtered inputs are also described. A simple linear stochastic system identification technique had a variance accounted for (VAF) of less than 75%. Representations using the first and second Volterra kernels had a much higher VAF (90-97%) as well as a lower Akaike information criteria (AICc) indicating that the Volterra kernel models were more efficient. The experimental second Volterra kernel matches well with results from a dynamic-parameter nonlinearity model with fixed mass as a function of depth as well as stiffness and damping that increase with depth into the skin. A study with 16 subjects showed that the kernel peak values have mean coefficients of variation (CV) that ranged from 3 to 8% and showed that the kernel principal components were correlated with location on the body, subject mass, body mass index (BMI), and gender. These fast and robust methods for Volterra kernel stochastic system identification can be applied to the characterization of biological tissues, diagnosis of skin diseases, and determination of consumer product efficacy. PMID:23264003

Chen, Yi; Hunter, Ian W

2013-04-01

340

Sensor network based vehicle classification and license plate identification system  

SciTech Connect

Typically, for energy efficiency and scalability purposes, sensor networks have been used in the context of environmental and traffic monitoring applications in which operations at the sensor level are not computationally intensive. But increasingly, sensor network applications require data and compute intensive sensors such video cameras and microphones. In this paper, we describe the design and implementation of two such systems: a vehicle classifier based on acoustic signals and a license plate identification system using a camera. The systems are implemented in an energy-efficient manner to the extent possible using commercially available hardware, the Mica motes and the Stargate platform. Our experience in designing these systems leads us to consider an alternate more flexible, modular, low-power mote architecture that uses a combination of FPGAs, specialized embedded processing units and sensor data acquisition systems.

Frigo, Janette Rose [Los Alamos National Laboratory; Brennan, Sean M [Los Alamos National Laboratory; Rosten, Edward J [Los Alamos National Laboratory; Raby, Eric Y [Los Alamos National Laboratory; Kulathumani, Vinod K [WEST VIRGINIA UNIV.

2009-01-01

341

Protein-protein interactions in two potyviruses using the yeast two-hybrid system.  

PubMed

Interactions between all ten mature proteins of the potyviruses Soybean mosaic virus (Pinellia ternata isolate) and Shallot yellow stripe virus were investigated using yeast two-hybrid (Y2H) assays. Consistently strong self-interactions were found between the pairs of HC-Pro, VPg, NIa-Pro, NIb and CP in both viruses. Apart from the NIb, such interactions have been previously reported for some other potyviruses. The 6K1/NIa-Pro combination gave a consistently moderate to strong interaction in both directions for both viruses. This interaction occurred even when the 6K1 of SMV-P was truncated to eliminate the C-terminal motif that acts as a recognition site for cleavage by the NIa-Pro. Many other interactions occurred only in one direction or only for one of the two viruses. When taken together with other published reports, the data suggest that interactions detected by Y2H should be regarded as only preliminary indications. PMID:19189854

Lin, Lin; Shi, Yuhong; Luo, Zhaopeng; Lu, Yuwen; Zheng, Hongying; Yan, Fei; Chen, Jiong; Chen, Jianping; Adams, M J; Wu, Yunfeng

2009-06-01

342

Biopharmaceutical discovery and production in yeast.  

PubMed

The selection of an expression platform for recombinant biopharmaceuticals is often centered upon suitable product titers and critical quality attributes, including post-translational modifications. Although notable differences between microbial, yeast, plant, and mammalian host systems exist, recent advances have greatly mitigated any inherent liabilities of yeasts. Yeast expression platforms are important to both the supply of marketed biopharmaceuticals and the pipelines of novel therapeutics. In this review, recent advances in yeast-based expression of biopharmaceuticals will be discussed. The advantages of using glycoengineered yeast as a production host and in the discovery space will be illustrated. These advancements, in turn, are transforming yeast platforms from simple production systems to key technological assets in the discovery and selection of biopharmaceutical lead candidates. PMID:25014890

Meehl, Michael A; Stadheim, Terrance A

2014-12-01

343

Terahertz imaging system performance model for concealed weapon identification  

NASA Astrophysics Data System (ADS)

The U.S. Army Night Vision and Electronic Sensors Directorate and the U.S. Army Research Laboratory have developed a terahertz-band imaging system performance model for detection and identification of concealed weaponry. The MATLAB-based model accounts for the effects of all critical sensor and display components, and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination. The model is based on recent U.S. Army NVESD sensor performance models that couple system design parameters to observer-sensor field performance using the acquire methodology for weapon identification performance predictions. This THz model has been developed in support of the Defense Advanced Research Project Agencies' Terahertz Imaging Focal-Plane-Array Technology (TIFT) program and is presently being used to guide the design and development of a 0.650 THz active/passive imaging system. This paper will describe the THz model in detail, provide and discuss initial modeling results for a prototype THz imaging system, and outline plans to validate and calibrate the model through human perception testing.

Murrill, Steven R.; Jacobs, Eddie L.; Moyer, Steven K.; Halford, Carl E.; Griffin, Steven T.; De Lucia, Frank C.; Petkie, Douglas T.; Franck, Charmaine C.

2005-11-01

344

Terahertz imaging system performance model for concealed-weapon identification  

NASA Astrophysics Data System (ADS)

The U.S. Army Night Vision and Electronic Sensors Directorate (NVESD) and the U.S. Army Research Laboratory have developed a terahertz (THz) -band imaging system performance model for detection and identification of concealed weaponry. The MATLAB-based model accounts for the effects of all critical sensor and display components and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination. The model is based on recent U.S. Army NVESD sensor performance modeling technology that couples system design parameters to observer-sensor field performance by using the acquire methodology for weapon identification performance predictions. This THz model has been developed in support of the Defense Advanced Research Project Agencies' Terahertz Imaging Focal-Plane Technology (TIFT) program and is currently being used to guide the design and development of a 0.650 THz active-passive imaging system. This paper will describe the THz model in detail, provide and discuss initial modeling results for a prototype THz imaging system, and outline plans to calibrate and validate the model through human perception testing.

Murrill, Steven R.; Jacobs, Eddie L.; Moyer, Steven K.; Halford, Carl E.; Griffin, Steven T.; De Lucia, Frank C.; Petkie, Douglas T.; Franck, Charmaine C.

2008-03-01

345

Visual identification system for homeland security and law enforcement support  

NASA Astrophysics Data System (ADS)

This paper describes the basic configuration for a visual identification system (VIS) for Homeland Security and law enforcement support. Security and law enforcement systems with an integrated VIS will accurately and rapidly provide identification of vehicles or containers that have entered, exited or passed through a specific monitoring location. The VIS system stores all images and makes them available for recall for approximately one week. Images of alarming vehicles will be archived indefinitely as part of the alarming vehicle"s or cargo container"s record. Depending on user needs, the digital imaging information will be provided electronically to the individual inspectors, supervisors, and/or control center at the customer"s office. The key components of the VIS are the high-resolution cameras that capture images of vehicles, lights, presence sensors, image cataloging software, and image recognition software. In addition to the cameras, the physical integration and network communications of the VIS components with the balance of the security system and client must be ensured.

Samuel, Todd J.; Edwards, Don; Knopf, Michael

2005-05-01

346

Linear system identification via an asymptotically stable observer  

NASA Technical Reports Server (NTRS)

This paper presents a formulation for identification of linear multivariable systems from single or multiple sets of input-output data. The system input-output relationship is expressed in terms of an observer, which is made asymptotically stable by an embedded eigenvalue assignment procedure. The prescribed eigenvalues for the observer may be real, complex, mixed real and complex, or zero. In this formulation, the Markov parameters of the observer are identified from input-output data. The Markov parameters of the actual system are then recovered from those of the observer, and used to obtain a state space model of the system by standard realization techniques. The basic mathematical formulation is derived, and numerical examples using simulated noise-free data are presented to illustrate the proposed method.

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

1991-01-01

347

Abnormal condition detection in a cement rotary kiln with system identification methods  

Microsoft Academic Search

In this paper, we use system identification methods for abnormal condition detection in a cement rotary kiln. After selecting proper inputs and output, an input–output model is identified for the plant’s normal conditions. A novel approach is used in order to estimate the delays of the input channels of the kiln before identification part. This method eases the identification since

Iman Makaremi; Alireza Fatehi; Babak Nadjar Araabi; Morteza Azizi; Ahmad Cheloeian

2009-01-01

348

Quantitative description of ion transport via plasma membrane of yeast and small cells  

E-print Network

Modelling of ion transport via plasma membrane needs identification and quantitative understanding of the involved processes. Brief characterisation of ion transport systems of a yeast cell (Pma1, Ena1, TOK1, Nha1, Trk1, Trk2, non-selective cation conductance) and estimates concerning the number of molecules of each transporter per a cell allow predicting the corresponding ion flows. Comparison of ion transport in small yeast cell and several animal cell types is provided and importance of cell volume to surface ratio is stressed. Role of cell wall and lipid rafts is discussed in aspect of required increase in spatial and temporary resolution of measurements. Conclusions are formulated to describe specific features of ion transport in a yeast cell. Potential directions of future research are outlined based on the assumptions.

Vadim Volkov

2012-12-18

349

A Feast for Yeast  

NSDL National Science Digital Library

In this activity on page 6 of the PDF, learners investigate yeast. Learners prepare an experiment to observe what yeast cells like to eat. Learners feed the yeast cells various ingredients in plain bread--water, flour, sugar, and salt--to discover yeast's favorite food.

Society, American C.

2000-01-01

350

Yeast-Air Balloons  

NSDL National Science Digital Library

In this activity, learners make a yeast-air balloon to get a better idea of what yeast can do. Learners discover that the purpose of leaveners like yeast is to produce the gas that makes bread rise. Learners discover that as yeast feeds on sugar, it produces carbon dioxide which slowly fills the balloon.

The Exploratorium

2012-03-10

351

Fuzzy membership function optimization for system identification using an extended Kalman filter  

E-print Network

Fuzzy membership function optimization for system identification using an extended Kalman filter an extended Kalman filter to optimize the membership functions for system modeling, or system identification is that the proposed system acts as a noise-reducing filter. We demonstrate that the extended Kalman filter can

Simon, Dan

352

Tapping into yeast diversity.  

PubMed

Domesticated organisms demonstrate our capacity to influence wild species but also provide us with the opportunity to understand rapid evolution in the context of substantially altered environments and novel selective pressures. Recent advances in genetics and genomics have brought unprecedented insights into the domestication of many organisms and have opened new avenues for further improvements to be made. Yet, our ability to engineer biological systems is not without limits; genetic manipulation is often quite difficult. The budding yeast, Saccharomyces cerevisiae, is not only one of the most powerful model organisms, but is also the premier producer of fermented foods and beverages around the globe. As a model system, it entertains a hefty workforce dedicated to deciphering its genome and the function it encodes at a rich mechanistic level. As a producer, it is used to make leavened bread, and dozens of different alcoholic beverages, such as beer and wine. Yet, applying the awesome power of yeast genetics to understanding its origins and evolution requires some knowledge of its wild ancestors and the environments from which they were derived. A number of surprisingly diverse lineages of S. cerevisiae from both primeval and secondary forests in China have been discovered by Wang and his colleagues. These lineages substantially expand our knowledge of wild yeast diversity and will be a boon to elucidating the ecology, evolution and domestication of this academic and industrial workhorse. PMID:23281494

Fay, Justin C

2012-11-01

353

Explosives identification model in reflection mode for THz security system  

NASA Astrophysics Data System (ADS)

The aim of this paper was to obtain the identification model in refection mode. Results Time Domain Spectroscopy were used to prepare our algorithm. This study has focused on developing several feature extraction methods with intuitive justifications in the problem space. A related problem to feature extraction is that of feature selection. For this reasons this extraction and selection methods of THz spectra are introduced. Then a complete THz classification framework including feature extraction scheme and Mahalanobis classifier was presented. Our results confirm the possibility of application of the model in real THz stand-off security system.

Ryniec, Radoslaw; Zagrajek, Przemyslaw; Trzcinski, Tomasz; Szustakowski, Mieczyslaw

2011-10-01

354

Identification of clinical isolates of gram-negative nonfermentative bacteria by an automated cellular fatty acid identification system.  

PubMed Central

An automated cellular fatty acid (CFA) bacterial identification system, Microbial Identification System (MIS; Microbial ID, Newark, Del.), was compared with a conventional system for the identification of 573 strains of gram-negative nonfermentative bacteria. MIS identifications were based exclusively on the CFA composition following 22 to 26 h of growth at 28 degrees C on Trypticase soy agar. MIS identifications were listed with a confidence measurement (similarity index [SI]) on a scale of 0 to 1.0. A value of greater than or equal to 0.5 was considered a good match. The MIS correctly listed as the first choice 478 of 532 (90%) strains contained in the data base. However, only 314 (59%) had SI values of greater than or equal to 0.5. Of the 54 strains in which there was not agreement, 37 belonged to the genera Acinetobacter, Moraxella, or Alcaligenes or were Pseudomonas pickettii. Reproducibility studies suggest that SI variation is most likely a function of a difference in culture age at the time of analysis, which is due to the relatively low temperature and time of incubation. Other discrepancies were attributable to insufficiently characterized library entries or an inability to differentiate chemotaxonomically closely related species. The MIS, as the first automated CFA identification system, is an accurate, efficient, and relatively rapid method for the identification of gram-negative nonfermentative bacteria. The development of a CFA library with the media and incubation conditions routinely used for the isolation of clinical pathogens could further decrease the identification time and provide an increase in accuracy. PMID:1774302

Osterhout, G J; Shull, V H; Dick, J D

1991-01-01

355

Identification and robust control of linear parameter-varying systems  

NASA Astrophysics Data System (ADS)

This dissertation deals with linear parameter-varying (LPV) systems: linear dynamic systems that depend on time-varying parameters. These systems appear in gain scheduling problems, and much recent research has been devoted to their prospective usefulness for systematic gain scheduling. We primarily focus on robust control of uncertain LPV systems and identification of LPV systems that are modelable as linear-fractional transformations (LFTs). Using parameter-dependent quadratic Lyapunov functions, linear matrix inequalities (LMIs), and scaled small-gain arguments, we define notions of stability and induced-{cal L}sb2 performance for uncertain LPV systems whose parameters and rates of parameter variation satisfy given bounds. The performance criterion involves integral quadratic constraints and implies naturally parameter-dependent induced-{cal L}sb2 norm bounds. We formulate and solve an {cal H}sb{infty}-like control problem for an LPV plant with measurable parameters and an "Output/State Feedback" structure: the feedback outputs include some noiselessly measured states. Necessary and sufficient solvability conditions reduce to LMIs that can be solved approximately using finite-dimensional convex programming. Reduced-order LPV controllers are constructed from the LMI solutions. A D-K iteration-like procedure provides robustness to structured, time-varying, parametric uncertainty. The design method is applied to a motivating example: flight control for the F-16 VISTA throughout its subsonic flight envelope. Parameter-dependent weights and {cal H}sb{infty} design principles describe the performance objectives. Closed-loop responses exhibited by nonlinear simulations indicate satisfactory flying qualities. Identification of linear-fractional LPV systems is treated using maximum-likelihood parameter estimation. Computing the gradient and Hessian of a maximum-likelihood cost function reduces to simulating one LPV filter per identified parameter. We use nonlinear programming to (locally) minimize the cost function, paying careful attention to the need for good initial estimates. This identification scheme generalizes to all linear systems that can be written as LFTs (e.g., time-invariant, parameter-varying, multidimensional, uncertain). We also address the critical issue of identifiability. We characterize the well-known redundancy of LFT models by manifolds (generated by structured similarity transformations) in the parameter space. Restricting the nonlinear programming for iterative parameter estimation to directions that are orthogonal to the corresponding tangent spaces produces an identifiable local canonical form that greatly reduces the computational burden.

Lee, Lawton Hubert

356

A Method for Sporulating Budding Yeast Cells That Allows for Unbiased Identification of Kinase Substrates Using Stable Isotope Labeling by Amino Acids in Cell Culture  

PubMed Central

Quantitative proteomics has been widely used to elucidate many cellular processes. In particular, stable isotope labeling by amino acids in cell culture (SILAC) has been instrumental in improving the quality of data generated from quantitative high-throughput proteomic studies. SILAC uses the cell’s natural metabolic pathways to label proteins with isotopically heavy amino acids. Incorporation of these heavy amino acids effectively labels a cell’s proteome, allowing the comparison of cell cultures treated under different conditions. SILAC has been successfully applied to a variety of model organisms including yeast, fruit flies, plants, and mice to look for kinase substrates as well as protein–protein interactions. In budding yeast, several kinases are known to play critical roles in different aspects of meiosis. Therefore, the use of SILAC to identify potential kinase substrates would be helpful in the understanding the specific mechanisms by which these kinases act. Previously, it has not been possible to use SILAC to quantitatively study the phosphoproteome of meiotic Saccharomyces cerevisiae cells, because yeast cells sporulate inefficiently after pregrowth in standard synthetic medium. In this study we report the development of a synthetic, SILAC-compatible, pre-sporulation medium (RPS) that allows for efficient sporulation of S. cerevisiae SK1 diploids. Pre-growth in RPS supplemented with heavy amino acids efficiently labels the proteome, after which cells proceed relatively synchronously through meiosis, producing highly viable spores. As proof of principle, SILAC experiments were able to identify known targets of the meiosis-specific kinase Mek1. PMID:25168012

Suhandynata, Ray; Liang, Jason; Albuquerque, Claudio. P.; Zhou, Huilin; Hollingsworth, Nancy M.

2014-01-01

357

Retrograde lipid traffic in yeast: identification of two distinct pathways for internalization of fluorescent-labeled phosphatidylcholine from the plasma membrane  

PubMed Central

Digital, video-enhanced fluorescence microscopy and spectrofluorometry were used to follow the internalization into the yeast Saccharomyces cerevisiae of phosphatidylcholine molecules labeled on one acyl chain with the fluorescent probe 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD). Two pathways were found: (1) transport by endocytosis to the vacuole and (2) transport by a non-endocytic pathway to the nuclear envelope and mitochondria. The endocytic pathway was inhibited at low temperature (< 2 degrees C) and by ATP depletion. Mutations in secretory (SEC) genes that are necessary for membrane traffic through the secretory pathway (including SEC1, SEC2, SEC4, SEC6, SEC7, SEC12, SEC14, SEC17, SEC18, and SEC21) almost completely blocked endocytic uptake. In contrast, mutations in the SEC63, SEC65, or SEC11 genes, required for translocation of nascent secretory polypeptides into the ER or signal peptide processing in the ER, only slightly reduced endocytic uptake. Phospholipid endocytosis was also independent of the gene encoding the clathrin heavy chain, CHC1. The correlation of biochemical analysis with fluorescence microscopy indicated that the fluorescent phosphatidylcholine was degraded in the vacuole and that degradation was, at least in part, dependent on the vacuolar proteolytic cascade. The non-endocytic route functioned with a lower cellular energy charge (ATP levels 80% reduced) and was largely independent of the SEC genes. Non-endocytic transport of NBD-phosphatidylcholine to the nuclear envelope and mitochondria was inhibited by pretreatment of cells with the sulfhydryl reagents N-ethylmaleimide and p- chloromercuribenzenesulfonic acid, suggesting the existence of protein- mediated transmembrane transfer (flip-flop) of phosphatidylcholine across the yeast plasma membrane. These data establish a link between lipid movement during secretion and endocytosis in yeast and suggest that phospholipids may also gain access to intracellular organelles through non-endocytic, protein-mediated events. PMID:8253840

1993-01-01

358

Improved solution for system identification equations by Epsilon-Decomposition  

NASA Technical Reports Server (NTRS)

Matrix eigenvalue theory is used to examine the source of ill-conditioning in linear algebraic equations. This approach highlights the crucial role played by the zero and near-zero eigenvalues and corresponding eigenvectors of poorly conditioned systems. Insight gained from this approach is used to significantly improve a recently developed solution procedure called Epsilon-Decomposition (E-D). E-D is an efficient alternative to Singular Value Decomposition (SVD) for ill-conditioned systems arising in parameter estimation and system identification studies. The efficiency of the improved E-D over SVD resides in the need to only obtain the zero and near-zero eigenvalues of the coefficient matrix as opposed to all of its eigenvalues and vectors (as required by SVD). Thus, the efficiency of E-D is significant for large matrices with small rank deficiency.

Ojalvo, Irving U.

1990-01-01

359

Part identification in robotic assembly using vision system  

NASA Astrophysics Data System (ADS)

Machine vision system acts an important role in making robotic assembly system autonomous. Identification of the correct part is an important task which needs to be carefully done by a vision system to feed the robot with correct information for further processing. This process consists of many sub-processes wherein, the image capturing, digitizing and enhancing, etc. do account for reconstructive the part for subsequent operations. Interest point detection of the grabbed image, therefore, plays an important role in the entire image processing activity. Thus it needs to choose the correct tool for the process with respect to the given environment. In this paper analysis of three major corner detection algorithms is performed on the basis of their accuracy, speed and robustness to noise. The work is performed on the Matlab R2012a. An attempt has been made to find the best algorithm for the problem.

Balabantaray, Bunil Kumar; Biswal, Bibhuti Bhusan

2013-12-01

360

Studying Functions of All Yeast Genes Simultaneously  

NASA Technical Reports Server (NTRS)

A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain.

Stolc, Viktor; Eason, Robert G.; Poumand, Nader; Herman, Zelek S.; Davis, Ronald W.; Anthony Kevin; Jejelowo, Olufisayo

2006-01-01

361

The putative electrogenic nitrate-proton symport of the yeast Candida utilis. Comparison with the systems absorbing glucose or lactate.  

PubMed Central

Strain N.C.Y.C. 193 of Candida utilis was grown aerobically at 30 degrees C with nitrate as limiting nutrient in a chemostat. The washed yeast cells depleted of ATP absorbed up to 5 nmol of nitrate/mg dry wt. of yeast. At pH 4-6, extra protons and nitrate entered the yeast cells together, in a ratio of about 2:1. Charge balance was maintained by an outflow of about 1 equiv. of K+. Nitrate stimulated the uptake of about 1 proton equivalent during glycolysis or aerobic energy metabolism. Studies with 3,3'-dipropylthiadicarbocyanine indicated that the proton-linked absorption of nitrate, amino acids or glucose depolarized the yeast cells. Proton uptake along with lactate led neither to net expulsion of K+ nor to membrane depolarization. PMID:2998345

Eddy, A A; Hopkins, P G

1985-01-01

362

Advanced Techniques for Power System Identification from Measured Data  

SciTech Connect

Time-synchronized measurements provide rich information for estimating a power-system's electromechanical modal properties via advanced signal processing. This information is becoming critical for the improved operational reliability of interconnected grids. A given mode's properties are described by its frequency, damping, and shape. Modal frequencies and damping are useful indicators of power-system stress, usually declining with increased load or reduced grid capacity. Mode shape provides critical information for operational control actions. This project investigated many advanced techniques for power system identification from measured data focusing on mode frequency and damping ratio estimation. Investigators from the three universities coordinated their effort with Pacific Northwest National Laboratory (PNNL). Significant progress was made on developing appropriate techniques for system identification with confidence intervals and testing those techniques on field measured data and through simulation. Experimental data from the western area power system was provided by PNNL and Bonneville Power Administration (BPA) for both ambient conditions and for signal injection tests. Three large-scale tests were conducted for the western area in 2005 and 2006. Measured field PMU (Phasor Measurement Unit) data was provided to the three universities. A 19-machine simulation model was enhanced for testing the system identification algorithms. Extensive simulations were run with this model to test the performance of the algorithms. University of Wyoming researchers participated in four primary activities: (1) Block and adaptive processing techniques for mode estimation from ambient signals and probing signals, (2) confidence interval estimation, (3) probing signal design and injection method analysis, and (4) performance assessment and validation from simulated and field measured data. Subspace based methods have been use to improve previous results from block processing techniques. Bootstrap techniques have been developed to estimate confidence intervals for the electromechanical modes from field measured data. Results were obtained using injected signal data provided by BPA. A new probing signal was designed that puts more strength into the signal for a given maximum peak to peak swing. Further simulations were conducted on a model based on measured data and with the modifications of the 19-machine simulation model. Montana Tech researchers participated in two primary activities: (1) continued development of the 19-machine simulation test system to include a DC line; and (2) extensive simulation analysis of the various system identification algorithms and bootstrap techniques using the 19 machine model. Researchers at the University of Alaska-Fairbanks focused on the development and testing of adaptive filter algorithms for mode estimation using data generated from simulation models and on data provided in collaboration with BPA and PNNL. There efforts consist of pre-processing field data, testing and refining adaptive filter techniques (specifically the Least Mean Squares (LMS), the Adaptive Step-size LMS (ASLMS), and Error Tracking (ET) algorithms). They also improved convergence of the adaptive algorithms by using an initial estimate from block processing AR method to initialize the weight vector for LMS. Extensive testing was performed on simulated data from the 19 machine model. This project was also extensively involved in the WECC (Western Electricity Coordinating Council) system wide tests carried out in 2005 and 2006. These tests involved injecting known probing signals into the western power grid. One of the primary goals of these tests was the reliable estimation of electromechanical mode properties from measured PMU data. Applied to the system were three types of probing inputs: (1) activation of the Chief Joseph Dynamic Brake, (2) mid-level probing at the Pacific DC Intertie (PDCI), and (3) low-level probing on the PDCI. The Chief Joseph Dynamic Brake is a 1400 MW disturbance to the system and is injected for a ha

Pierre, John W.; Wies, Richard; Trudnowski, Daniel

2008-11-25

363

Detection of bacterial and yeast species with the Bactec 9120 automated system with routine use of aerobic, anaerobic, and fungal media.  

PubMed

During the period 2006 and 2007, all blood cultures required by four units at high infective risk and most of those required by other units of the University Hospital of Palermo, Palermo, Italy were performed using a Bactec 9120 automated blood culture system with a complete set of Plus Aerobic/F, Plus Anaerobic/F, and Mycosis IC/F bottles. The aim of the study was to enable the authors to gain firsthand experience of the culture potentialities of the three different media, to obtain information regarding the overall and specific recovery of bacteria and yeasts from blood cultures in the hospital, and to reach a decision as to whether and when to utilize anaerobic and fungal bottles. Although very few bloodstream infections (1.8%) were associated with obligate anaerobes, the traditional routine use of anaerobic bottles was confirmed because of their usefulness, not only in the detection of anaerobes, but also in that of gram-positive cocci and fermentative gram-negative bacilli. In this study, Mycosis IC/F bottles detected 77.4% of all the yeast isolates, 87.0% of yeasts belonging to the species Candida albicans, and 45.7% of nonfermentative gram-negative bacilli resistant to chloramphenicol and tobramycin. In order to improve the diagnosis of fungemia in high-risk patients, the additional routine use of fungal bottles was suggested when, as occurred in the intensive-care unit and in the hematology unit of the University Hospital of Palermo, high percentages of bloodstream infections are associated with yeasts, and/or antibiotic-resistant bacteria and/or multiple bacterial isolates capable of inhibiting yeast growth in aerobic bottles. PMID:18923011

Chiarini, Alfredo; Palmeri, Angelo; Amato, Teresa; Immordino, Rita; Distefano, Salvatore; Giammanco, Anna

2008-12-01

364

Identification of linear multivariable systems from a single set of data by identification of observers with assigned real eigenvalues  

NASA Technical Reports Server (NTRS)

This paper presents a formulation for identification of linear multivariable systems from a single set of input-output data. The identification method is formulated with the mathematical framework of learning identification, by extension of the repetition domain concept to include shifting time intervals. This contrasts existing learning approaches that require data from multiple experiments. In this method, the system input-output relationship is expressed in terms of an observer, which is made asymptotically stable by an embedded real eigenvalue assignment procedure. Through this relationship, the Markov parameters of the observer are identified. The Markov parameters of the actual system are recovered from those of the observer, and then used to obtain a state space model of the system by standard realization techniques. The basic mathematical formulation is derived, and numerical examples presented to illustrate the proposed method.

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

1991-01-01

365

A System of Shuttle Vectors and Yeast Host Strains Designed for Efficient Manipulation of DNA in Saccharomyces ceratisiae  

Microsoft Academic Search

A series of yeast shuttle vectors and host strains has been created to allow more efficient manipu- lation of DNA in Saccharomyces cereuisiae. Transplacement vectors were constructed and used to derive yeast strains containing nonreverting his3, trpl, leu2 and ura3 mutations. A set of YCp and YIP vectors (pRS series) was then made based on the backbone of the multipurpose

Robert S. Sikorski; Philip Hieter

366

Unscented Kalman filtering for wave energy converters system identification  

NASA Astrophysics Data System (ADS)

A model for a oscillating flap wave energy converter (WEC) is as a single degree of freedom system with a non-linear term to allow for the drag of the device through the water, known as the Morison term. The focus of this system identification is on estimating the dynamic state of the system and estimating the non-linear parameter from observations of the wave elevation and the vertical displacement of the device. It is assumed that the mass, stiffness and damping of the system, without the Morison term, are known from the physical characteristics of the device. The Kalman Filter (KF) can be used to estimate the states of a linear system, however, it is not directly applicable to a non-linear system. Various adaptations have been proposed for non-linear systems. One of the first was the extended Kalman Filter (EKF) which relied on a linearization about the current state values. However, an alternative approach, known as the unscented Kalman Filter (UKF) has been found to give a better performance and is easier to implement. We apply the UKF to estimate the dynamic states of the system together with the non-linear parameter. The fitted model can be used to predict the performance of the device in different wave environments.

Bakar, Mohd Aftar Abu; Green, David A.; Metcalfe, Andrew V.; Ariff, Noratiqah Mohd

2014-06-01

367

Prevention of Yeast Spoilage in Feed and Food by the Yeast Mycocin HMK  

PubMed Central

The yeast Williopsis mrakii produces a mycocin or yeast killer toxin designated HMK; this toxin exhibits high thermal stability, high pH stability, and a broad spectrum of activity against other yeasts. We describe construction of a synthetic gene for mycocin HMK and heterologous expression of this toxin in Aspergillus niger. Mycocin HMK was fused to a glucoamylase protein carrier, which resulted in secretion of biologically active mycocin into the culture media. A partial purification protocol was developed, and a comparison with native W. mrakii mycocin showed that the heterologously expressed mycocin had similar physiological properties and an almost identical spectrum of biological activity against a number of yeasts isolated from silage and yoghurt. Two food and feed production systems prone to yeast spoilage were used as models to assess the ability of mycocin HMK to act as a biocontrol agent. The onset of aerobic spoilage in mature maize silage was delayed by application of A. niger mycocin HMK on opening because the toxin inhibited growth of the indigenous spoilage yeasts. This helped maintain both higher lactic acid levels and a lower pH. In yoghurt spiked with dairy spoilage yeasts, A. niger mycocin HMK was active at all of the storage temperatures tested at which yeast growth occurred, and there was no resurgence of resistant yeasts. The higher the yeast growth rate, the more effective the killing action of the mycocin. Thus, mycocin HMK has potential applications in controlling both silage spoilage and yoghurt spoilage caused by yeasts. PMID:10698773

Lowes, K. F.; Shearman, C. A.; Payne, J.; MacKenzie, D.; Archer, D. B.; Merry, R. J.; Gasson, M. J.

2000-01-01

368

[Regulation of gene expression in methylotrophic yeasts].  

PubMed

Methylotrophic yeasts are unique eukaryotic organisms, that can metabolize toxic one-carbon substrate, methyl alcohol or methanol. About 50 species of methylotrophic yeasts is known, among them 4 species are the best studied: Pichia methanolica, Hansenula polymorpha, Pichia pastoris i Candida boidinii. These organisms, especially P. pastoris i H. polymorpha appeared to be very perspective overproducers of heterologous proteins and nowadays are used for industrial production of some of them. In this review, we provide information on the organization of the genome, mechanisms of regulation of gene expression and the use of strong promoters of these yeast species to construct the producers of heterologous proteins. In more details, we analyze genetic control of carbon and nitrogen catabolic repression in H. polymorpha and also the identification of metabolites inducing catabolite repression or peroxisome selective autophagy in the medium with ethanol in the Pichia methanolica yeast. PMID:23821948

Grabek-Lejko, Dorota; Sibirny, Vladimir; Sibirny, Andriy

2013-01-01

369

Next Generation Trusted Radiation Identification System (NG-TRIS).  

SciTech Connect

The original Trusted Radiation Identification System (TRIS) was developed from 1999-2001, featuring information barrier technology to collect gamma radiation template measurements useful for arms control regime operations. The first TRIS design relied upon a multichannel analyzer (MCA) that was external to the protected volume of the system enclosure, undesirable from a system security perspective. An internal complex programmable logic device (CPLD) contained data which was not subject to software authentication. Physical authentication of the TRIS instrument case was performed by a sensitive but slow eddy-current inspection method. This paper describes progress to date for the Next Generation TRIS (NG-TRIS), which improves the TRIS design. We have incorporated the MCA internal to the trusted system volume, achieved full authentication of CPLD data, and have devised rapid methods to authenticate the system enclosure and weld seals of the NG-TRIS enclosure. For a complete discussion of the TRIS system and components upon which NG-TRIS is based, the reader is directed to the comprehensive user's manual and system reference of Seager, et al.

Flynn, Adam J.; Amai, Wendy A.; Merkle, Peter Benedict; Anderson, Lawrence Frederick; Strother, Jerry D.; Weber, Thomas M.; Etzkin, Joshua L.

2010-05-01

370

On-Line Fault Diagnosis of Dynamic Systems via Robust Parameter Identification Gerard Blocha  

E-print Network

On-Line Fault Diagnosis of Dynamic Systems via Robust Parameter Identification G´erard Blocha of faults, their isolation and their identification is presented. The systems considered are MISO systems knowledge of the faults which can occur is used. The faults modeled here are outliers, biases or drifts

Paris-Sud XI, Université de

371

Auxiliary model based multi-innovation stochastic gradient identification for multirate multi-input systems  

Microsoft Academic Search

The multirate multi-input systems have different updating periods and sampling periods such that the traditional identification algorithms cannot be used to identify such multirate systems. By using the auxiliary model identification idea, the multi-innovation stochastic gradient algorithm is developed to estimate the parameters of multirate systems. Finally, an illustrative example is given to verify the effectiveness of the proposed algorithm.

Lili Han; Jie Ding; Feng Ding

2010-01-01

372

OPT: Optimal Protocol Tree for Efficient Tag Identification in Dense RFID Systems  

E-print Network

OPT: Optimal Protocol Tree for Efficient Tag Identification in Dense RFID Systems Girish Khandelwal is based on the tree search algorithm for RFID systems. The basic principle of OPT relies on taking is to significantly reduce the total identification time, in order to render the deployment of dense RFID systems

Yener, Aylin

373

Scalable RFID Systems: A Privacy-Preserving Protocol with Constant-Time Identification  

E-print Network

1 Scalable RFID Systems: A Privacy-Preserving Protocol with Constant-Time Identification Basel,awclark,rp3}@uw.edu, jorge.cuellar@siemens.com Abstract--In RFID literature, most "privacy-complexity of private identification in large-scale RFID systems. We utilize the special architecture of RFID systems

Poovendran, Radha

374

From yeast to patient neurons and back again: powerful new discovery platform.  

PubMed

No disease-modifying therapies are available for synucleinopathies, including Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple systems atrophy (MSA). The lack of therapies has been impeded by a paucity of validated drug targets and problematic cell-based model systems. New approaches are therefore needed to identify genes and compounds that directly target the underlying cellular pathologies elicited by the pathological protein, ?-synuclein (?-syn). This small, lipid-binding protein impinges on evolutionarily conserved processes such as vesicle trafficking and mitochondrial function. For decades, the genetically tractable, single-cell eukaryote, budding yeast, has been used to study nearly all aspects of cell biology. More recently, yeast has revealed key insights into the underlying cellular pathologies caused by ?-syn. The robust cellular toxicity caused by ?-syn expression facilitates unbiased high-throughput small-molecule screening. Critically, one must validate the discoveries made in yeast in disease-relevant neuronal models. Here, we describe two recent reports that together establish yeast-to-human discovery platforms for synucleinopathies. In this exemplar, genes and small molecules identified in yeast were validated in patient-derived neurons that present the same cellular phenotypes initially discovered in yeast. On validation, we returned to yeast, where unparalleled genetic approaches facilitated the elucidation of a small molecule's mode of action. This approach enabled the identification and neuronal validation of a previously unknown "druggable" node that interfaces with the underlying, precipitating pathologies caused by ?-syn. Such platforms can provide sorely needed leads and fresh ideas for disease-modifying therapy for these devastating diseases. PMID:25131316

Tardiff, Daniel F; Khurana, Vikram; Chung, Chee Yeun; Lindquist, Susan

2014-09-01

375

Identification of veterinary pathogens by use of commercial identification systems and new trends in antimicrobial susceptibility testing of veterinary pathogens.  

PubMed Central

Veterinary diagnostic microbiology is a unique specialty within microbiology. Although isolation and identification techniques are similar to those used for human pathogens, many veterinary pathogens require unique cultivation or identification procedures. Commercial identification systems provide rapid, accurate identification of human pathogens. However, the accuracy of these systems with veterinary pathogens varies widely depending on the bacterial species and the host animal from which it was isolated. Increased numbers of veterinary strains or species in the data bases of the various systems would improve their accuracy. Current procedures and interpretive criteria used for antimicrobial susceptibility testing of veterinary pathogens are based on guidelines used for human pathogens. The validity of these guidelines for use with veterinary pathogens has not been established. As with fastidious human pathogens, standardized methodologies and quality control isolates are needed for tests of organisms such as Actinobacillus pleuropneumoniae and Haemophilus somnus. Furthermore, interpretive criteria for veterinary antimicrobial agents based on the MIC for veterinary pathogens, the pharmacokinetics of the antimicrobial agent in the host animal, and in vivo efficacy of the antimicrobial agent are needed. This article reviews both the commercial identification systems evaluated with veterinary pathogens and current methods for performing and interpreting antimicrobial susceptibility tests with veterinary pathogens. Recommendations for future improvements in both areas are discussed. PMID:7923054

Watts, J L; Yancey, R J

1994-01-01

376

A Kinase Anchoring Protein (AKAP) Interaction and Dimerization of the RI? and RI? Regulatory Subunits of Protein Kinase A In vivo by the Yeast Two Hybrid System  

Microsoft Academic Search

Protein kinase A (PKA) regulatory (R) subunits dimerize through an N-terminal motif. Such dimerization is necessary for binding to PKA anchoring proteins (AKAPs) and targeting of PKA to its site of action. In the present study, we used the yeast two-hybrid system as an in vivo bio-reporter assay and analyzed the formation of homo- and heterodimeric complexes of RI? and

Cathrine R. Carlson; Anja Ruppelt; Kjetil Taskén

2003-01-01

377

Force-chain identification in quasi-2D granular systems  

NASA Astrophysics Data System (ADS)

Understanding the properties of force-chains is essential in understanding the physical and mechanical properties of granular materials. The key is to identify force-chains. In this study, we describe a systematic method to identify individual force-chains in 2D granular systems under different external load-pure shear or isotropic compression, where bi-disperse photo-elastic particles were used in order to measure vector contact forces between particles. Using this method, we studied the statistics of force-chain size distribution in these two systems: in pure shear, the distribution shows a fat tail that deviates from an exponential distribution function, whereas in isotropic compression, the distribution decays exponentially. In addition, we also investigated the dependence of various force-chain statistics on two main parameters defined in the force-chain identification algorithm.

Zhang, Ling; Wu, Jun-Qi; Zhang, Jie

2013-06-01

378

Modeling, identification, and control of rapid thermal processing systems  

NASA Astrophysics Data System (ADS)

A wafer temperature control system is developed for rapid thermal processing (RTP) semiconductor manufacturing equipment. The control algorithm is based on a physical model describing the heat transfer effects in advanced RTP equipment. A model identification procedure is proposed to estimate the uncertain parameters of the model from a set of experiments. Through singular value analysis, the impact of equipment design on feedback controller development is studied. An internal model control (IMC) design methodology is used to develop a low-order multivariable feedback control algorithm. The feedback controller is coordinated with additional modules including feedforward control and gain scheduling to achieve improved performance and flexibility. The algorithms are applied to three different multizone RTP systems. Temperature controlled ramps are demonstrated from 20 to 900 C at 45 C /s with less than +/- 5 C during the ramp at high temperatures and less than +/- 1 C average nonuniformity during steady state as measured by three radially distributed temperature sensors.

Schaper, Charles D.; Moslehi, Mehrdad M.; Saraswat, Krishna C.; Kailath, Thomas

1994-11-01

379

Identification of linear multivariable systems from a single set of data by identification of observers with assigned real eigenvalues  

NASA Technical Reports Server (NTRS)

A formulation is presented for identification of linear multivariable from a single set of input-output data. The identification method is formulated with the mathematical framework of learning identifications, by extension of the repetition domain concept to include shifting time intervals. This method contrasts with existing learning approaches that require data from multiple experiments. In this method, the system input-output relationship is expressed in terms of an observer, which is made asymptotically stable by an embedded real eigenvalue assignment procedure. Through this relationship, the Markov parameters of the observer are identified. The Markov parameters of the actual system are recovered from those of the observer, and then used to obtain a state space model of the system by standard realization techniques. The basic mathematical formulation is derived, and numerical examples presented to illustrate.

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

1991-01-01

380

Molecular dissection of step 2 catalysis of yeast pre-mRNA splicing investigated in a purified system  

PubMed Central

Step 2 catalysis of pre-mRNA splicing entails the excision of the intron and ligation of the 5? and 3? exons. The tasks of the splicing factors Prp16, Slu7, Prp18, and Prp22 in the formation of the step 2 active site of the spliceosome and in exon ligation, and the timing of their recruitment, remain poorly understood. Using a purified yeast in vitro splicing system, we show that only the DEAH-box ATPase Prp16 is required for formation of a functional step 2 active site and for exon ligation. Efficient docking of the 3? splice site (3?SS) to the active site requires only Slu7/Prp18 but not Prp22. Spliceosome remodeling by Prp16 appears to be subtle as only the step 1 factor Cwc25 is dissociated prior to step 2 catalysis, with its release dependent on docking of the 3?SS to the active site and Prp16 action. We show by fluorescence cross-correlation spectroscopy that Slu7/Prp18 and Prp16 bind early to distinct, low-affinity binding sites on the step-1-activated B* spliceosome, which are subsequently converted into high-affinity sites. Our results shed new light on the factor requirements for step 2 catalysis and the dynamics of step 1 and 2 factors during the catalytic steps of splicing. PMID:23685439

Ohrt, Thomas; Odenwälder, Peter; Dannenberg, Julia; Prior, Mira; Warkocki, Zbigniew; Schmitzová, Jana; Karaduman, Ramazan; Gregor, Ingo; Enderlein, Jörg; Fabrizio, Patrizia; Lührmann, Reinhard

2013-01-01

381

Perfume and flavor identification by odor sensing system using quartz-resonator sensor array and neural-network pattern recognition  

Microsoft Academic Search

A quartz-resonator sensor array and neural-network pattern recognition system previously used for whisky-aroma identification has been applied to perfume and flavor identification. Perfume and flavor identification by this odor sensing system was successfully performed although sensing membranes tuned up for whisky-aroma identification were used. Good separation among the samples was obtained

T. Nakamoto; A. Fukuda; T. Moriizumi

1991-01-01

382

Revised Culture-Based System for Identification of Malassezia Species?  

PubMed Central

Forty-six strains of Malassezia spp. with atypical biochemical features were isolated from 366 fresh clinical isolates from human subjects and dogs. Isolates obtained in this study included 2 (4.7%) lipid-dependent M. pachydermatis isolates; 1 (2.4%) precipitate-producing and 6 (14.6%) non-polyethoxylated castor oil (Cremophor EL)-assimilating M. furfur isolates; and 37 (34.3%) M. slooffiae isolates that were esculin hydrolyzing, 17 (15.7%) that were non-tolerant of growth at 40°C, and 2 (1.9%) that assimilated polyethoxylated castor oil. Although their colony morphologies and sizes were characteristic on CHROMagar Malassezia medium (CHROM), all strains of M. furfur developed large pale pink and wrinkled colonies, and all strains of M. slooffiae developed small (<1 mm) pale pink colonies on CHROM. These atypical strains were distinguishable by the appearance of their colonies grown on CHROM. Three clinically important Malassezia species, M. globosa, M. restricta, and M. furfur, were correctly identified by their biochemical characteristics and colony morphologies. The results presented here indicate that our proposed identification system will be useful as a routine tool for the identification of clinically important Malassezia species in clinical laboratories. PMID:17881545

Kaneko, Takamasa; Makimura, Koichi; Abe, Michiko; Shiota, Ryoko; Nakamura, Yuka; Kano, Rui; Hasegawa, Atsuhiko; Sugita, Takashi; Shibuya, Shuichi; Watanabe, Shinichi; Yamaguchi, Hideyo; Abe, Shigeru; Okamura, Noboru

2007-01-01

383

Using the Yeast Three-Hybrid System to Identify Proteins that Interact with a Phloem-Mobile mRNA  

PubMed Central

Heterografting and RNA transport experiments have demonstrated the long-distance mobility of StBEL5 RNA, its role in controlling tuber formation, and the function of the 503-nt 3? untranslated region (UTR) of the RNA in mediating transport. Because the 3? UTR of StBEL5 is a key element in regulating several aspects of RNA metabolism, a potato leaf cDNA library was screened using the 3? UTR of StBEL5 as bait in the yeast three-hybrid (Y3H) system to identify putative partner RNA-binding proteins (RBPs). From this screen, 116 positive cDNA clones were isolated based on nutrient selection, HIS3 activation, and lacZ induction and were sequenced and classified. Thirty-five proteins that were predicted to function in either RNA- or DNA-binding were selected from this pool. Seven were monitored for their expression profiles and further evaluated for their capacity to bind to the 3? UTR of StBEL5 using ?-galactosidase assays in the Y3H system and RNA gel-shift assays. Among the final selections were two RBPs, a zinc finger protein, and one protein, StLSH10, from a family involved in light signaling. In this study, the Y3H system is presented as a valuable tool to screen and verify interactions between target RNAs and putative RBPs. These results can shed light on the dynamics and composition of plant RNA-protein complexes that function to regulate RNA metabolism. PMID:22969782

Cho, Sung Ki; Kang, Il-Ho; Carr, Tyrell; Hannapel, David J.

2012-01-01

384

p53 Transactivation and the Impact of Mutations, Cofactors and Small Molecules Using a Simplified Yeast-Based Screening System  

PubMed Central

Background The p53 tumor suppressor, which is altered in most cancers, is a sequence-specific transcription factor that is able to modulate the expression of many target genes and influence a variety of cellular pathways. Inactivation of the p53 pathway in cancer frequently occurs through the expression of mutant p53 protein. In tumors that retain wild type p53, the pathway can be altered by upstream modulators, particularly the p53 negative regulators MDM2 and MDM4. Methodology/Principal Findings Given the many factors that might influence p53 function, including expression levels, mutations, cofactor proteins and small molecules, we expanded our previously described yeast-based system to provide the opportunity for efficient investigation of their individual and combined impacts in a miniaturized format. The system integrates i) variable expression of p53 proteins under the finely tunable GAL1,10 promoter, ii) single copy, chromosomally located p53-responsive and control luminescence reporters, iii) enhanced chemical uptake using modified ABC-transporters, iv) small-volume formats for treatment and dual-luciferase assays, and v) opportunities to co-express p53 with other cofactor proteins. This robust system can distinguish different levels of expression of WT and mutant p53 as well as interactions with MDM2 or 53BP1. Conclusions/Significance We found that the small molecules Nutlin and RITA could both relieve the MDM2-dependent inhibition of WT p53 transactivation function, while only RITA could impact p53/53BP1 functional interactions. PRIMA-1 was ineffective in modifying the transactivation capacity of WT p53 and missense p53 mutations. This dual-luciferase assay can, therefore, provide a high-throughput assessment tool for investigating a matrix of factors that can influence the p53 network, including the effectiveness of newly developed small molecules, on WT and tumor-associated p53 mutants as well as interacting proteins. PMID:21674059

Bisio, Alessandra; Lion, Mattia; Jordan, Jennifer; Fronza, Gilberto; Menichini, Paola; Resnick, Michael A.; Inga, Alberto

2011-01-01

385

Assembly of eukaryotic algal chromosomes in yeast  

PubMed Central

Background Synthetic genomic approaches offer unique opportunities to use powerful yeast and Escherichia coli genetic systems to assemble and modify chromosome-sized molecules before returning the modified DNA to the target host. For example, the entire 1 Mb Mycoplasma mycoides chromosome can be stably maintained and manipulated in yeast before being transplanted back into recipient cells. We have previously demonstrated that cloning in yeast of large (>?~?150 kb), high G?+?C (55%) prokaryotic DNA fragments was improved by addition of yeast replication origins every ~100 kb. Conversely, low G?+?C DNA is stable (up to at least 1.8 Mb) without adding supplemental yeast origins. It has not been previously tested whether addition of yeast replication origins similarly improves the yeast-based cloning of large (>150 kb) eukaryotic DNA with moderate G?+?C content. The model diatom Phaeodactylum tricornutum has an average G?+?C content of 48% and a 27.4 Mb genome sequence that has been assembled into chromosome-sized scaffolds making it an ideal test case for assembly and maintenance of eukaryotic chromosomes in yeast. Results We present a modified chromosome assembly technique in which eukaryotic chromosomes as large as ~500 kb can be assembled from cloned ~100 kb fragments. We used this technique to clone fragments spanning P. tricornutum chromosomes 25 and 26 and to assemble these fragments into single, chromosome-sized molecules. We found that addition of yeast replication origins improved the cloning, assembly, and maintenance of the large chromosomes in yeast. Furthermore, purification of the fragments to be assembled by electroelution greatly increased assembly efficiency. Conclusions Entire eukaryotic chromosomes can be successfully cloned, maintained, and manipulated in yeast. These results highlight the improvement in assembly and maintenance afforded by including yeast replication origins in eukaryotic DNA with moderate G?+?C content (48%). They also highlight the increased efficiency of assembly that can be achieved by purifying fragments before assembly. PMID:24325901

2013-01-01

386

Yeast: An Experimental Organism for Modern Biology.  

ERIC Educational Resources Information Center

Discusses the applicability and advantages of using yeasts as popular and ideal model systems for studying and understanding eukaryotic biology at the cellular and molecular levels. Cites experimental tractability and the cooperative tradition of the research community of yeast biologists as reasons for this success. (RT)

Botstein, David; Fink, Gerald R.

1988-01-01

387

Assimilation of protocatechuic acid and p-hydroxybenzoic acid as an aid to laboratory identification of Candida parapsilosis and other medically important yeasts.  

PubMed Central

Test for the ability of yeasts isolated from clinical specimens to utilize protocatechuic acid and p-hydroxybenzoic acid were carried out by using techniques that are commonly employed to test assimilation of carbon sources. A total of 60 isolates of Candida parapsilosis and 5 isolates of Candida humicola readily assimilated these two phenolic acids, whereas other Candida species gave uniformly negative results. Cryptococcus albidus, Cryptococcus terreus, and some isolates of Cryptococcus laurentii also assimilated protocatechuate and p-hydroxybenzoate, whereas Cryptococcus neoformans did not. Results of these tests suggest that assimilation of protocatechuate and p-hydroxybenzoate may be a useful characteristic, when used in conjunction with traditional tests, for identifying C. parapsilosis and C. albidus. PMID:489723

Cooper, B H; Land, G A

1979-01-01

388

Identification of the rapamycin-sensitive phosphorylation sites within the Ser/Thr-rich domain of the yeast Npr1 protein kinase.  

PubMed

The Saccharomyces cerevisae nitrogen permease reactivator Npr1 is a hyperphosphorylated protein that belongs to a fungus-specific family of Ser/Thr protein kinases dedicated to the regulation of plasma membrane transporters. Its activity is regulated by the TOR (target of rapamycin) signalling pathway. Inhibition of the TOR proteins by treating yeast cells with the immunosuppressant drug rapamycin promotes rapid dephosphorylation of Npr1. To identify the rapamycin-sensitive phosphorylation sites in yeast Npr1, glutathione-S-transferase (GST)-tagged Npr1 was isolated from untreated or rapamycin-treated cells, and analyzed by mass spectrometry. Here, we report for the first time 22 phosphorylation sites that are clustered in two regions of the N-terminal serine-rich domain. All phosphorylation sites, except two, were found to be rapamycin-sensitive. Some phosphorylation sites are contained in motifs that closely resemble those in mammalian S6K (serines followed by a tyrosine or a phenylalanine) and 4E-BP1 (serines followed by a proline). Other sites, such as serines followed by Ala, Asn, Gln, His, Ile, Leu, or Val, appear to define new motifs. Thus, TOR controls an unusually broad array of phosphorylation sites in Npr1. In addition to phosphorylation by upstream kinases, Npr1 undergoes autophosphorylation that was mapped to three distinct serines in the N-terminal domain of which Ser257 appears to be the main autophosphorylation site. Site-directed mutagenesis confirmed the mass spectral assignments of the autophosphorylation sites and shows that Ser257 is specifically involved in forming an in vitro substrate-binding site. PMID:18980262

Gander, Stefan; Bonenfant, Debora; Altermatt, Patrick; Martin, Dietmar E; Hauri, Simon; Moes, Suzette; Hall, Michael N; Jenoe, Paul

2008-12-01

389

Glucuronidation does not suppress the estrogenic activity of quercetin in yeast and human breast cancer cell model systems.  

PubMed

Several plant-derived molecules, referred to as phytoestrogens, are thought to mimic the actions of endogenous estrogens. Among these, quercetin, one of the most widespread flavonoids in the plant kingdom, has been reported as estrogenic in some occasions. However, quercetin occurs in substantial amounts as glycosides such as quercetin-3-O-glucoside (isoquercitrin) and quercetin-3-O-rutinoside (rutin) in dietary sources. It is now well established that quercetin undergoes substantial phase II metabolism after ingestion by humans, with plasma metabolites after a normal dietary intake rarely exceeding nmol/L concentrations. Therefore, attributing phytoestrogenic activity to flavonoids without taking into account the fact that it is their phase II metabolites that enter the circulatory system, will almost certainly lead to misleading conclusions. With the aim of clarifying the above issue, the goal of the present study was to determine if plant-associated quercetin glycosides and human phase II quercetin metabolites, actually found in human biological fluids after intake of quercetin containing foods, are capable of interacting with the estrogen receptors (ER). To this end, we used a yeast-based two-hybrid system and an estrogen response element-luciferase reporter assay in an ER-positive human cell line (MCF-7) to probe the ER interaction capacities of quercetin and its derivatives. Our results show that quercetin-3-O-glucuronide, one of the main human phase II metabolites produced after intake of dietary quercetin, displays ER?- and ER?-dependent estrogenic activity, the functional consequences of which might be related to the protective activity of diets rich in quercetin glycosides. PMID:24657077

Ruotolo, Roberta; Calani, Luca; Brighenti, Furio; Crozier, Alan; Ottonello, Simone; Del Rio, Daniele

2014-10-01

390

Comparison of Automated and Nonautomated Systems for Identification of Burkholderia pseudomallei  

Microsoft Academic Search

identification of uncommonly encountered organisms such as B. pseudomallei critically important. This study compares the manual API 20NE and 20E identification systems with the automated Vitek 1 and 2 systems. A total of 103 B. pseudomallei isolates were tested and correctly identified in 98%, 99%, 99%, and 19% of cases, respectively. The failure of the Vitek 2 to correctly identify

Peter Lowe; Catherine Engler; Robert Norton

2002-01-01

391

Multivariable identification and controller design of an integrated flight control system  

Microsoft Academic Search

This paper investigates the multivariable identification and controller design for the longitudinal channel of a Boeing 747 transport. The transfer function matrix of the system is identified using the prediction error (PE) identification method with multivariable ARX model. An ellipsoidal parametric uncertainty set is constructed from the covariance matrix of the identified parameters. It contains the parameters of actual system

D. T. W. Yau; E. H. K. Fung; Y. K. Wong; H. H. T. Liu

2007-01-01

392

A Hierarchical Genetic Algorithm for System Identification and Curve Fitting with a Supercomputer Implementation  

E-print Network

A Hierarchical Genetic Algorithm for System Identification and Curve Fitting with a Supercomputer;1 A Hierarchical Genetic Algorithm for System Identification and Curve Fitting with a Supercomputer Implementation implemented on a Cray supercomputer. The GA code was vectorized for parallel processing of 128 array elements

Smith, Alice E.

393

Genetic algorithm based system identification and PID tuning for optimum adaptive control  

Microsoft Academic Search

In this paper the genetic algorithm optimization technique, is successfully applied in system identification and PID tuning for optimum adaptive control. In the proposed approach, two independent genetic algorithms were used sequentially. The first one is used for system model identification and the second one for PID controller tuning. Once the plant model was identified the parameters found are used

Dionisio S. Pereira; João O. P. Pinto

2005-01-01

394

Disadvantaged-Handicapped Identification and Supportive Service Delivery System, Southwestern College, Spring 1974.  

ERIC Educational Resources Information Center

A system of identification and notification designed and implemented at Southwestern College to speed supportive services to the disadvantaged and handicapped students in vocational programs is discussed. The system is comprised of the following procedures: (1) Self-identification (Student Services Information Form filled out by each student at…

MacDougall, Allan

395

An artificial neural network-based expert system for network topological error identification  

Microsoft Academic Search

An artificial neural network (ANN)-based expert system for network topological error identification is proposed in this paper. A concept of artificial neural network management system (ANNMS) is also introduced in the paper. Network topological error identification is not only a hard problem but also a key problem in real time state estimation. How to acquire and use human expert's knowledge

Tian Tian; Minzhe Zhu; Boming Zhang

1995-01-01

396

Comparison of Striking Distance Models Architectures using a System Identification Approach  

Microsoft Academic Search

This paper introduces the use of a system identification approach to the lightning striking distance problem. After a brief introduction to system identification and nonlinear parameter estimation methodology, a comparison of some striking distance models architectures in the literature is presented. The model architectures were compared based on how well they approximated the data collected by Eriksson from 2D and

B. Rodriguez-Medina; S. Grzybowski

2006-01-01

397

COMPARISON OF SYSTEM IDENTIFICATION TECHNIQUES FOR A SPHERICAL AIR-BEARING  

E-print Network

AAS 03-611 COMPARISON OF SYSTEM IDENTIFICATION TECHNIQUES FOR A SPHERICAL AIR-BEARING SPACECRAFT independent spher- ical air-bearing platforms for formation flying attitude control simula- tion is impractical. We document the process to determine an appropriate system identification technique for an air-bearing

Hall, Christopher D.

398

Automatic feature-queried bird identification system based on entropy and fuzzy similarity  

E-print Network

Automatic feature-queried bird identification system based on entropy and fuzzy similarity Xingqi not have any intelligence and cannot tolerate noises either. A bird identification system, BirdID is proposed and implemented. To identify birds, BirdID imitates bird experts to automatically direct

Yao, Xin

399

Decoupling Identification for Serial Two-Link Two-Inertia System  

NASA Astrophysics Data System (ADS)

The purpose of our study is to develop a precise model by applying the technique of system identification for the model-based control of a nonlinear robot arm, under taking joint-elasticity into consideration. We previously proposed a systematic identification method, called “decoupling identification,” for a “SCARA-type” planar two-link robot arm with elastic joints caused by the Harmonic-drive® reduction gears. The proposed method serves as an extension of the conventional rigid-joint-model-based identification. The robot arm is treated as a serial two-link two-inertia system with nonlinearity. The decoupling identification method using link-accelerometer signals enables the serial two-link two-inertia system to be divided into two linear one-link two-inertia systems. The MATLAB®'s commands for state-space model estimation are utilized in the proposed method. Physical parameters such as motor inertias, link inertias, joint-friction coefficients, and joint-spring coefficients are estimated through the identified one-link two-inertia systems using a gray-box approach. This paper describes accuracy evaluations using the two-link arm for the decoupling identification method under introducing closed-loop-controlled elements and varying amplitude-setup of identification-input. Experimental results show that the identification method also works with closed-loop-controlled elements. Therefore, the identification method is applicable to a “PUMA-type” vertical robot arm under gravity.

Oaki, Junji; Adachi, Shuichi

400

Yeast Education Network  

NSDL National Science Digital Library

The Yeast Education Network provides a variety of resources to facilitate use of the budding yeast Saccharomyces cerevisiae in undergraduate science curricula. Laboratory, classroom, and computer-based activities can be used with college and advanced high school students.

401

Computational yeast systems biology: a case study for the MAP kinase cascade.  

PubMed

Cellular networks and processes can be mathematically described and analyzed in various ways. Here, the case example of a MAP kinase (MAPK) cascade is used to detail steps in the formulation of a system of ordinary differential equations governing the temporal behavior of a signal transduction pathway after stimulation. Different analysis methods for the model are explained and demonstrated, such as stoichiometric analysis, sensitivity analysis, or studying the effect of deletions and protein overexpression. Finally, a perspective on standards concerning modeling in systems biology is given. PMID:21863496

Klipp, Edda

2011-01-01

402

The Impact of Early Design Phase Risk Identification Biases on Space System Project Performance  

NASA Technical Reports Server (NTRS)

Risk identification during the early design phases of complex systems is commonly implemented but often fails to result in the identification of events and circumstances that truly challenge project performance. Inefficiencies in cost and schedule estimation are usually held accountable for cost and schedule overruns, but the true root cause is often the realization of programmatic risks. A deeper understanding of frequent risk identification trends and biases pervasive during space system design and development is needed, for it would lead to improved execution of existing identification processes and methods.

Reeves, John D., Jr.; Eveleigh, Tim; Holzer, Thomas; Sarkani, Shahryar

2012-01-01

403

Using yeast two hybrid system to study protein-protein interactions  

Technology Transfer Automated Retrieval System (TEKTRAN)

Protein-protein interactions are essential for many complex signaling systems that are involved in all levels of cellular processes. Defining, characterizing, and understanding the nature of these protein-protein interactions is a challenging task. Many advanced methodologies, such as tandem affinit...

404

Network topological reordering revealing systemic patterns in yeast protein interaction networks  

Microsoft Academic Search

Identifying candidate genes\\/proteins involved in human disease specific molecular pathways or networks has been a primary focus of biomedical research. Although node ranking and graph clustering methods can help identify localized topological properties in a network, it remains unclear how the results should be interpreted in biological functional context in systems-level. In complex biomolecular interaction networks, biomolecular entities may not

Xiaogang Wu; Ragini Pandey; Jake Yue Chen

2009-01-01

405

Heterologous expression systems for P-glycoprotein: E. coli , yeast, and baculovirus  

Microsoft Academic Search

Chemotherapy, though it remains one of the front-line weapons used to treat human cancer, is often ineffective due to drug resistance mechanisms manifest in tumor cells. One common pattern of drug resistance, characterized by simultaneous resistance to multiple amphipathic, but otherwise structurally dissimilar anticancer drugs, is termed multidrug resistance. Multidrug resistance in various model systems, covering the phylogenetic range from

Gregory L. Evans; Baofu Ni; Christine A. Hrycyna; David Chen; Suresh V. Ambudkar; Ira Pastan; Ursula A. Germann; Michael M. Gottesman

1995-01-01

406

Effect of Dietary Supplementation of Brewer's Yeast and GroBiotic®-A on Growth, Immune Responses, and Low-Salinity Tolerance of Pacific White Shrimp Litopenaeus vannamei Cultured in Recirculating Systems  

Microsoft Academic Search

Two separate trials were conducted in clean recirculating systems at salinities of 32.9 (optimal) and 2 ppt (low-salinity challenge) to evaluate brewer's yeast and GroBiotic®-A, a commercial prebiotic, as dietary supplements for growth and health management of Pacific white shrimp Litopenaeus vannamei. The growth-promoting influences of brewer's yeast or GroBiotic®-A previously observed with fish were not demonstrated in these trials

Peng Li; Xiaoxue Wang; Shivananda Murthy; Delbert M. Gatlin III; Frank L. Castille; Addison L. Lawrence

2009-01-01

407

Advanced terahertz imaging system performance model for concealed weapon identification  

NASA Astrophysics Data System (ADS)

The U.S. Army Night Vision and Electronic Sensors Directorate (NVESD) and the U.S. Army Research Laboratory (ARL) have developed a terahertz-band imaging system performance model for detection and identification of concealed weaponry. The details of this MATLAB-based model which accounts for the effects of all critical sensor and display components, and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination, were reported on at the 2005 SPIE Europe Security and Defence Symposium. The focus of this paper is to report on recent advances to the base model which have been designed to more realistically account for the dramatic impact that target and background orientation can have on target observability as related to specular and Lambertian reflections captured by an active-illumination-based imaging system. The advanced terahertz-band imaging system performance model now also accounts for target and background thermal emission, and has been recast into a user-friendly, Windows-executable tool. This advanced THz model has been developed in support of the Defense Advanced Research Project Agency's (DARPA) Terahertz Imaging Focal-Plane Technology (TIFT) program. This paper will describe the advanced THz model and its new radiometric sub-model in detail, and provide modeling and experimental results on target observability as a function of target and background orientation.

Murrill, Steven R.; Redman, Brian; Espinola, Richard L.; Franck, Charmaine C.; Petkie, Douglas T.; De Lucia, Frank C.; Jacobs, Eddie L.; Griffin, Steven T.; Halford, Carl E.; Reynolds, Joe

2007-04-01

408

Usefulness of the MicroSeq 500 16S rDNA bacterial identification system for identification of anaerobic Gram positive bacilli isolated from blood cultures  

PubMed Central

Using full 16S ribosomal RNA (rRNA) gene sequencing as the gold standard, 20 non?duplicating anaerobic Gram positive bacilli isolated from blood cultures were analysed by the MicroSeq 500 16S rDNA bacterial identification system. The MicroSeq system successfully identified 13 of the 20 isolates. Four and three isolates were misidentified at the genus and species level, respectively. Although the MicroSeq 500 16S rDNA bacterial identification system is better than three commercially available identification systems also evaluated, its database needs to be expanded for accurate identification of anaerobic Gram positive bacilli. PMID:16443743

Lau, S K P; Ng, K H L; Woo, P C Y; Yip, K?t; Fung, A M Y; Woo, G K S; Chan, K?m; Que, T?l

2006-01-01

409

Rice Mitogen-Activated Protein Kinase Interactome Analysis Using the Yeast Two-Hybrid System1[C][W  

PubMed Central

Mitogen-activated protein kinase (MAPK) cascades support the flow of extracellular signals to intracellular target molecules and ultimately drive a diverse array of physiological functions in cells, tissues, and organisms by interacting with other proteins. Yet, our knowledge of the global physical MAPK interactome in plants remains largely fragmented. Here, we utilized the yeast two-hybrid system and coimmunoprecipitation, pull-down, bimolecular fluorescence complementation, subcellular localization, and kinase assay experiments in the model crop rice (Oryza sativa) to systematically map what is to our knowledge the first plant MAPK-interacting proteins. We identified 80 nonredundant interacting protein pairs (74 nonredundant interactors) for rice MAPKs and elucidated the novel proteome-wide network of MAPK interactors. The established interactome contains four membrane-associated proteins, seven MAP2Ks (for MAPK kinase), four MAPKs, and 59 putative substrates, including 18 transcription factors. Several interactors were also validated by experimental approaches (in vivo and in vitro) and literature survey. Our results highlight the importance of OsMPK1, an ortholog of tobacco (Nicotiana benthamiana) salicyclic acid-induced protein kinase and Arabidopsis (Arabidopsis thaliana) AtMPK6, among the rice MAPKs, as it alone interacts with 41 unique proteins (51.2% of the mapped MAPK interaction network). Additionally, Gene Ontology classification of interacting proteins into 34 functional categories suggested MAPK participation in diverse physiological functions. Together, the results obtained essentially enhance our knowledge of the MAPK-interacting protein network and provide a valuable research resource for developing a nearly complete map of the rice MAPK interactome. PMID:22786887

Singh, Raksha; Lee, Mi-Ok; Lee, Jae-Eun; Choi, Jihyun; Park, Ji Hun; Kim, Eun Hye; Yoo, Ran Hee; Cho, Jung-Il; Jeon, Jong-Seong; Rakwal, Randeep; Agrawal, Ganesh Kumar; Moon, Jae Sun; Jwa, Nam-Soo

2012-01-01

410

The expression of a mountain cedar allergen comparing plant-viral apoplastic and yeast expression systems  

Microsoft Academic Search

Jun a 3, a major allergenic protein in mountain cedar pollen, causes seasonal allergic rhinitis in hypersensitive individuals.\\u000a Recombinant Jun a 3 was expressed in Nicotiana benthamiana interstitial fluid (300 ?g\\/g leaf material) and Pichia pastoris (100 ?g\\/ml media). Polyclonal anti-Jun a 3 and IgE antibodies from the sera of allergic patients both reacted with the recombinant\\u000a protein. Of the two systems,

Marcie H. Moehnke; Terumi Midoro-Horiuti; Randall M. Goldblum; Christopher M. Kearney

2008-01-01

411

Fep1 represses expression of the fission yeast Schizosaccharomyces pombe siderophore-iron transport system  

Microsoft Academic Search

When iron repletes, Schizosaccharomyces pombe cells repress transcription of genes encoding components involved in the reductive iron transport system. Fep1 mediates this transcriptional control by interacting specifically with GATA-type cis-acting elements. To further investigate the role that Fep1 plays in iron homeostasis, we searched for addi- tional Fep1-regulated genes. We found that str1+ is subject to negative transcriptional regulation, which

Benoit Pelletier; Jude Beaudoin; Caroline C. Philpott; Simon Labbe ´

2003-01-01

412

Segmental Dynamics of Forward Fall Arrests: System Identification Approach  

PubMed Central

Background Fall-related injuries are multifaceted problems, necessitating thorough biodynamic simulation to identify critical biomechanical factors. Methods A 2-degree-of-freedom discrete impact model was constructed through system identification and validation processes using the experimental data to understand dynamic interactions of various biomechanical parameters in bimanual forward fall arrests. Findings The bimodal reaction force response from the identified models had small identification errors for the first and second force peaks less than 3.5% and high coherence between the measured and identified model responses (R2=0.95). Model validation with separate experimental data also demonstrated excellent validation accuracy and coherence, less than 7% errors and R2=0.87, respectively. The first force peak was usually greater than the second force peak and strongly correlated with the impact velocity of the upper extremity, while the second force peak was associated with the impact velocity of the body. The impact velocity of the upper extremity relative to the body could be a major risk factor to fall-related injuries as observed from model simulations that a 75% faster arm movement relative to the falling speed of the body alone could double the first force peak from soft landing, thereby readily exceeding the fracture strength of the distal radius. Interpretation Considering that the time-critical nature of falling often calls for a fast arm movement, the use of the upper extremity in forward fall arrests is not biomechanically justified unless sufficient reaction time and coordinated protective motion of the upper extremity are available. PMID:19250726

Kim, Kyu-Jung; Ashton-Miller, James A.

2009-01-01

413

Identification of region-specific yeast artificial chromosomes using pools of Alu element-mediated polymerase chain reaction probes labeled via linear amplification  

SciTech Connect

The ability to identify large numbers of yeast artificial chromosomes (YACS) specific to any given genomic region rapidly and efficiently enhances both the construction of clone maps and the isolation of region-specific landmarks (e.g., polymorphic markers). The authors describe a method of preparing region-specific single-stranded hybridization probes from Alu element-mediated polymerase chain reaction (Alu-PCR) products of somatic cell hybrids for YAC library screening. Pools of up to 50 cloned Alu-PCR products from an irradiation-reduced hybrid containing 22q11.2-q13.1 were labeled to high specific activity by linear amplification using a single vector primer. The resulting single-stranded probes were extensively competed to remove repetitive sequences, while retaining the full complexity of the probe. Extensive coverage of the region by YACs using multiple probe pools was demonstrated as many YACs were detected more than once. In situ analysis using chosen YACs confirmed that the clones were specific for the region. Thus, this pooled probe approach constitutes a rapid method to identify large numbers of YACs relevant to a large chromosomal region. 29 refs., 4 figs.

Cole, C.G.; Bobrow, M.; Bentley, D.R.; Dunham, I. (United Medical and Dental Schools of Guy's and St. Thomas Hospitals, London Bridge, London, England (United Kingdom)); Patel, K.; Shipley, J.; Sheer, D. (Imperial Cancer Research Fund, London (United Kingdom))

1992-12-01

414

MOR Is Not Enough: Identification of Novel mu-Opioid Receptor Interacting Proteins Using Traditional and Modified Membrane Yeast Two-Hybrid Screens  

PubMed Central

The mu-opioid receptor (MOR) is the G-protein coupled receptor primarily responsible for mediating the analgesic and rewarding properties of opioid agonist drugs such as morphine, fentanyl, and heroin. We have utilized a combination of traditional and modified membrane yeast two-hybrid screening methods to identify a cohort of novel MOR interacting proteins (MORIPs). The interaction between the MOR and a subset of MORIPs was validated in pulldown, co-immunoprecipitation, and co-localization studies using HEK293 cells stably expressing the MOR as well as rodent brain. Additionally, a subset of MORIPs was found capable of interaction with the delta and kappa opioid receptors, suggesting that they may represent general opioid receptor interacting proteins (ORIPS). Expression of several MORIPs was altered in specific mouse brain regions after chronic treatment with morphine, suggesting that these proteins may play a role in response to opioid agonist drugs. Based on the known function of these newly identified MORIPs, the interactions forming the MOR signalplex are hypothesized to be important for MOR signaling and intracellular trafficking. Understanding the molecular complexity of MOR/MORIP interactions provides a conceptual framework for defining the cellular mechanisms of MOR signaling in brain and may be critical for determining the physiological basis of opioid tolerance and addiction. PMID:23840749

Jin, Jay; Wong, Victoria; Kittanakom, Saranya; Ferraro, Thomas N.; Stagljar, Igor; Levenson, Robert

2013-01-01

415

Identification of the major selenium compound, Se-Methionine, in three yeast (Saccharomyces cerevisiae) dietary supplements by on-line narrowbore liquid chromatography-electrospray tandem mass spectrometry.  

PubMed

On-line monitoring of six Se-compounds was accomplished by using an XTerra MS C18 column coupled to electrospray tandem mass spectrometry (ES-MS-MS). In view of the nature of the compounds, the positively charged ion pairing agent tetraethylammoniumchloride (TEACl) was added to the mobile phase. The HPLC-ES-MS-MS method was optimized with six commercially available Se-compounds. Substitution of the analytical column by the narrowbore type significantly enhanced the sensitivity of the method. We were able to detect the m/z of these six molecules on-line. Furthermore, all product ions could be monitored. The method was applied to three different yeast-based supplements. They were submitted to proteolytic digestion and screened for their Se-content by HPLC-HG-AFS (hydride generation-atomic fluorescence spectrometry). By application of on-line narrowbore HPLC-electrospray tandem mass spectrometry, the main compound present in these three supplements, Se-Methionine, could be measured on its m/z and its product ions. The method can be further extended for on-line measurement of different Se-species in complex matrices PMID:15865193

Dumont, Emmie; De Cremer, Koen; Van Hulle, Marijn; Chéry, Cyrille C; Vanhaecke, Frank; Cornelis, Rita

2005-04-15

416

Robustness and evolvability in natural chemical resistance: identification of novel systems properties, biochemical mechanisms and regulatory  

E-print Network

Robustness and evolvability in natural chemical resistance: identification of novel systems correlate with transcriptional noise), association with TFIID or SAGA, and propensity to function, systems robustness and evolvability are simultaneously active as general forces in tolerating

417

Compact Modeling of Nonlinear Analog Circuits using System Identification via Semi-Definite Programming and Robustness Certification  

E-print Network

This paper presents a system identification technique for generating stable compact models of typical analog circuit blocks in radio frequency systems. The identification procedure is based on minimizing the model error ...

Bond, Bradley N.

418

On the identification of continuous vibrating systems modelled by hyperbolic partial differential equations  

NASA Technical Reports Server (NTRS)

This paper deals with the identification of spatially varying parameters in systems of finite spatial extent which can be described by second order hyperbolic differential equations. Two questions have been addressed. The first deals with 'partial identification' and inquires into the possibility of retrieving all the eigenvalues of the system from response data obtained at one location x-asterisk epsilon (0, 1). The second deals with the identification of the distributed coefficients rho(x), a(x) and b(x). Sufficient conditions for unique identification of all the eigenvalues of the system are obtained, and conditions under which the coefficients can be uniquely identified using suitable response data obtained at one point in the spatial domain are determined. Application of the results and their usefulness is demonstrated in the identification of the properties of tall building structural systems subjected to dynamic load environments.

Udwadia, F. E.; Garba, J. A.

1983-01-01

419

System identification and trajectory optimization for guided store separation  

NASA Astrophysics Data System (ADS)

Combat aircraft utilize expendable stores such as missiles, bombs, flares, and external tanks to execute their missions. Safe and acceptable separation of these stores from the parent aircraft is essential for meeting the mission objectives. In many cases, the employed missile or bomb includes an onboard guidance and control system to enable precise engagement of the selected target. Due to potential interference, the guidance and control system is usually not activated until the store is sufficiently far away from the aircraft. This delay may result in large perturbations from the desired flight attitude caused by separation transients, significantly reducing the effectiveness of the store and jeopardizing mission objectives. The purpose of this research is to investigate the use of a transitional control system to guide the store during separation. The transitional control system, or "store separation autopilot", explicitly accounts for the nonuniform flow field through characterization of the spatially variant aerodynamics of the store during separation. This approach can be used to mitigate aircraft-store interference and leverage aerodynamic interaction to improve separation characteristics. This investigation proceeds in three phases. First, system identification is used to determine a parametric model for the spatially variant aerodynamics. Second, the store separation problem is recast into a trajectory optimization problem, and optimal control theory is used to establish a framework for designing a suitable reference trajectory with explicit dependence on the spatially variant aerodynamics. Third, neighboring optimal control is used to construct a linear-optimal feedback controller for correcting deviations from the nominal reference trajectory due varying initial conditions, modeling errors, and flowfield perturbations. An extended case study based on actual wind tunnel and flight test measurements is used throughout to illustrate the effectiveness of the approach and to highlight the anticipated benefits of guided store separation.

Carter, Ryan E.

420

Development of growth selection systems to isolate a-type or ?-type of yeast cells spontaneously emerging from MATa/? diploids  

PubMed Central

Background Manufacture of MATa and MAT? yeast cells is required for crossbreeding, a procedure that permits hybridization and the generation of new heterozygous strains. Crossbreeding also can be performed with a- and ?-type of cells, which have the same mating abilities as MATa and MAT? haploid cells, respectively. Results In this work, we describe a method to generate a- and ?-type of cells via the naturally-occurring chromosomal aberration in parental MATa/? diploids. We successfully designed suitable genetic circuits for expression of the URA3 selection marker gene to permit isolation of a- and ?-type of cells, respectively, on solid medium lacking uracil. Furthermore we succeeded in generation of zygotes by mating of both the manufactured a- and ?-type of yeast cells. Conclusions This process does not require exposure to mutagens such as UV irradiation, thereby avoiding the accumulation of undesirable mutations that would detract from the valuable traits that are under study. All the genetic modifications in the current study were introduced into yeast cells using plasmids, meaning that these traits can be removed without altering the genome sequence. This approach provides a reliable and versatile tool for scientific research and industrial yeast crossbreeding. PMID:24261936

2013-01-01

421

Continuous immobilized yeast reactor system for complete beer fermentation using spent grains and corncobs as carrier materials  

Microsoft Academic Search

Despite extensive research carried out in the last few decades, continuous beer fermentation has not yet managed to outperform the traditional batch technology. An industrial breakthrough in favour of continuous brewing using immobilized yeast could be expected only on achievement of the following process characteristics: simple design, low investment costs, flexible operation, effective process control and good product quality. The

Tomáš Brányik; Daniel P. Silva; António A. Vicente; Radek Lehnert; João B. Almeida e Silva; Pavel Dostálek; José A. Teixeira

2006-01-01

422

Wavelet features for failure detection and identification in vibration systems  

NASA Astrophysics Data System (ADS)

The result of this effort is an extremely flexible and powerful methodology for failure detection and identification (FDI) in vibrating systems. The essential elements of this methodology are: (1) an off-line set of techniques to identify high-energy, statistically significant features in the continuous wavelet transform (CWT); (2) a CWT-based preprocessor to extract the most useful features from the sensor signal; and (3) simple artificial neural networks (incorporating a mechanism to defer any decision if the current feature sample is determined to be ambiguous) for the subsequent classification task. For the helicopter intermediate gearbox test-stand data and centrifugal and fire pump shipboard (mild operating condition) data used, the algorithms designed using this method achieved perfect detection performance (1.000 probability of detection, and 0.000 false alarm probability), with a probability less than 0.04 that a decision would be deferred-based on only 500 milliseconds of data from each sample case. While this effort shows the exceptional promise of our wavelet-based method for FDI in vibrating systems, more demanding applications, which also have other sources of high-energy vibration, raise additional technical issues that could provide the focus for a Phase 2 effort.

Deckert, James C.; Rhenals, Alonso E.; Tenney, Robert R.; Willsky, Alan S.

1992-12-01

423

Multiinnovation least-squares identification for system modeling.  

PubMed

A multiinnovation least-squares (MILS) identification algorithm is presented for linear regression models with unknown parameter vectors by expanding the innovation length in the traditional recursive least-squares (RLS) algorithm from the viewpoint of innovation modification. Because the proposed MILS algorithm uses p innovations (not only the current innovation but also past innovations) at each iteration (with the integer p > 1 being an innovation length), the accuracy of parameter estimation is improved, compared with that of the RLS algorithm. Performance analysis and simulation results show that the proposed MILS algorithm is consistently convergent. Moreover, a new interval-varying MILS algorithm is proposed, for which the key is to dynamically change the interval in order to deal with cases where some measurement data are missing. Furthermore, an auxiliary-model-based MILS algorithm is derived for pseudolinear models corresponding to output error moving average systems with colored noises. Finally, the proposed algorithms are applied to model an experimental water level control system. PMID:19884093

Ding, Feng; Liu, Peter X; Liu, Guangjun

2010-06-01

424

Reduced-size kernel models for nonlinear hybrid system identification.  

PubMed

This brief paper focuses on the identification of nonlinear hybrid dynamical systems, i.e., systems switching between multiple nonlinear dynamical behaviors. Thus the aim is to learn an ensemble of submodels from a single set of input-output data in a regression setting with no prior knowledge on the grouping of the data points into similar behaviors. To be able to approximate arbitrary nonlinearities, kernel submodels are considered. However, in order to maintain efficiency when applying the method to large data sets, a preprocessing step is required in order to fix the submodel sizes and limit the number of optimization variables. This brief paper proposes four approaches, respectively inspired by the fixed-size least-squares support vector machines, the feature vector selection method, the kernel principal component regression and a modification of the latter, in order to deal with this issue and build sparse kernel submodels. These are compared in numerical experiments, which show that the proposed approach achieves the simultaneous classification of data points and approximation of the nonlinear behaviors in an efficient and accurate manner. PMID:22042154

Le, Van Luong; Bloch, Grard; Lauer, Fabien

2011-12-01

425

A global non-coding RNA system modulates fission yeast protein levels in response to stress  

PubMed Central

Non-coding RNAs (ncRNAs) are frequent and prevalent across the taxa. Although individual non-coding loci have been assigned a function, most are uncharacterized. Their global biological significance is unproven and remains controversial. Here we investigate the role played by ncRNAs in the stress response of Schizosaccharomyces pombe. We integrate global proteomics and RNA sequencing data to identify a systematic programme in which elevated antisense RNA arising both from ncRNAs and from 3?-overlapping convergent gene pairs is directly associated with substantial reductions in protein levels throughout the genome. We describe an extensive array of ncRNAs with trans associations that have the potential to influence multiple pathways. Deletion of one such locus reduces levels of atf1, a transcription factor downstream of the stress-activated mitogen-activated protein kinase (MAPK) pathway, and alters sensitivity to oxidative stress. These non-coding transcripts therefore regulate specific stress responses, adding unanticipated information-processing capacity to the MAPK signalling system. PMID:24853205

Leong, Hui Sun; Dawson, Keren; Wirth, Chris; Li, Yaoyong; Connolly, Yvonne; Smith, Duncan L.; Wilkinson, Caroline R. M.; Miller, Crispin J.

2014-01-01

426

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast  

PubMed Central

The diauxic shift in Saccharomyces cerevisiae is an ideal model to study how eukaryotic cells readjust their metabolism from glycolytic to gluconeogenic operation. In this work, we generated time-resolved physiological data, quantitative metabolome (69 intracellular metabolites) and proteome (72 enzymes) profiles. We found that the diauxic shift is accomplished by three key events that are temporally organized: (i) a reduction in the glycolytic flux and the production of storage compounds before glucose depletion, mediated by downregulation of phosphofructokinase and pyruvate kinase reactions; (ii) upon glucose exhaustion, the reversion of carbon flow through glycolysis and onset of the glyoxylate cycle operation triggered by an increased expression of the enzymes that catalyze the malate synthase and cytosolic citrate synthase reactions; and (iii) in the later stages of the adaptation, the shutting down of the pentose phosphate pathway with a change in NADPH regeneration. Moreover, we identified the transcription factors associated with the observed changes in protein abundances. Taken together, our results represent an important contribution toward a systems-level understanding of how this adaptation is realized. PMID:23549479

Zampar, Guillermo G; Kümmel, Anne; Ewald, Jennifer; Jol, Stefan; Niebel, Bastian; Picotti, Paola; Aebersold, Ruedi; Sauer, Uwe; Zamboni, Nicola; Heinemann, Matthias

2013-01-01

427

Optical Verification Laboratory Demonstration System for High Security Identification Cards  

NASA Technical Reports Server (NTRS)

Document fraud including unauthorized duplication of identification cards and credit cards is a serious problem facing the government, banks, businesses, and consumers. In addition, counterfeit products such as computer chips, and compact discs, are arriving on our shores in great numbers. With the rapid advances in computers, CCD technology, image processing hardware and software, printers, scanners, and copiers, it is becoming increasingly easy to reproduce pictures, logos, symbols, paper currency, or patterns. These problems have stimulated an interest in research, development and publications in security technology. Some ID cards, credit cards and passports currently use holograms as a security measure to thwart copying. The holograms are inspected by the human eye. In theory, the hologram cannot be reproduced by an unauthorized person using commercially-available optical components; in practice, however, technology has advanced to the point where the holographic image can be acquired from a credit card-photographed or captured with by a CCD camera-and a new hologram synthesized using commercially-available optical components or hologram-producing equipment. Therefore, a pattern that can be read by a conventional light source and a CCD camera can be reproduced. An optical security and anti-copying device that provides significant security improvements over existing security technology was demonstrated. The system can be applied for security verification of credit cards, passports, and other IDs so that they cannot easily be reproduced. We have used a new scheme of complex phase/amplitude patterns that cannot be seen and cannot be copied by an intensity-sensitive detector such as a CCD camera. A random phase mask is bonded to a primary identification pattern which could also be phase encoded. The pattern could be a fingerprint, a picture of a face, or a signature. The proposed optical processing device is designed to identify both the random phase mask and the primary pattern [1-3]. We have demonstrated experimentally an optical processor for security verification of objects, products, and persons. This demonstration is very important to encourage industries to consider the proposed system for research and development.

Javidi, Bahram

1997-01-01

428

In-vitro bacterial identification using fluorescence spectroscopy with an optical fiber system  

NASA Astrophysics Data System (ADS)

Acute otitis media (AOM) remains a source of significant morbidity in children. With the emergence of antibiotic resistant strains of bacteria, tympanocentesis has become an important method of bacterial identification in the setting of treatment failures. Previous studies described a prototype system for the non-invasive fluorescence identification of bacteria in vitro. We demonstrate the addition of an optical fiber to allow for the identification of a specimen distant to the spectrofluorometer. Emission spectra from three bacteria, Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus were successfully obtained in vitro. This represents a necessary step prior to the study of in vivo identification of bacteria in AOM using fluorescence spectroscopy.

Spector, Brian C.; Werkhaven, Jay A.; Smith, Dana; Reinisch, Lou

2000-05-01

429

Bootstrapping a Spoken Language Identification System Using Unsupervised Integrated Sensing and  

E-print Network

identification task on the CallFriend1 and 2003 NIST Language Recognition Evaluation corpora [3], we demonstrateBootstrapping a Spoken Language Identification System Using Unsupervised Integrated Sensing Language Technology Center of Excellence, Johns Hopkins University 1-4 {shuaihuang

430

Stability Analysis of Fuzzy Identification for Nonlinear Discrete Systems - Part I: Theoretical Study  

Microsoft Academic Search

This paper presents the stability analysis of parameter identification. The Takagi Sugeno fuzzy model is employed to represent the discrete time nonlinear dynamical systems. Once the structure of the fuzzy model is fixed, the parameters can be optimized. The parameter identification is accomplished by applying the gradient method where the iteration rates are specific to each parameter. The stability of

Sonia ALIMI; Mohamed CHTOUROU

2009-01-01

431

Fast Identification of the Missing Tags in a Large RFID System  

E-print Network

Fast Identification of the Missing Tags in a Large RFID System Rui Zhang, Yunzhong Liu, Yanchao University of Tennessee, Knoxville, TN, USA jysun@eecs.utk.edu Abstract--RFID (radio-frequency identification, and inventory management. How to quickly identify the missing RFID tags and thus their associated objects

Zhang, Rui

432

Secure Human-Computer Identification (Interface) Systems against Peeping Attacks: SecHCI  

Microsoft Academic Search

This paper focuses on human-computer identification systems against peeping attacks, in which adversaries can observe (and even control) interactions between humans (provers) and computers (verifiers). Real cases on peeping attacks were reported by Ross J. Anderson ten years before. Fixed passwords are insecure to peeping attacks since adversaries can simply replay the observed passwords. Some identification techniques can be used

Shujun Li; Heung-Yeung Shum

2004-01-01

433

Analysis and application of minimum variance discrete time system identification  

NASA Technical Reports Server (NTRS)

An on-line minimum variance parameter identifier was developed which embodies both accuracy and computational efficiency. The new formulation resulted in a linear estimation problem with both additive and multiplicative noise. The resulting filter is shown to utilize both the covariance of the parameter vector itself and the covariance of the error in identification. It is proven that the identification filter is mean square covergent and mean square consistent. The MV parameter identification scheme is then used to construct a stable state and parameter estimation algorithm.

Kotob, S.; Kaufman, H.

1976-01-01

434

Identification of a yeast artificial chromosome clone spanning a translocation breakpoint at 7q32.1 in a Smith-Lemli-Opitz syndrome patient  

SciTech Connect

Smith-Lemli-Opitz syndrome (SLOS) is a mental retardation/multiple congenital anomaly syndrome. The gene(s) involved has not been mapped or cloned, but, recently, a biochemical abnormality in cholesterol biosynthesis has been shown to occur in most SLOS patients. The defect is suspected to occur in the penultimate step of the cholesterol pathway, involving the enzyme 7-dehydrocholesterol reductase, which has not been isolated. On the basis of the hypothesis that a de novo balanced translocation (t(7;20)(q32.1; q13.2)) in an SLOS patient directly interrupts the SLOS gene, positional cloning techniques are being employed to localize and identify the SLOS gene. We report the identification of a chromosome 7-specific YAC that spans the translocation breakpoint, as detected by FISH. This is the first study narrowing a candidate SLOS region and placing it on physical and genetic maps of the human genome. 19 refs., 2 figs., 1 tab.

Alley, T.L.; Gray, B.A.; Lee, S.H. [Univ. of Florida College of Medicine, Gainesville, FL (United States)] [and others

1995-06-01

435

Recombinant protein production in yeasts.  

PubMed

Recombinant protein production is a multibillion-dollar market. The development of a new product begins with the choice of a production host. While one single perfect host for every protein does not exist, several expression systems ranging from bacterial hosts to mammalian cells have been established. Among them, yeast cell factories combine the advantages of being single cells, such as fast growth and easy genetic manipulation, as well as eukaryotic features including a secretory pathway leading to correct protein processing and post-translational modifications. In this respect, especially the engineering of yeast glycosylation to produce glycoproteins of human-like glycan structures is of great interest. Additionally, different attempts of cellular engineering as well as the design of different production processes that are leading to improved productivities are presented. With the advent of cheaper next-generation sequencing techniques, systems biotechnology approaches focusing on genome scale analyses will advance and accelerate yeast cell factories and thus recombinant protein production processes in the near future. In this review we summarize advantages and limitations of the main and most promising yeast hosts, including Saccharomyces cerevisiae, Pichia pastoris, and Hansenula polymorpha as those presently used in large scale production of heterologous proteins. PMID:22160907