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1

Evaluation of Automated Yeast Identification System  

NASA Technical Reports Server (NTRS)

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

McGinnis, M. R.

1996-01-01

2

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

PubMed

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

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

2007-01-01

3

Evaluation of the Biolog MicroStation system for yeast identification  

NASA Technical Reports Server (NTRS)

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

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

1996-01-01

4

Evaluation of the MicroScan enzyme-based system for the identification of foodborne yeasts.  

PubMed

Eighty-nine strains representing 36 species of foodborne yeasts isolated from fruit juice concentrates were identified using the Baxter MicroScan enzyme-based kit, conventional tests according to a simplified identification method (SIM), and the API 20C kit. Of the 15 test species included in the MicroScan database, only 40% were correctly identified; 13% gave scores of unacceptably low probabilities, 20% were misidentified, and 27% could not be identified. Of the 21 test species not in the MicroScan database, 38% were misidentified and 62% produced biocodes with between-species differences not larger than differences between strains within species. The reliability of the MicroScan enzyme-based system is questioned, in that different results were sometimes obtained upon retesting the same strains. The MicroScan enzyme-based system is rapid, providing results within 4 h. However, because of its restricted and specific database and unreliability, the system appears to be unsuited for the identification of foodborne yeasts. PMID:7592137

Deak, T; Beuchat, L R

1995-10-01

5

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

PubMed

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

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

2014-05-01

6

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

PubMed

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

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

2014-06-01

7

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

PubMed Central

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

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

2013-01-01

8

[Comparison of Phoenix™ Yeast ID Panel and API® ID 32C commercial systems for the identification of Candida species isolated from clinical samples].  

PubMed

Opportunistic fungal pathogens are one of the important causes of nosocomial infections, and several different types of yeasts, especially Candida species are increasingly recovered from immunocompromised patients. Since many of the yeasts are resistant to the commonly used antifungal agents, the introduction of appropriate therapy depends on rapid and accurate identification. The aims of this study were to compare the commercial identification systems namely API® ID 32C (bioMerieux, France) and Phoenix™ Yeast ID Panel (Becton Dickinson Diagnostics, USA) for the identification of Candida species and to evaluate the effect of morphological findings in the identification process. A total of 211 yeast strains isolated from different clinical samples (111 urine, 34 blood/vascular catheter, 27 upper/lower respiratory tract, 16 abscess/pus, 13 throat/vagina swabs and 10 sterile body fluids) of 137 patients hospitalized in Uludag University Health and Research Center between October 2013 to January 2014, were included in the study. Samples were cultured on blood agar, chromogenic agar (CHROMagar Candida, BD, USA) and Saboraud's dextrose agar (SDA), and isolated yeast colonies were evaluated with germ tube test and morphological examination by microscopy on cornmeal/Tween-80 agar. The isolates were identified as well by two commercial systems according to the manufacturers' recommendations. Discrepant results between the systems were tried to be resolved by using morphological characteristics of the yeasts. Of the isolates 159 were identified identical by both of the systems, and the concordance between those systems were estimated as 75.4%. According to the concordant identification, the most frequently isolated species was C.albicans (44.1%) followed by C.tropicalis (9.9%), C.glabrata (9.5%), C.parapsilosis (8.5%) and C.kefyr (8.1%). The concordance rate was 81.7% in identification of frequently isolated species (C.albicans, C.tropicalis, C.parapsilosis, C.glabrata, C.kefyr), however it was 38.7% for the rarely isolated ones (C.krusei, C.lusitaniae, C.inconspicua/C.norvagensis, C.catenulata), representing statistical significance (p= 0.034; x2 test). Although not significant (p= 0.31; x2 test), the rate of concordance was increased (88.1%), when adding the morphological findings to the identification process. Of 211 isolates 37 (17.5%), 50 (23.7%) and 124 (58.8%) were identified according to their growth characteristics on chromogenic agar, blood agar and SDA, respectively, indicating no statistically significant difference between the media (p> 0.05). Although genotypic identification is essential, phenotypic methods are more commonly used in routine laboratories for the identification of yeast species. However, since genotypic identification could not be performed in this study, none of the systems were accepted as the standard method and therefore the sensitivity and specificity of the systems were not calculated. On the other hand, our data indicated that the two identification systems were comparable and careful observation of yeast morphology could add confidence to the identification. In conclusion, since the Phoenix™ Yeast ID system was found more practical with easier interpretation, and the results were obtained earlier than those of the API® ID 32C system (16 hours versus 48 hours), it was thought that Phoenix™ Yeast ID system may be used reliably in the routine laboratories. However, as none of the methods evaluated was completely reliable as a stand-alone, careful evaluation is necessary for species identification. PMID:25052110

Gayibova, Ülkü; Dalyan C?lo, Burcu; A?ca, Harun; Ener, Beyza

2014-07-01

9

[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

10

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

11

Improved Identification of Yeast Species Directly from Positive Blood Culture Media by Combining Sepsityper Specimen Processing and Microflex Analysis with the Matrix-Assisted Laser Desorption Ionization Biotyper System?  

PubMed Central

Current methods for identification of yeast from blood cultures may take several days after these microorganisms have been observed by Gram stain smears from positive blood cultures. We explored the use of a matrix-assisted laser desorption ionization (MALDI) Biotyper system in combination with Sepsityper specimen processing and Microflex analysis for improved detection and identification of yeast species directly from positive blood culture specimens demonstrating yeast-like organisms by Gram stain. The limit of detection of yeast species in blood culture medium was determined to be 5.9 × 105 CFU, with intra- and interstrain coefficients of variation of 1.8 to 3.6% and 2.9%, respectively. A total of 42 yeast-containing positive blood culture specimens were processed, and the identification results were compared to those obtained by routinely used phenotypic methods. Specimens with discrepant results between the Biotyper and phenotypic methods were identified on the basis of internal transcribed spacer region sequencing. The MALDI Biotyper system correctly identified the 42 specimens to species level, including 28 (66.7%) Candida albicans, 8 (19.0%) Candida parapsilosis, and 5 (11.9%) Candida tropicalis isolates and 1 (2.4%) Cryptococcus neoformans isolate. The entire procedure, from specimen extraction to final result reporting, can be completed within 1 h. Our data indicated that the Sepsityper specimen processing and Microflex analysis by the MALDI Biotyper system provide a rapid and reliable tool for yeast species identification directly from positive blood culture media. PMID:21543564

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

2011-01-01

12

Identification of human sperm proteins that interact with human zona pellucida3 (ZP3) using yeast two-hybrid system  

PubMed Central

Sperm proteins that interact with zona pellucida 3 (ZP3) have not been clearly identified in humans. In the present study, the yeast two-hybrid (Y2H) system was used to identify human sperm proteins that interact with human ZP3. Human ZP3 cDNA was cloned into pAS2-1 yeast vector and used as bait to find reactive proteins in the human testis cDNA library. Six specific clones were obtained that were further confirmed for interaction using the mammalian two-hybrid system. These six clones showed homologies with several proteins in the GenBank database. Of these, the strongest ZP3 interacting protein, that shows 97% homology with ubiquitin associated protein-2 like (UBAP2L), was tested in the hemizona assay. UBAP2L antibodies significantly (p < 0.001) inhibited human sperm-zona binding in this assay. We conclude that the Y2H system is a useful strategy for identifying novel genes encoding proteins that interact with ZP proteins. To our knowledge, this is the first study using the Y2H system to identify sperm proteins that interact with human oocyte ZP3. Novel proteins identified using this system may find applications in elucidating the fertilization cascade, development of a new generation of non-steroidal contraceptives, and specific diagnosis and treatment of human infertility. PMID:19945174

Naz, Rajesh K.; Dhandapani, Latha

2010-01-01

13

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

PubMed

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

Holcroft, James; Ganss, Bernhard

2011-12-01

14

Yeast metabolic state identification using micro-fiber optics spectroscopy  

NASA Astrophysics Data System (ADS)

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

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

2011-05-01

15

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

16

[Molecular identification methods of yeasts of biotechnological interest].  

PubMed

Yeasts have numerous applications in modern and traditional biotechnology. They take place in production of food, unicellular protein and products with added value, and in the last decades they have been incorporated to the biotechnology industry as host in the production of eukaryotes proteins. Apart from their advantages, some genera are the causes of mycosis on man and in some cases, are opportunistic pathogens associated to diseases such as HIV. They are also agents responsible for the damaging of fresh and elaborated food for human consumption. For these reasons, the quick and accurate identification of industrially, environmentally and clinically significant yeasts is important. Yeast taxonomy has been supported by conventional techniques, based on morphological and physiological descriptions of species and genera, but depend on strain culture conditions, therefore they have introduced errors in yeast taxonomy and originated the duality of their nomenclature. These difficulties have been solved with the application of molecular techniques, based on the sequence analysis of nucleic acid, specially karyotiping electrophoresis, microsatellite analysis, mitochondrial DNA length polymorphism, restriction fragment length polymorphism of ribosomal RNA, ramdom amplified polymorphic DNA and low molecular weight RNA. In this review all those methods are described, which have allowed the development of identification kits for clinical and industrial application for the clearance of phylogenetic relationships among species and genera of yeasts of biotechnological interest. PMID:15458357

Orbera-Ratón, Teresa

2004-03-01

17

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

SciTech Connect

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

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

1988-12-01

18

Prospective Evaluation of a Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System in a Hospital Clinical Microbiology Laboratory for Identification of Bacteria and Yeasts: a Bench-by-Bench Study for Assessing the Impact on Time to Identification and Cost-Effectiveness  

PubMed Central

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been found to be an accurate, rapid, and inexpensive method for the identification of bacteria and yeasts. Previous evaluations have compared the accuracy, time to identification, and costs of the MALDI-TOF MS method against standard identification systems or commercial panels. In this prospective study, we compared a protocol incorporating MALDI-TOF MS (MALDI protocol) with the current standard identification protocols (standard protocol) to determine the performance in actual practice using a specimen-based, bench-by-bench approach. The potential impact on time to identification (TTI) and costs had MALDI-TOF MS been the first-line identification method was quantitated. The MALDI protocol includes supplementary tests, notably for Streptococcus pneumoniae and Shigella, and indications for repeat MALDI-TOF MS attempts, often not measured in previous studies. A total of 952 isolates (824 bacterial isolates and 128 yeast isolates) recovered from 2,214 specimens were assessed using the MALDI protocol. Compared with standard protocols, the MALDI protocol provided identifications 1.45 days earlier on average (P < 0.001). In our laboratory, we anticipate that the incorporation of the MALDI protocol can reduce reagent and labor costs of identification by $102,424 or 56.9% within 12 months. The model included the fixed annual costs of the MALDI-TOF MS, such as the cost of protein standards and instrument maintenance, and the annual prevalence of organisms encountered in our laboratory. This comprehensive cost analysis model can be generalized to other moderate- to high-volume laboratories. PMID:22855510

Tan, K. E.; Ellis, B. C.; Lee, R.; Stamper, P. D.; Zhang, S. X.

2012-01-01

19

YEAST VOL. 14: 409417 (1998) Identification and Analysis of Homologues of  

E-print Network

YEAST VOL. 14: 409­417 (1998) Identification and Analysis of Homologues of Saccharomyces cerevisiae September 1997 Spt3 of Saccharomyces cerevisiae is a factor required for normal transcription from, TFIIA, TFIIB, TBP, TFIIE, TFIIF, TFIIG and TFIIH, are conserved in the yeast Saccharomyces cerevisiae

Winston, Fred

20

[Effects of nitrogen on performance and yeast morphology of yeast-SBR system].  

PubMed

Effects of nitrogen on yeast cell morphology, settleability and performance of wastewater treatment were investigated in treating oil-containing wastewater by yeast-SBR system. The results show that: nitrogen supply affects directly yeast biomass, settleability, pH and treatment efficiency of system; the absence of nitrogen induces the transformation of certain yeast cells from single cell to hypha morphology. Based on an overall consideration of efficiency and stability of yeast-SBR system, the optimum BOD/N ratio of influent is 20/1. The optimum nitrogen supply can improve wastewater treatment efficiency of systems with different degrees of nitrogen absence and make yeast morphology become the predominant morphology for slightly mycelial system over a short time, but for severe mycelial system, the hypha morphology still keeps dominant. PMID:18624205

Lü, Wen-Zhou; Liu, Ying; Chen, He-Ping; Zhu, Jian-Lin

2008-05-01

21

Quantum identification system  

Microsoft Academic Search

A secure quantum identification system combining a classical identification procedure and quantum key distribution is proposed. Each identification sequence is always used just once and sequences are ``refueled'' from a shared provably secret key transferred through the quantum channel. Two identification protocols are devised. The first protocol can be applied when legitimate users have an unjammable public channel at their

Miloslav Dusek; Ondrej Haderka; Martin Hendrych; Robert Myska

1999-01-01

22

Identification of propulsion systems  

NASA Technical Reports Server (NTRS)

This paper presents a tutorial on the use of model identification techniques for the identification of propulsion system models. These models are important for control design, simulation, parameter estimation, and fault detection. Propulsion system identification is defined in the context of the classical description of identification as a four step process that is unique because of special considerations of data and error sources. Propulsion system models are described along with the dependence of system operation on the environment. Propulsion system simulation approaches are discussed as well as approaches to propulsion system identification with examples for both air breathing and rocket systems.

Merrill, Walter; Guo, Ten-Huei; Duyar, Ahmet

1991-01-01

23

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

24

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

25

The power of the yeast two-hybrid system in the identification of novel drug targets: building and modulating PPP1 interactomes.  

PubMed

Since the description of the yeast two-hybrid (Y2H) method, it has become more and more evident that it is the most commonly used method to identify protein-protein interactions (PPIs). The improvements in the original Y2H methodology in parallel with the idea that PPIs are promising drug targets, offer an excellent opportunity to apply the principles of this molecular biology technique to the pharmaceutical field. Additionally, the theoretical developments in the networks field make PPI networks very useful frameworks that facilitate many discoveries in biomedicine. This review highlights the relevance of Y2H in the determination of PPIs, specifically phosphoprotein phosphatase 1 interactions, and its possible outcomes in pharmaceutical research. PMID:25795147

Silva, Joana Vieira; Freitas, Maria João; Felgueiras, Juliana; Fardilha, Margarida

2015-04-01

26

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

PubMed Central

Rapid, accurate identification of yeast isolates from clinical samples has always been important given their innately variable antifungal susceptibility profiles. Recently, this has become paramount with the proposed introduction of species-specific interpretive breakpoints for MICs obtained in yeast antifungal susceptibility tests (M. A. Pfaller, D. Andes, D. J. Diekema, A. Espinel–Ingroff, D. Sheehan, and CLSI Subcommittee for Antifungal Susceptibility Testing, Drug Resist. Updat. 13:180–195, 2010). Here, we present the results of a 12-month evaluation of the accuracy of identifications that accompany yeast isolates submitted to the Mycology Reference Laboratory (United Kingdom) for either confirmation of identity or susceptibility testing. In total, 1,781 yeast isolates were analyzed, and the robustness of prior identifications obtained in microbiology laboratories throughout the United Kingdom was assessed using a combination of culture on chromogenic agar, morphology on cornmeal agar, and molecular identification by pyrosequencing. Over 40% of isolates (755) were submitted without any suggested identification. Of those isolates with a prior identification, 100 (9.7%) were incorrectly identified. Error rates ranged from 5.2% (for organisms submitted for antifungal susceptibility testing) to 18.2% (for organisms requiring confirmation of identity) and varied in a strictly species-specific manner. At least 50% of identification errors would be likely to affect interpretation of MIC data, with a possible impact on patient management. In addition, 2.3% of submitted cultures were found to contain mixtures of at least two yeast species. The vast majority of mixtures had gone undetected in the referring laboratory and would have impacted the interpretation of antifungal susceptibility profiles and patient management. Some of the more common misidentifications are discussed according to the identification method employed, with suggestions for avoiding such misinterpretations. PMID:22649009

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

2012-01-01

27

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

28

Genetic Algorithms based Parameter Identification of Yeast Fed-Batch Cultivation  

E-print Network

Genetic Algorithms based Parameter Identification of Yeast Fed-Batch Cultivation Maria Angelova of a fermentation process. Altogether eight realizations of genetic algorithms have been presented - four of simple the others. 1 INTRODUCTION Fermentation processes (FP) are widely used in different branches of industry, i

Mustakerov, Ivan

29

Author Identification Systems  

ERIC Educational Resources Information Center

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

Wagner, A. Ben

2009-01-01

30

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

PubMed

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

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

2014-03-01

31

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

32

Quantum System Identification  

E-print Network

The aim of quantum system identification is to estimate the ingredients inside a black box, in which some quantum-mechanical unitary process takes place, by just looking at its input-output behavior. Here we establish a basic and general framework for quantum system identification, that allows us to classify how much knowledge about the quantum system is attainable, in principle, from a given experimental setup. Prior knowledge on some elements of the black box helps the system identification. We present an example in which a Bell measurement is more efficient to identify the system. When the topology of the system is known, the framework enables us to establish a general criterion for the estimability of the coupling constants in its Hamiltonian.

Daniel Burgarth; Kazuya Yuasa

2011-04-04

33

Systematic identification of cell size regulators in budding yeast.  

PubMed

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

34

Global identification of yeast chromosome interactions using Genome conformation capture.  

PubMed

The association of chromosomes with each other and other nuclear components plays a critical role in nuclear organization and Genome function. Here, using a novel and generally applicable methodology (Genome conformation capture [GCC]), we reveal the network of chromosome interactions for the yeast Saccharomyces cerevisiae. Inter- and intra-chromosomal interactions are non-random and the number of interactions per open reading frame depends upon the dispensability of the gene product. Chromosomal interfaces are organized and provide evidence of folding within chromosomes. Interestingly, the genomic connections also involve the 2 microm plasmid and the mitochondrial genome. Mitochondrial interaction partners include genes of alpha-proteobacterial origin and the ribosomal DNA. Organization of the 2 microm plasmid aligns two inverted repeats (IR1 and IR2) and displays the stability locus on a prominent loop thus making it available for plasmid clustering. Our results form the first global map of chromosomal interactions in a eukaryotic nucleus and demonstrate the highly connected nature of the yeast genome. These results have significant implications for understanding eukaryotic genome organization. PMID:19628047

Rodley, C D M; Bertels, F; Jones, B; O'Sullivan, J M

2009-11-01

35

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

36

Optimized System Identification  

NASA Technical Reports Server (NTRS)

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

Juang, Jer-Nan; Longman, Richard W.

1999-01-01

37

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

PubMed Central

The clinical impact of severe infections with yeasts and yeast-like fungi has increased, especially in immunocompromised hosts. In recent years, new antifungal agents with different and partially species-specific activity patterns have become available. Therefore, rapid and reliable species identification is essential for antifungal treatment; however, conventional biochemical methods are time-consuming and require considerable expertise. We evaluated matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the rapid routine identification of clinical yeast isolates. A total of 18 type collection strains and 267 recent clinical isolates of Candida (n = 250), Cryptococcus, Saccharomyces, Trichosporon, Geotrichum, Pichia, and Blastoschizomyces spp. were identified by MALDI-TOF MS. The results were compared with those obtained by conventional phenotyping and biochemical tests, including the API ID 32C system (bioMérieux, Nürtingen, Germany). Starting with cells from single colonies, accurate species identification by MALDI-TOF MS was achieved for 247 of the clinical isolates (92.5%). The remaining 20 isolates required complementation of the reference database with spectra for the appropriate reference strains which were obtained from type culture collections or identified by 26S rRNA gene sequencing. The absence of a suitable reference strain from the MALDI-TOF MS database was clearly indicated by log(score) values too low for the respective clinical isolates; i.e., no false-positive identifications occurred. After complementation of the database, all isolates were unambiguously identified. The established API ID 32C biochemical diagnostic system identified 244 isolates in the first round. Overall, MALDI-TOF MS proved a most rapid and reliable tool for the identification of yeasts and yeast-like fungi, with the method providing a combination of the lowest expenditure of consumables, easy interpretation of results, and a fast turnaround time. PMID:19571014

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

2009-01-01

38

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

Microsoft Academic Search

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

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

1997-01-01

39

Automated Microbiological Detection/Identification System  

PubMed Central

An automated, computerized system, the AutoMicrobic System, has been developed for the detection, enumeration, and identification of bacteria and yeasts in clinical specimens. The biological basis for the system resides in lyophilized, highly selective and specific media enclosed in wells of a disposable plastic cuvette; introduction of a suitable specimen rehydrates and inoculates the media in the wells. An automated optical system monitors, and the computer interprets, changes in the media, with enumeration and identification results automatically obtained in 13 h. Sixteen different selective media were developed and tested with a variety of seeded (simulated) and clinical specimens. The AutoMicrobic System has been extensively tested with urine specimens, using a urine test kit (Identi-Pak) that contains selective media for Escherichia coli, Proteus species, Pseudomonas aeruginosa, Klebsiella-Enterobacter species, Serratia species, Citrobacter freundii, group D enterococci, Staphylococcus aureus, and yeasts (Candida species and Torulopsis glabrata). The system has been tested with 3,370 seeded urine specimens and 1,486 clinical urines. Agreement with simultaneous conventional (manual) cultures, at levels of 70,000 colony-forming units per ml (or more), was 92% or better for seeded specimens; clinical specimens yielded results of 93% or better for all organisms except P. aeruginosa, where agreement was 86%. System expansion in progress includes antibiotic susceptibility testing and compatibility with most types of clinical specimens. Images PMID:334798

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

1977-01-01

40

Toward Genome-Wide Identification of Bateson–Dobzhansky–Muller Incompatibilities in Yeast: A Simulation Study  

PubMed Central

The Bateson–Dobzhansky–Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen our understanding of the molecular genetic basis of reproductive isolation and speciation. However, despite repeated efforts, BDM incompatibilities between nuclear genes have never been identified between S. cerevisiae and its sister species S. paradoxus. Such negative results have led to the belief that simple nuclear BDM incompatibilities do not exist between the two yeast species. Here, we explore an alternative explanation that such incompatibilities exist but were undetectable due to limited statistical power. We discover that previously employed statistical methods were not ideal and that a redesigned method improves the statistical power. We determine, under various sample sizes, the probabilities of identifying BDM incompatibilities that cause F1 spore inviability with incomplete penetrance, and confirm that the previously used samples were too small to detect such incompatibilities. Our findings call for an expanded experimental search for yeast BDM incompatibilities, which has become possible with the decreasing cost of genome sequencing. The improved methodology developed here is, in principle, applicable to other organisms and can help detect epistasis in general. PMID:23742870

Li, Chuan; Wang, Zhi; Zhang, Jianzhi

2013-01-01

41

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

PubMed Central

Genetic interaction networks that underlie most human diseases are highly complex and poorly defined. Better-defined networks will allow identification of a greater number of therapeutic targets. Here we introduce our Yeast Augmented Network Analysis (YANA) approach and test it with the X-linked spinal muscular atrophy (SMA) disease gene UBA1. First, we express UBA1 and a mutant variant in fission yeast and use high-throughput methods to identify fission yeast genetic modifiers of UBA1. Second, we analyze available protein-protein interaction network databases in both fission yeast and human to construct UBA1 genetic networks. Third, from these networks we identified potential therapeutic targets for SMA. Finally, we validate one of these targets in a vertebrate (zebrafish) SMA model. This study demonstrates the power of combining synthetic and chemical genetics with a simple model system to identify human disease gene networks that can be exploited for treating human diseases. PMID:25075304

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

2014-01-01

42

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

43

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

44

Comparison of the Accuracy of Two Conventional Phenotypic Methods and Two MALDI-TOF MS Systems with That of DNA Sequencing Analysis for Correctly Identifying Clinically Encountered Yeasts  

PubMed Central

We assessed the accuracy of species-level identification of two commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Bruker Biotyper and Vitek MS) and two conventional phenotypic methods (Phoenix 100 YBC and Vitek 2 Yeast ID) with that of rDNA gene sequencing analysis among 200 clinical isolates of commonly encountered yeasts. The correct identification rates of the 200 yeast isolates to species or complex (Candida parapsilosis complex, C. guilliermondii complex and C. rugosa complex) levels by the Bruker Biotyper, Vitek MS (using in vitro devices [IVD] database), Phoenix 100 YBC and Vitek 2 Yeast ID (Sabouraud's dextrose agar) systems were 92.5%, 79.5%, 89%, and 74%, respectively. An additional 72 isolates of C. parapsilosis complex and 18 from the above 200 isolates (30 in each of C. parapsilosis, C. metapsilosis, and C. orthopsilosis) were also evaluated separately. Bruker Biotyper system could accurately identify all C. parapsilosis complex to species level. Using Vitek 2 MS (IVD) system, all C. parapsilosis but none of C. metapsilosis, or C. orthopsilosis could be accurately identified. Among the 89 yeasts misidentified by the Vitek 2 MS (IVD) system, 39 (43.8%), including 27 C. orthopsilosis isolates, could be correctly identified Using the Vitek MS Plus SARAMIS database for research use only. This resulted in an increase in the rate of correct identification of all yeast isolates (87.5%) by Vitek 2 MS. The two species in C. guilliermondii complex (C. guilliermondii and C. fermentati) isolates were correctly identified by cluster analysis of spectra generated by the Bruker Biotyper system. Based on the results obtained in the current study, MALDI-TOF MS systems present a promising alternative for the routine identification of yeast species, including clinically commonly and rarely encountered yeast species and several species belonging to C. parapsilosis complex, C. guilliermondii complex, and C. rugosa complex. PMID:25330370

Chao, Qiao-Ting; Lee, Tai-Fen; Teng, Shih-Hua; Peng, Li-Yun; Chen, Ping-Hung; Teng, Lee-Jene; Hsueh, Po-Ren

2014-01-01

45

Yeast prions: structure, biology, and prion-handling systems.  

PubMed

A prion is an infectious protein horizontally transmitting a disease or trait without a required nucleic acid. Yeast and fungal prions are nonchromosomal genes composed of protein, generally an altered form of a protein that catalyzes the same alteration of the protein. Yeast prions are thus transmitted both vertically (as genes composed of protein) and horizontally (as infectious proteins, or prions). Formation of amyloids (linear ordered ?-sheet-rich protein aggregates with ?-strands perpendicular to the long axis of the filament) underlies most yeast and fungal prions, and a single prion protein can have any of several distinct self-propagating amyloid forms with different biological properties (prion variants). Here we review the mechanism of faithful templating of protein conformation, the biological roles of these prions, and their interactions with cellular chaperones, the Btn2 and Cur1 aggregate-handling systems, and other cellular factors governing prion generation and propagation. Human amyloidoses include the PrP-based prion conditions and many other, more common amyloid-based diseases, several of which show prion-like features. Yeast prions increasingly are serving as models for the understanding and treatment of many mammalian amyloidoses. Patients with different clinical pictures of the same amyloidosis may be the equivalent of yeasts with different prion variants. PMID:25631286

Wickner, Reed B; Shewmaker, Frank P; Bateman, David A; Edskes, Herman K; Gorkovskiy, Anton; Dayani, Yaron; Bezsonov, Evgeny E

2015-03-01

46

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

PubMed

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

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

2011-08-01

47

Rapid Identification of Candida dubliniensis with Commercial Yeast Identification Systems  

Microsoft Academic Search

Candida dubliniensis is a newly described species that is closely related phylogenetically to Candida albicans and that is commonly associated with oral candidiasis in human immunodeficiency virus-positive patients. Several recent studies have attempted to elucidate phenotypic and genotypic characteristics of use in sepa- rating the two species. However, results obtained with simple phenotypic tests were too variable and tests that

D. H. PINCUS; D. C. COLEMAN; W. R. PRUITT; A. A. PADHYE; I. F. SALKIN; M. GEIMER; A. BASSEL; D. J. SULLIVAN; M. CLARKE; V. HEARN

1999-01-01

48

Detection and identification of wild yeasts in Champús, a fermented Colombian maize beverage.  

PubMed

The aim of this study was to identify and characterise the predominant yeasts in Champús, a traditional Colombian cereal-based beverage with a low alcoholic content. Samples of Champús from 20 production sites in the Cauca Valley region were analysed. A total of 235 yeast isolates were identified by conventional microbiological analyses and by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of ITS1-5.8S rDNA-ITS2. The dominant species were: Saccharomyces cerevisiae, Issatchenkia orientalis, Pichia fermentans, Pichia kluyveri var. kluyveri, Zygosaccharomyces fermentati, Torulospora delbruekii, Galactomyces geotrichum and Hanseniaspora spp. Model Champús systems were inoculated with single strains of some isolated sporogenus species and the aromatic profiles were analysed by SPME. Analysis of data showed that Champús strains produced high amounts of esters. The aromatic compounds produced by Saccharomyces and non-Saccharomyces yeasts from Champús can exert a relevant influence on the sensory characteristics of the fermented beverage. The Champús strains could thus represent an important source for new yeast biotypes with potential industrial applications. PMID:18620968

Osorio-Cadavid, Esteban; Chaves-López, Clemencia; Tofalo, Rosanna; Paparella, Antonello; Suzzi, Giovanna

2008-09-01

49

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

50

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

51

Identification of a Small Molecule Yeast TORC1 Inhibitor with a Multiplex Screen Based on Flow Cytometry  

E-print Network

Identification of a Small Molecule Yeast TORC1 Inhibitor with a Multiplex Screen Based on Flow TOR inhibitors. Here we report a high-throughput flow cytometry multiplexed screen using five GFP was measured simultaneously by flow cytometry, which allows rapid prioritization of compounds that likely act

Halazonetis, Thanos

52

System identification of jet engines  

Microsoft Academic Search

System identification plays an important role in advanced control systems for jet engines, in which controls are performed adaptively using data from the actual engine and the identified engine. An identification technique for jet engine using the Constant Gain Extended Kalman Filter (CGEKF) is described. The filter is constructed for a two-spool turbofan engine. The CGEKF filter developed here can

N. Sugiyama

2000-01-01

53

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

54

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 Central

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

2014-01-01

55

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...

56

Spoilage yeasts.  

PubMed

Yeasts are best known for their beneficial contributions to society, and the literature abounds with discussions of their role in the fermentation of alcoholic beverages, bread, and other products. Yeasts also cause spoilage, but, with a few exceptions, this unwanted activity often goes unrecognized and underestimated as a major problem in the food and beverage industries. In some cases, there is only a fine line between what is perceived as either a spoilage or beneficial activity. This review examines the occurrence and growth of yeasts in foods and beverages with respect to their spoilage activities, the biochemistry of this spoilage, and technologies for the enumeration and identification of spoilage yeasts. PMID:1733519

Fleet, G

1992-01-01

57

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

PubMed Central

A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers. PMID:9399515

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

1997-01-01

58

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system  

PubMed Central

Background Mass spectrometry has become a powerful tool for the analysis of large numbers of proteins in complex samples, enabling much of proteomics. Due to various analytical challenges, so far no proteome has been sequenced completely. O'Shea, Weissman and co-workers have recently determined the copy number of yeast proteins, making this proteome an excellent model system to study factors affecting coverage. Results To probe the yeast proteome in depth and determine factors currently preventing complete analysis, we grew yeast cells, extracted proteins and separated them by one-dimensional gel electrophoresis. Peptides resulting from trypsin digestion were analyzed by liquid chromatography mass spectrometry on a linear ion trap-Fourier transform mass spectrometer with very high mass accuracy and sequencing speed. We achieved unambiguous identification of more than 2,000 proteins, including very low abundant ones. Effective dynamic range was limited to about 1,000 and effective sensitivity to about 500 femtomoles, far from the subfemtomole sensitivity possible with single proteins. We used SILAC (stable isotope labeling by amino acids in cell culture) to generate one-to-one pairs of true peptide signals and investigated if sensitivity, sequencing speed or dynamic range were limiting the analysis. Conclusion Advanced mass spectrometry methods can unambiguously identify more than 2,000 proteins in a single proteome. Complex mixture analysis is not limited by sensitivity but by a combination of dynamic range (high abundance peptides preventing sequencing of low abundance ones) and by effective sequencing speed. Substantially increased coverage of the yeast proteome appears feasible with further development in software and instrumentation. PMID:16784548

de Godoy, Lyris MF; Olsen, Jesper V; de Souza, Gustavo A; Li, Guoqing; Mortensen, Peter; Mann, Matthias

2006-01-01

59

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

60

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

61

[Efficiency and yeast community structure of oil-containing treatment system inoculated by different yeast strains complex wastewater].  

PubMed

Ten yeast stains were grouped and applied in pilot-scale sequencing batch reactors to treat oil-containing wastewater. The efficiency and stability of different reactors were discussed and yeast community structure was investigated by PCR-DGGE method. The results show: the group consisting of O2, G1 and W1 is markedly superior to others in efficiency and stability respects; the group absence of these 3 stains fails to form a system with high efficiency and good stability; O4 and G2 strains lead to turbid supernatant fluid and are eliminated from system step by step; the distribution of yeast cells in settlement sludge varies with different stains. When aeration is stopped, G1 deposits into lower layer but O2 or W1 distributes evenly. PMID:19068631

Lü, Wen-zhou; Liu, Ying; Zhu, Jian-lin

2008-09-01

62

New and emerging yeast pathogens.  

PubMed Central

The most common yeast species that act as agents of human disease are Candida albicans, Candida tropicalis, Candida glabrata, Candida parapsilosis, and Cryptococcus neoformans. The incidence of infections by other yeasts has increased during the past decade. The most evident emerging pathogens are Malassezia furfur, Trichosporon beigelii, Rhodotorula species, Hansenula anomala, Candida lusitaniae, and Candida krusei. Organisms once considered environmental contaminants or only industrially important, such as Candida utilis and Candida lipolytica, have now been implicated as agents of fungemia, onychomycosis, and systemic disease. The unusual yeasts primarily infect immunocompromised patients, newborns, and the elderly. The role of central venous catheter removal and antifungal therapy in patient management is controversial. The antibiograms of the unusual yeasts range from resistant to the most recent azoles and amphotericin B to highly susceptible to all antifungal agents. Current routine methods for yeast identification may be insufficient to identify the unusual yeasts within 2 days after isolation. The recognition of unusual yeasts as agents of sometimes life-threatening infection and their unpredictable antifungal susceptibilities increase the burden on the clinical mycology laboratory to pursue complete species identification and MIC determinations. Given the current and evolving medical practices for management of seriously ill patients, further evaluations of the clinically important data about these yeasts are needed. PMID:8665465

Hazen, K C

1995-01-01

63

Yeast Systems Biology: Our Best Shot at Modeling a Cell  

PubMed Central

THE Genetics Society of America’s Edward Novitski Prize recognizes an extraordinary level of creativity and intellectual ingenuity in the solution of significant problems in genetics research. The 2014 recipient, Charles Boone, has risen to the top of the emergent discipline of postgenome systems biology by focusing on the global mapping of genetic interaction networks. Boone invented the synthetic genetic array (SGA) technology, which provides an automated method to cross thousands of strains carrying precise mutations and map large-scale yeast genetic interactions. These network maps offer researchers a functional wiring diagram of the cell, which clusters genes into specific pathways and reveals functional connections. PMID:25316779

Boone, Charles

2014-01-01

64

Yeast three-hybrid screening for identifying anti-tuberculosis drug targets.  

PubMed

Mycobacterium goes yeast: Target deconvolution of anti-tuberculosis drugs can be a very challenging task. Here we report a yeast 3-hybrid system that allows promising small molecules to be screened for protein targets of a pathogen in nontoxic yeast cells. The system employs libraries of randomly fragmented bacterial DNA and offers a technically simple alternative approach for target identification. PMID:24133019

Moser, Simone; Johnsson, Kai

2013-11-25

65

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

SciTech Connect

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

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

1994-05-01

66

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

PubMed

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

Koh, Yvonne Y; Wickens, Marvin

2014-01-01

67

From genomes to systems: the path with yeast.  

PubMed

Metabolic Control Analysis (MCA) is a conceptual and mathematical formalism that models the relative contributions of individual effectors in a pathway to both the flux through the pathway and the concentrations of individual intermediates within it. To exploit MCA in an initial Systems Biology analysis of the eukaryotic cell, two categories of experiments are required. In category 1 experiments, flux is changed and the impact on the levels of the direct and indirect products of gene action is measured. We have measured the impact of changing the flux on the transcriptome, proteome and metabolome of Saccharomyces cerevisiae. In this whole-cell analysis, flux equates to growth rate. In category 2 experiments, the levels of individual gene products are altered, and the impact on the flux is measured. We have used competition analyses between the complete set of heterozygous yeast deletion mutants to reveal genes encoding proteins with high flux control coefficients. These genes may be exploited, in a top-down analysis, to build a coarse-grained model of the eukaryotic cell, as exemplified by yeast. More detailed modelling requires that 'natural' biological systems be identified. The combination of flux balance analysis with both genetics and metabolomics in the definition of metabolic systems is discussed. PMID:16524836

Oliver, Stephen G

2006-03-29

68

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

PubMed

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

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

2014-03-01

69

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

70

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

71

Systems identification - reprise and projections  

NASA Technical Reports Server (NTRS)

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

Taylor, L. W., Jr.

1974-01-01

72

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

73

Comparison of Equivalent System Mass of Yeast and Flat Bread Systems  

Microsoft Academic Search

The Equivalent System Mass (ESM) metric developed by NASA describes and compares individual system impact on a closed system in terms of a single parameter, mass. The food system of a Mars mission may encompass a large percentage of total mission ESM, and decreasing this ESM would be beneficial. Yeast breads were made using three methods (hand & oven, bread

Ilan Weiss; Banu F. Ozen; Michele H. Perchonok; Kirby D. Hayes; Lisa J. Mauer

2003-01-01

74

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...

75

Automated Hardware-Identification System  

NASA Technical Reports Server (NTRS)

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

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

1995-01-01

76

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...

77

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

78

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

79

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

PubMed

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

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

2011-05-01

80

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

81

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

82

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

PubMed Central

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

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

2010-01-01

83

Multiple polyamine transport systems on the vacuolar membrane in yeast.  

PubMed

We recently identified a gene (TPO1, YLL028w) that encodes a polyamine transport protein on the vacuolar membrane in yeast [Tomitori, Kashiwagi, Sakata, Kakinuma and Igarashi (1999) J. Biol. Chem. 274, 3265-3267]. Because the existence of one or more other genes for a polyamine transport protein on the vacuolar membrane was expected, we searched sequence databases for homologues of the protein encoded by TPO1. Membrane proteins encoded by the open reading frames YGR138c (TPO2), YPR156c (TPO3) and YOR273c (TPO4) were postulated to be polyamine transporters and, indeed, were subsequently shown to be polyamine transport proteins on the vacuolar membrane. Cells overexpressing these genes were resistant to polyamine toxicity and showed an increase in polyamine uptake activity and polyamine content in vacuoles. Furthermore, cells in which these genes were disrupted showed an increased sensitivity to polyamine toxicity and a decrease in polyamine uptake activity and polyamine content in vacuoles. Resistance to polyamine toxicity in cells overexpressing the genes was overcome by bafilomycin A(1), an inhibitor of the vacuolar H(+)-ATPase. Among the four polyamine transporters, those encoded by TPO2 and TPO3 were specific for spermine, whereas those encoded by TPO1 and TPO4 recognized spermidine and spermine. These results suggest that polyamine content in the cytoplasm of yeast is elaborately regulated by several polyamine transport systems in vacuoles. Furthermore, it was shown that Glu-207, Glu-324 (or Glu-323) and Glu-574 of TPO1 protein were important for the transport activity. PMID:11171066

Tomitori, H; Kashiwagi, K; Asakawa, T; Kakinuma, Y; Michael, A J; Igarashi, K

2001-02-01

84

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

Microsoft Academic Search

BACKGROUND: Yeasts provide attractive expression platforms in combining ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. However, early restriction to a single yeast platform can result in costly and time-consuming failures. It is therefore advisable to assess several selected systems in parallel for

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

2006-01-01

85

Automated systems for identification of microorganisms.  

PubMed Central

Automated instruments for the identification of microorganisms were introduced into clinical microbiology laboratories in the 1970s. During the past two decades, the capabilities and performance characteristics of automated identification systems have steadily progressed and improved. This article explores the development of the various automated identification systems available in the United States and reviews their performance for identification of microorganisms. Observations regarding deficiencies and suggested improvements for these systems are provided. PMID:1498768

Stager, C E; Davis, J R

1992-01-01

86

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

87

In-Flight System Identification  

NASA Technical Reports Server (NTRS)

A method is proposed and studied whereby the system identification cycle consisting of experiment design and data analysis can be repeatedly implemented aboard a test aircraft in real time. This adaptive in-flight system identification scheme has many advantages, including increased flight test efficiency, adaptability to dynamic characteristics that are imperfectly known a priori, in-flight improvement of data quality through iterative input design, and immediate feedback of the quality of flight test results. The technique uses equation error in the frequency domain with a recursive Fourier transform for the real time data analysis, and simple design methods employing square wave input forms to design the test inputs in flight. Simulation examples are used to demonstrate that the technique produces increasingly accurate model parameter estimates resulting from sequentially designed and implemented flight test maneuvers. The method has reasonable computational requirements, and could be implemented aboard an aircraft in real time.

Morelli, Eugene A.

1998-01-01

88

On-orbit system parameter identification  

NASA Technical Reports Server (NTRS)

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

Simonian, Stepan S.

1988-01-01

89

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

90

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

91

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

PubMed

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

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

2006-10-01

92

System/observer/controller identification toolbox  

NASA Technical Reports Server (NTRS)

System Identification is the process of constructing a mathematical model from input and output data for a system under testing, and characterizing the system uncertainties and measurement noises. The mathematical model structure can take various forms depending upon the intended use. The SYSTEM/OBSERVER/CONTROLLER IDENTIFICATION TOOLBOX (SOCIT) is a collection of functions, written in MATLAB language and expressed in M-files, that implements a variety of modern system identification techniques. For an open loop system, the central features of the SOCIT are functions for identification of a system model and its corresponding forward and backward observers directly from input and output data. The system and observers are represented by a discrete model. The identified model and observers may be used for controller design of linear systems as well as identification of modal parameters such as dampings, frequencies, and mode shapes. For a closed-loop system, an observer and its corresponding controller gain directly from input and output data.

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

1992-01-01

93

Nonlinear system identification of a twin rotor MIMO system  

Microsoft Academic Search

This work presents system identification using neural network approaches for modelling a laboratory based twin rotor multi-input multi-output system (TRMS). Here we focus on a memetic algorithm based approach for training the multilayer perceptron neural network (NN) applied to nonlinear system identification. In the proposed system identification scheme, we have exploited three global search methods namely genetic algorithm (GA), Particle

Bidyadhar Subudhi; Debashisha Jena

2009-01-01

94

Parameter identification for nonlinear aerodynamic systems  

NASA Technical Reports Server (NTRS)

Work continues on frequency analysis for transfer function identification, both with respect to the continued development of the underlying algorithms and in the identification study of two physical systems. Some new results of a theoretical nature were recently obtained that lend further insight into the frequency domain interpretation of the research. Progress in each of those areas is summarized. Although not related to the system identification problem, some new results were obtained on the feedback stabilization of linear time lag systems.

Pearson, Allan E.

1991-01-01

95

A thiamine-regulatable epitope-tagged protein expression system in fission yeast.  

PubMed

Schizosaccharomyces pombe, the fission yeast, has been a popular and useful model system for investigating the mechanisms of biological processes for a long time. To facilitate purification, localization, and functional analysis of gene products, a wide range of expression vectors have been developed. Several of these vectors utilize the inducible/repressible promoter systems and enable the episomal expression of proteins as fusion proteins with epitope tags attached to their N terminus or C terminus.This chapter provides a detailed protocol for expression of the epitope-tagged proteins from thiamine-regulatable nmt promoter in fission yeast. The yeast culture conditions and procedures for yeast transformation, expression induction, preparation of whole-cell extracts, and analysis of epitope-tagged protein expression by Western blotting are described. PMID:22160912

Tamm, Tiina

2012-01-01

96

Personal identification credential system (PICS)  

NASA Astrophysics Data System (ADS)

A pilot Personal Identification Credential System (PICS) has been developed and fielded. The PICS is a wireless biometric credential that interfaces with access control systems. The PICS consists of individual handheld Personal Identification Credentials (PIC), a PICS Reader located at a facility entry control point that interfaces with the facility entry control system, and a PICS Enrollment Station. In operation, an individual approaching a facility entry point in a vehicle picks up the PIC handheld unit and places a finger on its sensor. The PIC then authenticates the user and from within the vehicle initiates two-way, secure RF communication with the PICS Reader as the vehicle approaches the gate. The PICS Reader then verifies that the individual is authorized for admittance and notifies the facility gate entry control system, which informs the sentry that the request for access was successful or unsuccessful. If the request for access is unsuccessful, the gate entry control system automatically will close the gate. This sequence of events takes place while the car is moving through a normally open entry lane. The PIC is a small, handheld device which contains the biometric sensor (fingerprint sensor), wireless RF transceiver, processor, encryption and battery. The PIC may be used while traveling in a vehicle or may be used while on foot for access to a PICS controlled man gate or secure area access portal. The PIC is small enough to be carried in a shirt pocket, or it can be left in the user's vehicle. The PIC battery will power the PIC for months and is rechargeable. Up to 10 fingers may be stored in the PIC.

Pressley, Jackson R.; Cantrell, Thomas; Page, Lochlin; Cudlitz, Stephen; Higgins, Roy

2005-03-01

97

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

98

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

NASA Astrophysics Data System (ADS)

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

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

1984-06-01

99

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

PubMed Central

The specification and maintenance of cell fates is essential to the development of multicellular organisms. However, the precise molecular mechanisms in cell fate selection are, to our knowledge, poorly understood due to the complexity of multiple interconnected pathways. In this study, model-based quantitative analysis is used to explore how to maintain distinguished cell fates between cell-cycle commitment and mating arrest in budding yeast. We develop a full mathematical model of an interlinked regulatory network based on the available experimental data. By theoretically defining the Start transition point, the model is able to reproduce many experimental observations of the dynamical behaviors in wild-type cells as well as in Ste5-8A and Far1-S87A mutants. Furthermore, we demonstrate that a moderate ratio between Cln1/2?Far1 inhibition and Cln1/2?Ste5 inhibition is required to ensure a successful switch between different cell fates. We also show that the different ratios of the mutual Cln1/2 and Far1 inhibition determine the different cell fates. In addition, based on a new, definition of network entropy, we find that the Start point in wild-type cells coincides with the system’s point of maximum entropy. This result indicates that Start is a transition point in the network entropy. Therefore, we theoretically explain the Start point from a network dynamics standpoint. Moreover, we analyze the biological bistablity of our model through bifurcation analysis. We find that the Cln1/2 and Cln3 production rates and the nonlinearity of SBF regulation on Cln1/2 production are potential determinants for irreversible entry into a new cell fate. Finally, the quantitative computations further reveal that high specificity and fidelity of the cell-cycle and mating pathways can guarantee specific cell-fate selection. These findings show that quantitative analysis and simulations with a mathematical model are useful tools for understanding the molecular mechanisms in cell-fate decisions. PMID:23708368

Li, Yongkai; Yi, Ming; Zou, Xiufen

2013-01-01

100

Identification and characterization of DGA2, an acyltransferase of the DGAT1 acyl-CoA:diacylglycerol acyltransferase family in the oleaginous yeast Yarrowia lipolytica. New insights into the storage lipid metabolism of oleaginous yeasts.  

PubMed

Triacylglycerols (TAG) and steryl esters (SE) are the principal storage lipids in all eukaryotic cells. In yeasts, these storage lipids accumulate within special organelles known as lipid bodies (LB). In the lipid accumulation-oriented metabolism of the oleaginous yeast Yarrowia lipolytica, storage lipids are mostly found in the form of TAG, and only small amounts of SE accumulate. We report here the identification of a new DAG acyltransferase gene, DGA2, homologous to the ARE genes of Saccharomyces cerevisiae. This gene encodes a member of the type 1 acyl-CoA:diacylglycerol acyltransferase family (DGAT1), which has not previously been identified in yeasts, but is commonly found in mammals and plants. Unlike the Are proteins in S. cerevisiae, Dga2p makes a major contribution to TAG synthesis via an acyl-CoA-dependent mechanism and is not involved in SE synthesis. This enzyme appears to affect the size and morphology of LB, suggesting a direct role of storage lipid proteins in LB formation. We report that the Are1p of Y. lipolytica was essential for sterol esterification, as deletion of the encoding gene (ARE1) completely abolished SE synthesis. Unlike its homologs in yeasts, YlARE1 has no DAG acyltransferase activity. We also reconsider the role and function of all four acyltransferase enzymes involved in the final step of neutral lipid synthesis in this oleaginous yeast. PMID:21808970

Beopoulos, Athanasios; Haddouche, Ramdane; Kabran, Philomene; Dulermo, Thierry; Chardot, Thierry; Nicaud, Jean-Marc

2012-02-01

101

[Treatment of oil-manufacturing wastewater by yeast-SBR system].  

PubMed

Eight yeast strains were applied to a sequencing batch reactor (SBR) to treat high-strength oil-containing wastewater. The removal performance, yeast cultivation method and key factors affecting the stability of system were discussed. The results show yeast sludge with MLSS of 19 g/L and SVI of 35 mL/g can be obtained in 6 d in an open system without any molds and bacteria inhibitor addition; In 30 d continuous wastewater treatment, COD and oil removal rate achieve 86.8%-96.9% and above 99.5% respectively under the influent conditions of the COD of 9000-23000 mg/L and oil of 4500-16000 mg/L; Short period of pH impact brings reversible effects on the system and the sludge retention time can affect the SVI of the yeast; Absence of nitrogen induces morphology conversion of some yeast cells from single cell to filamentous one and impairs the settling capability of the yeast. PMID:18637347

Lü, Wen-zhou; Liu, Ying; Huang, Yi-zhen

2008-04-01

102

Experimental facilities for system identification  

NASA Technical Reports Server (NTRS)

Future space vehicles will differ significantly from the space systems used in the past. The planned spacecraft configurations will include extremely large structures, up to 100-200 meters across. Because the allowable launch weights are limited, the large space structures must be constructed of lightweight, flexible elements, and active control of the shape and attitude of the spacecraft will be required. The behavior of large structures is characterized by many closely spaced natural modes, and some applications may also include large on-board disturbances. Consequently, the control and disturbance forces will invariably spill over to a large number of modes. Structural identification will be necessary for precision pointing and shape controls to be effective. An accurate mathematical model of a structure is essential for the success of precision control system design. However, the currently available analytical modeling codes, such as NASTRAN, are incapable of producing numerical models of the required precision. The favored approach for model determination is to refine the mathematical model based on experiments in the orbital environment. It is to this effect that we must develop techniques to reliably generate the accurate models required for future missions, and the arena in which these methods will be developed and proved is through ground-based system identification experiments and demonstrations. The Air Force Astronautics Laboratory (AFAL) has expanded the on-site ground-test facilities in recent years, and additional sites are planned for the immediate future. We shall review the plans for laboratory growth at AFAL with regard to the type of experiments proposed and the availability of the new facilities.

Das, Alok; Thompson, Roger C.

1988-01-01

103

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

104

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

105

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

PubMed Central

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

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

1989-01-01

106

Identification and characterization of genes related to the production of organic acids in yeast.  

PubMed

Organic acids contribute to the flavor of many foods and drinks including alcoholic beverages. To study the cellular processes affecting organic acid production, here we screened collections of Saccharomyces cerevisiae deletion mutants and identified 36 yeast mutants forming a yellow halo on YPD plates containing bromocresol purple, indicating that the pH of the medium had been lowered. The disrupted genes encoded TCA cycle enzymes, transcription factors, signal transducers, and ubiquitin-related proteins. Acetate, pyruvate, and succinate are produced by yeast fermentation in rich medium, and their production was affected by mutations of the genes GTR1, GTR2, LIP5, LSM1, PHO85, PLM2, RTG1, RTG2 and UBP3, and also succinate dehydrogenase-related genes including EMI5, SDH1, SDH2, SDH4, TCM62 and YDR379C-A. Among the genes identified, overexpression of only LIP5 affected the production of acetate in S. cerevisiae. However, overexpression of EMI5, LIP5, RTG2 and UBP3 had a significant effect on the production of acetate, citrate, lactate, and succinate in the bottom-fermenting yeast Saccharomyces pastorianus. Furthermore, phenotypic analysis of the S. cerevisiae disruptants involved in organic acid production showed that azaserine, citrate, ethionine, and sulfite are useful compounds by which mutants with altered organic acid production might be selected. Taken together, these results suggest that the regulation of many organic acids might be simultaneously achieved by activation or inactivation of a single gene. PMID:22277779

Yoshida, Satoshi; Yokoyama, Aki

2012-05-01

107

Identification of a functional homolog of the yeast copper homeostasis gene ATX1 from Arabidopsis  

SciTech Connect

A cDNA clone encoding a homolog of the yeast (Saccharomyces cerevisiae) gene Anti-oxidant 1 (ATX1) has been identified from Arabidopsis. This gene, referred to as Copper CHaperone (CCH), encodes a protein that is 36% identical to the amino acid sequence of ATX1 and has a 48-amino acid extension at the C-terminal end, which is absent from ATX1 homologs identified in animals. ATX1-deficient yeast (atx1) displayed a loss of high-affinity iron uptake. Expression of CCH in the atx1 strain restored high-affinity iron uptake, demonstrating that CCH is a functional homolog of ATX1. When overexpressed in yeast lacking the superoxide dismutase gene SOD1, both ATX1 and CCH protected the cell from the reactive oxygen toxicity that results from superoxide dismutase deficiency. CCH was unable to rescue the sod1 phenotype in the absence of copper, indicating that CCH function is copper dependent. In Arabidopsis CCH mRNA is present in the root, leaf, and in fluorescence and is up-regulated 7-fold in leaves undergoing senescence. In plants treated with 800 nL/L ozone for 30 min, CCH mRNA levels increased by 30%. In excised leaves and whole plants treated with high levels of exogenous CuSO{sub 4}, CCH mRNA levels decreased, indicating that CCH is regulated differently than characterized metallothionein proteins in Arabidopsis.

Himelblau, E.; Amasino, R.M. [Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry] [Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry; Mira, H.; Penarrubia, L. [Univ. de Valencia (Spain). Dept. de Bioquimica i Biologia Molecular] [Univ. de Valencia (Spain). Dept. de Bioquimica i Biologia Molecular; Lin, S.J.; Culotta, V.C. [Johns Hopkins Univ. School of Public Health, Bethesda, MD (United States)] [Johns Hopkins Univ. School of Public Health, Bethesda, MD (United States)

1998-08-01

108

Radio Frequency Identification Based Library Management System  

Microsoft Academic Search

Radio frequency identification (RFID) is a term that is used to describe a system that transfers the identity of an object or person wirelessly, using radio waves. It falls under the category of automatic identification technologies. This paper proposes RFID Based Library Management System that would allow fast transaction flow and will make easy to handle the issue and return

Anshul Ahuja Priyanka Grover

2010-01-01

109

Stochastic system identification in structural dynamics  

USGS Publications Warehouse

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

Safak, Erdal

1988-01-01

110

Functional Analysis With a Barcoder Yeast Gene Overexpression System  

PubMed Central

Systematic analysis of gene overexpression phenotypes provides an insight into gene function, enzyme targets, and biological pathways. Here, we describe a novel functional genomics platform that enables a highly parallel and systematic assessment of overexpression phenotypes in pooled cultures. First, we constructed a genome-level collection of ~5100 yeast barcoder strains, each of which carries a unique barcode, enabling pooled fitness assays with a barcode microarray or sequencing readout. Second, we constructed a yeast open reading frame (ORF) galactose-induced overexpression array by generating a genome-wide set of yeast transformants, each of which carries an individual plasmid-born and sequence-verified ORF derived from the Saccharomyces cerevisiae full-length EXpression-ready (FLEX) collection. We combined these collections genetically using synthetic genetic array methodology, generating ~5100 strains, each of which is barcoded and overexpresses a specific ORF, a set we termed “barFLEX.” Additional synthetic genetic array allows the barFLEX collection to be moved into different genetic backgrounds. As a proof-of-principle, we describe the properties of the barFLEX overexpression collection and its application in synthetic dosage lethality studies under different environmental conditions. PMID:23050238

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

2012-01-01

111

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

112

Study of amyloids using yeast  

PubMed Central

Summary Saccharomyces cerevisiae has been a useful model organism in such fields as the cell cycle, regulation of transcription, protein trafficking and cell biology, primarily because of its ease of genetic manipulation. This is no less so in the area of amyloid studies. The endogenous yeast amyloids described to date include prions, infectious proteins (Table 1), and some cell wall proteins (1). and amyloids of humans and a fungal prion have also been studied using the yeast system. Accordingly, the emphasis of this chapter will be on genetic, biochemical, cell biological and physical methods particularly useful in the study of yeast prions and other amyloids studied in yeast. We limit our description of these methods to those aspects which have been most useful in studying yeast prions, citing more detailed expositions in the literature. Volumes on yeast genetics methods (2–4), and on amyloids and prions (5, 6) are useful, and Masison has edited a volume of Methods on “Identification, analysis and characterization of fungal prions” which covers some of this territory (7). We also outline some useful physical methods, pointing the reader to more extensive and authoratative descriptions. PMID:22528100

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

2012-01-01

113

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

PubMed

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

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

2012-06-01

114

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

PubMed

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

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

2011-08-30

115

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

PubMed Central

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

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

1999-01-01

116

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

PubMed

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

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

1999-10-01

117

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

PubMed Central

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

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

2011-01-01

118

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

PubMed

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

Sorenson, Matthew R; Stevens, Scott W

2014-05-01

119

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

120

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

121

MALDI-TOF MS-based identification of black yeasts of the genus Exophiala.  

PubMed

In this study, we investigated the applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Exophiala species. The analysis included a total of 110 Exophiala isolates, including 15 CBS strains representing 4 species, Exophiala dermatitidis (61), E. phaeomuriformis (36), E. crusticola (9), and E. heteromorpha (4), that had been previously identified based on internal transcribed spacer (ITS) regions. We also compared the relative efficacies of Sabouraud glucose agar (SGA) and Columbia agar (CA) for use in MALDI-TOF MS. Remarkably, we obtained a log-score value ?2.0 by using either SGA or CA for all 15 CBS strains, indicating species-level identification. The remaining 95 Exophiala strains were identified to the genus or species levels, with identification rates of 96.8% and 90.5%, using SGA or CA, respectively. Most of the E. dermatitidis (100% and 92.9%), E. phaeomuriformis (80.6% and 83.9%), E. crusticola (50% and 100%), and E. heteromorpha (100% and 100%) isolates were correctly identified using SGA or CA, respectively. Furthermore, 58.9% and 26.3% of the strains had log-score values of ?2.0 by using SGA and CA, respectively. Our results indicate that MALDI-TOF MS is a rapid and reliable technique with high rates of correct taxonomic identification. PMID:25851261

Özhak-Baysan, Betil; Ö?ünç, Dilara; Dö?en, Aylin; Ilkit, Macit; de Hoog, G Sybren

2015-05-01

122

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

Microsoft Academic Search

The adenylyl-cyclase-associated protein, CAP, was originally identified in yeasts as a protein that functions in both signal transduction and cytoskeletal organization. This paper reports the identification of a cDNA and genomic DNA that encodes a CAP homologue from the mushroom Lentinus edodes. The L. edodes cap gene contains eight introns and an ORF encoding a 518 amino acid protein. The

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

1998-01-01

123

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

124

Security approaches for Radio Frequency Identification systems  

E-print Network

In this thesis, I explore the challenges related to the security of the Electronic Product Code (EPC) class of Radio Frequency Identification (RFID) tags and associated data. RFID systems can be used to improve supply chain ...

Foley, Joseph Timothy, 1976-

2007-01-01

125

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

PubMed Central

Background Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for yeast identification is limited by the requirement for protein extraction and for robust reference spectra across yeast species in databases. We evaluated its ability to identify a range of yeasts in comparison with phenotypic methods. Methods MALDI-TOF MS was performed on 30 reference and 167 clinical isolates followed by prospective examination of 67 clinical strains in parallel with biochemical testing (total n?=?264). Discordant/unreliable identifications were resolved by sequencing of the internal transcribed spacer region of the rRNA gene cluster. Principal Findings Twenty (67%; 16 species), and 24 (80%) of 30 reference strains were identified to species, (spectral score ?2.0) and genus (score ?1.70)-level, respectively. Of clinical isolates, 140/167 (84%) strains were correctly identified with scores of ?2.0 and 160/167 (96%) with scores of ?1.70; amongst Candida spp. (n?=?148), correct species assignment at scores of ?2.0, and ?1.70 was obtained for 86% and 96% isolates, respectively (vs. 76.4% by biochemical methods). Prospectively, species-level identification was achieved for 79% of isolates, whilst 91% and 94% of strains yielded scores of ?1.90 and ?1.70, respectively (100% isolates identified by biochemical methods). All test scores of 1.70–1.90 provided correct species assignment despite being identified to “genus-level”. MALDI-TOF MS identified uncommon Candida spp., differentiated Candida parapsilosis from C. orthopsilosis and C. metapsilosis and distinguished between C. glabrata, C. nivariensis and C. bracarensis. Yeasts with scores of <1.70 were rare species such as C. nivariensis (3/10 strains) and C. bracarensis (n?=?1) but included 4/12 Cryptococcus neoformans. There were no misidentifications. Four novel species-specific spectra were obtained. Protein extraction was essential for reliable results. Conclusions MALDI-TOF MS enabled rapid, reliable identification of clinically-important yeasts. The addition of spectra to databases and reduction in identification scores required for species-level identification may improve its utility. PMID:22022438

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

2011-01-01

126

Identification of power steering system dynamic models  

Microsoft Academic Search

This paper presents the identification of the dynamic model for a power steering system constructed using a rotary valve. The steering system is divided into two subsystems: mechanical and hydraulic. Each subsystem is modeled separately. An experimental setup is designed and built to instrument the steering system. The parameters of the steering system are identified using experimental data. Several methods

Amuliu Bogdan Proca; Ali Keyhani

1998-01-01

127

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

PubMed Central

Background Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in China and Southeast Asia. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less well studied and their potential roles in fungal dimorphism were largely unknown. Based on P. marneffei genome sequence, we hypothesize that miRNA-like RNAs (milRNAs) may be expressed in the dimorphic fungus. Methodology/Principal Findings We attempted to identify milRNAs in P. marneffei in both mycelial and yeast phase using high-throughput sequencing technology. Small RNAs were more abundantly expressed in mycelial than yeast phase. Sequence analysis revealed 24 potential milRNA candidates, including 17 candidates in mycelial and seven in yeast phase. Two genes, dcl-1 and dcl-2, encoding putative Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were identified in P. marneffei. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp., suggesting the co-evolution of dcl-2 among the thermal dimorphic fungi. Moreover, dcl-2 demonstrated higher mRNA expression levels in mycelial than yeast phase by 7 folds (P<0.001). Northern blot analysis confirmed the expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase. Using dcl-1KO, dcl-2KO, dclDKO and qde-2KO deletion mutants, we showed that the biogenesis of both milRNAs were dependent on dcl-2 but not dcl-1 or qde-2. The mRNA expression levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1KD, supporting regulatory function of milRNAs. Conclusions/Significance Our findings provided the first evidence for differential expression of milRNAs in different growth phases of thermal dimorphic fungi and shed light on the evolution of fungal proteins involved in milRNA biogenesis and possible role of post-transcriptional control in governing thermal dimorphism. PMID:23991243

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

2013-01-01

128

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

129

The odontology victim identification skill assessment system.  

PubMed

Mass fatality identification efforts involving forensic odontology can involve hundreds of dental volunteers. A literature review was conducted and forensic odontologists and dental educators consulted to identify lessons learned from past mass fatality identification efforts. As a result, the authors propose a skill assessment system, the Odontology Victim Identification Skill Assessment System (OVID-SAS), which details qualifications required to participate on the Antemortem, Postmortem, Ante/Postmortem Comparison, Field, and Shift Leader/Initial Response Teams. For each qualification, specific skills have been identified along with suggested educational pedagogy and skill assessment methods. Courses and assessments can be developed by dental schools, professional associations, or forensic organizations to teach and test for the skills required for dental volunteers to participate on each team. By implementing a system, such as OVID-SAS, forensic odontologists responsible for organizing and managing a forensic odontology mass fatality identification effort will be able to optimally utilize individuals presenting with proven skills. PMID:20345802

Zohn, Harry K; Dashkow, Sheila; Aschheim, Kenneth W; Dobrin, Lawrence A; Glazer, Howard S; Kirschbaum, Mitchell; Levitt, Daniel; Feldman, Cecile A

2010-05-01

130

Candida ciferrii , a new fluconazole-resistant yeast causing systemic mycosis in immunocompromised patients  

Microsoft Academic Search

Systemic infections related to fluconazole-resistant yeasts are increasingly observed in immunocompromised patients receiving fluconazole as a prophylactic antifungal treatment. Here, we report a case of invasive candidiasis caused by Candida ciferrii in a patient with acute myeloid leukemia and who suffered a relapse after autologous peripheral blood progenitor cell transplantation. Erythematous skin papulae and spotted pulmonary infiltrations were present. A

E. Gunsilius; C. Lass-Flörl; C. M. Kähler; G. Gastl; A. L. Petzer

2001-01-01

131

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

Microsoft Academic Search

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

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

2001-01-01

132

Identification of Chinese cabbage sentrin as a suppressor of Bax-induced cell death in yeast.  

PubMed

Studies into the cell death program termed apoptosis have resulted in new information regarding how cells control and execute their own demise, including insights into the mechanism by which death-preventing factors can inhibit Bax-induced caspase activation. We investigated high temperature stress-induced cell death in Brassica rapa. Using a yeast functional screening from a Brassica rapa cDNA library, the BH5-127 EST clone encoding an apoptotic suppressor peptide was identified. However, a phylogenic tree showed that BH5-127 clusters within a clade containing SUMO-1 (Small Ubiquitin-like Modifier- 1). BH5-127 was confirmed similar to have function to SUMO-1 as Fas suppression. Expression of BH5-127 showed that substantial suppression of cell death survived on SD-galactose-Leu--Ura- medium. The results suggest that BrSE (Brassica rapa Sentrin EST, BH5-127) is one of the important regulatory proteins in programming cell death, especially in the seedling stage of Chinese cabbage. PMID:22561852

Sawitri, Widhi Dyah; Slameto, Slameto; Sugiharto, Bambang; Kim, Kyung-Min

2012-05-01

133

Identification of two different RNase H activities associated with yeast RNA polymerase A.  

PubMed

Two ribonuclease H activities have been found in yeast RNA polymerase A. The nuclease activities comigrated with subunits A49 (Mr = 49,000) and A40 (Mr = 40,000), after electrophoresis in a sodium dodecyl sulfate polyacrylamide gel containing [32P](rG)n . (dC)n as substrate. Both activities were also found, among other nucleases, in a high salt chromatin extract. Several lines of evidence suggest that the chromatin RNase H of 49,000 daltons (RNase H49) is the same protein as subunit A49. They co-migrate on sodium dodecyl sulfate-gel electrophoresis, have the same chromatographic properties, and dissociate simultaneously from RNA polymerase A. Fractions containing RNase H49 stimulate RNA synthesis by RNA polymerase A* lacking A49 and A34.5 subunits. Finally, limited proteolysis of the protein band having RNase H49 activity yields the characteristic fingerprint of the A49 subunit. This subunit, therefore, exists in two states: bound to chromatin and associated with RNA polymerase A. On the other hand, it is not yet clear whether the RNase H activity of 40,000 daltons, associated with RNA polymerase A, is due to the A40 subunit or whether it represents a trace contamination by a very active nuclease tightly bound to the enzyme. PMID:387760

Iborra, F; Huet, J; Breant, B; Sentenac, A; Fromageot, P

1979-11-10

134

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...

135

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

136

Modeling, system identification, and control of ASTREX  

NASA Technical Reports Server (NTRS)

The modeling, system identification and controller design aspects of the ASTREX precision space structure are presented in this work. Modeling of ASTREX is performed using NASTRAN, TREETOPS and I-DEAS. The models generated range from simple linear time-invariant models to nonlinear models used for large angle simulations. Identification in both the time and frequency domains are presented. The experimental set up and the results from the identification experiments are included. Finally, controller design for ASTREX is presented. Simulation results using this optimal controller demonstrate the controller performance. Finally the future directions and plans for the facility are addressed.

Abhyankar, Nandu S.; Ramakrishnan, J.; Byun, K. W.; Das, A.; Cossey, Derek F.; Berg, J.

1993-01-01

137

Multi-level RF identification system  

SciTech Connect

A radio frequency identification system having a radio frequency transceiver for generating a continuous wave RF interrogation signal that impinges upon an RF identification tag. An oscillation circuit in the RF identification tag modulates the interrogation signal with a subcarrier of a predetermined frequency and modulates the frequency-modulated signal back to the transmitting interrogator. The interrogator recovers and analyzes the subcarrier signal and determines its frequency. The interrogator generates an output indicative of the frequency of the subcarrier frequency, thereby identifying the responding RFID tag as one of a "class" of RFID tags configured to respond with a subcarrier signal of a predetermined frequency.

Steele, Kerry D.; Anderson, Gordon A.; Gilbert, Ronald W.

2004-07-20

138

On Markov parameters in system identification  

NASA Technical Reports Server (NTRS)

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

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

1991-01-01

139

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

140

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...

141

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

142

Model-driven system identification of transcritical vapor compression systems  

Microsoft Academic Search

This brief uses an air conditioning system to illustrate the benefits of iteratively combining first principles and system identification techniques to develop control-oriented models of complex systems. A transcritical vapor compression system is initially modeled with first principles and then verified with experimental data. Both single-input-single-output (SISO) and multi-input-multi-output (MIMO) system identification techniques are then used to construct locally linear

Bryan P. Rasmussen; Andrew G. Alleyne; Andrew B. Musser

2005-01-01

143

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

144

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

145

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

146

Continuous ethanol fermentation using flocculent yeast entrapped in Horizontal Parallel Flow bioreactor system  

Microsoft Academic Search

Summary Continuous ethanol fermentations were conducted in single-stage and three-stage Horizontal Parallel Flow (HOPAF) bioreactor systems. Biological entrapment of yeast could be achieved by virtue of its growth and flocculence in reusable porous stainless steel fiber sheets. Twenty-five g·l-1·h-1 productivity was obtained in three-stage system. Distributions of ethanol and glucose in reactors were examined.

Lekh Raj Juneja; Minoru Terasawa; Tsuneo Yamane; Shoichi Shimizu

1986-01-01

147

Structural system identification based on multibranch BPNN  

Microsoft Academic Search

System identification is especially important for structural health monitoring and vibration control. It is one of the critical factors to control structural vibration with high quality and evaluate whether control method can be applied or not. In this paper, a kind of multi-branch BPNN model is proposed to identify structural dynamic system. In this model, the primary factors that affect

Hongnan Li; Hao Yang; Dongsheng Li

2004-01-01

148

Identification and isolation of the cytochrome oxidase subunit II gene in mitochondria of the yeast Hansenula saturnus  

Microsoft Academic Search

Mitochondrial DNA from the petite negative yeast Hansenula saturnus has been isolated and sized by digestion with restriction enzymes. The size of the mitochondrial genome is approximately 47 kb. The gene for subunit II of cytochrome oxidase was localized in the genome by Southern blotting using a [32P]-labeled probe containing the subunit II gene of the yeast Saccharomyces cerevisiae. The

Janet E. Lawson; Donald W. Deters

1985-01-01

149

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...

150

A practical approach to rotorcraft systems identification  

NASA Technical Reports Server (NTRS)

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

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

1984-01-01

151

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

152

Continuous-Time Bilinear System Identification  

NASA Technical Reports Server (NTRS)

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

Juang, Jer-Nan

2003-01-01

153

Direct alcoholic fermentation of starchy biomass using amylolytic yeast strains in batch and immobilized cell systems  

Microsoft Academic Search

Direct alcoholic fermentation of dextrin or soluble starch with selected amylolytic yeasts was studied in both batch and immobilized cell systems. In batch fermentations, Saccharomyces diastaticus was capable of fermenting high dextrin concentrations much more efficiently than Schwanniomyces castellii. From 200 g·l-1 of dextrin S. diastaticus produced 77 g·l-1 of ethanol (75% conversion efficiency). The conversion efficiency decreased to 59%

G. Amin; R. De Mot; K. Van Dijck; H. Verachtert

1985-01-01

154

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

E-print Network

: Uncoupling protein 3; Yeast expression system; Energy expenditure 1. Introduction Uncoupling proteins (UCPs)2 proteins with 59% and 57% homology to UCP1 were identi¢ed, UCP2 [10,11] and UCP3 [12^14]. The UCP3 gene generates two mRNA transcripts, UCP3L, which encodes a protein similar in length to UCP1 and UCP2, and UCP3S

155

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

156

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

157

A novel alkali-tolerant Yarrowia lipolytica strain for dissecting Na +-coupled phosphate transport systems in yeasts  

Microsoft Academic Search

The newly isolated osmo-, salt- and alkali-tolerant Yarrowia lipolytica yeast strain is remarkable by its capacity to grow at alkaline pH values (pH 9.7), which makes it an excellent model system for studying Na+-coupled phosphate transport systems in yeast cells grown at alkaline conditions. In cells Y. lipolytica grown at pH 9.7, phosphate uptake was mediated by several kinetically discrete

Renata Zvyagilskaya; Bengt L. Persson

2005-01-01

158

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

159

Authentication Without Identification using Anonymous Credential System  

E-print Network

Privacy and security are often intertwined. For example, identity theft is rampant because we have become accustomed to authentication by identification. To obtain some service, we provide enough information about our identity for an unscrupulous person to steal it (for example, we give our credit card number to Amazon.com). One of the consequences is that many people avoid e-commerce entirely due to privacy and security concerns. The solution is to perform authentication without identification. In fact, all on-line actions should be as anonymous as possible, for this is the only way to guarantee security for the overall system. A credential system is a system in which users can obtain credentials from organizations and demonstrate possession of these credentials. Such a system is anonymous when transactions carried out by the same user cannot be linked. An anonymous credential system is of significant practical relevance because it is the best means of providing privacy for users.

Damodaram, A

2009-01-01

160

System identification of a natural gas engine  

Microsoft Academic Search

Simulation results are shown for linear system identification carried out to identify key model parameters of a lean-burn natural gas engine with transmission. The natural gas engine can be described by a nonlinear plant with three states. The dynamic state equations of the model involve parameters that might vary depending on ambient conditions, type of transmission connected to the engine,

Anupam Gangopadhyay; Peter Meckl

1998-01-01

161

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

162

Music Emotion Identification from Lyrics Systems Science  

E-print Network

Music Emotion Identification from Lyrics Dan Yang Systems Science University of Ottawa Ottawa aspect of research which combines different classifiers of musical emotion such as acoustics and lyrical text. Keywords: Text Mining, Text Classification, Music Information Retrieval, Lyrical Text, Emotion. I

Lee, WonSook

163

Aircraft System Identification Using Artificial Neural Networks  

E-print Network

Aircraft System Identification Using Artificial Neural Networks Kenton Kirkpatrick Jim May Jr. John Networks 2 Artificial Neural Networks ANNSID Conclusions and Open Challenges #12;Motivation 3 #12;Motivating Questions Is it possible to use artificial neural networks to determine a linear model

Valasek, John

164

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

165

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

166

System identification: A question of uniqueness, revisited  

NASA Technical Reports Server (NTRS)

Questions of uniqueness of parameters which were obtained from a system identification algorithm were investigated. The local properties of the surface defined by the error function were used. Static and dynamic numerical experiments on determinate and indeterminate trusses and on shear buildings illustrate the procedure. Examples are given of loading and sensor configurations which produce unique parameters

Hardee, J. E.; Matzen, V. C.

1982-01-01

167

System identification, observer identification, and data-based controller design  

NASA Astrophysics Data System (ADS)

Three basic aspects of modern control are the development of a state space model from data, the development of an observer based on the model and assumed or somehow separately measured plant and measurement noise levels, and the design of an optimal control law. Here we develop algorithms that relate each process more directly to data, and obtain substantially improved results. Regarding identification, in state space model identification a Hankel matrix is needed, which is usually constructed from Markov parameters obtained by some process from data. Here we directly identify the Hankel matrix from data. The resulting algorithm is shown to give significantly improved order determination, which simplifies the model identification process by eliminating the common need for a model reduction step. For observer design, a method of developing observers directly from data is presented, which benefits from the above improved order determination, and in addition eliminates the very troublesome assignment of plant and measurement noise covariances in a Kalman filter design. The data is used to directly determine the needed observer gain without the need to assign values for these covariances. In numerical examples, the performance of the identified estimator is shown to compare very favorably with that of a Kalman filter that knows exactly the true system model and the true measurement and plant noise statistics. Multi-step observers are also developed which are useful in predictive control. The design of a modern controller would normally require model identification, then estimator choice based on the model, and then optimal control design based on the model and using the estimator as part of the control process. Regarding controller design, the contributions in this thesis bypass this multistage process and directly produce the control gains directly from data. There is no need for a model and no need for an observer. The results are optimal predictive control laws. The benefits of each of these new algorithms are demonstrated on real data for the Hubble telescope, or a truss structure at NASA Langley Research Center, or in experiments run on a very flexible spine structure.

Lim, Ryoung Kyu

168

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

169

Impact of yeast systems biology on industrial biotechnology  

Microsoft Academic Search

Systems biology is yet an emerging discipline that aims to quantitatively describe and predict the functioning of a biological system. This nascent discipline relies on the recent advances in the analytical technology (such as DNA microarrays, mass spectromety, etc.) to quantify cellular characteristics (such as gene expression, protein and metabolite abundance, etc.) and computational methods to integrate information from these

Dina Petranovic; Goutham N. Vemuri

2009-01-01

170

Phenotypic and molecular identification and clustering of lactic acid bacteria and yeasts from wheat (species Triticum durum and Triticum aestivum) sourdoughs of Southern Italy.  

PubMed

The microflora of 25 wheat sourdoughs from the Apulia region, Southern Italy, was characterized. The sourdoughs were mainly produced from Triticum durum wheat. The number of lactic acid bacteria and yeasts ranged from ca. log 7.5 to log 9.3 colony forming units (cfu)/g and from log 5.5 to log 8.4 cfu/g, respectively. About 38% of the 317 isolates of lactic acid bacteria were identified by conventional physiological and biochemical tests. Phenotypic identification was confirmed by 16S rDNA and 16S/23S rRNA spacer region PCR. Overall, 30% of the isolates were identified as Lactobacillus sanfranciscensis, 20% as Lb. alimentarius, 14% as Lb. brevis, 12% as Leuconostoc citreum, 7% as Lb. plantarum, 6% as Lactococcus lactis subsp. lactis, 4% as Lb. fermentum and Lb. acidophilus, 2% as Weissella confusa and 1% as Lb. delbrueckii subsp. delbrueckii. Some of these species have not been previously isolated from sourdoughs. Since bakers yeast is widely used in sourdough production, Saccharomyces cerevisiae was largely found. The phenotypical relationships within the main lactic acid bacteria identified were established by using cluster analysis. A microbial map of the 25 sourdoughs was plotted showing characteristic associations among lactic acid bacteria and differences in the lactic acid bacteria species which were mainly due to the species of wheat flour, use of bakers yeast and type of bread. PMID:11252516

Corsetti, A; Lavermicocca, P; Morea, M; Baruzzi, F; Tosti, N; Gobbetti, M

2001-02-28

171

The tandem affinity purification method: an efficient system for protein complex purification and protein interaction identification.  

PubMed

Isolation and identification of protein partners in multi-protein complexes are important in gaining further insights into the cellular roles of proteins and determining the possible mechanisms by which proteins have an effect in the molecular environment. The tandem affinity purification (TAP) method was originally developed in yeast for the purification of protein complexes and identification of protein-protein interactions. With modifications to this method and many variations in the original tag made over the past few years, the TAP system could be applied in mammalian, plant, bacteria and other systems for protein complex analysis. In this review, we describe the application of the TAP method in various organisms, the modification in the tag, the disadvantages, the developments and the future prospects of the TAP method. PMID:20399864

Xu, Xiaoli; Song, Yuan; Li, Yuhua; Chang, Jianfeng; Zhang, Hua; An, Lizhe

2010-08-01

172

NON-LINEAR SYSTEM IDENTIFICATION USING UNCOUPLED STATE  

E-print Network

NON-LINEAR SYSTEM IDENTIFICATION USING UNCOUPLED STATE MULTIPLE-MODEL APPROACH Rodolfo Orjuela deals with the off-line identification of non-linear systems employing the multiple-model approach. We is proposed to avoid this phenomenon. Keywords: Multiple-models, Non-linear system identification, Model

Paris-Sud XI, Université de

173

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

174

Structural system identification: Structural dynamics model validation  

SciTech Connect

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

Red-Horse, J.R.

1997-04-01

175

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

176

Identification of multivariate linear systems  

SciTech Connect

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

Griffith, J.M.

1981-01-01

177

Deformable Contour Tracking & System Identification  

E-print Network

. Vaswani 3 Brain MRI slices: Tumor sequence (actual deformations) Perspective effect: Plane tracked by UAV,... ­ Animals such as a fish ­ Medical sequences: ROIs in brain or heart · Changing region of partial occlusions a UAV #12;Deformable Contour Tracking & System Id ­ N. Vaswani 14 Separate clutter (mul

Vaswani, Namrata

178

Unique device identification system. Final rule.  

PubMed

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

2013-09-24

179

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

180

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

181

Automated fuzzy neural networks for nonlinear system identification  

Microsoft Academic Search

This paper discusses the identification of nonlinear dynamic system using fuzzy neural networks. It focuses on both the structure uncertainty and the parameter uncertainty which have been widely explored in the literature of nonlinear system identification. The main contribution is that an integrated analytic framework is proposed for automated fuzzy neural network structure selection, parameter identification and hysteresis network switching

Wen Yu

2008-01-01

182

NEURAL NETWORK BASED HAMMERSTEIN SYSTEM IDENTIFICATION USING PARTICLE SWARM SUBSPACE  

E-print Network

, Neural Network Training, Subspace Identification, Static Nonlinearity, Dynamic Linearity, Radial BasisNEURAL NETWORK BASED HAMMERSTEIN SYSTEM IDENTIFICATION USING PARTICLE SWARM SUBSPACE ALGORITHM S Function (RBF) Neural Networks. Abstract: This paper presents a new method for modeling of Hammerstein

Rizvi, Syed Z.

183

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

184

Realization-Based System Identification with Applications  

NASA Astrophysics Data System (ADS)

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

Miller, Daniel N.

185

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

186

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

187

Identification of Pseudomonas syringae type III effectors that can suppress programmed cell death in plants and yeast.  

PubMed

The Pseudomonas syringae pv. tomato DC3000 type III secretion system (TTSS) is required for bacterial pathogenicity on plants and elicitation of the hypersensitive response (HR), a programmed cell death (PCD) that occurs on resistant plants. Cosmid pHIR11 enables non-pathogens to elicit an HR dependent upon the TTSS and the effector HopPsyA. We used pHIR11 to determine that effectors HopPtoE, avirulence AvrPphEPto, AvrPpiB1Pto, AvrPtoB, and HopPtoF could suppress a HopPsyA-dependent HR on tobacco and Arabidopsis. Mixed inoculum and Agrobacterium-mediated transient expression experiments confirmed that suppressor action occurred within plant cells. These suppressors, with the exception of AvrPpiB1Pto, inhibited the expression of the tobacco pathogenesis-related (PR) gene PR1a. DC3000 suppressor mutants elicited an enhanced HR consistent with these mutants lacking an HR suppressor. Additionally, HopPtoG was identified as a suppressor on the basis of an enhanced HR produced by a hopPtoG mutant. Remarkably, these proteins functioned to inhibit the ability of the pro-apoptotic protein, Bax to induce PCD in plants and yeast, indicating that these effectors function as anti-PCD proteins in a trans-kingdom manner. The high proportion of effectors that suppress PCD suggests that suppressing plant immunity is one of the primary roles for DC3000 effectors and a central requirement for P. syringae pathogenesis. PMID:14756767

Jamir, Yashitola; Guo, Ming; Oh, Hye-Sook; Petnicki-Ocwieja, Tanja; Chen, Shaorong; Tang, Xiaoyang; Dickman, Martin B; Collmer, Alan; Alfano, James R

2004-02-01

188

An in-house assay is superior to sepsityper for direct matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry identification of yeast species in blood cultures.  

PubMed

We developed an in-house assay for the direct identification, by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, of yeasts in blood culture. Sixty-one representative strains from 12 species were analyzed in spiked blood cultures. Our assay accurately identified 95 of 107 (88.8%) positive blood cultures and outperformed the commercial Sepsityper kit (81.7% identification). PMID:25762771

Bidart, Marie; Bonnet, Isabelle; Hennebique, Aurélie; Kherraf, Zine Eddine; Pelloux, Hervé; Berger, François; Cornet, Muriel; Bailly, Sébastien; Maubon, Danièle

2015-05-01

189

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

190

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

191

Identification of a novel pathway involving a GATA transcription factor in yeast and possibly plant Zn uptake and homeostasis  

Technology Transfer Automated Retrieval System (TEKTRAN)

To gain a better understanding of the regulation of Zn homeostasis in plants and the degree of conservation of Zn homeostasis between plants and yeast, a cDNA library from the Zn/Cd hyperaccumulating plant species, Nocceae caerulescens, was screened for its ability to restore growth under Zn limitin...

192

System Identification Using Embedded Dynamic Signal Analyzer  

NASA Astrophysics Data System (ADS)

The effect of model uncertainty is increased in optical disc drives (ODDs) because the mechanical and electrical components are manufactured with a wide error tolerance to reduce production costs. In this paper, we introduce a new technique for system identification whereby an embedded dynamic signal analyzer (EDSA) is used for the estimation of the system frequency characteristics. The estimated transfer function can be utilized to adapt a controller and improve the performance and stability of the system in terms of the model uncertainty. The EDSA comprises a sine generator, system identifier, and band-pass filter. A design methodology is proposed for the production of an accurate and cost-effective sine signal, which minimizes error and prevents overflow. Moreover, the proposed algorithms are implemented in a system-on-chip for an ODD. The experimental results show that the EDSA exhibits good performance and reliability.

Kim, Soo-Yong; Koo, Keunhwi; Huh, Junho; Cho, Hyeonwoo; Kim, Sang Woo

2012-08-01

193

Yeast killer toxins and dimorphism.  

PubMed

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. PMID:2754015

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

1989-06-01

194

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

PubMed Central

Background Yeasts provide attractive expression platforms in combining ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. However, early restriction to a single yeast platform can result in costly and time-consuming failures. It is therefore advisable to assess several selected systems in parallel for the capability to produce a particular protein in desired amounts and quality. A suitable vector must contain a targeting sequence, a promoter element and a selection marker that function in all selected organisms. These criteria are fulfilled by a wide-range integrative yeast expression vector (CoMed™) system based on A. adeninivorans- and H. polymorpha-derived elements that can be introduced in a modular way. Results The vector system and a selection of modular elements for vector design are presented. Individual single vector constructs were used to transform a range of yeast species. Various successful examples are described. A vector with a combination of an rDNA sequence for genomic targeting, the E. coli-derived hph gene for selection and the A. adeninivorans-derived TEF1 promoter for expression control of a GFP (green fluorescent protein) gene was employed in a first example to transform eight different species including Hansenula polymorpha, Arxula adeninivorans and others. In a second example, a vector for the secretion of IL-6 was constructed, now using an A. adeninivorans-derived LEU2 gene for selection of recombinants in a range of auxotrophic hosts. In this example, differences in precursor processing were observed: only in A. adeninivorans processing of a MF?1/IL-6 fusion was performed in a faithful way. Conclusion rDNA targeting provides a tool to co-integrate up to 3 different expression plasmids by a single transformation step. Thus, a versatile system is at hand that allows a comparative assessment of newly introduced metabolic pathways in several organisms or a comparative co-expression of bottleneck genes in cases where production or secretion of a certain product is impaired. PMID:17105649

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

2006-01-01

195

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

196

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

PubMed Central

Yeasts are largely used as bioreactors for vaccine production. Usually, antigens are produced in yeast then purified and mixed with adjuvants before immunization. However, the purification costs and the safety concerns recently raised by the use of new adjuvants argue for alternative strategies. To this end, the use of whole yeast as both production and delivery system appears attractive. Here, we evaluated Pichia pastoris yeast as an alternative vaccine production and delivery system for the circumsporozoite protein (CS) of Plasmodium, the etiologic agent of malaria. The CS protein from Plasmodium berghei (Pb) was selected given the availability of the stringent C57Bl/6 mouse model of infection by Pb sporozoites, allowing the evaluation of vaccine efficacy in vivo. PbCS was multimerized by fusion to the measles virus (MV) nucleoprotein (N) known to auto-assemble in yeast in large-size ribonucleoprotein rods (RNPs). Expressed in P. pastoris, the N-PbCS protein generated highly multimeric and heterogenic RNPs bearing PbCS on their surface. Electron microscopy and immunofluorescence analyses revealed the shape of these RNPs and their localization in peripheral cytoplasmic inclusions. Subcutaneous immunization of C57Bl/6 mice with heat-inactivated whole P. pastoris expressing N-PbCS RNPs provided significant reduction of parasitemia after intradermal challenge with a high dose of parasites. Thus, in the absence of accessory adjuvants, a very low amount of PbCS expressed in whole yeast significantly decreased clinical damages associated with Pb infection in a highly stringent challenge model, providing a proof of concept of the intrinsic adjuvancy of this vaccine strategy. In addition to PbCS multimerization, the N protein contributed by itself to parasitemia delay and long-term mice survival. In the future, mixtures of whole recombinant yeasts expressing relevant Plasmodium antigens would provide a multivalent formulation applicable for antigen combination screening and possibly for large-scale production, distribution and delivery of a malaria vaccine in developing countries. PMID:24475165

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

2014-01-01

197

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

198

Compressive Topology Identification of Large-Scale Interconnected Dynamical Systems  

E-print Network

Compressive Topology Identification of Large-Scale Interconnected Dynamical Systems Borhan M) Compressive Topology Identification CEEMS Seminar - 4/06/12 1 / 38 #12;Outline Gene Network BMS (CSM) Compressive Topology Identification CEEMS Seminar - 4/06/12 2 / 38 #12;Outline Compressive Topology

Sanandaji, Borhan M.

199

A secure identification system using coherent states  

NASA Astrophysics Data System (ADS)

A quantum identification system based on the transformation of polarization of a mesoscopic coherent state is proposed. Physically, an initial polarization state which carries the identity information is transformed into an arbitrary elliptical polarization state. To verify the identity of a communicator, a reverse procedure is performed by the receiver. For simply describing the transformation procedure, the analytical methods of Poincaré sphere and quaternion are adopted. Since quantum noise provides such a measurement uncertainty for the eavesdropping that the identity information cannot be retrieved from the elliptical polarization state, the proposed scheme is secure.

He, Guang-Qiang; Zeng, Gui-Hua

2006-02-01

200

A recent case study in system identification  

NASA Technical Reports Server (NTRS)

Results of a recent study of a ten-bay truss structure at the NASA Langley Research Center are reported. First, the conditioning of complex eigenvectors derived by the ERA method is discussed. Results of parameter estimation using the SSID (Structural System Identification) code are then presented. Based on the results of the study, it is concluded that (1) parameter estimation based on modal data should include eigenvectors as well as eigenvalues; (2) the eigenvectors should be orthogonalized when orthogonality is poor due to closely spaced modes; and (3) the parameters used in the estimation should enable the model to match the data.

Hasselman, T. K.; Chrostowski, J. D.

1991-01-01

201

Parameter identification for nonlinear aerodynamic systems  

NASA Technical Reports Server (NTRS)

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

Pearson, Allan E.

1993-01-01

202

Purification and Properties of an Esterase from the Yeast Saccharomyces cerevisiae and Identification of the Encoding Gene  

Microsoft Academic Search

We purified an intracellular esterase that can function as an S-formylglutathione hydrolase from the yeast Saccharomyces cerevisiae. Its molecular mass was 40 kDa, as determined by gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The isoelectric point was 5.0 by isoelectric focusing. The enzyme activity was optimal at 50°C and pH 7.0. The corresponding gene, YJLO68C, was identified by its

GIULIANO DEGRASSI; LASSE UOTILA; RAFFAELLA KLIMA; VITTORIO VENTURI

1999-01-01

203

Endocytosis is required for the growth of vacuolar H(+)ATPase defective yeast: identification of six new END genes  

Microsoft Academic Search

Yeast mutants that are defective in acidification of the lysosome-like vacuole are able to grow at pH 5.5, but not at pH 7. Here, we present evi- dence that endocytosis is required for this low pH- dependent growth and use this observation to develop a screen for mutants defective in endocytosis. By iso- lating mutants that cannot grow when they

Alan L. Munn; Howard Riezman

1994-01-01

204

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

PubMed Central

In fission yeast, regulation of p34(cdc2) plays an important role in the checkpoint coupling mitosis to completion of DNA replication. The cdc2 mutations cdc2-3w (C67Y) and cdc2-4w (C67F) abolish checkpoint control without seriously affecting normal cell proliferation. However the molecular basis of this phenotype is not known. To better understand the role of p34(cdc2) in checkpoint control, we have screened for more mutations in Schizosaccharomyces pombe cdc2 with this phenotype. We have isolated cdc2-3w and cdc2-4w, as well as three new cdc2 alleles: cdc2-6w (N66I), cdc2-7w (E8V) and cdc2-8w (K9E). The altered residues map to two different regions on opposite faces of the protein, suggesting that the interaction between p34(cdc2) and components of the checkpoint pathway may be complex. In contrast to cdc2-3w and cdc2-4w, the new mutations alter residues that are conserved between the fission yeast cdc2(+) and other cdks, including the human CDC2 protein. Expression of the equivalent human CDC2 mutants in fission yeast abolishes checkpoint control, suggesting that these residues could be involved in checkpoint-dependent regulation of other eukaryotic cdks. PMID:8978030

Basi, G.; Enoch, T.

1996-01-01

205

System Identification of a Vortex Lattice Aerodynamic Model  

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

206

Fractional System Identification: An Approach Using Continuous Order-Distributions  

NASA Technical Reports Server (NTRS)

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

Hartley, Tom T.; Lorenzo, Carl F.

1999-01-01

207

Construction of Helicopter-loop Simulation System and Model Identification  

Microsoft Academic Search

3-DOF helicopter experimental teaching system components were introduced in the paper and the freedom of three helicopters system modeling were executed by using theoretical modeling method and the equation of state system was educed. The pitch axis for the model identification was introduced by using identification of modern. Application of linear quadratic optimal control strategy designed controller and expatiated that

Li Qing; Yin Xiuyun; Liu Zhengao; Song Fanfan

2007-01-01

208

System Identification of X-33 Neural Network  

NASA Technical Reports Server (NTRS)

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

Aggarwal, Shiv

2003-01-01

209

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

210

Urmylation and tRNA thiolation functions of ubiquitin-like Uba4·Urm1 systems are conserved from yeast to man.  

PubMed

The ubiquitin-like protein Urm1 from budding yeast and its E1-like activator Uba4 have dual roles in protein urmylation and tRNA thiolation pathways. To study whether these are conserved among eukaryotes, we used gene shuffles to replace the yeast proteins by their human counterparts, hURM1 and hUBA4/MOCS3. As judged from biochemical and genetical assays, hURM1 and hUBA4 are functional in yeast, albeit at reduced efficiencies. They mediate urmylation of the peroxiredoxin Ahp1, a known urmylation target in yeast, and support tRNA thiolation. Similar to hUBA4, yeast Uba4 itself is modified by Urm1 and hURM1 suggesting target overlap between eukaryal urmylation pathways. In sum, our study shows that dual-function ubiquitin-like Urm1·Uba4 systems are conserved and exchangeable between human and yeast cells. PMID:25747390

Jüdes, André; Ebert, Folke; Bär, Christian; Thüring, Kathrin L; Harrer, Aileen; Klassen, Roland; Helm, Mark; Stark, Michael J R; Schaffrath, Raffael

2015-04-01

211

Identification and biophysical characterization of a very-long-chain-fatty-acid-substituted phosphatidylinositol in yeast subcellular membranes  

PubMed Central

Morphological analysis of a conditional yeast mutant in acetyl-CoA carboxylase acc1ts/mtr7, the rate-limiting enzyme of fatty acid synthesis, suggested that the synthesis of C26 VLCFAs (very-long-chain fatty acids) is important for maintaining the structure and function of the nuclear membrane. To characterize this C26-dependent pathway in more detail, we have now examined cells that are blocked in pathways that require C26. In yeast, ceramide synthesis and remodelling of GPI (glycosylphosphatidylinositol)-anchors are two pathways that incorporate C26 into lipids. Conditional mutants blocked in either ceramide synthesis or the synthesis of GPI anchors do not display the characteristic alterations of the nuclear envelope observed in acc1ts, indicating that the synthesis of another C26-containing lipid may be affected in acc1ts mutant cells. Lipid analysis of isolated nuclear membranes revealed the presence of a novel C26-substituted PI (phosphatidylinositol). This C26-PI accounts for approx. 1% of all the PI species, and is present in both the nuclear and the plasma membrane. Remarkably, this C26-PI is the only C26-containing glycerophospholipid that is detectable in wild-type yeast, and the C26-substitution is highly specific for the sn-1 position of the glycerol backbone. To characterize the biophysical properties of this lipid, it was chemically synthesized. In contrast to PIs with normal long-chain fatty acids (C16 or C18), the C26-PI greatly reduced the bilayer to hexagonal phase transition of liposomes composed of 1,2-dielaidoyl-sn-glycero-3-phosphoethanolamine (DEPE). The biophysical properties of this lipid are thus consistent with a possible role in stabilizing highly curved membrane domains. PMID:15270698

2004-01-01

212

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

PubMed Central

Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule participating in cellular regulatory events and having implications for disease. A challenge in deciphering ceramide signaling emanates from the myriad of ceramide species that exist and the possibility that many of them may have distinct functions. Here, we applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast (Saccharomyces cerevisiae) and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We find that during heat stress distinct metabolic mechanisms control the abundance of different groups of ceramide species. Additionally, distinct groups of ceramide species regulated different sets of functionally related genes, indicating that specific sub-groups of lipids participated in different regulatory pathways. These results indicate a previously unrecognized complexity and versatility of lipid-mediated cell regulation. PMID:24170935

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

2014-01-01

213

Genotoxicity of chemical compounds identification and assessment by yeast cells transformed with GFP reporter constructs regulated by the PLM2 or DIN7 promoter.  

PubMed

Yeast cells transformed with high-copy number plasmids comprising a green fluorescent protein (GFP)-encoding gene optimized for yeast under the control of the new DIN7 or PLM2 and the established RNR2 and RAD54 promoters were used to assess the genotoxic potential of chemical compounds. The activity of potential DNA-damaging agents was investigated by genotoxicity assays and by OxoPlate assay in the presence of various test compounds. The fluorescence signal generated by GFP in response to DNA damage was related to the different concentrations of analytes and the analyte-dependent GFP synthesis. The use of distinct DNA damage-inducible promoters presents alternative genotoxicity testing strategies by selective induction of promoters in response to DNA damage. The new DIN7 and PLM2 systems show higher sensitivity than the RNR2 and RAD54 systems in detecting 4-nitroquinoline-N-oxide and actinomycin D. Both DIN7 and PLM2 systems are able to detect camptothecin while RNR2 and RAD54 systems are not. Automated laboratory systems with assay performance on 384-well microplates provide for cost-effective high-throughput screening of DNA-damaging agents, reducing compound consumption to about 53% as compared with existing eukaryotic genotoxicity bioassays. PMID:25691521

Bui, Van Ngoc; Nguyen, Thi Thu Huyen; Bettarel, Yvan; Nguyen, Thi Hoai Thu; Pham, Thuy Linh; Hoang, Thi Yen; Nguyen, Vu Thanh Thanh; Nghiem, Ngoc Minh; Wölfl, Stefan

2015-01-01

214

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

NASA Astrophysics Data System (ADS)

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

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

215

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

NASA Astrophysics Data System (ADS)

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

Pisman, T.; Somova, L.

216

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

PubMed

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

Pisman, T I; Somova, L A

2003-01-01

217

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

PubMed Central

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

2012-01-01

218

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

PubMed

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

Kotani, Tetsuya; Takagi, Hiroshi

2008-06-01

219

Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog.  

PubMed

Aminoacyl-tRNA synthetases (aaRSs) are a group of ancient enzymes catalyzing aminoacylation and editing reactions for protein biosynthesis. Increasing evidence suggests that these critical enzymes are often associated with mammalian disorders. Therefore, complete determination of the enzymes functions is essential for informed diagnosis and treatment. Here, we show that a yeast knock-out strain for the threonyl-tRNA synthetase (ThrRS) gene is an excellent platform for such an investigation. Saccharomyces cerevisiae ThrRS has a unique modular structure containing four structural domains and a eukaryote-specific N-terminal extension. Using randomly mutated libraries of the ThrRS gene (thrS) and a genetic screen, a set of loss-of-function mutants were identified. The mutations affected the synthetic and editing activities and influenced the dimer interface. The results also highlighted the role of the N-terminal extension for enzymatic activity and protein stability. To gain insights into the pathological mechanisms induced by mutated aaRSs, we systematically introduced the loss-of-function mutations into the human cytoplasmic ThrRS gene. All mutations induced similar detrimental effects, showing that the yeast model could be used to study pathology-associated point mutations in mammalian aaRSs. PMID:25416776

Ruan, Zhi-Rong; Fang, Zhi-Peng; Ye, Qing; Lei, Hui-Yan; Eriani, Gilbert; Zhou, Xiao-Long; Wang, En-Duo

2015-01-16

220

Orthogonal approaches to time-series analysis and system identification  

Microsoft Academic Search

Some recent, efficient approaches to nonlinear system identification, ARMA modeling, and time-series analysis are described and illustrated. Sufficient detail and references are furnished to enable ready implementation, and examples are provided to demonstrate superiority over established classical techniques. The ARMA identification algorithm presented does not require a priori knowledge of, or assumptions about, the order of the system to be

M. J. Korenberg; L. D. Paarmann

1991-01-01

221

Early Identification System: Predictive Validity. Research Report 80-14.  

ERIC Educational Resources Information Center

During the academic year 1978-79 school teams implemented a newly developed early identification system in all kindergarten and grade one classes in London, Ontario schools. After analysis and revision of the system, the short-term predictive validity of the process was investigated by comparing school team identification ratings made in January…

Stennett, R. G.; Earl, L. M.

222

33 CFR 164.46 - Automatic Identification System (AIS).  

Code of Federal Regulations, 2011 CFR

...2011-07-01 false Automatic Identification System (AIS). 164.46 Section 164...164.46 Automatic Identification System (AIS). (a) The following vessels...speed without the input of an external positioning device (e.g. dGPS); the use of other...

2011-07-01

223

33 CFR 164.46 - Automatic Identification System (AIS).  

Code of Federal Regulations, 2012 CFR

...2012-07-01 false Automatic Identification System (AIS). 164.46 Section 164...164.46 Automatic Identification System (AIS). (a) The following vessels...speed without the input of an external positioning device (e.g. dGPS); the use of other...

2012-07-01

224

33 CFR 164.46 - Automatic Identification System (AIS).  

Code of Federal Regulations, 2014 CFR

...2014-07-01 false Automatic Identification System (AIS). 164.46 Section 164...164.46 Automatic Identification System (AIS). (a) The following vessels...speed without the input of an external positioning device (e.g. dGPS); the use of other...

2014-07-01

225

A Method of Visualizing Three-Dimensional Distribution of Yeast in Bread Dough  

NASA Astrophysics Data System (ADS)

A novel technique was developed to monitor the change in three-dimensional (3D) distribution of yeast in frozen bread dough samples in accordance with the progress of mixing process. Application of a surface engineering technology allowed the identification of yeast in bread dough by bonding EGFP (Enhanced Green Fluorescent Protein) to the surface of yeast cells. The fluorescent yeast (a biomarker) was recognized as bright spots at the wavelength of 520 nm. A Micro-Slicer Image Processing System (MSIPS) with a fluorescence microscope was utilized to acquire cross-sectional images of frozen dough samples sliced at intervals of 1 ?m. A set of successive two-dimensional images was reconstructed to analyze 3D distribution of yeast. Samples were taken from each of four normal mixing stages (i.e., pick up, clean up, development, and final stages) and also from over mixing stage. In the pick up stage yeast distribution was uneven with local areas of dense yeast. As the mixing progressed from clean up to final stages, the yeast became more evenly distributed throughout the dough sample. However, the uniformity in yeast distribution was lost in the over mixing stage possibly due to the breakdown of gluten structure within the dough sample.

Maeda, Tatsurou; Do, Gab-Soo; Sugiyama, Junichi; Oguchi, Kosei; Shiraga, Seizaburou; Ueda, Mitsuyoshi; Takeya, Koji; Endo, Shigeru

226

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

227

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

228

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

PubMed

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

Rösel, H; Kunze, G

1996-09-30

229

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

Code of Federal Regulations, 2010 CFR

...Implantable radiofrequency transponder system for patient identification and health information...Implantable radiofrequency transponder system for patient identification and health information...implantable radiofrequency transponder system for patient identification and health...

2010-04-01

230

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

231

Identification for multirate multi-input systems using the multi-innovation identification theory  

Microsoft Academic Search

This paper considers identification problems of multirate multi-input sampled-data systems. Using the continuous-time system discretization technique with zero-order holds, the mapping relationship (state–space model) between available multirate input and output data is set up. The multi-innovation identification theory is applied to estimate the parameters of the obtained multirate models and to present a multi-innovation stochastic gradient algorithm for the multirate

Lili Han; Feng Ding

2009-01-01

232

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics  

E-print Network

1 Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative systems amenable to genetic and biochemical analysis (5-16). The budding yeast Saccharomyces cerevisiae@genetics.wustl.edu Abstract We screened for new structural non-coding RNAs in the genome sequence of the yeast Saccharomyces

Eddy, Sean

233

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

234

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

NASA Astrophysics Data System (ADS)

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.; Bai, Zhong-Chen; Zhang, Xin; Mai, John D.

2013-11-01

235

Modeling, validation and system identification of a natural gas engine  

Microsoft Academic Search

In this paper, a model of a central fuel injected natural gas engine with transmission is developed and linear system identification is carried out to identify key model parameters that could lead to automated identification of transmission dynamics. The paper has two major components. First, the natural gas engine is modeled with an extension of the mean value engine model

Anupam Gangopadhyay; Peter Meckl

1997-01-01

236

Marked for Success?: Identification Systems Impact Poultry Welfare  

Technology Transfer Automated Retrieval System (TEKTRAN)

Individual identification is a common method used in animal research. This study was designed to examine if various common identification systems, i.e., leg bands (LB), wing bands (WB), neck tags (ST), and livestock marker (LM), have different effects on hens' behavioral and physiological homeostasi...

237

Identification and control of dynamical systems using neural networks  

Microsoft Academic Search

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

KUMPATI S. NARENDRA; KANNAN PARTHASARATHY

1990-01-01

238

Modal identification of linear non-proportionally damped systems by  

E-print Network

Modal identification of linear non-proportionally damped systems by wavelet transform Silvano is used. Frequencies, modal damping ratios and complex mode shapes are identified from output-only free-proportional) damping is significant. Key words: Modal identification, Complex modes, Shock response, Time

Paris-Sud XI, Université de

239

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

240

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

241

Neural system prediction and identification challenge  

PubMed Central

Can we infer the function of a biological neural network (BNN) if we know the connectivity and activity of all its constituent neurons?This question is at the core of neuroscience and, accordingly, various methods have been developed to record the activity and connectivity of as many neurons as possible. Surprisingly, there is no theoretical or computational demonstration that neuronal activity and connectivity are indeed sufficient to infer the function of a BNN. Therefore, we pose the Neural Systems Identification and Prediction Challenge (nuSPIC). We provide the connectivity and activity of all neurons and invite participants (1) to infer the functions implemented (hard-wired) in spiking neural networks (SNNs) by stimulating and recording the activity of neurons and, (2) to implement predefined mathematical/biological functions using SNNs. The nuSPICs can be accessed via a web-interface to the NEST simulator and the user is not required to know any specific programming language. Furthermore, the nuSPICs can be used as a teaching tool. Finally, nuSPICs use the crowd-sourcing model to address scientific issues. With this computational approach we aim to identify which functions can be inferred by systematic recordings of neuronal activity and connectivity. In addition, nuSPICs will help the design and application of new experimental paradigms based on the structure of the SNN and the presumed function which is to be discovered. PMID:24399966

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

2013-01-01

242

Automated frequency domain system identification of a large space structure  

NASA Technical Reports Server (NTRS)

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

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

1989-01-01

243

Substructure System Identification for Finite Element Model Updating  

NASA Technical Reports Server (NTRS)

This report summarizes research conducted under a NASA grant on the topic 'Substructure System Identification for Finite Element Model Updating.' The research concerns ongoing development of the Substructure System Identification Algorithm (SSID Algorithm), a system identification algorithm that can be used to obtain mathematical models of substructures, like Space Shuttle payloads. In the present study, particular attention was given to the following topics: making the algorithm robust to noisy test data, extending the algorithm to accept experimental FRF data that covers a broad frequency bandwidth, and developing a test analytical model (TAM) for use in relating test data to reduced-order finite element models.

Craig, Roy R., Jr.; Blades, Eric L.

1997-01-01

244

Rapid identification of pathogenic yeast isolates by real-time PCR and two-dimensional melting-point analysis  

Microsoft Academic Search

There is a need in the clinical microbiological laboratory for rapid and reliable methods for the universal identification\\u000a of fungal pathogens. Two different regions of the rDNA gene complex, the highly polymorphic ITS1 and ITS2, were amplified\\u000a using primers targeting conserved regions of the 18S, 5.8S and 28S genes. After melting-point analysis of the amplified products,\\u000a the Tm of the

A. Bergman; V. Fernandez; K. O. Holmström; B. E. B. Claesson; H. Enroth

2007-01-01

245

High Throughput Identification of Monoclonal Antibodies to Membrane Bound and Secreted Proteins Using Yeast and Phage Display  

PubMed Central

Antibodies are ubiquitous and essential reagents for biomedical research. Uses of antibodies include quantifying proteins, identifying the temporal and spatial pattern of expression in cells and tissue, and determining how proteins function under normal or pathological conditions. Specific antibodies are only available for a small portion of the proteome, limiting study of those proteins for which antibodies do not exist. The technologies to generate target-specific antibodies need to be improved to obtain high quality antibodies to the proteome at reasonable cost. Here we show that renewable, validated, and standardized monoclonal antibodies can be generated at high throughput, without the need for antigen production or animal immunizations. In this study, 60 protein domains from 24 selected secreted proteins were expressed on the surface of yeast and used for selection of phage antibodies, over 400 monoclonal antibodies were identified within 3 weeks. A subset of these antibodies was validated for binding to cancer cells that overexpress the target protein by flow cytometry or immunohistochemistry. This approach will be applicable to many of the membrane-bound and the secreted proteins, 20–40% of the proteome, accelerating the timeline for Ab generation while reducing the cost. PMID:25353955

Zhao, Lequn; Qu, Liang; Zhou, Jing; Sun, Zhengda; Zou, Hao; Chen, Yunn-Yi; Marks, James D.; Zhou, Yu

2014-01-01

246

A cloning method to identify caspases and their regulators in yeast: Identification of Drosophila IAP1 as an inhibitor of the Drosophila caspase DCP-1  

PubMed Central

Site-specific proteases play critical roles in regulating many cellular processes. To identify novel site-specific proteases, their regulators, and substrates, we have designed a general reporter system in Saccharomyces cerevisiae in which a transcription factor is linked to the intracellular domain of a transmembrane protein by protease cleavage sites. Here, we explore the efficacy of this approach by using caspases, a family of aspartate-specific cysteine proteases, as a model. Introduction of an active caspase into cells that express a caspase-cleavable reporter results in the release of the transcription factor from the membrane and subsequent activation of a nuclear reporter. We show that known caspases activate the reporter, that an activator of caspase activity stimulates reporter activation in the presence of an otherwise inactive caspase, and that caspase inhibitors suppress caspase-dependent reporter activity. We also find that, although low or moderate levels of active caspase expression do not compromise yeast cell growth, higher level expression leads to lethality. We have exploited this observation to isolate clones from a Drosophila embryo cDNA library that block DCP-1 caspase-dependent yeast cell death. Among these clones, we identified the known cell death inhibitor DIAP1. We showed, by using bacterially synthesized proteins, that glutathione S-transferase–DIAP1 directly inhibits DCP-1 caspase activity but that it had minimal effect on the activity of a predomainless version of a second Drosophila caspase, drICE. PMID:10077606

Hawkins, Christine J.; Wang, Susan L.; Hay, Bruce A.

1999-01-01

247

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

248

System Identification: Time Varying and Nonlinear Methods  

E-print Network

to develop first few time step models is detailed, providing a unified solution to the time varying identification problem. The practical problem of identifying the time varying generalized Markov parameters required for TVERA is presented as the next result...

Majji, Manoranjan

2010-07-14

249

A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast  

Technology Transfer Automated Retrieval System (TEKTRAN)

A linear discrete dynamic system model is constructed to represent the temporal interactions among significantly expressed genes in response to bioethanol conversion inhibitor 5-hydroxymethylfurfural for ethanologenic yeast Saccharomyces cerevisiae. This study identifies the most significant linear...

250

Red yeast  

MedlinePLUS

... problems. Other conditions. More evidence is needed to rate the effectiveness of red yeast for these uses. ... can affect the muscles. Red yeast can also affect the muscles. Taking niacin along with ... cautious with this combination.Talk with your health provider.

251

Dry yeast  

NSDL National Science Digital Library

Yeast is a type of eukaryotic organism that can live in a dormant state. It can be activated from its dormant state by water and sugar. The yeast uses the sugar to grow and produces carbon dioxide gas as a byproduct.

Ranveig Thattai (None; )

2005-09-27

252

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

253

Complete and Fast Unknown Tag Identification in Large RFID Systems  

E-print Network

, Bin Xiao The Hong Kong Polytechnic University Central South University Abstract--The RFID technologyComplete and Fast Unknown Tag Identification in Large RFID Systems Xuan Liu, Shigeng Zhang, Kai Bu

Xiao, Bin

254

Radio Frequency Identification (RFID) System 333 [2] . RFID. , ,  

E-print Network

http://www.martindaleassoc.com/barcode_readers.php#psc [5] Retrieved July 14, 2008, from http://www.zbausa.com/security_card_reader Identification (RFID) System334 [14] Retrieved July 14, 2008, from http://www.automaticleasing.com/images/ Cards

Kovintavewat, Piya

255

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

256

Frequency-based structural damage identification and dynamic system characterisation   

E-print Network

This thesis studies structural dynamic system identification in a frequency-based framework. The basic consideration stems from the fact that frequencies may generally be measured with higher accuracy than other pertinent ...

Mao, Lei

2012-11-29

257

System Identification and the Modeling of Sailing Yachts  

E-print Network

This research represents an exploration of sailing yacht dynamics with full-scale sailing motion data, physics-based models, and system identification techniques. The goal is to provide a method of obtaining and validating ...

Legursky, Katrina

2013-12-31

258

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

259

S-adenosyl-L-homocysteine hydrolase and methylation disorders: Yeast as a model system  

PubMed Central

S-adenosyl-L-methionine (AdoMet)-dependent methylation is central to the regulation of many biological processes: more than 50 AdoMet-dependent methyltransferases methylate a broad spectrum of cellular compounds including nucleic acids, proteins and lipids. Common to all AdoMet-dependent methyltransferase reactions is the release of the strong product inhibitor S-adenosyl-L-homocysteine (AdoHcy), as a by-product of the reaction. S-adenosyl-L-homocysteine hydrolase is the only eukaryotic enzyme capable of reversible AdoHcy hydrolysis to adenosine and homocysteine and, thus, relief from AdoHcy inhibition. Impaired S-adenosyl-L-homocysteine hydrolase activity in humans results in AdoHcy accumulation and severe pathological consequences. Hyperhomocysteinemia, which is characterized by elevated levels of homocysteine in blood, also exhibits a similar phenotype of AdoHcy accumulation due to the reversal of the direction of the S-adenosyl-L-homocysteine hydrolase reaction. Inhibition of S-adenosyl-L-homocysteine hydrolase is also linked to antiviral effects. In this review the advantages of yeast as an experimental system to understand pathologies associated with AdoHcy accumulation will be discussed. PMID:23017368

Tehlivets, Oksana; Malanovic, Nermina; Visram, Myriam; Pavkov-Keller, Tea; Keller, Walter

2013-01-01

260

Parameter estimation techniques for LTP system identification  

NASA Astrophysics Data System (ADS)

LISA Pathfinder (LPF) is the precursor mission of LISA (Laser Interferometer Space Antenna) and the first step towards gravitational waves detection in space. The main instrument onboard the mission is the LTP (LISA Technology Package) whose scientific goal is to test LISA's drag-free control loop by reaching a differential acceleration noise level between two masses in ? geodesic motion of 3 × 10-14 ms-2 / Hz in the milliHertz band. The mission is not only challenging in terms of technology readiness but also in terms of data analysis. As with any gravitational wave detector, attaining the instrument performance goals will require an extensive noise hunting campaign to measure all contributions with high accuracy. But, opposite to on-ground experiments, LTP characterisation will be only possible by setting parameters via telecommands and getting a selected amount of information through the available telemetry downlink. These two conditions, high accuracy and high reliability, are the main restrictions that the LTP data analysis must overcome. A dedicated object oriented Matlab Toolbox (LTPDA) has been set up by the LTP analysis team for this purpose. Among the different toolbox methods, an essential part for the mission are the parameter estimation tools that will be used for system identification during operations: Linear Least Squares, Non-linear Least Squares and Monte Carlo Markov Chain methods have been implemented as LTPDA methods. The data analysis team has been testing those methods with a series of mock data exercises with the following objectives: to cross-check parameter estimation methods and compare the achievable accuracy for each of them, and to develop the best strategies to describe the physics underlying a complex controlled experiment as the LTP. In this contribution we describe how these methods were tested with simulated LTP-like data to recover the parameters of the model and we report on the latest results of these mock data exercises.

Nofrarias Serra, Miquel

261

Research of Uncertainty Reasoning in Pineapple Disease Identification System  

NASA Astrophysics Data System (ADS)

In order to deal with the uncertainty of evidences mostly existing in pineapple disease identification system, a reasoning model based on evidence credibility factor was established. The uncertainty reasoning method is discussed,including: uncertain representation of knowledge, uncertain representation of rules, uncertain representation of multi-evidences and update of reasoning rules. The reasoning can fully reflect the uncertainty in disease identification and reduce the influence of subjective factors on the accuracy of the system.

Liu, Liqun; Fan, Haifeng

262

PWL approximation of nonlinear dynamical systems, part II: identification issues  

NASA Astrophysics Data System (ADS)

This paper and its companion address the problem of the approximation/identification of nonlinear dynamical systems depending on parameters, with a view to their circuit implementation. The proposed method is based on a piecewise-linear approximation technique. In particular, this paper describes a black-box identification method based on state space reconstruction and PWL approximation, and applies it to some particularly significant dynamical systems (two topological normal forms and the Colpitts oscillator).

DeFeo, O.; Storace, M.

2005-01-01

263

System identification of suspension bridge from ambient vibration response  

Microsoft Academic Search

The paper addresses and evaluates the application of system identification to a suspension bridge using ambient vibration response. To obtain dynamic characteristics of the bridge, two output-only time-domain system identification methods are employed namely, the Random Decrement Method combined with the Ibrahim Time Domain (ITD) method and the Natural Excitation Technique (NExT) combined with the Eigensystem Realization Algorithm (ERA). Accuracy

Dionysius M. Siringoringo; Yozo Fujino

2008-01-01

264

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

PubMed Central

The performances of five automated microbial identification systems, relative to that of a reference identification system, for their ability to accurately and repeatedly identify six common food-borne pathogens were assessed. The systems assessed were the MicroLog system (Biolog Inc., Hayward, Calif.), the Microbial Identification System (MIS; MIDI Inc., Newark, Del.), the VITEK system (bioMérieux Vitek, Hazelwood, Mo.), the MicroScan WalkAway 40 system (Dade-MicroScan International, West Sacramento, Calif.), and the Replianalyzer system (Oxoid Inc., Nepean, Ontario, Canada). The sensitivities and specificities of these systems for the identification of food-borne isolates of Bacillus cereus, Campylobacter jejuni, Listeria monocytogenes, Staphylococcus aureus, Salmonella spp., and verotoxigenic Escherichia coli were determined with 40 reference positive isolates and 40 reference negative isolates for each pathogen. The sensitivities of these systems for the identification of these pathogens ranged from 42.5 to 100%, and the specificities of these systems for the identification of these pathogens ranged from 32.5 to 100%. Some of the systems had difficulty correctly identifying the reference isolates when the results were compared to those from the reference identification tests. The sensitivity of MIS for the identification of S. aureus, B. cereus, E. coli, and C. jejuni, for example, ranged from 47.5 to 72.5%. The sensitivity of the Microlog system for the identification of E. coli was 72.5%, and the sensitivity of the VITEK system for the identification of B. cereus was 42.5%. The specificities of four of the five systems for the identification of all of the species tested with the available databases were greater than or equal to 97.5%; the exception was MIS for the identification of C. jejuni, which displayed a specificity of 32.5% when it was tested with reference negative isolates including Campylobacter coli and other Campylobacter species. All systems had >80% sensitivities for the identification of Salmonella species and Listeria species at the genus level. The repeatability of these systems for the identification of test isolates ranged from 30 to 100%. Not all systems included all six pathogens in their databases; thus, some species could not be tested with all systems. The choice of automated microbial identification system for the identification of a food-borne pathogen would depend on the availability of identification libraries within the systems and the performance of the systems for the identification of the pathogen. PMID:10074506

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

1999-01-01

265

Identification of active magnetic bearing system with a flexible rotor  

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

266

Selection of Intracellular Single-Domain Antibodies Targeting the HIV-1 Vpr Protein by Cytoplasmic Yeast Two-Hybrid System  

PubMed Central

The targeting of HIV-1 using antibodies is of high interest as molecular tools to better understand the biology of the virus or as a first step toward the design of new inhibitors targeting critical viral intracellular proteins. Small and highly stable llama-derived single-domain antibodies can often be functionally expressed as intracellular antibodies in the cytoplasm of eukaryotic cells. Using a selection method based on the Sos Recruitment System, a cytoplasmic yeast two-hybrid approach, we have isolated single-domain antibodies able to bind HIV-1 Vpr and Capside proteins in the yeast cytoplasm. One anti-Vpr single domain antibody was able to bind the HIV-1 regulatory Vpr protein in the cytoplasm of eukaryotic cells, leading to its delocalization from the nucleus to the cytoplasm. To our knowledge, this is the first description of a functional single-domain intrabody targeting HIV-1 Vpr, isolated using an in vivo cytoplasmic selection method that alleviates some limitations of the conventional yeast two-hybrid system. PMID:25436999

Matz, Julie; Hérate, Cécile; Bouchet, Jérôme; Dusetti, Nelson; Gayet, Odile; Baty, Daniel; Benichou, Serge; Chames, Patrick

2014-01-01

267

Identification of regions involved in substrate binding and dimer stabilization within the central domains of yeast Hsp40 Sis1.  

PubMed

Protein folding, refolding and degradation are essential for cellular life and are regulated by protein homeostatic processes such those that involve the molecular chaperone DnaK/Hsp70 and its co-chaperone DnaJ. Hsp70 action is initiated when proteins from the DnaJ family bind an unfolded protein for delivery purposes. In eukaryotes, the DnaJ family can be divided into two main groups, Type I and Type II, represented by yeast cytosolic Ydj1 and Sis1, respectively. Although sharing some unique features both members of the DnaJ family, Ydj1 and Sis1 are structurally and functionally distinct as deemed by previous studies, including the observation that their central domains carry the structural and functional information even in switched chimeras. In this study, we combined several biophysical tools for evaluating the stability of Sis1 and mutants that had the central domains (named Gly/Met rich domain and C-terminal Domain I) deleted or switched to those of Ydj1 to gain insight into the role of these regions in the structure and function of Sis1. The mutants retained some functions similar to full length wild-type Sis1, however they were defective in others. We found that: 1) Sis1 unfolds in at least two steps as follows: folded dimer to partially folded monomer and then to an unfolded monomer. 2) The Gly/Met rich domain had intrinsically disordered characteristics and its deletion had no effect on the conformational stability of the protein. 3) The deletion of the C-terminal Domain I perturbed the stability of the dimer. 4) Exchanging the central domains perturbed the conformational stability of the protein. Altogether, our results suggest the existence of two similar subdomains in the C-terminal domain of DnaJ that could be important for stabilizing each other in order to maintain a folded substrate-binding site as well as the dimeric state of the protein. PMID:23227221

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

2012-01-01

268

Structural parameter identification of distributed systems using finite element approximation  

NASA Technical Reports Server (NTRS)

A system identification technique is developed for classes of distributed systems using finite element approximations. Vibrating systems represented by partial differential equations have physical parameters associated with mass, stiffness, and damping distributions which need to be known in order to properly control and design mathematical models of the system. In order to identify these parameters a weighted least-squares algorithm and modified Newton-Raphson method is used for the identification process. The theory and technique is demonstrated by estimating the system parameters of a vibrating cantilever beam made up of several different structural properties.

Lee, K. Y.; Walker, D. K.; Hossain, S. A.

1985-01-01

269

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

270

A Yeast-Based Genetic System for Functional Analysis of Viral mRNA Capping Enzymes  

PubMed Central

Virus-encoded mRNA capping enzymes are attractive targets for antiviral therapy, but functional studies have been limited by the lack of genetically tractable in vivo systems that focus exclusively on the RNA-processing activities of the viral proteins. Here we have developed such a system by engineering a viral capping enzyme—vaccinia virus D1(1-545)p, an RNA triphosphatase and RNA guanylyltransferase—to function in the budding yeast Saccharomyces cerevisiae in lieu of the endogenous fungal triphosphatase (Cet1p) and guanylyltransferase (Ceg1p). This was accomplished by fusion of D1(1-545)p to the C-terminal guanylyltransferase domain of mammalian capping enzyme, Mce1(211-597)p, which serves as a vehicle to target the viral capping enzyme to the RNA polymerase II elongation complex. An inactivating mutation (K294A) of the mammalian guanylyltransferase active site in the fusion protein had no impact on genetic complementation of cet1?ceg1? cells, thus proving that (i) the viral guanylyltransferase was active in vivo and (ii) the mammalian domain can serve purely as a chaperone to direct other proteins to the transcription complex. Alanine scanning had identified five amino acids of vaccinia virus capping enzyme—Glu37, Glu39, Arg77, Glu192, and Glu194—that are essential for ? phosphate cleavage in vitro. Here we show that the introduction of mutation E37A, R77A, or E192A into the fusion protein abrogates RNA triphosphatase function in vivo. The essential residues are located within three motifs that define a family of viral and fungal metal-dependent phosphohydrolases with a distinctive capacity to hydrolyze nucleoside triphosphates to nucleoside diphosphates in the presence of manganese or cobalt. The acidic residues Glu37, Glu39, and Glu192 likely comprise the metal-binding site of vaccinia virus triphosphatase, insofar as their replacement by glutamine abolishes the RNA triphosphatase and ATPase activities. PMID:10823853

Ho, C. Kiong; Martins, Alexandra; Shuman, Stewart

2000-01-01

271

System identification methods for aircraft flight control development and validation  

NASA Technical Reports Server (NTRS)

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

Tischler, Mark B.

1995-01-01

272

A portable air jet actuator device for mechanical system identification  

NASA Astrophysics Data System (ADS)

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

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

2011-03-01

273

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2010 CFR

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

2010-10-01

274

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2011 CFR

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

2011-10-01

275

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

SciTech Connect

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

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

1993-01-01

276

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

277

Molecular Phylogeny of the Yeasts: Impact on Classification and Prediction of Biotechnological Properties  

Technology Transfer Automated Retrieval System (TEKTRAN)

DNA sequence analysis and other DNA-based methodologies have transformed the way in which yeasts are identified and classified. Development of species-specific gene sequence databases has provided a barcode system for rapid identification of known species and the recognition of undescribed species. ...

278

Prerequisites: Control Systems I&II, System Modeling, Knowledge in system identification and engine  

E-print Network

Prerequisites: Control Systems I&II, System Modeling, Knowledge in system identification and engine algorithms should then be implemented in Matlab/Simulink® and tested on a simulation model of the engine systems, MATLAB/Simulink® experience Contact: Michael Moser, ML K41, +41 44 632 65 57, mimoser

Lygeros, John

279

Volume 14 Number 17 1986 Nucleic Acids Research Analysis of the yeast SPT3 gene and Identification of its product, a positive regulator of Ty  

E-print Network

mutations have b«en identified in yeast (9,13,14), Drosophila (15-18) and mice (19). In yeast, Ty and solo of retrovlruses (2-4), transpose via an RNA intermediate (5) and appear to encode a reverse transcriptase (6). Insertion mutations caused by Ty elements, copia-like elements and mammalian proviruses can inhibit

Winston, Fred

280

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

281

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

282

Biology of the Heat Shock Response and Protein Chaperones: Budding Yeast (Saccharomyces cerevisiae) as a Model System  

PubMed Central

Summary: The eukaryotic heat shock response is an ancient and highly conserved transcriptional program that results in the immediate synthesis of a battery of cytoprotective genes in the presence of thermal and other environmental stresses. Many of these genes encode molecular chaperones, powerful protein remodelers with the capacity to shield, fold, or unfold substrates in a context-dependent manner. The budding yeast Saccharomyces cerevisiae continues to be an invaluable model for driving the discovery of regulatory features of this fundamental stress response. In addition, budding yeast has been an outstanding model system to elucidate the cell biology of protein chaperones and their organization into functional networks. In this review, we evaluate our understanding of the multifaceted response to heat shock. In addition, the chaperone complement of the cytosol is compared to those of mitochondria and the endoplasmic reticulum, organelles with their own unique protein homeostasis milieus. Finally, we examine recent advances in the understanding of the roles of protein chaperones and the heat shock response in pathogenic fungi, which is being accelerated by the wealth of information gained for budding yeast. PMID:22688810

Verghese, Jacob; Abrams, Jennifer; Wang, Yanyu

2012-01-01

283

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

PubMed

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

Böer, Erik; Piontek, Michael; Kunze, Gotthard

2009-09-01

284

System Identification of Small-Size Unmanned Helicopter Dynamics  

Microsoft Academic Search

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

Bernard Mettler; Mark B. Tischler; Takeo Kanade

285

Regulation of yeast trehalase by a monocyclic, cyclic AMP-dependent phosphorylation-dephosphorylation cascade system.  

PubMed Central

Mutation at the GLC1 locus in Saccharomyces cerevisiae resulted in simultaneous deficiencies in glycogen and trehalose accumulation. Extracts of yeast cells containing the glc1 mutation exhibited an abnormally high trehalase activity. This elevated activity was associated with a defective cyclic AMP (cAMP)-dependent monocyclic cascade which, in normal cells, regulates trehalase activity by means of protein phosphorylation and dephosphorylation. Trehalase in extracts of normal cells was largely in a cryptic form which could be activated in vitro by ATP . Mg in the presence of cAMP. Normal extracts also exhibited a correlated cAMP-dependent protein kinase which catalyzed incorporation of label from [gamma-32P]ATP into protamine. In contrast, cAMP had little or no additional activating effect on trehalase or on protamine phosphorylation in extracts of glc1 cells. Similar, unregulated activation of cryptic trehalase was also found in glycogen-deficient strains bearing a second, independently isolated mutant allele, glc1-2. Since trehalase activity was not directly affected by cAMP, the results indicate that the glc1 mutation results in an abnormally active protein kinase which has lost its normal dependence on cAMP. Trehalase in extracts of either normal or mutant cells underwent conversion to a cryptic form in an Mg2+-dependent, fluoride-sensitive reaction. Rates of this reversible reduction of activity were similar in extracts of mutant and normal cells. This same, unregulated protein kinase would act on glycogen synthase, maintaining it in the phosphorylated low-activity D-form. The glc1 mutants provide a novel model system for investigating the in vivo metabolic functions of a specific, cAMP-dependent protein kinase. PMID:6296049

Ortiz, C H; Maia, J C; Tenan, M N; Braz-Padrão, G R; Mattoon, J R; Panek, A D

1983-01-01

286

System identification of the Arabidopsis plant circadian system  

NASA Astrophysics Data System (ADS)

The circadian system generates an endogenous oscillatory rhythm that governs the daily activities of organisms in nature. It offers adaptive advantages to organisms through a coordination of their biological functions with the optimal time of day. In this paper, a model of the circadian system in the plant Arabidopsis (species thaliana) is built by using system identification techniques. Prior knowledge about the physical interactions of the genes and the proteins in the plant circadian system is incorporated in the model building exercise. The model is built by using primarily experimentally-verified direct interactions between the genes and the proteins with the available data on mRNA and protein abundances from the circadian system. Our analysis reveals a great performance of the model in predicting the dynamics of the plant circadian system through the effect of diverse internal and external perturbations (gene knockouts and day-length changes). Furthermore, we found that the circadian oscillatory rhythm is robust and does not vary much with the biochemical parameters except those of a light-sensitive protein P and a transcription factor TOC1. In other words, the circadian rhythmic profile is largely a consequence of the network's architecture rather than its particular parameters. Our work suggests that the current experimental knowledge of the gene-to-protein interactions in the plant Arabidopsis, without considering any additional hypothetical interactions, seems to suffice for system-level modeling of the circadian system of this plant and to present an exemplary platform for the control of network dynamics in complex living organisms.

Foo, Mathias; Somers, David E.; Kim, Pan-Jun

2015-02-01

287

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

E-print Network

strains FY250yEGFPpst1 (A) and 2 (B), and plasmid reporter pDCUdyEGFP (C). Background fluorescence from induced yeast lacking LexA-B42 (red) was used to determine the background threshold, as described previously. (D) Table of relevant statistics... ......................................................................................................................... 1 Affinity Chromatography of Cell Lysates .......................................................................... 1 Affinity Assays of Expressed cDNA Libraries ................................................................... 6 Tag...

Bailey, Kyle

2011-05-27

288

Cloning and Expression in Yeast of a Plant Potassium Ion Transport System  

Microsoft Academic Search

A membrane polypeptide involved in K^+ transport in a higher plant was cloned by complementation of a yeast mutant defective in K^+ uptake with a complementary DNA library from Arabidopsis thaliana. A 2.65-kilobase complementary DNA conferred ability to grow on media with K^+ concentration in the micromolar range and to absorb K^+ (or 86Rb^+) at rates similar to those in

Herve Sentenac; Nathalie Bonneaud; Michele Minet; Francois Lacroute; Jean-Michel Salmon; Frederic Gaymard; Claude Grignon

1992-01-01

289

Bioremediation of petroleum-contaminated soil by a combined system of biostimulation-bioaugmentation with yeast.  

PubMed

This paper presents a study of the effect of a combined biostimulation-bioaugmentation treatment applied to a clay-loam soil contaminated with 16,300 mg/kg of total petroleum hydrocarbons (TPH), which comprised 51% saturated hydrocarbons and 31% aromatic hydrocarbons. The bioaugmentation was performed with yeast Candida tropicalis SK21 isolated from petroleum-contaminated soil. The strain was able to grow in a pH range of 3-9 in liquid culture, and the optimum pH was found to be 6 for both growth and biosurfactant production. At pH 6, 96% and 42% of TPH were degraded by the strain at the initial diesel oil concentrations of 0.5% and 5% (v/v), respectively. The remediation via inoculating the yeast removed 83% of TPH in 180 days while the experiment with the indigenous microorganisms alone removed 61%. Microbial enumeration showed that the yeast SK21 could grow good in the soil. It was also found that dehydrogenase and polyphenoloxidase activities in soil were remarkably enhanced by the inoculation of the yeast. PMID:24600879

Fan, Mei-Ying; Xie, Rui-Jie; Qin, Gang

2014-01-01

290

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

291

Application of unsymmetric block Lanczos vectors in system identification  

NASA Technical Reports Server (NTRS)

This paper demonstrates a new system identification approach of using Lanczos coordinates in place of modal coordinates. Identified experimental Lanczos vectors can be directly used in many structural dynamics analysis applications. A multi-input, multi-output frequency-domain technique was used to extract system matrices and an unsymmetric block Lanczos algorithm was used to reduce the order of the experimental model. A cantilever beam example showed promising results, indicating that a new system identification approach using Lanczos coordinates is worthy of further study.

Kim, H. M., Jr.; Craig, R. R.

1992-01-01

292

Application of unsymmetric block Lanczos vectors in system identification  

NASA Astrophysics Data System (ADS)

This paper demonstrates a new system identification approach of using Lanczos coordinates in place of modal coordinates. Identified experimental Lanczos vectors can be directly used in many structural dynamics analysis applications. A multi-input, multi-output frequency-domain technique was used to extract system matrices and an unsymmetric block Lanczos algorithm was used to reduce the order of the experimental model. A cantilever beam example showed promising results, indicating that a new system identification approach using Lanczos coordinates is worthy of further study.

Kim, H. M., Jr.; Craig, R. R.

1992-10-01

293

70 FR 24358 - Minimum Uniform Standards for a Biometric Identification System To Ensure Identification of...  

Federal Register 2010, 2011, 2012, 2013, 2014

...Standards for a Biometric Identification System To Ensure...ANPRM) on using biometric identifiers to provide...The Transportation Security Administration...mandating use of a biometric identifier to mandating...satisfied the unique identifier standard in TEA-21...following seven personal identifiers: Name, date of...color, and......

2005-05-09

294

Barcoding the Yeasts – Which Genes?  

Technology Transfer Automated Retrieval System (TEKTRAN)

Old style yeast identification, as many know, is an onerous process requiring determination of growth reactions on 60-100 different media. Once completed, there is still a high degree of uncertainty about species identity. With the determination of sequences for domains 1 and 2 (D1/D2) of the nucl...

295

A neural network approach to identification of structural systems  

Microsoft Academic Search

Artificial neural networks are widely used for identification of nonlinear control systems. Two common approaches are multichannel neural networks and recurrent networks. The nonlinear autoregressive moving averages with exogenous input (NARMAX) model is usually used as a general input-output representation. Using the NARMAX model it is not necessary to make any assumptions regarding the structure of identified system except for

Jozef Korbicz; Andrzej Janczak

1996-01-01

296

A contamination source identification model for water distribution system security  

Microsoft Academic Search

This article presents and demonstrates a simple, straightforward genetic algorithm (GA) scheme for contamination source identification to enhance the security of water distribution systems. Related previous work on this subject has concentrated on developing analytical water quality inverse models with two major restrictions: the ability to disclose unique solutions and to handle water distribution systems of large size. These two

A. Preis; A. Ostfeld

2007-01-01

297

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

298

Risk Identification and Analysis Using a Group Support System  

Microsoft Academic Search

This paper describes the use of a specific Group Support System (GroupSystems) for Risk Identification and Analysis, sometimes called Control Risk Self Assessment (CRSA). The process can be applied to an entire organization, a department or a project. In this process, the key people involved enter the risks into networked laptop computers. The risks are discussed and the definitions refined.

Alan Weatherall; Frank Hailstones

2002-01-01

299

Distortion sources identification in power systems with capacitor banks  

Microsoft Academic Search

The identification of distortion sources in a power system is a topic unsolved. The problem has a difficult solution because there are elements in the system that do not produce harmonic but amplifies the existing in the electrical network. The most common of those elements is the capacitor, very used to compensate power factor at fundamental frequency. The capacitor behaviour

Reyes S. Herrera; Patricio Salmeron; Salvador P. Litran

2011-01-01

300

System Identification and Modelling of a High Performance Hydraulic Actuator  

E-print Network

hydraulic systems on the part of robot designers in the research community. Hydraulic actuation is often actuators. However, hydraulic actuators specifically designed for robotics and other demanding applicationsSystem Identification and Modelling of a High Performance Hydraulic Actuator Benoit Boulet, Laeeque

Hayward, Vincent

301

Numerical studies of identification in nonlinear distributed parameter systems  

NASA Technical Reports Server (NTRS)

An abstract approximation framework and convergence theory for the identification of first and second order nonlinear distributed parameter systems developed previously by the authors and reported on in detail elsewhere are summarized and discussed. The theory is based upon results for systems whose dynamics can be described by monotone operators in Hilbert space and an abstract approximation theorem for the resulting nonlinear evolution system. The application of the theory together with numerical evidence demonstrating the feasibility of the general approach are discussed in the context of the identification of a first order quasi-linear parabolic model for one dimensional heat conduction/mass transport and the identification of a nonlinear dissipation mechanism (i.e., damping) in a second order one dimensional wave equation. Computational and implementational considerations, in particular, with regard to supercomputing, are addressed.

Banks, H. T.; Lo, C. K.; Reich, Simeon; Rosen, I. G.

1989-01-01

302

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

303

Fission yeast Schizosaccharomyces pombe as a new system for the investigation of corticosterone methyloxidase deficiency-causing mutations.  

PubMed

The aldosterone synthase, CYP11B2, catalyses the conversion of 11-deoxycorticosterone to aldosterone, a process that requires three steps: a hydroxylation at position 11? to form corticosterone, another one at position 18 to produce 18-hydroxycorticosterone, and, finally, an oxidation at position 18 to form aldosterone. Aldosterone synthase deficiency usually finds its expression in infancy as a life-threatening electrolyte imbalance, caused by mutations in the CYP11B2 gene. Therefore, in depth studies of mutations and their enzymatic activities will provide information for the diagnosis and management of hypoaldosteronism caused by CYP11B2 deficiencies. Here, we report the development of a fast and cheap whole-cell technology for the enzymatic characterisation of CYP11B2 mutations. The principle of the new system is the heterologous expression of the mutants of CYP11B2 in fission yeast (Schizosaccharomyces pombe) followed by steroid bioconversion assays for the enzymatic characterisation of the investigated mutants. The new system was validated and 10 known mutations of CYP11B2 have been investigated, two of them for the first time concerning their effect on the CYP11B2 three-step reaction. The results of the fission yeast system were in good agreement with the cell culture results presenting this new system as an alternative non radioactive method that can be applied for the enzymatic characterisation of CYP11B2 mutations. PMID:21237269

Tin, Ming Kwai; Hakki, Tarek; Bernhardt, Rita

2011-03-01

304

Improving glutathione extraction from crude yeast extracts by optimizing aqueous two-phase system composition and operation conditions  

Microsoft Academic Search

PEG-Dextran and PEG-salt aqueous two-phase systems (ATPS) have been applied to separate glutathione (GSH) from crude yeast\\u000a extracts. Single-factor experiments were carried out to determine the important factors influencing the partition coefficient\\u000a and extraction yield. The effect of PEG molecular weight, phase-forming components, PEG and Dextran concentration, pH value,\\u000a and temperature on the GSH partitioning behavior in ATPS was investigated.

Xiangting Wu; Linmei Tang; Yinming Du; Zhinan Xu

2010-01-01

305

Modeling and Identification of a Large Gap Magnetic Suspension System  

NASA Technical Reports Server (NTRS)

This paper presents the results of modeling and system identification efforts on the NASA Large-Angle Magnetic Suspension Test Fixture (LAMSTF). The LAMSTF consists of a cylindrical permanent magnet which is levitated above a planar array of five electromagnets mounted in a circular configuration. The analytical model is first developed and open-loop characteristics are described. The system is shown to be highly unstable and requires feedback control in order to apply system identification. Limitations on modeling accuracy due to the effect of eddy-currents on the system are discussed. An algorithm is derived to identify a state-space model for the system from input/output data acquired during closed-loop operation. The algorithm is tested on both the baseline system and a perturbed system which has an increased presence of eddy currents. It is found that for the baseline system the analytic model adequately captures the dynamics, although the identified model improves the simulation accuracy. For the system perturbed by additional unmodeled eddy-currents the analytic model is no longer adequate and a higher-order model, determined through system identification, is required to accurately predict the system's time response.

Cox, David E. (Editor); Groom, Nelson J. (Editor); Hsiao, Min-Hung; Huang, Jen-Kuang

1996-01-01

306

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

307

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

308

Intelligent Parking Identification System Based on Embedded Video Acquisition  

Microsoft Academic Search

In this paper, it introduces a intelligent identification system based on embedded video acquisition aiming at non-parking zone control in ITS(intelligent transportation system).Background differencing method is adopted to control the non-parking zone and pick up the effective information automatically and intelligently. The system uses embedded XScale micro-frame processor of Intel and some embedded periphery chip so that it operates easily

Chen Wei; Ye Zhinan; Hao Ping

2007-01-01

309

Cryopreservation of yeast cultures.  

PubMed

A method is described that allows a wide range of yeast species to be stored in liquid nitrogen while maintaining a high level of viability. Yeast cultures are sealed in commercially available polypropylene straws after having been mixed with a glycerol-based cryoprotectant. Once placed in a secondary cryotube the temperature of the sealed straws is reduced slowly to -30 degrees C in a methanol bath over a period of up to 3 h. The straws are then transferred directly to the liquid nitrogen and placed in a racking system for long-term storage. PMID:18080465

Bond, Chris

2007-01-01

310

Identification of barriers to rotation of DNA segments in yeast from the topology of DNA rings excised by an inducible site-specific recombinase.  

PubMed Central

Controlled excision of DNA segments to yield intracellular DNA rings of well-defined sequences was utilized to study the determinants of transcriptional supercoiling of closed circular DNA in the yeast Saccharomyces cerevisiae. In delta top1 top2ts strains of S. cerevisiae expressing Escherichia coli DNA topoisomerase I, accumulation of positive supercoils in intracellular DNA normally occurs upon thermal inactivation of DNA topoisomerase II because of the simultaneous generation of positively and negatively supercoiled domains by transcription and the preferential relaxation of the latter by the bacterial enzyme. Positive supercoil accumulation in DNA rings is shown to depend on the presence of specific sequence elements; one likely cause of this dependence is that the persistence of oppositely supercoiled domains in an intracellular DNA ring requires the presence of barriers to rotation of the DNA segments connecting the domains. Analysis of the S. cerevisiae 2-microns plasmid partition system by this approach suggests that the plasmid-encoded REP1 and REP2 proteins are involved in forming such a barrier in DNA containing the REP3 sequence. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:8248138

Gartenberg, M R; Wang, J C

1993-01-01

311

Control and dynamic systems. Volume 27. System identification and adaptive control. Part 3  

SciTech Connect

The conference presents papers on a new approach to adaptive control, a linear programming approach to constrained multivariable process control, techniques for the identification of distributed systems using the finite element approximation, an identification scheme for linear control systems with wave-form type disturbances, realizations for generalized state space singular systems, and discrete systems with multiple time scales. Particular attention is given to rapprochement with traditional adaptive control design, a general method for the mathematical formulation of endodynamic models, infinite-dimensional identification. Other topics include discrete multiple-time-scale systems and linear quadratic regulators.

Leondes, C.T.

1988-01-01

312

On neural networks in identification and control of dynamic systems  

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

313

Immune System Toxicity and Immunotoxicity Hazard Identification  

EPA Science Inventory

Exposure to chemicals may alter immune system health, increasing the risk of infections, allergy and autoimmune diseases. The chapter provides a concise overview of the immune system, host factors that affect immune system heal, and the effects that xenobiotic exposure may have ...

314

Temporal and spatial properties of a yeast multi-cellular amplification system based on signal molecule diffusion.  

PubMed

We report on the spatial and temporal signaling properties of a yeast pheromone-based cell communication and amplifier system. It utilizes the Saccharomyces cerevisiae mating response pathway and relies on diffusion of the pheromone ?-factor as key signaling molecule between two cell types. One cell type represents the ?-factor secreting sensor part and the other the reporter part emitting fluorescence upon activation. Although multi-cellular signaling systems promise higher specificity and modularity, the complex interaction of the cells makes prediction of sensor performance difficult. To test the maximum distance and response time between sensor and reporter cells, the two cell types were spatially separated in defined compartments of agarose hydrogel (5 x 5 mm) and reconnected by diffusion of the yeast pheromone. Different ratios of sensor to reporter cells were tested to evaluate the minimum amount of sensor cells required for signal transduction. Even the smallest ratio, one ?-factor-secreting cell to twenty reporter cells, generated a distinct fluorescence signal. When using a 1:1 ratio, the secreted pheromone induced fluorescence in a distance of up to four millimeters after six hours. We conclude from both our experimental results and a mathematical diffusion model that in our approach: (1) the maximum dimension of separated compartments should not exceed five millimeters in gradient direction; and (2) the time-limiting step is not diffusion of the signaling molecule but production of the reporter protein. PMID:24233076

Jahn, Michael; Mölle, Annett; Rödel, Gerhard; Ostermann, Kai

2013-01-01

315

Interaction of CSFV E2 Protein with Swine Host Factors as Detected by Yeast Two-Hybrid System  

PubMed Central

E2 is one of the envelope glycoproteins of pestiviruses, including classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV). E2 is involved in several critical functions, including virus entry into target cells, induction of a protective immune response and virulence in swine. However, there is no information regarding any host binding partners for the E2 proteins. Here, we utilized the yeast two-hybrid system and identified fifty-seven host proteins as positive binding partners which bound E2 from both CSFV and BVDV with the exception of two proteins that were found to be positive for binding only to CSFV E2. Alanine scanning of CSFV E2 demonstrated that the binding sites for these cellular proteins on E2 are likely non-linear binding sites. The possible roles of the identified host proteins are discussed as the results presented here will be important for future studies to elucidate mechanisms of host protein-virus interactions during pestivirus infection. However, due to the limitations of the yeast two hybrid system, the proteins identified is not exhaustive and each interaction identified needs to be confirmed by independent experimental approaches in the context of virus-infected cells before any definitive conclusion can be drawn on relevance for the virus life cycle. PMID:24416391

Gladue, Douglas P.; Baker-Bransetter, Ryan; Holinka, Lauren G.; Fernandez-Sainz, Ignacio J.; O’Donnell, Vivian; Fletcher, Paige; Lu, Zhiqiang; Borca, Manuel V.

2014-01-01

316

Temporal and Spatial Properties of a Yeast Multi-Cellular Amplification System Based on Signal Molecule Diffusion  

PubMed Central

We report on the spatial and temporal signaling properties of a yeast pheromone-based cell communication and amplifier system. It utilizes the Saccharomyces cerevisiae mating response pathway and relies on diffusion of the pheromone ?–factor as key signaling molecule between two cell types. One cell type represents the ?–factor secreting sensor part and the other the reporter part emitting fluorescence upon activation. Although multi-cellular signaling systems promise higher specificity and modularity, the complex interaction of the cells makes prediction of sensor performance difficult. To test the maximum distance and response time between sensor and reporter cells, the two cell types were spatially separated in defined compartments of agarose hydrogel (5 × 5 mm) and reconnected by diffusion of the yeast pheromone. Different ratios of sensor to reporter cells were tested to evaluate the minimum amount of sensor cells required for signal transduction. Even the smallest ratio, one ?–factor-secreting cell to twenty reporter cells, generated a distinct fluorescence signal. When using a 1:1 ratio, the secreted pheromone induced fluorescence in a distance of up to four millimeters after six hours. We conclude from both our experimental results and a mathematical diffusion model that in our approach: (1) the maximum dimension of separated compartments should not exceed five millimeters in gradient direction; and (2) the time-limiting step is not diffusion of the signaling molecule but production of the reporter protein. PMID:24233076

Jahn, Michael; Mölle, Annett; Rödel, Gerhard; Ostermann, Kai

2013-01-01

317

Training Sessions Provide Working Knowledge of National Animal Identification System  

ERIC Educational Resources Information Center

One in-service and two train-the-trainer workshops were conducted by University of Idaho Extension faculty, Idaho State Department of Agriculture personnel, and allied industry representatives to increase Extension educators' knowledge and awareness of the National Animal Identification System (NAIS) and related topics. Training sessions included…

Glaze, J. Benton, Jr.; Ahola, Jason K.

2010-01-01

318

Applying system identification using commercially available software and hardware  

Microsoft Academic Search

System identification methods are now incorporated into several commercially available products, including two MATLAB Toolboxes and a number of frequency response analyzers. This paper reports on the accuracy obtained with the two MATLAB Toolboxes, when used with idealized noisy data, and also on their performance when used with real measurement data. The performance of the curve-fitting algorithms on two commercial

K. R. Godfrey; A. S. McCormack; J. O. Flower

1995-01-01

319

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

320

Recurrent fuzzy neural networks for nonlinear system identification  

Microsoft Academic Search

In this paper, we propose a new recurrent fuzzy neural network, which has the standard state space form, we call it state-space recurrent neural networks. Input-to-state stability is applied to access robust training algorithms for system identification. Stable learning algorithms for the premise part and the consequence part of fuzzy rules are proved.

Wen Yu; Xiaoou Li

2007-01-01

321

Neural networks for functional approximation and system identification  

E-print Network

is a static neural network, L has a simple representation in terms of bounded linear functionalsNeural networks for functional approximation and system identification H. N. Mhaskar Department translation networks to uniformly approximate a class of nonlinear, continuous functionals defined on Lp ([-1

Mhaskar, Hrushikesh Narhar

322

SYSTEM IDENTIFICATION OF PHOTOSENSITISER UPTAKE KINETICS IN PHOTODYNAMIC THERAPY  

E-print Network

SYSTEM IDENTIFICATION OF PHOTOSENSITISER UPTAKE KINETICS IN PHOTODYNAMIC THERAPY T. Bastogne L to the experimental modelling of photosensitiser uptake kinetics in photodynamic therapy. The experimental framework is limited to one cancer cell line (HT29-A4), one photosensitiser (Chlorin e6), one photosensitiser dose (5µg

Paris-Sud XI, Université de

323

Identification problem of Klein-Gordon-Schrödinger quantum system control  

NASA Astrophysics Data System (ADS)

Identification for Klein-Gordon-Schrödinger quantum control system as one of inverse problems is considered in this work. In particular, unknown parameters appeared at electric control field need to be identified as our target. The existence of optimal parameters is proved for quadratic criteria function. The profile of external control is recovered theoretically at the framework of variational method in complex Hilbert spaces.

Wang, Quan-Fang

2015-02-01

324

A HIERARCHICAL GENETIC SYSTEM FOR SYMBOLIC FUNCTION IDENTIFICATION  

E-print Network

as Ohm's law, Newton's law of universal gravitation, Kepler's law, and Snell's law of refraction from learning systems to find empirical laws (function models) from the observations, such as BACON (Langley concept learning tasks of function identification problems and "rediscover" such classical scientific laws

Wright, Alden H.

325

FREQUENCY DOMAIN SYSTEM IDENTIFICATION OF A LIGHT HELICOPTER IN HOVER  

E-print Network

FREQUENCY DOMAIN SYSTEM IDENTIFICATION OF A LIGHT HELICOPTER IN HOVER Stefano Geluardia,b, Frank M-Input Single-Output fully coupled transfer function model of a civil light helicopter in hover. A frequency the capability to capture the main helicopter dynamic modes. It is concluded that models with order less than 6

326

A Recursive System Identification Method Based on Binary Measurements  

E-print Network

A Recursive System Identification Method Based on Binary Measurements Kian Jafari, Member, IEEE, such as This work was supported by the research grant of French Ministry of Higher Education and Research. K. Jafari-sur-Yvette Cedex, France (Phone: + 33 169851424, e-mail: Kian.Jafari@ieee.org). J. Juillard is with SUPELEC

Paris-Sud XI, Université de

327

System identification using modular neural network with improved learning  

Microsoft Academic Search

This paper addresses the problem of the identification of nonlinear dynamic systems using modularly structured neural network with the new learning algorithm for the learning of both gating and expert networks weights. Here we start with the standard learning procedure for such networks in the sense that the problem of learning is formulated and treated as a mixture estimation problem

Vojislav Kecman

1996-01-01

328

SUPPORT VECTOR MACHINE BASED SPEAKER IDENTIFICATION SYSTEMS USING GMM PARAMETERS  

E-print Network

SUPPORT VECTOR MACHINE BASED SPEAKER IDENTIFICATION SYSTEMS USING GMM PARAMETERS Vijendra Raj techniques, the Gaussian Mixture Model Universal Background Model (GMM-UBM) based approach and MAP adaptation- lation and is presently state-of-the-art technique [3]. GMM- UBMs provide a probabilistic model

De Leon, Phillip

329

SYSTEM IDENTIFICATION OF A SPHERICAL AIR-BEARING SPACECRAFT SIMULATOR  

E-print Network

resolution: for example, many programs include libraries of fasteners and commonly used commercial parts for the air-bearing spacecraft simulators at Georgia Tech1 and the Air Force Institute of Technology.2AAS 04-122 SYSTEM IDENTIFICATION OF A SPHERICAL AIR-BEARING SPACECRAFT SIMULATOR Jana L. Schwartz

Hall, Christopher D.

330

Identification of Protective Antigens for Vaccination against Systemic Salmonellosis.  

PubMed

There is an urgent medical need for improved vaccines with broad serovar coverage and high efficacy against systemic salmonellosis. Subunit vaccines offer excellent safety profiles but require identification of protective antigens, which remains a challenging task. Here, I review crucial properties of Salmonella antigens that might help to narrow down the number of potential candidates from more than 4000 proteins encoded in Salmonella genomes, to a more manageable number of 50-200 most promising antigens. I also discuss complementary approaches for antigen identification and potential limitations of current pre-clinical vaccine testing. PMID:25157252

Bumann, Dirk

2014-01-01

331

Biometric identification systems: the science of transaction facilitation  

NASA Astrophysics Data System (ADS)

The future ofthe "secure transaction" and the success ofall undertakings that depend on absolute certainty that the individuals involved really are who and what they represent themselves to be is dependent upon the successful development of absolutely accurate, low-cost and easy-to-operate Biometric Identification Systems. Whether these transactions are political, military, financial or administrative (e.g. health cards, drivers licenses, welfare entitlement, national identification cards, credit card transactions, etc.), the need for such secure and positive identification has never been greater -and yet we are only at the beginning ofan era in which we will see the emergence and proliferation of Biometric Identification Systems in nearly every field ofhuman endeavor. Proper application ofthese systems will change the way the world operates, and that is precisely the goal ofComparator Systems Corporation. Just as with the photo-copier 40 years ago and the personal computer 20 years ago, the potential applications for positive personal identification are going to make the Biometric Identification System a commonplace component in the standard practice ofbusiness, and in interhuman relationships ofall kinds. The development of new and specific application hardware, as well as the necessary algorithms and related software required for integration into existing operating procedures and newly developed systems alike, has been a more-than-a-decade-long process at Comparator -and we are now on the verge of delivering these systems to the world markets so urgently in need of them. An individual could feel extremely confident and satisfied ifhe could present his credit, debit, or ATM card at any point of sale and, after inserting his card, could simply place his finger on a glass panel and in less than a second be positively accepted as being the person that the card purported him to be; not to mention the security and satisfaction of the vendor involved in knowing that his fraud risk had been reduced to virtually zero. In highly sensitive security applications, such a system would be imperative -and when combined, if necessary, with other biometric identifiers such as signature and/or voice recognition for simultaneous verification, one would have a nearly foolproof system. These are the tools of what we call Transaction Facilitation, and this is the realm of Comparator Systems Corp. Our technological developments over the last ten years have moved our Company forward into a position of potential leadership in what is fast becoming a worldwide market, and it is toward this end that we have applied all of our efforts.

Rogers, Robert R.

1994-10-01

332

New HVAC control by system identification  

Microsoft Academic Search

Modern air-conditioning systems for commercial buildings commonly employ the concept of a “Central All-Air System” and the VAV system in particular is widely used in Hong Kong and other places around the world for energy conservation. In the lengthy wet summer season of Hong Kong, centralised air-handling units (AHUs) dehumidify and cool down the appropriate mixture of return air and

Albert T. P. So; W. L. Chan; T. T. Chow; W. L. Tse

1995-01-01

333

Linking yeast genetics to mammalian genomes: identification and mapping of the human homolog of CDC27 via the expressed sequence tag (EST) data base.  

PubMed Central

We describe a strategy for quickly identifying and positionally mapping human homologs of yeast genes to cross-reference the biological and genetic information known about yeast genes to mammalian chromosomal maps. Optimized computer search methods have been developed to scan the rapidly expanding expressed sequence tag (EST) data base to find human open reading frames related to yeast protein sequence queries. These methods take advantage of the newly developed BLOSUM scoring matrices and the query masking function SEG. The corresponding human cDNA is then used to obtain a high-resolution map position on human and mouse chromosomes, providing the links between yeast genetic analysis and mapped mammalian loci. By using these methods, a human homolog of Saccharomyces cerevisiae CDC27 has been identified and mapped to human chromosome 17 and mouse chromosome 11 between the Pkca and Erbb-2 genes. Human CDC27 encodes an 823-aa protein with global similarity to its fungal homologs CDC27, nuc2+, and BimA. Comprehensive cross-referencing of genes and mutant phenotypes described in humans, mice, and yeast should accelerate the study of normal eukaryotic biology and human disease states. Images Fig. 2 PMID:8234252

Tugendreich, S; Boguski, M S; Seldin, M S; Hieter, P

1993-01-01

334

A system identification approach to non-invasive central cardiovascular monitoring  

E-print Network

This thesis presents a new system identification approach to non-invasive central cardiovascular monitoring problem. For this objective, this thesis will develop and analyze blind system identification and input signal ...

Hahn, Jin-Oh, Ph. D. Massachusetts Institute of Technology

2008-01-01

335

Decentralized Output-only Modal Identification Techniques for Wireless Monitoring Systems  

E-print Network

natural frequencies, modal damping ratios, and mode shapes). INTRODUCTION Structural health monitoringDecentralized Output-only Modal Identification Techniques for Wireless Monitoring Systems Michihito-only modal identification methods are advantageous for use in characterizing system properties. This paper

Lynch, Jerome P.

336

An overview of the essential differences and similarities of system identification techniques  

NASA Technical Reports Server (NTRS)

Information is given in the form of outlines, graphs, tables and charts. Topics include system identification, Bayesian statistical decision theory, Maximum Likelihood Estimation, identification methods, structural mode identification using a stochastic realization algorithm, and identification results regarding membrane simulations and X-29 flutter flight test data.

Mehra, Raman K.

1991-01-01

337

Non-linear system identification using neural networks  

Microsoft Academic Search

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

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

1990-01-01

338

A Subspace Method for Blind Channel Identification in OFDM Systems  

Microsoft Academic Search

It has been shown that cyclostationarity in the received signal allows the receiver to blindly identify the channel impulse response using only second-order statistics. In orthogonal frequency-division multiplexing (OFDM) systems, cyclostationarity is embedded at the transmitter due to cyclic prefix. In this paper, a subspace approach based on second-order statistics is proposed for blind channel identification in OFDM systems. We

Xiaodong Cai; Ali N. Akansu

2000-01-01

339

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

340

Early identification systems for emerging foodborne hazards.  

PubMed

This paper provides a non-exhausting overview of early warning systems for emerging foodborne hazards that are operating in the various places in the world. Special attention is given to endpoint-focussed early warning systems (i.e. ECDC, ISIS and GPHIN) and hazard-focussed early warning systems (i.e. FVO, RASFF and OIE) and their merit to successfully identify a food safety problem in an early stage is discussed. Besides these early warning systems which are based on monitoring of either disease symptoms or hazards, also early warning systems and/or activities that intend to predict the occurrence of a food safety hazard in its very beginning of development or before that are described. Examples are trend analysis, horizon scanning, early warning systems for mycotoxins in maize and/or wheat and information exchange networks (e.g. OIE and GIEWS). Furthermore, recent initiatives that aim to develop predictive early warning systems based on the holistic principle are discussed. The assumption of the researchers applying this principle is that developments outside the food production chain that are either directly or indirectly related to the development of a particular food safety hazard may also provide valuable information to predict the development of this hazard. PMID:18272277

Marvin, H J P; Kleter, G A; Prandini, A; Dekkers, S; Bolton, D J

2009-05-01

341

Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway.  

PubMed Central

This review focuses on the gene-enzyme relationships and the regulation of different levels of the aromatic amino acid biosynthetic pathway in a simple eukaryotic system, the unicellular yeast Saccharomyces cerevisiae. Most reactions of this branched pathway are common to all organisms which are able to synthesize tryptophan, phenylalanine, and tyrosine. The current knowledge about the two main control mechanisms of the yeast aromatic amino acid biosynthesis is reviewed. (i) At the transcriptional level, most structural genes are regulated by the transcriptional activator GCN4, the regulator of the general amino acid control network, which couples transcriptional derepression to amino acid starvation of numerous structural genes in multiple amino acid biosynthetic pathways. (ii) At the enzyme level, the carbon flow is controlled mainly by modulating the enzyme activities at the first step of the pathway and at the branch points by feedback action of the three aromatic amino acid end products. Implications of these findings for the relationship of S. cerevisiae to prokaryotic as well as to higher eukaryotic organisms and for general regulatory mechanisms occurring in a living cell such as initiation of transcription, enzyme regulation, and the regulation of a metabolic branch point are discussed. PMID:1943992

Braus, G H

1991-01-01

342

Real-time monitoring of relative peptide-protein interaction strengths in the yeast two-hybrid system.  

PubMed

The yeast two-hybrid (Y2H) system is one of the most technically straightforward, effective, and widely used tools for the discovery of the binary peptide or protein interactions. However, its exceptional detection sensitivity poses a serious challenge for affinity ranking and hence prioritizing the resultant large number of putative interactors for follow-up analyses. To overcome this apparent bottleneck, we describe here a novel yeast growth curve-based interaction-monitoring approach that permits semiautomatic quantification, comparison, and statistically ascertained scoring of a large collection of Y2H interactions under real-time conditions. Initially, we conducted a proof-of-concept test of five literature-validated peptide-protein interactions with known affinities in the low ?M range, and subsequently used the method to classify 88 novel vitamin D receptor-binding peptides derived from high-throughput screening of a highly diverse artificial peptide aptamer library. Based on our in-depth data evaluation, we conclude that real-time monitoring of clone growth as a measure of relative binding strength offers a facile, cost-effective, accurate, reproducible, and further adaptable complement to standard Y2H-derived clone management. PMID:23679850

Rid, Raphaela; Herzog, Julia; Maier, Richard H; Hundsberger, Harald; Eger, Andreas; Hintner, Helmut; Bauer, Johann W; Onder, Kamil

2013-05-01

343

Purification of fructooligosaccharides by immobilized yeast cells and identification of ethyl ?-D-fructofuranoside as a novel glycoside formed during the process.  

PubMed

A yeast strain (XS1) capable of selective utilization of fructooligosaccharides (FOSs) syrup was identified as Wickerhamomyces anomala. Cells of W. anomala XS1 were immobilized in calcium alginate and incubated with an FOS mixture at 30 °C. The purity of the FOS increased from 54.4% to 80.1% (w/w) as 93.6% of monosaccharides were metabolized while the oligosaccharides were not affected. The immobilized yeast cells could be recycled 10 times and the corresponding batch treatments achieved FOS purities around 80%. Thus, the method could be promising for large-scale purification of FOS syrup at low cost. A byproduct formed by the yeast was identified as ethyl ?-D-fructofuranoside by MS and NMR spectroscopy. PMID:23186684

Lu, Lili; Wu, Jian; Song, Deyong; Zhao, Han; Gu, Guofeng; Guo, Yuchuan; Lan, Jin; Xiao, Min

2013-03-01

344

Overexpression of multisubunit replication factors in yeast.  

PubMed

Facile genetic and biochemical manipulation coupled with rapid cell growth and low cost of growth media has established the yeast Saccharomyces cerevisiae as a versatile workhorse. This article describes the use of yeast expression systems for the overproduction of complex multipolypeptide replication factors. The regulated overexpression of these factors in yeast provides for a readily accessible and inexpensive source of these factors in large quantities. The methodology is illustrated with the five-subunit replication factor C. Whole-cell extracts are prepared by blending yeast cells with glass beads or frozen yeast with dry ice. Procedures are described that maximize the yield of these factors while minimizing proteolytic degradation. PMID:10454996

Burgers, P M

1999-07-01

345

Development of pilot scale nanofiltration system for yeast industry wastewater treatment  

PubMed Central

The treatment of the yeast industry wastewater was investigated by nanofiltration (NF) membrane process on a pilot scale. Two wastewaters were used as feed: (i) dilute wastewater with COD 2000 mg/L and (ii) concentrate wastewater with COD 8000 mg/L. The permeate flux, COD retention, color and electrical conductivity (EC) removal were evaluated in relation to trans-membrane pressure and long-term filtration. A linear growth in permeate flux was found with increasing in trans-membrane pressure for wastewaters. In addition, the COD retention, color and EC removal increased with trans-membrane pressure enhancement. The results obtained from the long-term nanofiltration of dilute wastewater indicated that the permeate flux decreased from 2300 L/day to 1250 L/day and COD retention increased from 86% to 92%. The quality of the permeate in term of COD is lower than the discharge standard in river (200 mg/L). Thus, this process is useful for treatment of wastewaters produced by yeast industry. PMID:24593865

2014-01-01

346

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

347

System and Method for Automatic Singer Identification  

NSDL National Science Digital Library

Individuals' music collections that are stored on a computer, whether legal or not, are often quite large and consist of many different artists. This unique research paper from Hewlett-Packard outlines a system that can automatically identify the singer of a song based upon digital samples of that song, allowing for hassle-free sorting of many titles. The system is first trained by exposing it to a representative sample of songs from a wide range of artists. Then, by extracting sound features from different songs and analyzing them, the software can make a best guess as to which artist is singing. The system is shown to have an accuracy of 80 percent when trained with a single song for eight singers and tested on 45 other songs by the same singers.

Zhang, Tong

348

On-orbit system identification using active members  

NASA Technical Reports Server (NTRS)

The capability to perform accurate on-orbit system identification for both open loop (passive) and closed loop (active) structural systems will be required for future NASA missions; especially those missions which require large precision structures. The information is required to accurately establish the dynamic characteristics of the operational structure in order to adjust the structure itself using the concepts of Adaptive Structures and/or the control system. This paper presents the test results of using Active Members in an adaptive structural system to excite a free-free structure to determine both open and closed loop dynamic characteristics.

Kuo, C. P.; Chen, G.-S.; Pham, P.; Wada, B. K.

1990-01-01

349

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

350

Rapid identification of Listeria spp.: an AOAC performance test of the MIT 1000 rapid microbial identification system  

Technology Transfer Automated Retrieval System (TEKTRAN)

Methods that rapidly confirm the identification of foodborne pathogens are highly desired. The Micro Imaging Technology (MIT) 1000 Rapid Microbial Identification (RMID) System is a benchtop instrument that detects laser light scattered from individual bacterial cells in solution with an array of 35 ...

351

Production of interleukin-6 in Arxula adeninivorans, Hansenula polymorpha and Saccharomyces cerevisiae by applying the wide-range yeast vector (CoMed) system to simultaneous comparative assessment.  

PubMed

A wide-range yeast vector (CoMed) system has been applied to the comparative assessment of three different yeast platforms for the production of human interleukin-6. A vector equipped with an rRNA gene targeting sequence and an Arxula adeninivorans-derived LEU2 gene was used for simultaneous transformation of auxotrophic A. adeninivorans, Hansenula polymorpha and Saccharomyces cerevisiae strains. IL6 was expressed under control of the strong constitutive A. adeninivorans-derived TEF1 promoter, which is functional in all yeast species analyzed so far. Secreted IL-6 was found to be correctly processed from an MFalpha1-IL6 precursor in A. adeninivorans only, whereas N-terminally truncated proteins were observed in H. polymorpha and S. cerevisiae. PMID:17537181

Böer, Erik; Steinborn, Gerhard; Matros, Andrea; Mock, Hans-Peter; Gellissen, Gerd; Kunze, Gotthard

2007-10-01

352

Effect of sterol metabolism in the yeast-Drosophila system on the frequency of radiation-induced aneuploidy in the Drosophila melanogaster oocytes  

SciTech Connect

The effect of sterol metabolism on induced mutagenesis of Drosophila melanogaster was studied in the ecogenetic system of yeast-Drosophila. Sterol deficiency was created in Drosophila by using the biomass of live cells of Saccharomyces cerevisiae strain 9-2-P712 till mutation in locus nys/sup r1/ blocking the synthesis of ergosterol as the food. It was found that rearing of Drosophila females on the mutant yeast increases the frequency of loss and nondisjunction of X chromosomes induced in mature oocytes by X rays (1000 R). Addition of 0.1% of cholesterol solution in 10% ethanol to the yeast biomass restores the resistance of oocyte to X irradiation to the control level. The possible hormonal effect on membrane leading to increased radiation-induced aneuploidy in Drosophila and the role of sterol metabolism in determining the resistance to various damaging factors are discussed.

Savitskii, V.V.; Luchnikova, E.M.; Inge-Vechtomov, S.G.

1986-01-01

353

Frequency domain state-space system identification  

NASA Technical Reports Server (NTRS)

An algorithm for identifying state-space models from frequency response data of linear systems is presented. A matrix-fraction description of the transfer function is employed to curve-fit the frequency response data, using the least-squares method. The parameters of the matrix-fraction representation are then used to construct the Markov parameters of the system. Finally, state-space models are obtained through the Eigensystem Realization Algorithm using Markov parameters. The main advantage of this approach is that the curve-fitting and the Markov parameter construction are linear problems which avoid the difficulties of nonlinear optimization of other approaches. Another advantage is that it avoids windowing distortions associated with other frequency domain methods.

Chen, Chung-Wen; Juang, Jer-Nan; Lee, Gordon

1992-01-01

354

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

355

Identification of Chaotic Systems by Neural Networks  

NASA Astrophysics Data System (ADS)

In this paper a traditional Multi Layer Perceptron with a tapped delay line as input is trained to identify the parameters of the Chua's circuit when fed with a sequence of values of a scalar state variable. The analysis of the a priori identifiability of the system, performed resorting to differential algebra, allows one to choose a suitable observable and the minimum number of taps. The results confirm the appropriateness of the proposed approach.

Cannas, B.; Montisci, A.; Pisano, F.

356

Closed Loop System Identification with Genetic Algorithms  

NASA Technical Reports Server (NTRS)

High performance control design for a flexible space structure is challenging since high fidelity plant models are di.cult to obtain a priori. Uncertainty in the control design models typically require a very robust, low performance control design which must be tuned on-orbit to achieve the required performance. Closed loop system identi.cation is often required to obtain a multivariable open loop plant model based on closed-loop response data. In order to provide an accurate initial plant model to guarantee convergence for standard local optimization methods, this paper presents a global parameter optimization method using genetic algorithms. A minimal representation of the state space dynamics is employed to mitigate the non-uniqueness and over-parameterization of general state space realizations. This control-relevant system identi.cation procedure stresses the joint nature of the system identi.cation and control design problem by seeking to obtain a model that minimizes the di.erence between the predicted and actual closed-loop performance.

Whorton, Mark S.

2004-01-01

357

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...

358

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 ...

359

Identification and analysis of the metabolic functions of a high-salt-tolerant halophilic aromatic yeast Candida etchellsii for soy sauce production.  

PubMed

Salt-tolerant yeasts are very important for the flavor formation in soy sauce fermentation production. A halophilic aromatic yeast was isolated on the basis of the molecular biological and metabolic functions from soy sauce. The ITS nucleotide sequence alignment method was used to identify the strain as Candida etchellsii by subjecting the sequence to NCBI-BLAST in comparison with that of the C. etchellsii strain Miso 0208 (a typical high-salt-tolerant halophilic aromatic yeast strain). Organic acids, amino acids and volatile flavor compounds were produced by the yeast strain which were analyzed by HPLC and SPME-GC/MS methods. Tartaric acid (0.979 ± 0.040 g/l), formic acid (0.636 ± 0.030 g/l), lactic acid (2.80 ± 0.10 g/l), ?-alkone glutaric acid (0.132 ± 0.015 g/l), citric acid (2.59 ± 0.10 g/l) and succinic acid (3.03 ± 0.20 g/l) were detected at 72 h of fermentation, respectively. Free and acid hydrolyzed amino acids at levels of 3.7355 ± 0.0027 and 11.5604 ± 0.0037 g/l, respectively, 4-ethyl guaiacols as well as other volatile flavor compounds were also detected. PMID:22805926

Feng, Jie; Zhan, Xiao-Bei; Wang, Dong; Zhang, Li-Min; Lin, Chi-Chung

2012-04-01

360

System Identification and POD Method Applied to Unsteady Aerodynamics  

NASA Technical Reports Server (NTRS)

The representation of unsteady aerodynamic flow fields in terms of global aerodynamic modes has proven to be a useful method for reducing the size of the aerodynamic model over those representations that use local variables at discrete grid points in the flow field. Eigenmodes and Proper Orthogonal Decomposition (POD) modes have been used for this purpose with good effect. This suggests that system identification models may also be used to represent the aerodynamic flow field. Implicit in the use of a systems identification technique is the notion that a relative small state space model can be useful in describing a dynamical system. The POD model is first used to show that indeed a reduced order model can be obtained from a much larger numerical aerodynamical model (the vortex lattice method is used for illustrative purposes) and the results from the POD and the system identification methods are then compared. For the example considered, the two methods are shown to give comparable results in terms of accuracy and reduced model size. The advantages and limitations of each approach are briefly discussed. Both appear promising and complementary in their characteristics.

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

2001-01-01

361

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

362

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation  

PubMed Central

Network analysis became a powerful tool giving new insights to the understanding of cellular behavior. Heat shock, the archetype of stress responses, is a well-characterized and simple model of cellular dynamics. S. cerevisiae is an appropriate model organism, since both its protein-protein interaction network (interactome) and stress response at the gene expression level have been well characterized. However, the analysis of the reorganization of the yeast interactome during stress has not been investigated yet. We calculated the changes of the interaction-weights of the yeast interactome from the changes of mRNA expression levels upon heat shock. The major finding of our study is that heat shock induced a significant decrease in both the overlaps and connections of yeast interactome modules. In agreement with this the weighted diameter of the yeast interactome had a 4.9-fold increase in heat shock. Several key proteins of the heat shock response became centers of heat shock-induced local communities, as well as bridges providing a residual connection of modules after heat shock. The observed changes resemble to a ‘stratus-cumulus’ type transition of the interactome structure, since the unstressed yeast interactome had a globally connected organization, similar to that of stratus clouds, whereas the heat shocked interactome had a multifocal organization, similar to that of cumulus clouds. Our results showed that heat shock induces a partial disintegration of the global organization of the yeast interactome. This change may be rather general occurring in many types of stresses. Moreover, other complex systems, such as single proteins, social networks and ecosystems may also decrease their inter-modular links, thus develop more compact modules, and display a partial disintegration of their global structure in the initial phase of crisis. Thus, our work may provide a model of a general, system-level adaptation mechanism to environmental changes. PMID:22022244

Mihalik, Ágoston; Csermely, Peter

2011-01-01

363

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

PubMed

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 B for selection of recombinants. Heterologous gene expression was assessed using a green fluorescent protein (GFP) reporter gene. The plasmid was found to be integrated into the genome of the various hosts tested; recombinant strains of all species exhibited heterologous gene expressions of a similar high level. PMID:15175929

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

2004-06-01

364

Parameter identification in noisy extended systems  

NASA Astrophysics Data System (ADS)

We study extended systems such as the coupled Landau equations with complex coefficients partialt An = ? An + g ( A_n+1 + A_n-1 - 2 An ) - l | An |^2 A_n, the Kuramoto-Sivashinsky equation or the Kardar-Parisi-Zhang model. Our purpose is to identify the parameters of these equation when given noisy observation of the solutions. This approach mimics the analysis of real experiments. We also apply directly to real experimental data. We use an inverse method based on the backpropagation of the gradient J = nabla \\cal L of a distance \\cal L between the noisy observations and a given solution( A detailed account of this work is available at the archive http://xyz.lanl.gov) in preprint chao-dyn/9601008. Our method is able to follow the data closely over a correlation time, is markedly noise resistant, and yields a reconstructed system with the same intermittent chaotic behavior over long times as the data. We discuss the difficulties that occur when the noise level is large or when one attempts to follow the data over long times.

Fullana, José María; Rossi, Maurice; Zaleski, Stéphane

1996-11-01

365

On some system identification techniques for adaptive filtering  

Microsoft Academic Search

Three different identification methods (the Steiglitz-McBride method, the output error method, and the instrumental variable method) are discussed in the context of adaptive filtering. They can be implemented by recursive algorithms with similar structures, either in gradient or Newton form as well as in various tracking variants for time-varying systems. Their properties are discussed and compared in terms of local

TORSTEN SODERSTROM; PETRE STOICA

1988-01-01

366

Terahertz imaging system performance model for concealed-weapon identification  

Microsoft Academic Search

The U.S. Army Night Vision and Electronic Sensors Directorate (NVESD) and the U.S. Army Research Laboratory have developed a terahertz (THz) -band imaging system performance model for detection and identification of concealed weaponry. The MATLAB-based model accounts for the effects of all critical sensor and display components and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination.

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

2008-01-01

367

Advanced terahertz imaging system performance model for concealed weapon identification  

Microsoft Academic Search

The U.S. Army Night Vision and Electronic Sensors Directorate (NVESD) and the U.S. Army Research Laboratory (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,

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

2007-01-01

368

Terahertz imaging system performance model for concealed weapon identification  

Microsoft Academic Search

The U.S. Army Night Vision and Electronic Sensors Directorate and the U.S. Army Research Laboratory have developed a terahertz-band imaging system performance model for detection and identification of concealed weaponry. The MATLAB-based model accounts for the effects of all critical sensor and display components, and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination. The model is

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

2005-01-01

369

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

370

Prefire identification for pulse power systems  

DOEpatents

Prefires in a high-power, high-frequency, multi-stage pulse generator are detected by a system having an EMI shielded pulse timing transmitter associated with and tailored to each stage of the pulse generator. Each pulse timing transmitter upon detection of a pulse triggers a laser diode to send an optical signal through a high frequency fiber optic cable to a pulse timing receiver which converts the optical signal to an electrical pulse. The electrical pulses from all pulse timing receivers are fed through an OR circuit to start a time interval measuring device and each electrical pulse is used to stop an individual channel in the measuring device thereby recording the firing sequence of the multi-stage pulse generator.

Longmire, Jerry L. (Los Alamos, NM); Thuot, Michael E. (Espanola, NM); Warren, David S. (Los Alamos, NM)

1985-01-01

371

Prefire identification for pulse-power systems  

DOEpatents

Prefires in a high-power, high-frequency, multi-stage pulse generator are detected by a system having an EMI shielded pulse timing transmitter associated with and tailored to each stage of the pulse generator. Each pulse timing transmitter upon detection of a pulse triggers a laser diode to send an optical signal through a high frequency fiber optic cable to a pulse timing receiver which converts the optical signal to an electrical pulse. The electrical pulses from all pulse timing receivers are fed through an OR circuit to start a time interval measuring device and each electrical pulse is used to stop an individual channel in the measuring device thereby recording the firing sequence of the multi-stage pulse generator.

Longmire, J.L.; Thuot, M.E.; Warren, D.S.

1982-08-23

372

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

373

System IDentification Programs for AirCraft (SIDPAC)  

NASA Technical Reports Server (NTRS)

A collection of computer programs for aircraft system identification is described and demonstrated. The programs, collectively called System IDentification Programs for AirCraft, or SIDPAC, were developed in MATLAB as m-file functions. SIDPAC has been used successfully at NASA Langley Research Center with data from many different flight test programs and wind tunnel experiments. SIDPAC includes routines for experiment design, data conditioning, data compatibility analysis, model structure determination, equation-error and output-error parameter estimation in both the time and frequency domains, real-time and recursive parameter estimation, low order equivalent system identification, estimated parameter error calculation, linear and nonlinear simulation, plotting, and 3-D visualization. An overview of SIDPAC capabilities is provided, along with a demonstration of the use of SIDPAC with real flight test data from the NASA Glenn Twin Otter aircraft. The SIDPAC software is available without charge to U.S. citizens by request to the author, contingent on the requestor completing a NASA software usage agreement.

Morelli, Eugene A.

2002-01-01

374

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

375

Genome and Transcriptome Analysis of the Food-Yeast Candida utilis  

PubMed Central

The industrially important food-yeast Candida utilis is a Crabtree effect-negative yeast used to produce valuable chemicals and recombinant proteins. In the present study, we conducted whole genome sequencing and phylogenetic analysis of C. utilis, which showed that this yeast diverged long before the formation of the CUG and Saccharomyces/Kluyveromyces clades. In addition, we performed comparative genome and transcriptome analyses using next-generation sequencing, which resulted in the identification of genes important for characteristic phenotypes of C. utilis such as those involved in nitrate assimilation, in addition to the gene encoding the functional hexose transporter. We also found that an antisense transcript of the alcohol dehydrogenase gene, which in silico analysis did not predict to be a functional gene, was transcribed in the stationary-phase, suggesting a novel system of repression of ethanol production. These findings should facilitate the development of more sophisticated systems for the production of useful reagents using C. utilis. PMID:22629373

Tomita, Yasuyuki; Ikeo, Kazuho; Tamakawa, Hideyuki; Gojobori, Takashi; Ikushima, Shigehito

2012-01-01

376

System Identification of Mistuned Bladed Disks from Traveling Wave Response Measurements  

NASA Technical Reports Server (NTRS)

A new approach to modal analysis is presented. By applying this technique to bladed disk system identification methods, one can determine the mistuning in a rotor based on its response to a traveling wave excitation. This allows system identification to be performed under rotating conditions, and thus expands the applicability of existing mistuning identification techniques from integrally bladed rotors to conventional bladed disks.

Feiner, D. M.; Griffin, J. H.; Jones, K. W.; Kenyon, J. A.; Mehmed, O.; Kurkov, A. P.

2003-01-01

377

Advances of the WITY system: yeast performance evaluation during the production of sweet wine using Mavrodafni and Carbarnet sauvignon.  

PubMed

The production of sweet wine from the Mavrodafni and Cabernet sauvignon varieties was explored. External inoculation with oenological yeast strains was employed. The performance of the two yeast strains were studied under batch and continuous mode and in free and immobilised states. The kinetics of the different carbohydrates was studied and the main oenological parameters were measured. PMID:15954665

Nerantzis, E T; Logothetis, S

2001-01-01

378

Identification and Analysis of National Airspace System Resource Constraints  

NASA Technical Reports Server (NTRS)

This analysis is the deliverable for the Airspace Systems Program, Systems Analysis Integration and Evaluation Project Milestone for the Systems and Portfolio Analysis (SPA) focus area SPA.4.06 Identification and Analysis of National Airspace System (NAS) Resource Constraints and Mitigation Strategies. "Identify choke points in the current and future NAS. Choke points refer to any areas in the en route, terminal, oceanic, airport, and surface operations that constrain actual demand in current and projected future operations. Use the Common Scenarios based on Transportation Systems Analysis Model (TSAM) projections of future demand developed under SPA.4.04 Tools, Methods and Scenarios Development. Analyze causes, including operational and physical constraints." The NASA analysis is complementary to a NASA Research Announcement (NRA) "Development of Tools and Analysis to Evaluate Choke Points in the National Airspace System" Contract # NNA3AB95C awarded to Logistics Management Institute, Sept 2013.

Smith, Jeremy C.; Marien, Ty V.; Viken, Jeffery K.; Neitzke, Kurt W.; Kwa, Tech-Seng; Dollyhigh, Samuel M.; Fenbert, James W.; Hinze, Nicolas K.

2015-01-01

379

System identification for modeling for control of flexible structures  

NASA Technical Reports Server (NTRS)

The major components of a design and operational flight strategy for flexible structure control systems are presented. In this strategy an initial distributed parameter control design is developed and implemented from available ground test data and on-orbit identification using sophisticated modeling and synthesis techniques. The reliability of this high performance controller is directly linked to the accuracy of the parameters on which the design is based. Because uncertainties inevitably grow without system monitoring, maintaining the control system requires an active on-line system identification function to supply parameter updates and covariance information. Control laws can then be modified to improve performance when the error envelopes are decreased. In terms of system safety and stability the covariance information is of equal importance as the parameter values themselves. If the on-line system ID function detects an increase in parameter error covariances, then corresponding adjustments must be made in the control laws to increase robustness. If the error covariances exceed some threshold, an autonomous calibration sequence could be initiated to restore the error enveloped to an acceptable level.

Mettler, Edward; Milman, Mark

1986-01-01

380

The Yin and Yang of Yeast Transcription: Elements of a Global Feedback System between Metabolism and Chromatin  

PubMed Central

When grown in continuous culture, budding yeast cells tend to synchronize their respiratory activity to form a stable oscillation that percolates throughout cellular physiology and involves the majority of the protein-coding transcriptome. Oscillations in batch culture and at single cell level support the idea that these dynamics constitute a general growth principle. The precise molecular mechanisms and biological functions of the oscillation remain elusive. Fourier analysis of transcriptome time series datasets from two different oscillation periods (0.7 h and 5 h) reveals seven distinct co-expression clusters common to both systems (34% of all yeast ORF), which consolidate into two superclusters when correlated with a compilation of 1,327 unrelated transcriptome datasets. These superclusters encode for cell growth and anabolism during the phase of high, and mitochondrial growth, catabolism and stress response during the phase of low oxygen uptake. The promoters of each cluster are characterized by different nucleotide contents, promoter nucleosome configurations, and dependence on ATP-dependent nucleosome remodeling complexes. We show that the ATP:ADP ratio oscillates, compatible with alternating metabolic activity of the two superclusters and differential feedback on their transcription via activating (RSC) and repressive (Isw2) types of promoter structure remodeling. We propose a novel feedback mechanism, where the energetic state of the cell, reflected in the ATP:ADP ratio, gates the transcription of large, but functionally coherent groups of genes via differential effects of ATP-dependent nucleosome remodeling machineries. Besides providing a mechanistic hypothesis for the delayed negative feedback that results in the oscillatory phenotype, this mechanism may underpin the continuous adaptation of growth to environmental conditions. PMID:22685547

Machné, Rainer; Murray, Douglas B.

2012-01-01

381

An approximation theory for the identification of linear thermoelastic systems  

NASA Technical Reports Server (NTRS)

An abstract approximation framework and convergence theory for the identification of thermoelastic systems is developed. Starting from an abstract operator formulation consisting of a coupled second order hyperbolic equation of elasticity and first order parabolic equation for heat conduction, well-posedness is established using linear semigroup theory in Hilbert space, and a class of parameter estimation problems is then defined involving mild solutions. The approximation framework is based upon generic Galerkin approximation of the mild solutions, and convergence of solutions of the resulting sequence of approximating finite dimensional parameter identification problems to a solution of the original infinite dimensional inverse problem is established using approximation results for operator semigroups. An example involving the basic equations of one dimensional linear thermoelasticity and a linear spline based scheme are discussed. Numerical results indicate how the approach might be used in a study of damping mechanisms in flexible structures.

Rosen, I. G.; Su, Chien-Hua Frank

1990-01-01

382

Multivariable adaptive identification and control for artificial pancreas systems.  

PubMed

A constrained weighted recursive least squares method is proposed to provide recursive models with guaranteed stability and better performance than models based on regular identification methods in predicting the variations of blood glucose concentration in patients with Type 1 Diabetes. Use of physiological information from a sports armband improves glucose concentration prediction and enables earlier recognition of the effects of physical activity on glucose concentration. Generalized predictive controllers (GPC) based on these recursive models are developed. The performance of GPC for artificial pancreas systems is illustrated by simulations with UVa-Padova simulator and clinical studies. The controllers developed are good candidates for artificial pancreas systems with no announcements from patients. PMID:24557689

Turksoy, Kamuran; Quinn, Laurie; Littlejohn, Elizabeth; Cinar, Ali

2014-03-01

383

Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5' end of the large-subunit (26S) ribosomal DNA gene.  

PubMed Central

Clinically important species of Candida and related organisms were compared for extent of nucleotide divergence in the 5' end of the large-subunit (26S) ribosomal DNA (rDNA) gene. This rDNA region is sufficiently variable to allow reliable separation of all known clinically significant yeast species. Of the 204 described species examined, 21 appeared to be synonyms of previously described organisms. Phylogenetic relationships among the species are presented. PMID:9114410

Kurtzman, C P; Robnett, C J

1997-01-01

384

Phenotypic and molecular identification and clustering of lactic acid bacteria and yeasts from wheat (species Triticum durum and Triticum aestivum) sourdoughs of Southern Italy  

Microsoft Academic Search

The microflora of 25 wheat sourdoughs from the Apulia region, Southern Italy, was characterized. The sourdoughs were mainly produced from Triticum durum wheat. The number of lactic acid bacteria and yeasts ranged from ca. log7.5 to log9.3 colony forming units (cfu)\\/g and from log5.5 to log8.4 cfu\\/g, respectively. About 38% of the 317 isolates of lactic acid bacteria were identified

A. Corsetti; P. Lavermicocca; M. Morea; F. Baruzzi; N. Tosti; M. Gobbetti

2001-01-01

385

Identification and characterization of a mitochondrial thioredoxin system in plants  

PubMed Central

Plants possess two well described thioredoxin systems: a cytoplasmic system including several thioredoxins and an NADPH-dependent thioredoxin reductase and a specific chloroplastic system characterized by a ferredoxin-dependent thioredoxin reductase. On the basis of biochemical activities, plants also are supposed to have a mitochondrial thioredoxin system as described in yeast and mammals, but no gene encoding plant mitochondrial thioredoxin or thioredoxin reductase has been identified yet. We report the characterization of a plant thioredoxin system located in mitochondria. Arabidopsis thaliana genome sequencing has revealed numerous thioredoxin genes among which we have identified AtTRX-o1, a gene encoding a thioredoxin with a potential mitochondrial transit peptide. AtTRX-o1 and a second gene, AtTRX-o2, define, on the basis of the sequence and intron positions, a new thioredoxin type up to now specific to plants. We also have characterized AtNTRA, a gene encoding a protein highly similar to the previously described cytosolic NADPH-dependent thioredoxin reductase AtNTRB but with a putative presequence for import into mitochondria. Western blot analysis of A. thaliana subcellular and submitochondrial fractions and in vitro import experiments show that AtTRX-o1 and AtNTRA are targeted to the mitochondrial matrix through their cleavable N-terminal signal. The two proteins truncated to the estimated mature forms were produced in Escherichia coli; AtTRX-o1 efficiently reduces insulin in the presence of DTT and is reduced efficiently by AtNTRA and NADPH. Therefore, the thioredoxin and the NADPH-dependent thioredoxin reductase described here are proposed to constitute a functional plant mitochondrial thioredoxin system. PMID:11717467

Laloi, Christophe; Rayapuram, Naganand; Chartier, Yvette; Grienenberger, Jean-Michel; Bonnard, Géraldine; Meyer, Yves

2001-01-01

386

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

387

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

388

Identification of Time-Varying Wiener Systems with Unknown Parameters  

NASA Astrophysics Data System (ADS)

Wiener systems which consist of a dynamic linear block followed by a static nonlinear element have been used in numerous applications. In many cases, the system parameters are affected by changes in the environmental conditions. This paper describes a new approach to the on-line identification of time-varying Wiener systems. The time-varying linear parameters and the static nonlinear characteristics are estimated by the neural networks which can represent various nonlinear characteristics. The initial states of the linear model in each estimation window are not available in the Wiener systems. Thus, the initial states and the other system parameters are estimated simultaneously by the nonlinear optimization techniques. Furthermore, the optimal numbers of hidden units in the neural networks are determined by the minimum description length (MDL) criterion. As the result of the simulation of this method, more accurate parameters can be obtained than the result without the estimation of initial states and MDL.

Kobayashi, Yasuhide; Shiotani, Yuzuru; Hikita, Shinichi; Nomura, Kazuya

389

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

390

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

391

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

392

Terahertz imaging system performance model for concealed-weapon identification.  

PubMed

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. PMID:18709076

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

2008-03-20

393

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

394

Identification of linear systems by an asymptotically stable observer  

NASA Technical Reports Server (NTRS)

A formulation is presented for the identification of a linear multivariable system 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 extensive numerical examples using simulated noise-free data are presented to illustrate the proposed method.

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

1992-01-01

395

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

396

Image processing and classification algorithm for yeast cell morphology in a microfluidic chip  

NASA Astrophysics Data System (ADS)

The study of yeast cell morphology requires consistent identification of cell cycle phases based on cell bud size. A computer-based image processing algorithm is designed to automatically classify microscopic images of yeast cells in a microfluidic channel environment. The images were enhanced to reduce background noise, and a robust segmentation algorithm is developed to extract geometrical features including compactness, axis ratio, and bud size. The features are then used for classification, and the accuracy of various machine-learning classifiers is compared. The linear support vector machine, distance-based classification, and k-nearest-neighbor algorithm were the classifiers used in this experiment. The performance of the system under various illumination and focusing conditions were also tested. The results suggest it is possible to automatically classify yeast cells based on their morphological characteristics with noisy and low-contrast images.

Yang Yu, Bo; Elbuken, Caglar; Ren, Carolyn L.; Huissoon, Jan P.

2011-06-01

397

PCR differentiation of commercial yeast strains using intron splice site primers.  

PubMed Central

The increased use of pure starter cultures in the wine industry has made it necessary to develop a rapid and simple identification system for yeast strains. A method based upon the PCR using oligonucleotide primers that are complementary to intron splice sites has been developed. Since most introns are not essential for gene function, introns have evolved with minimal constraint. By targeting these highly variable sequences, the PCR has proved to be very effective in uncovering polymorphisms in commercial yeast strains. The speed of the method and the ability to analyze many samples in a single day permit the monitoring of specific yeast strains during fermentations. Furthermore, the simplicity of the technique, which does not require the isolation of DNA, makes it accessible to industrial laboratories that have limited molecular expertise and resources. PMID:8953723

de Barros Lopes, M; Soden, A; Henschke, P A; Langridge, P

1996-01-01

398

Pentose fermentation by yeasts  

Microsoft Academic Search

66 different yeast strains were screened for glucose, xylose and xylulose fermentation in shake flask cultures. None of the tested yeasts was able to grow or produce significant amounts of ethanol on xylose anaerobically. The best ethanol yields from xylulose were obtained with a wine yeast, two distillery yeasts, and a strain of Saccharomyces uvarum. The best conversion of xylulose

M.-L. Suihko; M. Dra?i?

1983-01-01

399

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

400

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.

2013-07-08

401

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

402

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

403

Nonlinear system identification using the MRAS technique and hyperstability concepts  

E-print Network

. Example of a Nonlinear Function f (x ' ) 7. Example of F(x ) Functions 10 15 26 27 28 8. Comparison of Response/Equation Error in State Tracking With Measurement Noise 35 9. EE Identification of a Saturation With Dead lone Non- I ineari ty 10... the RE linear MRAS case to the nonlinear case has only been done by Tomizuka [29] for a special class of nonlinear systems of the form: Dm + f Dm I + . . . + f o + f x(t) = nm n m-I ''' ni no Dn + a Dn + . . . + a 0 + a n-I '' I o ~ Nn(u(t)) I for m...

Schatte, Alvin Robert

1982-01-01

404

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

405

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

406

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

407

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

408

Non-conventional yeasts.  

PubMed

In the beginning there was yeast, and it raised bread, brewed beer, and made wine. After many not days but centuries and even millenia later, it was named Saccharomyces cerevisiae. After more years and centuries there was another yeast, and it was named Schizosaccharomyces pombe; now there were two stars in the yeast heaven. In only a few more years there were other yeasts, and then more, and more, and more. The era of the non-conventional yeasts had begun. PMID:11878307

Spencer, J F T; Ragout de Spencer, A L; Laluce, C

2002-02-01

409

The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin  

PubMed Central

Chromatin dynamics crucially contributes to gene regulation. Studies of the yeast PHO5 promoter were key to establish this nowadays accepted view and continuously provide mechanistic insight in chromatin remodeling and promoter regulation, both on single locus as well as on systems level. The PHO5 promoter is a context independent chromatin switch module where in the repressed state positioned nucleosomes occlude transcription factor sites such that nucleosome remodeling is a prerequisite for and not consequence of induced gene transcription. This massive chromatin transition from positioned nucleosomes to an extensive hypersensitive site, together with respective transitions at the co-regulated PHO8 and PHO84 promoters, became a prime model for dissecting how remodelers, histone modifiers and chaperones co-operate in nucleosome remodeling upon gene induction. This revealed a surprisingly complex cofactor network at the PHO5 promoter, including five remodeler ATPases (SWI/SNF, RSC, INO80, Isw1, Chd1), and demonstrated for the first time histone eviction in trans as remodeling mode in vivo. Recently, the PHO5 promoter and the whole PHO regulon were harnessed for quantitative analyses and computational modeling of remodeling, transcription factor binding and promoter input-output relations such that this rewarding single-locus model becomes a paradigm also for theoretical and systems approaches to gene regulatory networks. PMID:25190457

Korber, Philipp; Barbaric, Slobodan

2014-01-01

410

Recursive form of the eigensystem realization algorithm for system identification  

NASA Technical Reports Server (NTRS)

An algorithm is developed for recursively calculating the minimum realization of a linear system from sampled impulse response data. The Gram-Schmidt orthonormalization technique is used to generate an orthonormal basis for factorization of the data matrix. The system matrix thus identified is in upper Hessenberg form, which has advantages for the identification of modal parameters including damping coefficients, frequencies, mode shapes, and modal participation factors. It also has the property that once an element of the system matrix is computed, it is never altered as the dimension of the model is increased in the recursive process. Numerical examples are presented for comparison of the recursive and nonrecursive forms of the eigensystem realization algorithm.

Longman, Richard W.; Juang, Jer-Nan

1989-01-01

411

A contamination source identification model for water distribution system security  

NASA Astrophysics Data System (ADS)

This article presents and demonstrates a simple, straightforward genetic algorithm (GA) scheme for contamination source identification to enhance the security of water distribution systems. Related previous work on this subject has concentrated on developing analytical water quality inverse models with two major restrictions: the ability to disclose unique solutions and to handle water distribution systems of large size. These two limitations are addressed in this study by coupling a GA with EPANET. The objective function is minimization of the least-squares of the differences between simulated and measured contaminant concentrations, with the decision variables being the contaminant event characteristics of intrusion location, starting time, duration and mass rate. The developed methodology is demonstrated through base runs and sensitivity analysis of three water distribution system example applications of increasing complexity.

Preis, A.; Ostfeld, A.

2007-12-01

412

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

413

A Gamma Memory Neural Network for System Identification  

NASA Technical Reports Server (NTRS)

A gamma neural network topology is investigated for a system identification application. A discrete gamma memory structure is used in the input layer, providing delayed values of both the control inputs and the network output to the input layer. The discrete gamma memory structure implements a tapped dispersive delay line, with the amount of dispersion regulated by a single, adaptable parameter. The network is trained using static back propagation, but captures significant features of the system dynamics. The system dynamics identified with the network are the Mach number dynamics of the 16 Foot Transonic Tunnel at NASA Langley Research Center, Hampton, Virginia. The training data spans an operating range of Mach numbers from 0.4 to 1.3.

Motter, Mark A.; Principe, Jose C.

1992-01-01

414

A Multimicroprocessor System for Myoelectric Signal Analysis/Identification  

PubMed Central

Use of Myoelectric signal as a control signal has found numerous applications for the disabled. A multimicroprocessor system which is useful for the analysis and identification of myoelectric signals is described. This system is also useful for the development of a controller which can provide the motion of prosthetic or orthotic limbs. In this paper, the theory, software and hardware design of a tightly coupled multimicroprocessor system with distributed common memory and private memory modules, to compute the values of auto-and crosscorrelation functions, to recover signals buried in noise, to compute cross and auto power spectral density at 128 points simultaneously on the time delay axis or frequency axis, are also described. Using these functions, EMG signals are identified and the motion of artificial limbs controlled.

Ganesan, S.; Ahmad, M.O.; Swamy, M.N.S.

1985-01-01

415

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

416

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

417

Nonlinear System Identification for Aeroelastic Systems with Application to Experimental Data  

NASA Technical Reports Server (NTRS)

Representation and identification of a nonlinear aeroelastic pitch-plunge system as a model of the Nonlinear AutoRegressive, Moving Average eXogenous (NARMAX) class is considered. A nonlinear difference equation describing this aircraft model is derived theoretically and shown to be of the NARMAX form. Identification methods for NARMAX models are applied to aeroelastic dynamics and its properties demonstrated via continuous-time simulations of experimental conditions. Simulation results show that (1) the outputs of the NARMAX model closely match those generated using continuous-time methods, and (2) NARMAX identification methods applied to aeroelastic dynamics provide accurate discrete-time parameter estimates. Application of NARMAX identification to experimental pitch-plunge dynamics data gives a high percent fit for cross-validated data.

Kukreja, Sunil L.

2008-01-01

418

Non-Linear System Identification for Aeroelastic Systems with Application to Experimental Data  

NASA Technical Reports Server (NTRS)

Representation and identification of a non-linear aeroelastic pitch-plunge system as a model of the NARMAX class is considered. A non-linear difference equation describing this aircraft model is derived theoretically and shown to be of the NARMAX form. Identification methods for NARMAX models are applied to aeroelastic dynamics and its properties demonstrated via continuous-time simulations of experimental conditions. Simulation results show that (i) the outputs of the NARMAX model match closely those generated using continuous-time methods and (ii) NARMAX identification methods applied to aeroelastic dynamics provide accurate discrete-time parameter estimates. Application of NARMAX identification to experimental pitch-plunge dynamics data gives a high percent fit for cross-validated data.

Kukreja, Sunil L.

2008-01-01

419

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

420

Yeast Genetics and Biotechnological Applications  

NASA Astrophysics Data System (ADS)

Yeast can be recognized as one of the very important groups of microorganisms on account of its extensive use in the fermentation industry and as a basic eukaryotic model cellular system. The yeast Saccharomyces cerevisiae has been extensively used to elucidate the genetics and regulation of several key functions in the cell such as cell mating, electron transport chain, protein trafficking, cell cycle events and others. Even before the genome sequence of the yeast was out, the structural organization and function of several of its genes was known. With the availability of the origin of replication from the 2 ?m plasmid and the development of transformation system, it became the host of choice for expression of a number of important proteins. A large number of episomal and integrative shuttle vectors are available for expression of mammalian proteins. The latest developments in genomics and micro-array technology have allowed investigations of individual gene function by site-specific deletion method. The application of metabolic profiling has also assisted in understanding the cellular network operating in this yeast. This chapter is aimed at reviewing the use of this system as an experimental tool for conducting classical genetics. Various vector systems available, foreign genes expressed and the limitations as a host will be discussed. Finally, the use of various yeast enzymes in biotechnology sector will be reviewed.

Mishra, Saroj; Baranwal, Richa

421

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

422

Advanced electric power systems. [Identification and preliminary evaluation; matching energy sources and conversion systems  

Microsoft Academic Search

An identification and preliminary evaluation was made of alternative advanced electric power systems that have been suggested for possible future use by the American electric utility industry. The motivation for interest in advanced power systems stems primarily from the rapidly rising costs of clean fossil fuels, especially conventional fuel oil, and uncertainties of fuel supply. Four basic energy sources have

A. J. Giramonti; R. D. Lessard

1975-01-01

423

Modelling and system identification of an experimental apparatus for anomaly detection in mechanical systems  

Microsoft Academic Search

This paper presents design, modelling and system identification of a laboratory test apparatus that has been constructed to experimentally validate the concepts of anomaly detection in complex mechanical systems. The test apparatus is designed to be complex in itself due to partially correlated interactions amongst its individual components and functional modules. The experiments are conducted on the test apparatus to

Amol M. Khatkhate; Asok Ray; Eric Keller

2007-01-01

424

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

425

Identification of human gene products containing Pro-Pro-x-Tyr (PY) motifs that enhance glutathione and endocytotic marker uptake in yeast.  

PubMed

In an attempt to identify genes involved in glutathione (GSH) transport, a human mammary gland cDNA library was screened for clones capable of complementing a defect in GSH uptake in yeast cells that lack Hgt1p, the primary yeast GSH uptake transporter. Five genes capable of rescuing growth on sulfur-deficient GSH-containing medium were identified: prostate transmembrane protein, androgen induced 1 (PMEPA1); lysosomal-associated protein transmembrane 4 alpha (LAPTM4alpha); solute carrier family 25, member 1 (SLC25A1); lipopolysaccharide-induced TNF factor (LITAF); and cysteine/tyrosine-rich-1 (CYYR1). All of these genes encode small integral membrane proteins of unknown function, although none appear to encode prototypical GSH transporters. Nevertheless, they all increased both intracellular glutathione levels and [(3)H]GSH uptake rates. [(3)H]GSH uptake was uniformly inhibited by high concentrations of unlabeled GSH, GSSG, and ophthalmic acid. Interestingly, each protein is predicted to contain Pro-Pro-x-Tyr (PY) motifs, which are thought to be important for regulating protein cell surface expression. Uptake of the endocytotic markers lucifer yellow and FM4-64 was also enhanced by each of the five genes. Mutations of the PY motifs in LITAF largely abolished all of its effects. In summary, although the results do not reveal novel GSH transporters, they identify five PY-containing human gene products that may influence plasma membrane transport activity. PMID:20110690

Shi, Shujie; Notenboom, Sylvia; Dumont, Mark E; Ballatori, Nazzareno

2010-01-01

426

High cell-density expression system: yeast cells in a phalanx efficiently produce a certain range of "difficult-to-express" secretory recombinant proteins.  

PubMed

Yeast's extracellular expression provides a cost-efficient means of producing recombinant proteins of academic or commercial interests. However, depending on the protein to be expressed, the production occasionally results in a poor yield, which is frequently accompanied with a deteriorated growth of the host. Here we describe our simple approach, high cell-density expression, to circumvent the cellular toxicity and achieve in a production of a certain range of "difficult-to-express" secretory protein in preparative amount. The system features an ease of performing: (1) precultivate yeast cells to the stationary phase in non-inducing condition, (2) suspend the cells to a small aliquot of inducing medium to form a high cell-density suspension or "a phalanx," and then (3) give a sufficient aeration to the phalanx. Factors and pitfalls that affect the system's performance are also described. PMID:25447864

Kawarasaki, Yasuaki; Kurose, Takeshi; Ito, Keisuke

2015-01-01

427

A Frequency-Domain Substructure System Identification Algorithm  

NASA Technical Reports Server (NTRS)

A new frequency-domain system identification algorithm is presented for system identification of substructures, such as payloads to be flown aboard the Space Shuttle. In the vibration test, all interface degrees of freedom where the substructure is connected to the carrier structure are either subjected to active excitation or are supported by a test stand with the reaction forces measured. The measured frequency-response data is used to obtain a linear, viscous-damped model with all interface-degree of freedom entries included. This model can then be used to validate analytical substructure models. This procedure makes it possible to obtain not only the fixed-interface modal data associated with a Craig-Bampton substructure model, but also the data associated with constraint modes. With this proposed algorithm, multiple-boundary-condition tests are not required, and test-stand dynamics is accounted for without requiring a separate modal test or finite element modeling of the test stand. Numerical simulations are used in examining the algorithm's ability to estimate valid reduced-order structural models. The algorithm's performance when frequency-response data covering narrow and broad frequency bandwidths is used as input is explored. Its performance when noise is added to the frequency-response data and the use of different least squares solution techniques are also examined. The identified reduced-order models are also compared for accuracy with other test-analysis models and a formulation for a Craig-Bampton test-analysis model is also presented.

Blades, Eric L.; Craig, Roy R., Jr.

1996-01-01

428

On the orthogonalised reverse path method for nonlinear system identification  

NASA Astrophysics Data System (ADS)

The problem of obtaining the underlying linear dynamic compliance matrix in the presence of nonlinearities in a general multi-degree-of-freedom (MDOF) system can be solved using the conditioned reverse path (CRP) method introduced by Richards and Singh (1998 Journal of Sound and Vibration, 213(4): pp. 673-708). The CRP method also provides a means of identifying the coefficients of any nonlinear terms which can be specified a priori in the candidate equations of motion. Although the CRP has proved extremely useful in the context of nonlinear system identification, it has a number of small issues associated with it. One of these issues is the fact that the nonlinear coefficients are actually returned in the form of spectra which need to be averaged over frequency in order to generate parameter estimates. The parameter spectra are typically polluted by artefacts from the identification of the underlying linear system which manifest themselves at the resonance and anti-resonance frequencies. A further problem is associated with the fact that the parameter estimates are extracted in a recursive fashion which leads to an accumulation of errors. The first minor objective of this paper is to suggest ways to alleviate these problems without major modification to the algorithm. The results are demonstrated on numerically-simulated responses from MDOF systems. In the second part of the paper, a more radical suggestion is made, to replace the conditioned spectral analysis (which is the basis of the CRP method) with an alternative time domain decorrelation method. The suggested approach - the orthogonalised reverse path (ORP) method - is illustrated here using data from simulated single-degree-of-freedom (SDOF) and MDOF systems.

Muhamad, P.; Sims, N. D.; Worden, K.

2012-09-01

429

A forward model-based analysis of cardiovascular system identification methods  

E-print Network

Cardiovascular system identification is a potentially powerful approach for intelligent patient monitoring of cardiovascular function. Rather than merely recording hemodynamic signals, the signals are mathematically analyzed ...

Mukkamala, Ramakrishna, 1971-

2000-01-01

430

Lack of interactions between amyloid precursor protein and hydrophilic domains of presenilin 1 and 2 using the yeast two hybrid system  

Microsoft Academic Search

Mutations in the two related genes, presenilin 1 (PS1) and presenilin 2 (PS2), which are predicted multispanning membrane\\u000a proteins, are responsible for the majority of early-onset familial Alzheimer's disease (FAD). To demonstrate direct interactions\\u000a between presenilins (PS) and amyloid precursor protein (APP), the authors utilized a yeast two-hybrid system. Various hydrophilic\\u000a domains derived from PS and those of APP were

Sung-Su Kim; Yoo-Mi Choi; Yoo-Hun Suh

1997-01-01

431

Improvements in ethanol concentration and fermentor ethanol productivity in yeast fermentations using whole soy flour in batch, and continuous recycle systems  

Microsoft Academic Search

Summary Ethanol concentrations and fermentor productivities were increased 20.2 and 15.5% at 90 and 95% recycle, respectively, when whole soy flour was added to the feed (2 g\\/l at 90% recycle, and 1 g\\/l at 95% recycle) of a continuous yeast fermentation system with recycle of cells and soy flour (soy flour concentrations were 2% at steady state in the

Dominick Damiano; Shaw S. Wang

1985-01-01

432

An in vivo detection system for transient and low-abundant protein interactions and their kinetics in budding yeast.  

PubMed

Methylation tracking (M-Track) is a protein-proximity assay in Saccharomyces cerevisiae, allowing the detection of transient protein-protein interactions in living cells. The bait protein is fused to a histone lysine methyl transferase and the prey protein to a methylation acceptor peptide derived from histone 3. Upon interaction, the histone 3 fragment is stably methylated on lysine 9 and can be detected by methylation-specific antibodies. Since methylation marking is irreversible in budding yeast and only takes place in living cells, the occurrence of artifacts during cell lysate preparation is greatly reduced, leading to a more accurate representation of native interactions. So far, this method has been limited to highly abundant or overexpressed proteins. However, many proteins of interest are low-abundant, and overexpression of proteins may interfere with their function, leading to an artificial situation. Here we report the generation of a toolbox including a novel cleavage-enrichment system for the analysis of very low-abundant proteins at their native expression levels. In addition, we developed a system for the parallel analysis of two prey proteins in a single cell, as well as an inducible methylation system. The inducible system allows precise control over the time during which the interaction is detected and can be used to determine interaction kinetics. Furthermore, we generated a set of constructs facilitating the cloning-free genomic tagging of proteins at their endogenous locus by homologous recombination, and their expression from centromeric plasmids. GenBank submissions: pCK900; KM407502, pCK901; KM407503, pCK902; KM407504, pCK903; KM407505, pCK904; KM407506, pCK905; KM407507, pCK906; KM407508, pCK907; KM407509, pCK908; KM407510, pCK909; KM407511, pCK910; KM407512, pCK911; KM407513. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25582094

Brezovich, Andrea; Schuschnig, Martina; Ammerer, Gustav; Kraft, Claudine

2015-03-01

433

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

434

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

435

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

436

Mixed Boiler-turbine Coordinated Control System Mathematical Model Based on Mechanism Modelling and Parameter Identification  

Microsoft Academic Search

Based on the excellence of mechanism mathematical model and system identification model, this paper established a mixed model of boiler-turbine coordinated control system (CCS), which combines mechanism analysis and parameter identification. To configure the model into a distributed control system (DCS) of the unit generator, by comparing the model parameters trend curve with the unit generator actual parameters trend curve

Han Zhong-xu; Qi Xiao-hong; Liu Min; Zhang Zhi; Zhou Chuan-xin

2006-01-01

437

A Gender Identification System for Customers in a Shop Using Infrared Area Scanners  

Microsoft Academic Search

Information about customers in shops plays an important role in marketing analysis. Currently, in convenience stores and supermarkets, the identification of customer's gender is examined by clerks. On the other hand, gender identification systems using camera images are investigated. However, these systems have a problem of invading human privacies in identifying attributes of customers. The proposed system identifies gender by

Takuya Tajima; Haruhiko Kimura; Takehiko Abe; Koji Abe; Yoshinori Nakamoto

2008-01-01

438

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

439

Autonomous identification of matrices in the APNea system  

SciTech Connect

The APNea System is a passive and active neutron assay device which features imaging to correct for nonuniform distributions of source material. Since the imaging procedure requires a detailed knowledge of both the detection efficiency and the thermal neutron flux for (sub)volumes of the drum of interest, it is necessary to identify which mocked-up matrix, to be used for detailed characterization studies, best matches the matrix of interest. A methodology referred to as the external matrix probe (EMP) has been established which links external measures of a drum matrix to those of mocked-up matrices. These measures by themselves are sufficient to identify the appropriate mock matrix, from which the necessary characterization data are obtained. This independent matrix identification leads to an autonomous determination of the required system response parameters for the assay analysis.

Hensley, D.

1995-12-31

440

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 identificatio