Sample records for yeast identification system

  1. Evaluation of Automated Yeast Identification System

    NASA Technical Reports Server (NTRS)

    McGinnis, M. R.

    1996-01-01

    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.

  2. Update and evaluation of the AutoMicrobic yeast identification system.

    PubMed Central

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

    1984-01-01

    The AutoMicrobic system (AMS) Yeast Biochemical Card (Vitek Systems Inc., Hazelwood, Mo.) is a system which has been designed for rapid and automated reporting of yeast identification in the clinical laboratory. Recent improvements have been implemented in the AMS data base to expand and enhance its yeast identification capabilities. These improvements include the addition of seven biotypes, changes in data analysis scheme, and construction of the taxonomic keys. The updated system was compared with the API 20C (Analytab Products, Plainview, N.Y.) yeast identification system and a rapid conventional method, using 1,106 clinical and stock yeast isolates. With these improvements, the AMS Yeast Biochemical Card had a correlation of 98.8% with the API 20C system and 93.4% with the rapid conventional method and significantly increased its capability of identifying Cryptococcus neoformans (98%). The most difficult organisms for the system to identify in 22 to 24 h were Cryptococcus terreus (58%) and Cryptococcus uniguttulatus (73%). The updated AMS not only provided more rapid results which were comparable to the other two systems but gave a substantial savings in set-up and reporting time as well. PMID:6386872

  3. Yeast-Plant Coupled Vector System for Identification of Nuclear Proteins1[OA

    E-print Network

    Citovsky, Vitaly

    clones into a multiple cloning site-compatible and reading frame-compatible plant expression vector be transferred, also by a one-step cloning, into a binary multigene expression vector for transient or stableYeast-Plant Coupled Vector System for Identification of Nuclear Proteins1[OA] Adi Zaltsman, Bu

  4. Multicenter Study Evaluating the Vitek MS System for Identification of Medically Important Yeasts

    PubMed Central

    Westblade, Lars F.; Jennemann, Rebecca; Branda, John A.; Bythrow, Maureen; Ferraro, Mary Jane; Garner, Omai B.; Ginocchio, Christine C.; Lewinski, Michael A.; Manji, Ryhana; Mochon, A. Brian; Procop, Gary W.; Richter, Sandra S.; Rychert, Jenna A.; Sercia, Linda

    2013-01-01

    The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates, including 58 C. albicans, 62 C. glabrata, and 53 C. krusei isolates), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n = 58) identified as Candida dubliniensis, one isolate of Candida parapsilosis (n = 73) identified as Candida pelliculosa, and three isolates of Geotrichum klebahnii (n = 6) identified as Geotrichum candidum. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories. PMID:23658267

  5. Evaluation of the Biolog MicroStation system for yeast identification

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

    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.

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

    PubMed

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

    1989-11-01

    Ninety-seven isolates of Cladosporium spp., Exophiala spp., Fonsecaea spp., Lecythophora hoffmannii, Phaeoannellomyces werneckii, Phialophora spp., Wangiella dermatitidis, and Xylohypha bantiana were used to evaluate the API 20C Yeast Identification System for the differentiation of dematiaceous fungi. Using the API 20C system, we were able to distinguish most species of Phialophora and Cladosporium and to separate L. hoffmannii from the species of Phialophora tested; X. bantiana from C. carrionii, C. resinae, and C. sphaerospermum; and W. dermatitidis from Exophiala jeanselmei and Exophiala spinifera. Ninety-two (60.1%) of 153 possible species-pair combinations were separated. PMID:2808678

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

    PubMed Central

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

    2013-01-01

    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

  8. Identification of yeasts from black olives in rapid system microtitre plates

    Microsoft Academic Search

    P. Kotzekidou

    1997-01-01

    A total of 125 yeasts were isolated from Greek-style black olives produced in different factories. Identification was based on 65 morphological and physiological characteristics. The majority of the tests were conducted in microtitration plates. The predominant species proved to be mainlyTorulaspora delbruekii,Debaryomyces hanseniiandCryptococcus laurentii. The speciesCryptococcus albidus,Dekkera bruxellensis,Sporobolomyces roseus,Bullera variabilis,Pichia farinosa,Pichia membranaefaciens, andZygosaccharomyces bailiiwere identified sporadically. A selection of the

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

    PubMed

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

    2014-07-01

    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

  10. Yeast killer systems.

    PubMed Central

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

    1997-01-01

    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

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

    Microsoft Academic Search

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

    2006-01-01

    In this study, we established an in-house database of yeast internal transcribed spacer (ITS) sequences. This database includes medically important as well as colonizing yeasts that frequently occur in the diagnostic laboratory. In a prospective study, we compared molecular identification with phenotypic identification by using the ID32C system (bioMerieux) for yeast strains that could not be identified by a combination

  12. Molecular identification of yeasts associated with traditional Egyptian dairy products.

    PubMed

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

    2009-09-01

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

  13. Yeast Identification Algorithm Based on Use of the Vitek MS System Selectively Supplemented with Ribosomal DNA Sequencing: Proposal of a Reference Assay for Invasive Fungal Surveillance Programs in China

    PubMed Central

    Zhang, Li; Xiao, Meng; Wang, He; Gao, Ran; Fan, Xin; Brown, Mitchell; Gray, Timothy J.; Kong, Fanrong

    2014-01-01

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

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

    Microsoft Academic Search

    Mine Yücesoy; Serhat Marol

    2003-01-01

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

  15. YEASTS OF THE WORLD - MORPHOLOGY, PHYSIOLOGY, SEQUENCES AND IDENTIFICATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This publication is a CD-ROM prepared by an international team of 12 scientists for the purpose of rapid identification of yeasts. Strains may be characterized from conventional growth tests or from sequences of selected genes. Test results are entered into the computer program where they are comp...

  16. Microfermentation Test For Identification Of Yeast

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

    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.

  17. Molecular Biological Identification of Malassezia Yeasts Using Pyrosequencing

    PubMed Central

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

    2013-01-01

    Background A Pyrosequencing assay has been used in identification of fungal species such as Candida or Aspergillus and diagnosis of pathogenic bacteria such as Helicobacter pylori but there has been no report on successful isolation and identification of Malassezia yeasts using the pyrosequencing method. Objective Examine the applicability and plausibility of the pyrosequencing method in identification of the Malassezia species. Methods At internal transcribed spacer (ITS) sites 1 and 2, three primers were developed using Pyrosequencing Assay Design Software (Biotage AB). Pyrosequencing was performed on 11 standard strains and 83 genomic DNA samples obtained from 66 healthy controls aged from 1 to 80. Results The eleven Malassezia standard species and 83 genomic DNA samples were successfully identified using the pyrosequencing assay. Conclusion The pyrosequencing method is a new tool for analysis of Malassezia yeasts, and its precision and rapidity suggests its clinical applicability. PMID:23467187

  18. Yeast on-target lysis (YOTL), a procedure for making auxiliary mass spectrum data sets for clinical routine identification of yeasts.

    PubMed

    Bernhard, Mareike; Weig, Michael; Zautner, Andreas E; Groß, Uwe; Bader, Oliver

    2014-12-01

    Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based species identification has become a reliable and fast tool for use in clinical diagnostics, including in mycology. To identify yeasts in the MALDI Biotyper system, a multistep extraction protocol, which is also used to generate the reference spectra, is recommended. Sample preparation by on-target lysis (OTL) requires significantly less hands-on time and is therefore highly desirable, but it results in too-low MALDI Biotyper log score values to allow automated species identification. To overcome this problem, we developed a procedure for generating and validating an OTL spectrum data set for the most relevant and frequently occurring yeast species in clinical specimens. The performance was evaluated against a set of OTL spectra derived during clinical routine procedures and from a set of closely related yeasts. In the diagnostic setting, the OTL procedure significantly decreased the workload but allowed species identification with high specificity and sensitivity. False identifications were not observed. The use of in-house-generated OTL reference spectra can highly accelerate MALDI-TOF MS-based yeast species identification using the MALDI Biotyper. PMID:25232169

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

    PubMed Central

    Ciardo, D. E.; Schär, G.; Böttger, E. C.; Altwegg, M.; Bosshard, P. P.

    2006-01-01

    In this study, we established an in-house database of yeast internal transcribed spacer (ITS) sequences. This database includes medically important as well as colonizing yeasts that frequently occur in the diagnostic laboratory. In a prospective study, we compared molecular identification with phenotypic identification by using the ID32C system (bioMérieux) for yeast strains that could not be identified by a combination of CHROMagar Candida and morphology on rice agar. In total, 113 yeast strains were included in the study. By sequence analysis, 98% of all strains were identified correctly to the species level. With the ID32C, 87% of all strains were identified correctly to the species or genus level, 7% of the isolates could not be identified, and 6% of the isolates were misidentified, most of them as Candida rugosa or Candida utilis. For a diagnostic algorithm, we suggest a three-step procedure which integrates morphological criteria, biochemical investigation, and sequence analysis of the ITS region. PMID:16390952

  20. Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts.

    PubMed

    Ciardo, D E; Schär, G; Böttger, E C; Altwegg, M; Bosshard, P P

    2006-01-01

    In this study, we established an in-house database of yeast internal transcribed spacer (ITS) sequences. This database includes medically important as well as colonizing yeasts that frequently occur in the diagnostic laboratory. In a prospective study, we compared molecular identification with phenotypic identification by using the ID32C system (bioMérieux) for yeast strains that could not be identified by a combination of CHROMagar Candida and morphology on rice agar. In total, 113 yeast strains were included in the study. By sequence analysis, 98% of all strains were identified correctly to the species level. With the ID32C, 87% of all strains were identified correctly to the species or genus level, 7% of the isolates could not be identified, and 6% of the isolates were misidentified, most of them as Candida rugosa or Candida utilis. For a diagnostic algorithm, we suggest a three-step procedure which integrates morphological criteria, biochemical investigation, and sequence analysis of the ITS region. PMID:16390952

  1. Yeast identification in routine clinical microbiology laboratory and its clinical relevance.

    PubMed

    Agarwal, S; Manchanda, V; Verma, N; Bhalla, P

    2011-01-01

    Rapid identification of yeast infections is helpful in prompt appropriate antifungal therapy. In the present study, the usefulness of chromogenic medium, slide culture technique and Vitek2 Compact (V2C) has been analysed. A total of 173 clinical isolates of yeast species were included in the study. An algorithm to identify such isolates in routine clinical microbiology laboratory was prepared and followed. Chromogenic medium was able to identify Candida albicans, C. tropicalis, C. krusei, C. parapsilosis and Trichosporon asahii. Chromogenic medium was also helpful in identifying "multi-species" yeast infections. The medium was unable to provide presumptive identification of C. pelliculosa, C. utilis, C. rugosa, C. glabrata and C. hemulonii. Vitek 2 compact (V2C) differentiated all pseudohypae non-producing yeast species. The algorithm followed was helpful in timely presumptive identification and final diagnosis of yeast infections, including multi-species yeast infections. PMID:21654115

  2. Identifying Candida and Other Yeast-Like Fungi: Utility of an Identification Algorithm in Resource Limited Setting

    PubMed Central

    Khan, Suveb; Kattungal, Sushma; Bhatia, Simi

    2014-01-01

    Aim: The increasing recovery rates of unusual yeasts with innate drug resistance make accurate identification crucial for successful therapy and infection control measures. The current study was undertaken to study the utility of CHROMagar Candida (CC) and evaluate an identification algorithm, using germ tube test (GT), CC and a commercial identification kit, API ID 32C. Settings and Design: The prospective study was carried out at a private laboratory in Mumbai, India. Materials and Methods: Identification of 533 yeast and yeast like isolates was carried out using an identification algorithm, comprising of the GT, CC and API tests. Results: CC was useful to detect mixed cultures. We were able to identify 393/533, i.e. 73.7 % of isolates using GT and CC Tests only. This was because C. albicans and C. tropicalis, which can be reliably identified using CC, constituted 75.2 % of the isolates. We were unable to identify 140 isolates, i.e. 26.3 %, using GT and CC tests only and performed additional testing using API ID 32C. CC was not found to be reliable in identifying C. krusei. Conclusion: The diverse identification profile obtained in our study substantiates the need for all diagnostic microbiology laboratories to be better prepared for identifying unusual yeasts. Though GT or CC testing cannot alone suffice for identification of all clinically encountered Candida and yeast-like fungi, use of GT, CC and automated identification systems in a step-wise algorithm can enable the same in a more cost effective manner. PMID:25653943

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

    PubMed Central

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

    2013-01-01

    Biochemical and molecular analysis was used for identification of different kefir yeasts species from Brazil, Canada and the United States of America. The sugar/ethanol-resistant activity of the yeasts was evaluated. Saccharomyces cerevisiae and Kluyveromyces marxianus had the highest growth rates, suggesting biotechnological applications possible for these strains. PMID:24159292

  4. Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts

    E-print Network

    Vale, Ronald D.

    Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts identified two mRNAs that localize to the bud tips of the yeast Saccharomyces cerevisiae. To identify reporter assay, identified 22 mRNAs that are localized to bud tips. These messages encode a wide variety

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

    Microsoft Academic Search

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

    2006-01-01

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

  6. Identification and antifungal susceptibility of a large collection of yeast strains isolated in Tunisian hospitals.

    PubMed

    Eddouzi, Jamel; Lohberger, Andrea; Vogne, Christelle; Manai, Mohamed; Sanglard, Dominique

    2013-10-01

    In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used as a rapid method to identify yeasts isolated from patients in Tunisian hospitals. When identification could not be exstablished with this procedure, sequencing of the internal transcribed spacer with 5.8S ribosomal DNA (rDNA) (ITS1-5.8S-ITS2) and D1/D2 domain of large-subunit (LSU rDNA) were employed as a molecular approach for species differentiation. Candida albicans was the dominant species (43.37% of all cases), followed by C. glabrata (16.55%), C. parapsilosis (13.23%), C. tropicalis (11.34%), C. dubliniensis (4.96%), and other species more rarely encountered in human diseases such as C. krusei, C. metapsilosis, C. lusitaniae, C. kefyr, C. palmioleophila, C. guilliermondii, C. intermedia, C. orthopsilosis, and C. utilis. In addition, other yeast species were obtained including Saccharomyces cerevisiae, Debaryomyces hansenii (anamorph known as C. famata), Hanseniaspora opuntiae, Kodamaea ohmeri, Pichia caribbica (anamorph known as C. fermentati), Trichosporon spp. and finally a novel yeast species, C. tunisiensis. The in vitro antifungal activities of fluconazole and voriconazole were determined by the agar disk diffusion test and Etest, while the susceptibility to additional antifungal agents was determined with the Sensititre YeastOne system. Our results showed low incidence of azole resistance in C. albicans (0.54%), C. tropicalis (2.08%) and C. glabrata (4.28%). In addition, caspofungin was active against most isolates of the collection with the exception of two K. ohmeri isolates. This is the first report to describe caspofungin resistant isolates of this yeast. PMID:23768242

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

    E-print Network

    Zhao, Huimin

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

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

    PubMed Central

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

    2013-01-01

    Yeast and mycobacteria can cause infections in immunocompromised patients and normal hosts. The rapid identification of these organisms can significantly improve patient care. There has been an increasing number of studies on using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for rapid yeast and mycobacterial identifications. However, studies on direct comparisons between the Bruker Biotyper and bioMérieux Vitek MS systems for the identification of yeast and mycobacteria have been limited. This study compared the performance of the two systems in their identification of 98 yeast and 102 mycobacteria isolates. Among the 98 yeast isolates, both systems generated species-level identifications in >70% of the specimens, of which Candida albicans was the most commonly cultured species. At a genus-level identification, the Biotyper system identified more isolates than the Vitek MS system for Candida (75/78 [96.2%]versus 68/78 [87.2%], respectively; P = 0.0426) and non-Candida yeasts (18/20 [90.0%]versus 7/20 [35.0%], respectively; P = 0.0008). For mycobacterial identification, the Biotyper system generated reliable identifications for 89 (87.3%) and 64 (62.8%) clinical isolates at the genus and species levels, respectively, from solid culture media, whereas the Vitek MS system did not generate any reliable identification. The MS method differentiated 12/21 clinical species, despite the fact that no differentiation between Mycobacterium abscessus and Mycobacterium chelonae was found by using 16S rRNA gene sequencing. In summary, the MALDI-TOF MS method provides short turnaround times and a standardized working protocol for the identification of yeast and mycobacteria. Our study demonstrates that MALDI-TOF MS is suitable as a first-line test for the identification of yeast and mycobacteria in clinical laboratories. PMID:24048537

  9. Advantages of using matrix-assisted laser desorption ionization-time of flight mass spectrometry as a rapid diagnostic tool for identification of yeasts and mycobacteria in the clinical microbiological laboratory.

    PubMed

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

    2013-12-01

    Yeast and mycobacteria can cause infections in immunocompromised patients and normal hosts. The rapid identification of these organisms can significantly improve patient care. There has been an increasing number of studies on using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid yeast and mycobacterial identifications. However, studies on direct comparisons between the Bruker Biotyper and bioMérieux Vitek MS systems for the identification of yeast and mycobacteria have been limited. This study compared the performance of the two systems in their identification of 98 yeast and 102 mycobacteria isolates. Among the 98 yeast isolates, both systems generated species-level identifications in >70% of the specimens, of which Candida albicans was the most commonly cultured species. At a genus-level identification, the Biotyper system identified more isolates than the Vitek MS system for Candida (75/78 [96.2%]versus 68/78 [87.2%], respectively; P = 0.0426) and non-Candida yeasts (18/20 [90.0%]versus 7/20 [35.0%], respectively; P = 0.0008). For mycobacterial identification, the Biotyper system generated reliable identifications for 89 (87.3%) and 64 (62.8%) clinical isolates at the genus and species levels, respectively, from solid culture media, whereas the Vitek MS system did not generate any reliable identification. The MS method differentiated 12/21 clinical species, despite the fact that no differentiation between Mycobacterium abscessus and Mycobacterium chelonae was found by using 16S rRNA gene sequencing. In summary, the MALDI-TOF MS method provides short turnaround times and a standardized working protocol for the identification of yeast and mycobacteria. Our study demonstrates that MALDI-TOF MS is suitable as a first-line test for the identification of yeast and mycobacteria in clinical laboratories. PMID:24048537

  10. Identification of yeasts associated with milk products using traditional and molecular techniques.

    PubMed

    Lopandic, K; Zelger, S; Bánszky, L K; Eliskases-Lechner, F; Prillinger, H

    2006-06-01

    An integrated approach including phenotypic (morphological, biochemical and physiological characterization) and genotypic (RAPD-PCR, sequencing of D1/D2 domain of 26S rRNA encoding gene) methods was used for the identification of yeasts isolated from different milk products. There were 513 isolates in all, 460 ascomycetous and 53 basidiomycetous yeasts. The yeast isolates were characterized on the basis of their biochemical and physiological properties, and the D1/D2 domain of 26S rDNA was sequenced in selected strains. Relying on the obtained results from both the data-sets, corresponding type strains were selected and compared with the respective yeast isolates from milk products by RAPD fingerprinting. The strains showing a degree of similarity >80% were considered conspecific. By means of the applied techniques it was possible to identify 92% yeast isolates at species level. Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces marxianus, Yarrowia lipolytica and Candida zeylanoides are the most frequently isolated species. The majority of the yeasts were isolated from fresh and sour curd cheese. A comparison of the results obtained by phenotypic and genotypic investigation revealed that the identification based on classical methods was supported by genotypic characterization in only 54% of examined isolates. The results described in this work show that the applied molecular identification is a reliable approach to the identification of yeasts associated with milk products in contrast to the conventional biochemical and physiological tests. The identification of new yeast species requires additional genetic markers such as sequencing of different genes or DNA:DNA hybridization. PMID:16943023

  11. Comparative Evaluation of the Bruker Biotyper and Vitek MS Matrix-Assisted Laser Desorption Ionization–Time Of Flight (MALDI-TOF) Mass Spectrometry Systems for Identification of Yeasts of Medical Importance

    PubMed Central

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

    2013-01-01

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

  12. 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

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

    2014-10-01

    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

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

    PubMed Central

    Kümmerle, Michael; Scherer, Siegfried; Seiler, Herbert

    1998-01-01

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

  14. Identification and functional analysis of chaperonin 10, the groES homolog from yeast mitochondria.

    PubMed

    Rospert, S; Glick, B S; Jenö, P; Schatz, G; Todd, M J; Lorimer, G H; Viitanen, P V

    1993-12-01

    Chaperonin 60 (cpn60) and chaperonin 10 (cpn10) constitute the chaperonin system in prokaryotes, mitochondria, and chloroplasts. In Escherichia coli, these two chaperonins are also termed groEL and groES. We have used a functional assay to identify the groES homolog cpn10 in yeast mitochondria. When dimeric ribulose-1,5-bisphosphate carboxylase (Rubisco) is denatured and allowed to bind to yeast cpn60, subsequent refolding of Rubisco is strictly dependent upon yeast cpn10. The heterologous combination of cpn60 from E. coli plus yeast cpn10 is also functional. In contrast, yeast cpn60 plus E. coli cpn10 do not support refolding of Rubisco. In the presence of MgATP, yeast cpn60 and yeast cpn10 form a stable complex that can be isolated by gel filtration and that facilitates refolding of denatured Rubisco. Although the potassium-dependent ATPase activity of E. coli cpn60 can be inhibited by cpn10 from either E. coli or yeast, neither of these cpn10s inhibits the ATPase activity of yeast cpn60. Amino acid sequencing of yeast cpn10 reveals substantial similarity to the corresponding cpn10 proteins from rat mitochondria and prokaryotes. PMID:7902576

  15. Identification and functional analysis of chaperonin 10, the groES homolog from yeast mitochondria.

    PubMed Central

    Rospert, S; Glick, B S; Jenö, P; Schatz, G; Todd, M J; Lorimer, G H; Viitanen, P V

    1993-01-01

    Chaperonin 60 (cpn60) and chaperonin 10 (cpn10) constitute the chaperonin system in prokaryotes, mitochondria, and chloroplasts. In Escherichia coli, these two chaperonins are also termed groEL and groES. We have used a functional assay to identify the groES homolog cpn10 in yeast mitochondria. When dimeric ribulose-1,5-bisphosphate carboxylase (Rubisco) is denatured and allowed to bind to yeast cpn60, subsequent refolding of Rubisco is strictly dependent upon yeast cpn10. The heterologous combination of cpn60 from E. coli plus yeast cpn10 is also functional. In contrast, yeast cpn60 plus E. coli cpn10 do not support refolding of Rubisco. In the presence of MgATP, yeast cpn60 and yeast cpn10 form a stable complex that can be isolated by gel filtration and that facilitates refolding of denatured Rubisco. Although the potassium-dependent ATPase activity of E. coli cpn60 can be inhibited by cpn10 from either E. coli or yeast, neither of these cpn10s inhibits the ATPase activity of yeast cpn60. Amino acid sequencing of yeast cpn10 reveals substantial similarity to the corresponding cpn10 proteins from rat mitochondria and prokaryotes. Images Fig. 1 Fig. 3 Fig. 4 PMID:7902576

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

    PubMed

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

    2014-10-01

    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?

  17. Highlights of CLSI Document – Abbreviated Identification of Bacteria and Yeast - M35-A2, Second Edition

    Microsoft Academic Search

    Mary K. York

    2010-01-01

    The second edition of M35-A2 Abbreviated identification of Bacteria and Yeast contains many more identifications than the first edition, including14 species from 11 genera. Biothreat agents and agents that can be highly infectious to laboratory personnel have been added to improve rapid detection of these agents and minimize exposure of personnel to them. User-friendly tables have been included, and safety

  18. Yeast metabolic state identification using micro-fiber optics spectroscopy

    Microsoft Academic Search

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

    2011-01-01

    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

  19. IDENTIFICATION OF YEASTS ISOLATED FROM MUKUMBI, A ZIMBABWEAN TRADITIONAL WINE

    Microsoft Academic Search

    A. Mpofu; J. L. F. Kock; E. E. Pretorious; C. H. Pohl; R. Zvauya

    The use and identity of microbes in traditional fermented beverages has attracted the interest of researchers and industrialists world-wide, probably due to their potential to reduce transmission of bacterial enteric pathogens, as well as improving their nutritional value. In the work done, yeasts were isolated from samples of Zimbabwean traditional wine, mukumbi, collected from rural households in Mberengwa, Zimbabwe. Isolates

  20. Author Identification Systems

    ERIC Educational Resources Information Center

    Wagner, A. Ben

    2009-01-01

    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…

  1. Automatic voice identification system

    Microsoft Academic Search

    Harvey Woodsum

    1987-01-01

    Advances in the basic science of voice identification when combined with the latest state-of-the-art digital electronics are discussed. The Sanders voice identification system prototype consisting of an audio input device, a microcomputer, and special hardware for computing spectrographic features is described. The Griffin Pattern classifier (GPC) for computing the likelihood of each identity is discussed. Results of the experimental testing

  2. A cyclohexanecarboxylic acid utilizing yeast: isolation, identification, and nutritional characteristics.

    PubMed

    Higuchi, K; Obata, H; Tokuyama, T

    1982-08-01

    A yeast capable of utilizing cyclohexanecarboxylic acid as sole carbon and energy source, strain KUY-6A, was isolated from soil by enrichment cultures. Taxonomical studies indicated that strain KUY-6A was Trichosporon cutaneum. Strain KUY-6A grew on a number of carboxylic acids. Among the cyclic compounds tested, cyclohexanecarboxylic acid was the best substrate. Cyclopentanecarboxylic acid, cycloheptanecarboxylic acid, cyclopentanone, cyclohexanone, and cyclopentanol also supported growth. In addition, the organism used the monocarboxylic acids, butyric, valeric, and caproic; the dicarboxylic acids succinic, glutaric, adipic, pimelic, and suberic; and the aromatic acids, benzoic and o-, m-, and p-hydroxybenzoic. The yeast did not require any vitamins for growth, although thiamine gave slight stimulation. The cell dry weight yield was 0.75 g from 1 g cyclohexanecarboxylic acid used. PMID:7139408

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

    PubMed

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

    2014-03-01

    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

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

    PubMed Central

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

    2014-01-01

    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

  5. Quantum System Identification

    E-print Network

    Daniel Burgarth; Kazuya Yuasa

    2011-04-04

    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.

  6. Systematic identification of cell size regulators in budding yeast.

    PubMed

    Soifer, Ilya; Barkai, Naama

    2014-01-01

    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

  7. Systematic identification of cell size regulators in budding yeast

    PubMed Central

    Soifer, Ilya; Barkai, Naama

    2014-01-01

    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

  8. Accurate identification of centromere locations in yeast genomes using Hi-C

    PubMed Central

    Varoquaux, Nelle; Liachko, Ivan; Ay, Ferhat; Burton, Joshua N.; Shendure, Jay; Dunham, Maitreya J.; Vert, Jean-Philippe; Noble, William S.

    2015-01-01

    Centromeres are essential for proper chromosome segregation. Despite extensive research, centromere locations in yeast genomes remain difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation capture assay, Hi-C, has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single genome from Hi-C data by exploiting the centromeres’ tendency to cluster in three-dimensional space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use Centurion to infer centromere locations in 14 yeast species. Across all microbes that we consider, Centurion predicts 89% of centromeres within 5 kb of their known locations. We also demonstrate the robustness of the approach in datasets with low sequencing depth. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results show that Centurion can be used for centromere identification for diverse species of yeast and possibly other microorganisms. PMID:25940625

  9. Accurate identification of centromere locations in yeast genomes using Hi-C.

    PubMed

    Varoquaux, Nelle; Liachko, Ivan; Ay, Ferhat; Burton, Joshua N; Shendure, Jay; Dunham, Maitreya J; Vert, Jean-Philippe; Noble, William S

    2015-06-23

    Centromeres are essential for proper chromosome segregation. Despite extensive research, centromere locations in yeast genomes remain difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation capture assay, Hi-C, has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single genome from Hi-C data by exploiting the centromeres' tendency to cluster in three-dimensional space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use Centurion to infer centromere locations in 14 yeast species. Across all microbes that we consider, Centurion predicts 89% of centromeres within 5 kb of their known locations. We also demonstrate the robustness of the approach in datasets with low sequencing depth. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results show that Centurion can be used for centromere identification for diverse species of yeast and possibly other microorganisms. PMID:25940625

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

    Microsoft Academic Search

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

    2002-01-01

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

  11. YeastMed: an XML-Based System for Biological Data Integration of Yeast

    E-print Network

    Briache, Abdelaali; Kerzazi, Amine; Navas-Delgado, Ismael; Montes, Jose F Aldana; Hassani, Badr D Rossi; Lairini, Khalid

    2010-01-01

    A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of biological data. SGD, Yeastract, CYGD-MIPS, BioGrid and PhosphoGrid are five of the most visited databases by the yeast community. These sources provide complementary data on biological entities. Biologists are brought systematically to query these data sources in order to analyse the results of their experiments. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned result is a complex and laborious task. To provide transparent and simultaneous access to these sources, we have developed a mediator-based system called YeastMed. In this paper, we present YeastMed focusing on its architecture.

  12. MALDI-TOF MS based identification of food-borne yeast isolates.

    PubMed

    Pavlovic, Melanie; Mewes, Anne; Maggipinto, Marzena; Schmidt, Wolfgang; Messelhäußer, Ute; Balsliemke, Joachim; Hörmansdorfer, Stefan; Busch, Ulrich; Huber, Ingrid

    2014-11-01

    In this study, food-borne yeast isolates (n=96), comprising at least 33 species, were identified using MALDI-TOF MS and conventional methods (API ID 32 C and Phoenix Yeast ID). Discrepancies of both methods were resolved by sequencing the ITS1-5.8S-rRNA-ITS2 region. For ten isolates, mainly classified to Rhodotorula and Trichosporon species, no clear final species identification was possible. 62 isolates were correctly identified to species level using either MALDI-TOF MS or conventional tests. 15 isolates were misidentified when applying conventional assays. In contrary, no species misidentifications were observed after MALDI-TOF MS based classification. In return, 16 isolates were not identifiable after matching their protein fingerprints against MALDI Biotyper 4.0.0.1 library. MALDI TOF MS in-house database update clearly improved the identification. In conclusion, the presented data suggest that MALDI-TOF MS is an appropriate platform for reliable classification and identification of food-borne yeast isolates. PMID:25193440

  13. Automated Microbiological Detection/Identification System

    PubMed Central

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

    1977-01-01

    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

  14. Strain differentiation of pathogenic yeasts by the killer system.

    PubMed

    Morace, G; Archibusacci, C; Sestito, M; Polonelli, L

    1984-02-15

    High sensitivity rates to the activity of killer toxins produced by 25 species of yeasts belonging to the genera Candida, Hansenula, Pichia, Rhodotorula, Saccharomyces and Trichosporon have been observed among 112 yeast isolates (25 Cryptococcus neoformans, 29 C. glabrata 16 C. parapsilosis, 20 C. pseudotropicalis and 22 C. tropicalis). The highest sensitivity has been observed among the C. parapsilosis isolates, the lowest in C. glabrata strains. Genera Pichia and Hansenula proved to have the greatest killer activity. A killer system, formerly used for differentiating C. albicans isolates within the species, proved to be valid as epidemiological marker when applied to 112 strains of pathogenic yeasts. PMID:6371541

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

    PubMed Central

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

    2009-01-01

    Background Malassezia yeasts are normal flora of the skin found in 75~98% of healthy subjects. The accurate identification of the Malassezia species is important for determining the pathogenesis of the Malassezia yeasts with regard to various skin diseases such as Malassezia folliculitis, seborrheic dermatitis, and atopic dermatitis. Objective This research was conducted to determine a more accurate and rapid molecular test for the identification and classification of Malassezia yeasts. Methods We compared the accuracy and efficacy of restriction fragment length polymorphism (RFLP) and the nested polymerase chain reaction (PCR) for the identification of Malassezia yeasts. Results Although both methods demonstrated rapid and reliable results with regard to identification, the nested PCR method was faster. However, 7 different Malassezia species (1.2%) were identified by the nested PCR compared to the RFLP method. Conclusion Our results show that RFLP method was relatively more accurate and reliable for the detection of various Malassezia species compared to the nested PCR. But, in the aspect of simplicity and time saving, the latter method has its own advantages. In addition, the 26S rDNA, which was targeted in this study, contains highly conserved base sequences and enough sequence variation for inter-species identification of Malassezia yeasts. PMID:20523823

  16. In vitro reconstruction of the mitochondrial translation system of yeast.

    PubMed Central

    Pfisterer, J; Buetow, D E

    1981-01-01

    We have isolated the translation system from yeast mitochondria and have reconstructed it in vitro. This submitochondrial system, composed of mitochondrial ribosomes, tRNA, pH 5 fraction and mRNA, is maximally active at 10 mM Mg2+ and 100 mM KCl or NH4Cl. NH4+ is more stimulatory than K+. Added Escherichia coli tRNA gives less than half the activity obtained with added mitochondrial tRNA. Activity is enhanced with protease inhibitors but not with Ca2+, spermine, or spermidine. In contrast to heterologous translation systems, the present system produces products with molecular weights similar to those of products synthesized by yeast mitochondria in vivo and by intact yeast mitochondria in vitro. The results support the idea that the unique coding features of the mitochondrial genome require a unique translation system for accurate translation of mitochondrial mRNAs. Images PMID:6946437

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

    PubMed Central

    Altun, Osman; Almuhayawi, Mohammed; Ullberg, Mĺns

    2013-01-01

    The FilmArray platform (FA; BioFire, Salt Lake City, UT) is a closed diagnostic system allowing high-order multiplex PCR analysis with automated readout of results directly from positive blood cultures in 1 h. In the present study, we evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel, which includes 19 bacteria, five yeasts, and three antibiotic resistance genes. In total, 206 blood culture bottles were included in the study. The FilmArray could identify microorganisms in 153/167 (91.6%) samples with monomicrobial growth. Thirteen of the 167 (7.8%) microorganisms were not covered by the FilmArray BCID panel. In 6/167 (3.6%) samples, the FilmArray detected an additional microorganism compared to blood culture. When polymicrobial growth was analyzed, the FilmArray could detect all target microorganisms in 17/24 (71%) samples. Twelve blood culture bottles that yielded a positive signal but showed no growth were also negative by FilmArray. In 3/206 (1.5%) bottles, the FilmArray results were invalid. The results of the FilmArray were reproducible, as demonstrated by the testing and retesting of five bottles in the same day and a longitudinal follow-up of five other blood cultures up to 4 weeks. The present study shows that the FilmArray is a rapid identification method with high performance in direct identification of bacteria and yeasts from positive blood culture bottles. PMID:24088863

  18. 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

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

    2014-01-01

    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

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

    PubMed

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

    2011-08-01

    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

  20. Potential of yeast secretory vesicles in biodelivery systems.

    PubMed

    Kutralam-Muniasamy, Gurusamy; Flores-Cotera, Luis B; Perez-Guevara, Fermin

    2015-06-01

    Membranous vesicular organelles (MVOs), such as secretory vesicles and exosomes, perform a variety of biological functions ranging from secretion to cellular communication in eukaryotic cells. Exosomes, particularly those of mammalian cells, have been widely studied as potential carriers in human therapeutic applications. However, no study has yet demonstrated the use of yeast secretory vesicles for such applications. Therefore, we explore here the current state of knowledge on yeast secretory vesicles and their potential use in therapeutic delivery systems. We focus on the characteristics shared by exosomes and yeast secretory vesicles to provide insights into the use of the latter as delivery vehicles. From this perspective, we speculate on the potential application of post-Golgi vesicles (PGVs) in the biomedical field. PMID:25843637

  1. RAPID IDENTIFICATION OF CANDIDA ALBICANS DIRECTLY FROM YEAST POSITIVE BLOOD CULTURE BOTTLES BY FLUORESCENCE IN SITU HYBRIDIZATION USING PNA PROBES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new fluorescence in situ hybridization (FISH) method using peptide nucleic acid (PNA) probes for identification of Candida albicans directly from yeast-positive blood culture bottles is described. The test (C. albicans PNA FISH) is based on a fluorescein-labeled PNA probe targeting C. albicans 26...

  2. System identification of jet engines

    Microsoft Academic Search

    N. Sugiyama

    2000-01-01

    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

  3. 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

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

    2014-01-01

    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

  4. 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

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

    2014-08-01

    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

  5. Dietary Yeasts Reduce Inflammation in Central Nerve System via Microflora

    PubMed Central

    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

    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

  6. Assessment of Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Bacterial and Yeast Identification.

    PubMed

    Westblade, Lars F; Garner, Omai B; MacDonald, Karen; Bradford, Constance; Pincus, David H; Mochon, A Brian; Jennemann, Rebecca; Manji, Ryhana; Bythrow, Maureen; Lewinski, Michael A; Burnham, Carey-Ann D; Ginocchio, Christine C

    2015-07-01

    Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has revolutionized the identification of clinical bacterial and yeast isolates. However, data describing the reproducibility of MALDI-TOF MS for microbial identification are scarce. In this study, we show that MALDI-TOF MS-based microbial identification is highly reproducible and can tolerate numerous variables, including differences in testing environments, instruments, operators, reagent lots, and sample positioning patterns. Finally, we reveal that samples of bacterial and yeast isolates prepared for MALDI-TOF MS identification can be repeatedly analyzed without compromising organism identification. PMID:25926486

  7. Identification of TRIO-GEFD1 chemical inhibitors using the Yeast Exchange Anne Blangy, *Nathalie Bouquier, *Ccile Gauthier-Rouvire, *Susanne

    E-print Network

    Paris-Sud XI, Université de

    1 Identification of TRIO-GEFD1 chemical inhibitors using the Yeast Exchange Assay. *§ Anne BlangyGEF inhibitors. Key words: RhoG, exchange factor, yeast, screen, nucleotide. #12;2 Abbreviations AMCA: amino. Results RhoG-T17N is a poor inhibitor of its exchange factor TRIO-GEFD1 in vivo: although it binds to TRIO

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

    PubMed Central

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

    1997-01-01

    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

  9. Presumptive identification of Clostridium difficile by detection of p-cresol in prepared peptone yeast glucose broth supplemented with p-hydroxyphenylacetic acid.

    PubMed Central

    Sivsammye, G; Sims, H V

    1990-01-01

    Prereduced, anaerobically sterilized peptone yeast glucose broth was supplemented with p-hydroxyphenylacetic acid and used for the presumptive identification of Clostridium difficile. Two hundred eighty-two organisms were grown in this medium for 18 h and tested for p-cresol production by gas-liquid chromatography. All 49 stock and reference strains of C. difficile and 19 organisms confirmed as C. difficile produced p-cresol. p-Cresol was not produced by 53 negative control or 161 test organisms. The system was convenient and effective. PMID:2394806

  10. Deformable Contour Tracking & System Identification

    E-print Network

    Vaswani, Namrata

    Deformable Contour Tracking & System Identification Namrata Vaswani Dept. of Electrical & Computer video or from spatial image sequences ­ Do this offline ("smoothing") or online ("tracking") ­ O (frequent camera viewpoint changes) Partial occlusion of car by street light #12;Deformable Contour Tracking

  11. Multisensor fusion for system identification

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  12. Studying protein complexes by the yeast two-hybrid system

    PubMed Central

    Rajagopala, Seesandra V.; Sikorski, Patricia; Caufield, J. Harry; Tovchigrechko, Andrey; Uetz, Peter

    2012-01-01

    Protein complexes are typically analysed by affinity purification and subsequent mass spectrometric analysis. However, in most cases the structure and topology of the complexes remains elusive from such studies. Here we investigate how the yeast two-hybrid system can be used to analyse direct interactions among proteins in a complex. First we tested all pairwise interactions among the seven proteins of Escherichia coli DNA polymerase III as well as an uncharacterized complex that includes MntR and PerR. Four and seven interactions were identified in these two complexes, respectively. In addition, we review Y2H data for three other complexes of known structure which serve as “gold-standards”, namely Varicella Zoster Virus (VZV) ribonucleotide reductase (RNR), the yeast proteasome, and bacteriophage lambda. Finally, we review an Y2H analysis of the human spliceosome which may serve as an example for a dynamic mega-complex. PMID:22841565

  13. Development and characterization of a reconstituted yeast translation initiation system.

    PubMed Central

    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

    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

  14. Advances in rotorcraft system identification

    NASA Astrophysics Data System (ADS)

    Hamel, Peter G.; Kaletka, Jürgen

    1997-03-01

    System identification can best be described as the extraction of system characteristics from measured flight test data. Therefore it provides an excellent tool for determining and improving mathematical models for a wide range of applications. The increasing need for accurate models for the design of high bandwidth control systems for rotorcraft has initiated a high interest in and a more intensive use of system identification. This development was supported by the AGARD FVP Working Group 18 on ‘Rotorcraft System Identification’, which brought together specialists from research organisations and industry, tasked with exploring the potential of this tool. In the Group, the full range of identification approaches was applied to dedicated helicopter flight-test-data including data quality checking and the determination and verification of flight mechanical models. It was mainly concentrated on the identification of six degrees of freedom rigid body models, which provide a realistic description of the rotorcraft dynamics for the lower and medium frequency range. The accomplishment of the Working Group has increased the demand for applying these techniques more routinely and, in addition, for extending the model order by including explicit rotor degrees of freedom. Such models also accurately characterize the higher frequency range needed for high bandwidth control system designs. In the specific case of the DLR In-Flight Simulator BO 105 ATTHeS, the application of the identified higher order models for the model-following control system was a major prerequisite for the obtained high simulation quality.

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

    PubMed Central

    Thornton, Mark A.; Thornton, Roy J.

    2013-01-01

    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

  16. Yeast Two-Hybrid, a Powerful Tool for Systems Biology

    PubMed Central

    Brückner, Anna; Polge, Cécile; Lentze, Nicolas; Auerbach, Daniel; Schlattner, Uwe

    2009-01-01

    A key property of complex biological systems is the presence of interaction networks formed by its different components, primarily proteins. These are crucial for all levels of cellular function, including architecture, metabolism and signalling, as well as the availability of cellular energy. Very stable, but also rather transient and dynamic protein-protein interactions generate new system properties at the level of multiprotein complexes, cellular compartments or the entire cell. Thus, interactomics is expected to largely contribute to emerging fields like systems biology or systems bioenergetics. The more recent technological development of high-throughput methods for interactomics research will dramatically increase our knowledge of protein interaction networks. The two most frequently used methods are yeast two-hybrid (Y2H) screening, a well established genetic in vivo approach, and affinity purification of complexes followed by mass spectrometry analysis, an emerging biochemical in vitro technique. So far, a majority of published interactions have been detected using an Y2H screen. However, with the massive application of this method, also some limitations have become apparent. This review provides an overview on available yeast two-hybrid methods, in particular focusing on more recent approaches. These allow detection of protein interactions in their native environment, as e.g. in the cytosol or bound to a membrane, by using cytosolic signalling cascades or split protein constructs. Strengths and weaknesses of these genetic methods are discussed and some guidelines for verification of detected protein-protein interactions are provided. PMID:19582228

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

    SciTech Connect

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

    1994-05-01

    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.

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

    Microsoft Academic Search

    Klaus Gori; Marina Kryger Bjřrklund; Nuria Canibe; Anni Řyan Pedersen; Lene Jespersen

    2011-01-01

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

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

    Microsoft Academic Search

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

    Transcriptional adaptor proteins are required for full function of higher eukaryotic acidic activators in the yeastSaccharomyces cerevisiae, suggesting that this pathway of activation is evolutionarily conserved. Consis- tent with this view, we have identified possible human homologs of yeast ADA2 (yADA2) and yeast GCN5 (yGCN5), components of a putative adaptor complex. While there is overall sequence similarity between the yeastandhumanproteins,perhapsmoresignificantisconservationofkeysequencefeatureswithotherknown

  20. 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...

  1. A yeast pheromone-based inter-species communication system.

    PubMed

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

    2015-02-01

    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

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

    Microsoft Academic Search

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

    2011-01-01

    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

  3. EFFICIENT AEROELASTIC CFD PREDICTIONS USING SYSTEM IDENTIFICATION

    E-print Network

    Jacob, Jamey

    EFFICIENT AEROELASTIC CFD PREDICTIONS USING SYSTEM IDENTIFICATION By TIMOTHY JOHN COWAN Bachelor of MASTER OF SCIENCE May, 1998 #12;ii EFFICIENT AEROELASTIC CFD PREDICTIONS USING SYSTEM IDENTIFICATION REVIEW........................................................................4 2.1. Piston Perturbation

  4. A Systems-Biology Approach to Yeast Actin Cables

    PubMed Central

    Drake, Tyler; Yusuf, Eddy; Vavylonis, Dimitrios

    2011-01-01

    We focus on actin cables in yeast as a model system for understanding cytoskeletal organization and the workings of actin itself. In particular, we highlight quantitative approaches on the kinetics of actin cable assembly and methods of measuring their morphology by image analysis. Actin cables described by these studies can span greater lengths than a thousand end-to-end actin monomers. Because of this difference in length scales, control of the actin-cable system constitutes a junction between short-range interactions—among actin monomers and nucleating, polymerization-facilitating, side-binding, severing, and cross-linking proteins—and the emergence of cell-scale physical form as embodied by the actin cables themselves. PMID:22161338

  5. System identification in experimental data

    SciTech Connect

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

    1996-06-01

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

  6. Automated drug identification system

    NASA Technical Reports Server (NTRS)

    Campen, C. F., Jr.

    1974-01-01

    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.

  7. Bimodal Biometric Person Identification System Under Perturbations

    E-print Network

    verification using face and voice information. We are interested in setting up a bimodal identification systemBimodal Biometric Person Identification System Under Perturbations Miguel Carrasco1 , Luis Pizarro2. Multibiometric person identification systems play a crucial role in environments where security must be ensured

  8. A bimodal biometric identification system

    NASA Astrophysics Data System (ADS)

    Laghari, Mohammad S.; Khuwaja, Gulzar A.

    2013-03-01

    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.

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

    Microsoft Academic Search

    ELKE HAMMER; DIRK KROWAS; ANNETT SCHAFER; MICHAEL SPECHT; WITTKO FRANCKE; FRIEDER SCHAUER

    1998-01-01

    We characterized the ability of a yeast to cleave the aromatic structure of the dioxin-like compound dibenzofuran. The yeast strain was isolated from a dioxin-contaminated soil sample and identified as Tricho- sporon mucoides. During incubation of glucose-pregrown cells with dibenzofuran, six major metabolites were detected by high-performance liquid chromatography. The formation of four different monohydroxylated dibenzofurans was proven by comparison

  10. Identification and functional analysis of hPRP17, the human homologue of the PRP17/CDC40 yeast gene involved in splicing and cell cycle control.

    PubMed

    Ben Yehuda, S; Dix, I; Russell, C S; Levy, S; Beggs, J D; Kupiec, M

    1998-10-01

    The PRP17 gene of the yeast Saccharomyces cerevisiae encodes a protein that participates in the second step of the splicing reaction. It was found recently that the yeast PRP17 gene is identical to the cell division cycle CDC40 gene. The PRP17/CDC40 gene codes for a protein with several copies of the WD repeat, a motif found in a large family of proteins that play important roles in signal transduction, cell cycle progression, splicing, transcription, and development. In this report, we describe the identification of human, nematode, and fission yeast homologues of the PRP17/CDC40 gene of S. cerevisiae. The newly identified proteins share homology with the budding yeast protein throughout their entire sequence, with the similarity being greatest in the C-terminal two thirds that includes the conserved WD repeats. We show that a yeast-human chimera, carrying the C-terminal two thirds of the hPRP17 protein, is able to complement the cell cycle and splicing defects of a yeast prp17 mutant. Moreover, the yeast and yeast-human chimeric proteins co-precipitate the intron-exon 2 lariat intermediate and the intron lariat product, providing evidence that these proteins are spliceosome-associated. These results show the functional conservation of the Prp17 proteins in evolution and suggest that the second step of splicing takes place by a similar mechanism throughout eukaryotes. PMID:9769104

  11. System identification of jet engines

    SciTech Connect

    Sugiyama, N.

    2000-01-01

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

  12. Molecular identification of yeast species associated with 'Hamei'--a traditional starter used for rice wine production in Manipur, India.

    PubMed

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

    2008-05-31

    In Manipur state of North-Eastern India, wine from glutinous rice using traditional solid state starter called 'Hamei' is particularly interesting because of its unique flavour. A total of 163 yeast isolates were obtained from fifty four 'Hamei' samples collected from household rice wine preparations in tribal villages of Manipur. Molecular identification of yeast species was carried out by analysis of the restriction digestion pattern generated from PCR amplified internal transcribed spacer region along with 5.8S rRNA gene (ITS1-5.8S-ITS2). Seventeen different restriction profiles were obtained from the size of PCR products and the restriction analysis with three endonucleases (Hae III, Cfo I and Hinf I). Nine groups were identified as S. cerevisiae, Pichia anomala, Trichosporon sp., Candida tropicalis, Pichia guilliermondi, Candida parapsilosis, Torulaspora delbrueckii, Pichia fabianii and Candida montana by comparing this ITS-RFLP profile with type strains of common wine yeasts, published data and insilico analysis of ITS sequence data available in CBS yeast database. ITS-RFLP profile of eight groups was not matching with available database of 288 common wine yeast species. The most frequent yeast species associated with 'Hamei' were S. cerevisiae (32.5%), P. anomala (41.7%) and Trichosporon sp. (8%). The identity of major groups was confirmed by additional restriction digestion of ITS region with Hind III, EcoRI, Dde I and Msp I. The genetic diversity of industrially important S. cerevisiae group was investigated using Pulsed Field Gel Electrophoresis (PFGE). Although most of the 53 strains of S. cerevisiae examined were exhibited a common species specific pattern, a distinct degree of chromosomal length polymorphism and variable number of chromosomal DNA fragments were observed with in the species. Cluster analysis showed seven major karyotypes (K1-K7) with more than 83% similarity. The karyotype pattern K1 was the most frequent (67.9%) among the strains from different samples. Other karyotypes K2-K7 were very unique with less than 80% similarity. Finally using mitochondrial DNA restriction analysis (mt-DNA RFLP), S. cerevisiae strains belonging to the major karyotype K1 were distinctly differentiated with highly polymorphic bands by Hinf I and Hae III endonucleases. PMID:18433905

  13. Identifiability and algebraic identification of time delay systems

    E-print Network

    Boyer, Edmond

    Identifiability and algebraic identification of time delay systems Lotfi Belkoura LAGIS(FRE 3303 and algebraic identification of time delay systems are investigated in this paper. Identifiability results: Time delay system, Identifiability, Identification. 1. INTRODUCTION The real time delay identification

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

    PubMed

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

    1997-02-01

    Coryneform bacteria and yeasts of 21 brick cheeses from six German dairies, produced by using undefined ripening cultures, were identified. Arthrobacter nicotianae, Brevibacterium linens, Corynebacterium ammoniagenes, Corynebacterium variabilis and Rhodococcus fascians were found in significant numbers. Out of 148 coryneform isolates 36 could not be identified at the species level. With the exception of a large rennet cheese, the coryneform microflora of rennet and acid cured cheeses were similar, but the cheeses had clearly different yeast populations. Debaryomyces hansenii and Galactomyces geotrichum prevailed in rennet cheeses while Kluyveromyces marxianus and Pichia membranaefaciens were the main species found in acid cured cheese. The dominance of Yarrowia lipolytica probably indicates an improper yeast population, resulting in poor cheese quality. Some of the species identified are potential candidates for designing a defined ripening culture for rennet red smear cheese. PMID:9039559

  15. Identification and molecular analysis of pathogenic yeasts in droppings of domestic pigeons in Beijing, China.

    PubMed

    Wu, Yuan; Du, Peng-Cheng; Li, Wen-Ge; Lu, Jin-Xing

    2012-09-01

    Feral pigeons are known as reservoirs of pathogenic yeasts that cause opportunistic infections in human. In the outskirts of Beijing, China, pigeons are more frequently raised at homes than are encountered in public areas. Many studies have focused on the presence of pathogenic yeasts in the excreta (fresh or withered) of a variety kinds of birds, pigeon crop and cloacae. One hundred and forty-three samples of fresh droppings were collected from three suburban pigeon-raising homes in an area of northern Beijing, China. The internal transcribed sequences (ITS) of all strains (except for 8 strains of Rhodotorula sp. ) were sequenced and compared with those of the databases of the National Center for Biotechnology Information website ( http://www.ncbi.nlm.nih.gov ) using the Basic Local Alignment Search Tool (BLAST). Yeasts representing 8 genera, Cryptococcus, Filobasidium, Rhodotorula, Candida, Debaryomyces, Saccaromyces, Trichosporon and Sporidiobolus, were identified from 120 isolates. Cryptococcus was the most prolific genera represented by eight species. The populations of yeast species isolated from fresh pigeon droppings were different among homes. Although it is well established that Cryptococcus neoformans exists mainly in old pigeon guano, several C. neoformans strains were still isolated from fresh pigeon excreta, providing a clue that live cryptococcal cells could move through the gastrointestinal tract of the pigeons. Eight genera identified from fresh droppings of domestic pigeons further confirm that pigeons serve as reservoirs, carriers and even spreaders of Cryptococcus species and other medically significant yeasts. The proportion of pathogenic yeasts in all isolates is more than 90 %. PMID:22476559

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

    Microsoft Academic Search

    Natalia Valdés-Stauber; Siegfried Scherer; Herbert Seiler

    1997-01-01

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

  17. Generation of an Isogenic Collection of Yeast Actin Mutants and Identification of Three Interrelated Phenotypes

    Microsoft Academic Search

    Johanna L. Whitacre; Dana A. Davis; Kurt A. Toenjes; Sharon M. Brower; Alison E. M. Adams

    2001-01-01

    A large collection of yeast actin mutations has been previously isolated and used in numerous studies of actin cytoskeletal function. However, the various mutations have been in congenic, rather than isogenic, backgrounds, making it difficult to compare the subtle phenotypes that are characteristic of these mutants. We have therefore placed 27 mutations in an isogenic background. We used a subset

  18. Yeast Functional Genomic Screens Lead to Identification of a Role for a Bacterial

    E-print Network

    Starnbach, Michael

    F inhibited both yeast and mammalian MAPK signaling cascades. Furthermore, inhibition of MAPK signaling by OspF is associated with attenuation of the host innate immune response to Shigella infection in a mouse model Bacterial pathogens have evolved numerous mechanisms to evade host cell defenses and promote infection. One

  19. Identification of Yju3p as functional orthologue of mammalian monoglyceride lipase in the yeast Saccharomycescerevisiae

    PubMed Central

    Heier, Christoph; Taschler, Ulrike; Rengachari, Srinivasan; Oberer, Monika; Wolinski, Heimo; Natter, Klaus; Kohlwein, Sepp D.; Leber, Regina; Zimmermann, Robert

    2010-01-01

    Monoacylglycerols (MAGs) are short-lived intermediates of glycerolipid metabolism. Specific molecular species, such as 2-arachidonoylglycerol, which is a potent activator of cannabinoid receptors, may also function as lipid signaling molecules. In mammals, enzymes hydrolyzing MAG to glycerol and fatty acids, resembling the final step in lipolysis, or esterifying MAG to diacylglycerol, are well known; however, despite the high level of conservation of lipolysis, the corresponding activities in yeast have not been characterized yet. Here we provide evidence that the protein Yju3p functions as a potent MAG hydrolase in yeast. Cellular MAG hydrolase activity was decreased by more than 90% in extracts of Yju3p-deficient cells, indicating that Yju3p accounts for the vast majority of this activity in yeast. Loss of this activity was restored by heterologous expression of murine monoglyceride lipase (MGL). Since yju3? mutants accumulated MAG in vivo only at very low concentrations, we considered the possibility that MAGs are re-esterified into DAG by acyltransferases. Indeed, cellular MAG levels were further increased in mutant cells lacking Yju3p and Dga1p or Lro1p acyltransferase activities. In conclusion, our studies suggest that catabolic and anabolic reactions affect cellular MAG levels. Yju3p is the functional orthologue of mammalian MGL and is required for efficient degradation of MAG in yeast. PMID:20554061

  20. Identification of the Zeo1 Protein as a Candidate Structural Homolog of ?-Synuclein in Budding Yeast

    E-print Network

    Sepehr Ehsani

    2015-05-23

    Human {\\alpha}-synuclein (SNCA) is a 140-amino-acid protein belonging to the three-member synuclein family. It has been extensively studied due to its misfolding/aggregation in and genetic linkage to neurodegenerative diseases, especially Parkinson's disease (PD). To better understand its biology, models of SNCA toxicity have been developed in budding yeast over the past decade, which have yielded insights into the protein's modes of action in specific pathways and potential therapeutic targets. Given that the synuclein gene family is not present in yeast, an extensive homology search was undertaken to determine if any yeast protein may possess structural homology to SNCA and whose native biology may shed more light on SNCA's pathomechanism in eukaryotes. We identified Zeo1, a membrane-associated protein involved in the cell wall integrity (CWI) pathway, as a candidate structural homolog. We show that Zeo1 overexpression is toxic in yeast and, similar to SNCA, localizes to lipid membranes. A number of biochemical similarities between Zeo1 and SNCA also become apparent in light of this potential structural connection. Moreover, the yeast PKC1 gene, a kinase acting as a downstream signaling hub in the CWI pathway, rescues both SNCA- and Zeo1-induced toxicities. Using the same homology search methods that identified Zeo1, we show that Pkc1 has a hybrid structural similarity to PINK1 and PARIS, two mitochondrial PD-implicated proteins not generally linked directly to synuclein-specific pathobiology. Overall, this proof-of-concept study shows the potential utility of hitherto uncharacterized cross-species structural homologs, identified using comparative proteome-wide structure prediction algorithms, in shedding light on abstruse connections among disease-relevant proteins.

  1. Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast.

    PubMed Central

    Isakoff, S J; Cardozo, T; Andreev, J; Li, Z; Ferguson, K M; Abagyan, R; Lemmon, M A; Aronheim, A; Skolnik, E Y

    1998-01-01

    Phosphatidylinositol 3-kinase (PI3K) mediates a variety of cellular responses by generating PtdIns(3,4)P2 and PtdIns(3,4,5)P3. These 3-phosphoinositides then function directly as second messengers to activate downstream signaling molecules by binding pleckstrin homology (PH) domains in these signaling molecules. We have established a novel assay in the yeast Saccharomyces cerevisiae to identify proteins that bind PtdIns(3,4)P2 and PtdIns(3,4,5)P3 in vivo which we have called TOPIS (Targets of PI3K Identification System). The assay uses a plasma membrane-targeted Ras to complement a temperature-sensitive CDC25 Ras exchange factor in yeast. Coexpression of PI3K and a fusion protein of activated Ras joined to a PH domain known to bind PtdIns(3,4)P2 (AKT) or PtdIns(3,4,5)P3 (BTK) rescues yeast growth at the non-permissive temperature of 37 degreesC. Using this assay, we have identified several amino acids in the beta1-beta2 region of PH domains that are critical for high affinity binding to PtdIns(3,4)P2 and/or PtdIns(3,4,5)P3, and we have proposed a structural model for how these PH domains might bind PI3K products with high affinity. From these data, we derived a consensus sequence which predicts high-affinity binding to PtdIns(3, 4)P2 and/or PtdIns(3,4,5)P3, and we have identified several new PH domain-containing proteins that bind PI3K products, including Gab1, Dos, myosinX, and Sbf1. Use of this assay to screen for novel cDNAs which rescue yeast at the non-permissive temperature should provide a powerful approach for uncovering additional targets of PI3K. PMID:9736615

  2. Robust identification of linear parameter varying systems

    Microsoft Academic Search

    Maria Cecilia Mazzaro; E. A. Movsichoff; R. S. S. Pena

    1999-01-01

    We study the robust identification problem for a special class of linear parameter varying systems, when it is assumed that there is only one varying parameter and all the states of the system under identification can be measured. We consider a worst-case approach, i.e., we look for a set of models in a class of systems defined a priori, which

  3. 77 FR 69393 - Unique Device Identification System

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-19

    ...Health, Food and Drug...identification system, as required...device through distribution and use...establishing a system of unique...medical device industry, and the...226 of the Food and Drug...or on the distribution of power...Identification System, Docket...the Federal Food,...

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

    Microsoft Academic Search

    Karlett Parra-Belky

    2002-01-01

    A biochemistry laboratory was designed for an undergraduate course to help students better understand the link between molecular engineering and biochemistry. Students identified unknown yeast strains with high specificity using SDS-PAGE and Western blot analysis of whole cell lysates. This problem-solving exercise is a common application of biochemistry in biotechnology research. Three different strains were used: a wild-type and two

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

    Microsoft Academic Search

    Jingjun Zhao; Jingsi Zeng; G. Sybren de Hoog; Derlene Attili-Angelis; Francesc X. Prenafeta-Boldú

    2010-01-01

    Black yeast members of the Herpotrichiellaceae present a complex ecological behavior: They are often isolated from rather extreme environments polluted with aromatic hydrocarbons,\\u000a while they are also regularly involved in human opportunistic infections. A selective technique to promote the in vitro growth\\u000a of herpotrichiellaceous fungi was applied to investigate their ecophysiology. Samples from natural ecological niches and man-made\\u000a environments that

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

    Microsoft Academic Search

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

    2003-01-01

    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

  7. Sequence of the small subunit of yeast carbamyl phosphate synthetase and identification of its catalytic domain.

    PubMed

    Nyunoya, H; Lusty, C J

    1984-08-10

    The yeast gene CPA1 coding for the small subunit of arginine-specific carbamyl phosphate synthetase has been cloned by complementation of a cpa 1 mutant with a plasmid library of total yeast chromosomal DNA. Two of the plasmids, pJL113/ST4 and pJL113/ST15, contain DNA inserts in opposite orientations with overlapping sequences of 2.6 kilobases. The nucleotide sequence of a 2.2-kilobase region of the DNA insert carrying the CPA1 gene has been determined. The CPA1 gene has been identified to be 1233 nucleotides long and to code for a polypeptide of 411 amino acids with a calculated molecular weight of 45,358. The amino acid sequence encoded in CPA1 is homologous to the recently determined sequence of the small subunit of Escherichia coli carbamyl phosphate synthetase (Piette, J., Nyunoya, H., Lusty, C.J., Cunin, R., Weyens, G., Crabeel, M., Charlier, D., Glandsdorff, N., and Pierard, A. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 4134-4138) over the entire length of the polypeptide chain. Comparison of the amino acid sequences of the small subunits of yeast and E. coli carbamyl phosphate synthetases to the sequences of Component II of anthranilate and p-aminobenzoate synthases suggests that these amidotransferases are evolutionarily related. The most highly conserved region of the yeast and E. coli enzymes includes a cysteine residue previously found to be at the active site of Pseudomonas putida anthranilate synthase Component II (Kawamura, M., Keim, P.S., Goto, Y., Zalkin, H., and Heinrikson, R.L. (1978) J. Biol. Chem. 253, 4659-4668). Based on the observed homologies in the primary sequences of the other amidotransferases examined, we propose a 13-amino acid long sequence to be part of the catalytic domain of this class of enzymes. PMID:6086650

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

    SciTech Connect

    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

    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.

  9. Identification and characterization of Drosophila relatives of the yeast transcriptional activator SNF2/SWI2.

    PubMed

    Elfring, L K; Deuring, R; McCallum, C M; Peterson, C L; Tamkun, J W

    1994-04-01

    The Drosophila brahma (brm) gene encodes an activator of homeotic genes that is highly related to the yeast transcriptional activator SWI2 (SNF2), a potential helicase. To determine whether brm is a functional homolog of SWI2 or merely a member of a family of SWI2-related genes, we searched for additional Drosophila genes related to SWI2 and examined their function in yeast cells. In addition to brm, we identified one other Drosophila relative of SWI2: the closely related ISWI gene. The 1,027-residue ISWI protein contains the DNA-dependent ATPase domain characteristic of the SWI2 protein family but lacks the three other domains common to brm and SWI2. In contrast, the ISWI protein is highly related (70% identical) to the human hSNF2L protein over its entire length, suggesting that they may be functional homologs. The DNA-dependent ATPase domains of brm and SWI2, but not ISWI, are functionally interchangeable; a chimeric SWI2-brm protein partially rescued the slow growth of swi2- cells and supported transcriptional activation mediated by the glucocorticoid receptor in vivo in yeast cells. These findings indicate that brm is the closest Drosophila relative of SWI2 and suggest that brm and SWI2 play similar roles in transcriptional activation. PMID:7908117

  10. Identification and characterization of Drosophila relatives of the yeast transcriptional activator SNF2/SWI2.

    PubMed Central

    Elfring, L K; Deuring, R; McCallum, C M; Peterson, C L; Tamkun, J W

    1994-01-01

    The Drosophila brahma (brm) gene encodes an activator of homeotic genes that is highly related to the yeast transcriptional activator SWI2 (SNF2), a potential helicase. To determine whether brm is a functional homolog of SWI2 or merely a member of a family of SWI2-related genes, we searched for additional Drosophila genes related to SWI2 and examined their function in yeast cells. In addition to brm, we identified one other Drosophila relative of SWI2: the closely related ISWI gene. The 1,027-residue ISWI protein contains the DNA-dependent ATPase domain characteristic of the SWI2 protein family but lacks the three other domains common to brm and SWI2. In contrast, the ISWI protein is highly related (70% identical) to the human hSNF2L protein over its entire length, suggesting that they may be functional homologs. The DNA-dependent ATPase domains of brm and SWI2, but not ISWI, are functionally interchangeable; a chimeric SWI2-brm protein partially rescued the slow growth of swi2- cells and supported transcriptional activation mediated by the glucocorticoid receptor in vivo in yeast cells. These findings indicate that brm is the closest Drosophila relative of SWI2 and suggest that brm and SWI2 play similar roles in transcriptional activation. Images PMID:7908117

  11. Experimental facilities for system identification

    NASA Technical Reports Server (NTRS)

    Das, Alok; Thompson, Roger C.

    1988-01-01

    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.

  12. Convex optimization techniques in system identification

    E-print Network

    Vandenberghe, Lieven

    ]. The 1-norm and nuclear norm techniques can be extended in several interesting ways. The two typesConvex optimization techniques in system identification Lieven Vandenberghe Electrical: In recent years there has been growing interest in convex optimization techniques for system identification

  13. System identification for passive linear quantum systems

    E-print Network

    Madalin Guta; Naoki Yamamoto

    2014-08-27

    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.

  14. Stochastic system identification in structural dynamics

    USGS Publications Warehouse

    Safak, Erdal

    1988-01-01

    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.

  15. Commercial systems for fluconazole susceptibility testing of yeasts: comparison with the broth microdilution method.

    PubMed

    Posteraro, B; Romano, L; Sanguinetti, M; Masucci, L; Morace, G; Fadda, G

    2000-09-01

    Fluconazole susceptibility was tested in 100 clinical yeast isolates (65 Candida albicans, 13 C. glabrata, 8 C. tropicalis, 7 C. parapsilosis, 3 Saccharomyces cerevisiae, 1 each of C. krusei, C. lusitaniae, Cryptococcus neoformans, Rhodotorula glutinis) and two control strains (Candida krusei ATCC 6258, C. parapsilosis ATCC 22019) using broth microdilution (reference method), disk diffusion, Etest strips, Sensititre YeastOne, Candifast, Integral System Yeasts. Using M27-A breakpoints, isolates were classified as susceptible (81%), susceptible-dose dependent or Resistant with broth dilution. Rates of concordance with the reference method were good for Sensititre YeastOne, Etest and disc-diffusion (81.2%-94.7%) but very low for the Candifast (3.1%) and Integral System (16.6%), which classified most susceptible isolates as resistant. Lack of standardisation (inoculum, medium composition) and non-objective interpretation schemes may be the cause of their poor performance. Sensititre YeastOne, Etest and disc-diffusion are potentially useful for fluconazole antifungal susceptibility testing of yeasts in clinical laboratories. PMID:11025181

  16. Identification of telomerase RNAs from filamentous fungi reveals conservation with vertebrates and yeasts.

    PubMed

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

    2013-01-01

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

  17. Study of amyloids using yeast

    PubMed Central

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

    2012-01-01

    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

  18. System Identification: Time Varying and Nonlinear Methods 

    E-print Network

    Majji, Manoranjan

    2010-07-14

    Novel methods of system identification are developed in this dissertation. First set of methods are designed to realize time varying linear dynamical system models from input-output experimental data. The preliminary results obtained in a recent...

  19. System Identification: Time Varying and Nonlinear Methods

    E-print Network

    Majji, Manoranjan

    2010-07-14

    Novel methods of system identification are developed in this dissertation. First set of methods are designed to realize time varying linear dynamical system models from input-output experimental data. The preliminary results obtained in a recent...

  20. System identification for robust control design

    SciTech Connect

    Dohner, J.L.

    1995-04-01

    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.

  1. Identification and characterization of genes involved in glutathione production in yeast.

    PubMed

    Suzuki, Takahiro; Yokoyama, Aki; Tsuji, Toshikazu; Ikeshima, Emiko; Nakashima, Keiko; Ikushima, Shigehito; Kobayashi, Chisa; Yoshida, Satoshi

    2011-08-01

    Glutathione is a major peptide protecting cells against oxidative stress. To study the cellular processes affecting intracellular glutathione production, we screened Saccharomyces cerevisiae mutant collections and identified new eight yeast deletion mutants that produced more than 1.2-fold higher levels of intracellular glutathione: chc1, cst6, ddc1, def1, pep12, rts1, ubp6, and yih1. Furthermore, overexpression of the DEF1 and CYS4 genes led to a higher production of glutathione, similar to overexpression of GSH1. A multiplier effect on activation of glutathione synthesis was observed by a combination of overexpression of GSH1 and deletion of one of the eight genes. Metabolome analysis of the def1, pep12, and ubp6 deletion mutant, and DEF1-overexpressing strains showed that levels of intracellular methionine and oxidized glutathione were higher than in the control strains, suggesting that methionine biosynthesis was activated and the oxidative stress response was increased in these glutathione-overproductive strains. Moreover, overexpression of GSH1, CYS4, and DEF1 also increased glutathione production in Candida utilis. Taken together, these results will significantly contribute to more effective industrial production of glutathione using yeasts. PMID:21601516

  2. Assay of vacuolar pH in yeast and identification of acidification-defective mutants.

    PubMed Central

    Preston, R A; Murphy, R F; Jones, E W

    1989-01-01

    As part of a genetic analysis of the biogenesis and function of the vacuole (lysosome) in the yeast Saccharomyces cerevisiae, assays of vacuolar pH were developed and used to identify mutants defective in vacuolar acidification. Vacuoles were labeled with 6-carboxyfluorescein with the membrane-permeant precursor 6-carboxyfluorescein diacetate. Dual-excitation flow cytometry was used to calibrate the pH-dependence of 6-carboxyfluorescein fluorescence in vivo. Vacuoles in wild-type yeast were mildly acidic, pH 6.2, in cells grown under several different conditions. Cultures labeled with 6-carboxyfluorescein were screened by fluorescence-ratio microscopy to detect mutants that had defects related to vacuolar acidification. A recessive nuclear mutation, vph1-1, caused an abnormally high vacuolar pH of 6.9, as assayed by flow cytometry, and eliminated vacuolar uptake of the weak base quinacrine. Acidification in a pep12::LEU2 mutant appeared defective by fluorescence-ratio microscopy and quinacrine-uptake assays, but the vacuolar pH in the pep12::LEU2 mutant was nearly normal (pH 6.3) in flow cytometric assays. Images PMID:2674942

  3. Heat Capacity Identification Method Using MT System

    NASA Astrophysics Data System (ADS)

    Suzuki, Arata; Sugimoto, Kenji

    This paper proposes a heat capacity identification method for cooking household appliances. Cooking household appliances select a cooking flow according to a cooking object capacity, hence the heat capacity identification is a very important function. However, a conventional heat capacity identification method has been based on one variable using “if-then rules”, hence it gives a low accuracy. This paper proposes a new heat capacity identification method that uses Mahalanobis-Taguchi System which is similar to discriminant analysis, and the effectiveness of this method is confirmed by the experiment.

  4. Dental orthopantomogram biometrics system for human identification.

    PubMed

    Singh, Sandeep; Bhargava, Darpan; Deshpande, Ashwini

    2013-07-01

    Fingerprinting is the most widely accepted method of identification of people. But in cases of disfigured, decomposed, burnt or fragmented bodies, it is of limited value. Teeth and dental restorations on the other hand are extremely resistant to destruction by fire. They retain a number of their original characteristics, which are often unique and hence offer a possibility of rather accurate and legally acceptable identification of such remains. This study was undertaken to evaluate the utility of orthopantomography for human identification and propose a coding system for orthopantomogram (OPG), which can be utilized as an identification tool in forensic sciences. PMID:23756505

  5. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for the rapid identification of yeasts causing bloodstream infections.

    PubMed

    Ghosh, A K; Paul, S; Sood, P; Rudramurthy, S M; Rajbanshi, A; Jillwin, T J; Chakrabarti, A

    2015-04-01

    Few studies have systematically standardised and evaluated matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of yeasts from bloodstream infections. This is rapidly becoming pertinent for early identification of yeasts and appropriate antifungal therapy. We used 354 yeast strains identified by polymerase chain reaction (PCR) sequencing for standardisation and 367 blind clinical strains for validation of our MALDI-TOF MS protocols. We also evaluated different sample preparation methods and found the on-plate formic acid extraction method as most cost- and time-efficient. The MALDI-TOF assay correctly identified 98.9% of PCR-sequenced yeasts. Novel main spectrum projections (MSP) were developed for Candida auris, C. viswanathii and Kodamaea ohmeri, which were missing from the Bruker MALDI-TOF MS database. Spectral cut-offs computed by receiver operating characteristics (ROC) analysis showed 99.4% to 100% accuracy at a log score of ?1.70 for C. tropicalis, C. parapsilosis, C. pelliculosa, C. orthopsilosis, C. albicans, C. rugosa, C. guilliermondii, C. lipolytica, C. metapsilosis, C. nivariensis. The differences in the species-specific scores of our standardisation and blind validation strains were not statistically significant, implying the optimal performance of our test protocol. The MSPs of the three new species also were validated. We conclude that MALDI-TOF MS is a rapid, accurate and reliable tool for identification of bloodstream yeasts. With proper standardisation, validation and regular database expansion, its efficiency can be further enhanced. PMID:25658527

  6. Identification of Medically Relevant Species of Arthroconidial Yeasts by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

    PubMed Central

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

    2013-01-01

    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

  7. An expanded tool kit for the auxin-inducible degron system in budding yeast

    PubMed Central

    Morawska, Magdalena; Ulrich, Helle D

    2013-01-01

    Fusion of inducible degradation signals, so-called degrons, to cellular proteins is an elegant method of controlling protein levels in vivo. Recently, a degron system relying on the plant hormone auxin has been described for use in yeast and vertebrate cells. We now report the construction of a series of vectors that significantly enhance the versatility of this auxin-inducible degron (AID) system in Saccharomyces cerevisiae. We have minimized the size of the degron and appended a series of additional epitope tags, allowing detection by commercial antibodies or fluorescence microscopy. The vectors are compatible with PCR-based genomic tagging strategies, allow for C- or N-terminal fusion of the degron, and provide a range of selection markers. Application to a series of yeast proteins, including essential replication factors, provides evidence for a general usefulness of the system. © 2013 The Authors. Yeast published by John Wiley & Sons, Ltd. PMID:23836714

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

    Microsoft Academic Search

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

    2006-01-01

    To identify essential host genes affecting replication of Tomato bushy stunt virus (TBSV), a small model plant virus, we screened 800 yeast genes present in the yeast Tet promoters Hughes Collection. In total, we have identified 30 new host genes whose down-regulation either increased or decreased the accumulation of a TBSV replicon RNA. The identified essential yeast genes are involved

  9. System identification of nonlinear resonant systems

    NASA Astrophysics Data System (ADS)

    Dunstan, Wayne John

    This dissertation addresses the problem of thermo-acoustic combustion instability modelling using nonlinear system identification. Specifically we are interested in the identification of closed loop limit cycling systems composed of a linear transfer function with a static nonlinearity in feedback. To begin we address the feasibility of the identification task, in terms of both data quality and dynamical capabilities of the model. Subsequently, we demonstrate that, despite the paucity of information available, a grey-box nonlinear model can be identified. The model correctly predicts the dominant system behavior. The nonlinear tools of describing functions, bifurcation theory and manifold analysis are used to further refine a low-complexity nonlinear model capable of describing the data and consistent with physical understanding. These tools are also used to better understand the identified model dynamical behavior. An atypical method for combining multiple experiments is considered. We construct a framework for combining multiple experiment information using bifurcation theory and follow an approach of successive deduction, hypothesis formulation and falsification testing in an attempt to invalidate the model. Model confidence is quantified in terms of bias and variance properties connecting the model, data and measures. The allows a more informed decision as to the model validity. We formulate a generic definition for the bias confidence, which gives an indication of overparametrization of the model or weak persistence of excitation in the data. We also formulate a generic definition for the variance confidence, which gives an indication of the parameter estimate variability due to different realizations of the underlying noise processes. These involve techniques for empirical estimation of the distribution of the estimated parameters. We reformulate these for dynamical system models by ensuring the correlation properties of the input-output data are preserved. Finally a multiplicative reference signal is introduced to increase identifiability of the model, at the expense of cyclostationary signals. Using cyclostationary signal analysis we develop the mapping of excitation properties in the scalar non-stationary data to the vector stationary lifted signals. The mapping of identifiability properties in the lifted vector system to the rank properties of the regression matrix is also created.

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

    PubMed Central

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

    2009-01-01

    The abundance of mitochondrial (mt) transcripts varies under different conditions, and is thought to depend upon rates of transcription initiation, transcription termination/attenuation and RNA processing/degradation. The requirement to maintain the balance between RNA synthesis and processing may involve coordination between these processes; however, little is known about factors that regulate the activity of mtRNA polymerase (mtRNAP). Recent attempts to identify mtRNAP–protein interactions in yeast by means of a generalized tandem affinity purification (TAP) protocol were not successful, most likely because they involved a C-terminal mtRNAP–TAP fusion (which is incompatible with mtRNAP function) and because of the use of whole-cell solubilization protocols that did not preserve the integrity of mt protein complexes. Based upon the structure of T7 RNAP (to which mtRNAPs show high sequence similarity), we identified positions in yeast mtRNAP that allow insertion of a small affinity tag, confirmed the mature N-terminus, constructed a functional N-terminal TAP–mtRNAP fusion, pulled down associated proteins, and identified them by LC–MS–MS. Among the proteins found in the pull-down were a DEAD-box protein (Mss116p) and an RNA-binding protein (Pet127p). Previous genetic experiments suggested a role for these proteins in linking transcription and RNA degradation, in that a defect in the mt degradadosome could be suppressed by overexpression of either of these proteins or, independently, by mutations in either mtRNAP or its initiation factor Mtf1p. Further, we found that Mss116p inhibits transcription by mtRNAP in vitro in a steady-state reaction. Our results support the hypothesis that Mss116p and Pet127p are involved in modulation of mtRNAP activity. Copyright © 2009 John Wiley & Sons, Ltd. PMID:19536766

  11. Isolation and identification of black yeasts by enrichment on atmospheres of monoaromatic hydrocarbons.

    PubMed

    Zhao, Jingjun; Zeng, Jingsi; de Hoog, G Sybren; Attili-Angelis, Derlene; Prenafeta-Boldú, Francesc X

    2010-07-01

    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

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

    PubMed Central

    1986-01-01

    We describe an in vitro system with all components derived from the yeast Saccharomyces cerevisiae that can translocate a yeast secretory protein across microsomal membranes. In vitro transcribed prepro-alpha- factor mRNA served to program a membrane-depleted yeast translation system. Translocation and core glycosylation of prepro-alpha-factor were observed when yeast microsomal membranes were added during or after translation. A membrane potential is not required for translocation. However, ATP is required for translocation and nonhydrolyzable analogues of ATP cannot serve as a substitute. These findings suggest that ATP hydrolysis may supply the energy required for translocation of proteins across the endoplasmic reticulum. PMID:3517001

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

    PubMed

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

    2015-05-01

    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

  14. Use of The Yeast Two-Hybrid System to Identify Targets of Fungal Effectors

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The yeast-two hybrid (Y2H) system is a binary method widely used to determine direct interactions between paired proteins. Although having certain limitations, this method has become one of the two main systemic tools (along with affinity purification/mass spectrometry) for interactome mapping in mo...

  15. Interactions between type III secretion apparatus components from Yersinia pestis detected using the yeast two-hybrid system

    Microsoft Academic Search

    Michael W. Jackson; Gregory V. Plano

    2000-01-01

    Interactions among the Yersinia secretion (Ysc) proteins of Yersinia pestis were explored using the yeast two-hybrid system. Various pairwise combinations of the yscEFGHIKLN and Q genes fused to the DNA-binding or activation domain of the yeast GAL4 gene were introduced into yeast, and expression of a reporter gene encoding ?-galactosidase was detected. Combinations of yscN and yscL, yscL and yscQ,

  16. A convolution approach for delay systems identification

    E-print Network

    Paris-Sud XI, Université de

    if the dead-time is known. On the other hand, most existing identification techniques for time-delay systems sometimes denote u(s), s C, the Laplace transform of u, and let denote for the convolution product

  17. The proteolytic system of the fission yeast Schizosaccharomyces pombe.

    PubMed

    Suárez-Rendueles, P; Villa, L; Arbesú, M J; Escudero, B

    1991-06-15

    Proteinase and peptidase activities of the fission yeast Schizosaccharomyces pombe were investigated. Several intracellular proteolytic enzymes were found: two endoproteinases, one carboxypeptidase, one aminopeptidase and one dipeptidyl-aminopeptidase. In addition, proteinase inhibitors were detected. In fresh crude extracts an activation procedure is needed to measure maximal activities of endoproteinases and carboxypeptidase, whose level is markedly dependent on growth medium composition and on growth phase, while aminopeptidase and dipeptidyl-aminopeptidase activities are very little, if at all, regulated by the carbon source. PMID:1884996

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

    PubMed Central

    2012-01-01

    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

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

    Microsoft Academic Search

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

    2001-01-01

    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

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

    PubMed

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

    2011-07-19

    Identification of the underlying molecular mechanisms for a derived phenotype by adaptive evolution is difficult. Here, we performed a systems-level inquiry into the metabolic changes occurring in the yeast Saccharomyces cerevisiae as a result of its adaptive evolution to increase its specific growth rate on galactose and related these changes to the acquired phenotypic properties. Three evolved mutants (62A, 62B, and 62C) with higher specific growth rates and faster specific galactose uptake were isolated. The evolved mutants were compared with a reference strain and two engineered strains, SO16 and PGM2, which also showed higher galactose uptake rate in previous studies. The profile of intermediates in galactose metabolism was similar in evolved and engineered mutants, whereas reserve carbohydrates metabolism was specifically elevated in the evolved mutants and one evolved strain showed changes in ergosterol biosynthesis. Mutations were identified in proteins involved in the global carbon sensing Ras/PKA pathway, which is known to regulate the reserve carbohydrates metabolism. We evaluated one of the identified mutations, RAS2(Tyr112), and this mutation resulted in an increased specific growth rate on galactose. These results show that adaptive evolution results in the utilization of unpredicted routes to accommodate increased galactose flux in contrast to rationally engineered strains. Our study demonstrates that adaptive evolution represents a valuable alternative to rational design in bioengineering of improved strains and, that through systems biology, it is possible to identify mutations in evolved strain that can serve as unforeseen metabolic engineering targets for improving microbial strains for production of biofuels and chemicals. PMID:21715660

  1. System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap*

    PubMed Central

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

    2012-01-01

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

  2. Identification of a novel casein kinase-1 homolog in fission yeast Schizosaccharomyces pombe.

    PubMed

    Kitamura, K; Yamashita, I

    1998-07-01

    Fission yeast cells lacking either the ste9+- or rum1+ function cannot enter the cell differentiation pathway upon nutritional starvation. Sterility in both mutants is suppressed by the srs1-S41 mutation. A gene encoding a novel casein kinase-1 (CK1) isoform, cki3+, was isolated as a high-copy-number suppressor gene of the srs1 mutation. Cki3 protein is structurally more related to the Cki/Yck subfamily proteins than those of the Hhp/Hrr25 subfamily. A mutant cki3 gene in which a highly conserved lysine residue in the kinase subdomain II was substituted to arginine lost the ability to recover the growth defect in the srs1 mutant, indicating that catalytic activity was necessary for suppression. Gene disruption revealed that cki3+ was dispensable for cell viability, and cells lacking functional cki3+ exhibited no characteristic phenotype. Thus, S. pombe has three highly related CK1 isoforms (Cki1, Cki2 and Cki3), but none of them has an essential function. PMID:9651503

  3. Identification and Characterization of Two Novel Proteins Affecting Fission Yeast ?-tubulin Complex FunctionV?

    PubMed Central

    Venkatram, Srinivas; Tasto, Joseph J.; Feoktistova, Anna; Jennings, Jennifer L.; Link, Andrew J.; Gould, Kathleen L.

    2004-01-01

    The ?-tubulin complex, via its ability to organize microtubules, is critical for accurate chromosome segregation and cytokinesis in the fission yeast, Schizosaccharomyces pombe. To better understand its roles, we have purified the S. pombe ?-tubulin complex. Mass spectrometric analyses of the purified complex revealed known components and identified two novel proteins (i.e., Mbo1p and Gfh1p) with homology to ?-tubulin–associated proteins from other organisms. We show that both Mbo1p and Gfh1p localize to microtubule organizing centers. Although cells deleted for either mbo1+ or gfh1+ are viable, they exhibit a number of defects associated with altered microtubule function such as defects in cell polarity, nuclear positioning, spindle orientation, and cleavage site specification. In addition, mbo1? and gfh1? cells exhibit defects in astral microtubule formation and anchoring, suggesting that these proteins have specific roles in astral microtubule function. This study expands the known roles of ?-tubulin complex components in organizing different types of microtubule structures in S. pombe. PMID:15004232

  4. Identification and characterization of two novel proteins affecting fission yeast gamma-tubulin complex function.

    PubMed

    Venkatram, Srinivas; Tasto, Joseph J; Feoktistova, Anna; Jennings, Jennifer L; Link, Andrew J; Gould, Kathleen L

    2004-05-01

    The gamma-tubulin complex, via its ability to organize microtubules, is critical for accurate chromosome segregation and cytokinesis in the fission yeast, Schizosaccharomyces pombe. To better understand its roles, we have purified the S. pombe gamma-tubulin complex. Mass spectrometric analyses of the purified complex revealed known components and identified two novel proteins (i.e., Mbo1p and Gfh1p) with homology to gamma-tubulin-associated proteins from other organisms. We show that both Mbo1p and Gfh1p localize to microtubule organizing centers. Although cells deleted for either mbo1(+) or gfh1(+) are viable, they exhibit a number of defects associated with altered microtubule function such as defects in cell polarity, nuclear positioning, spindle orientation, and cleavage site specification. In addition, mbo1Delta and gfh1Delta cells exhibit defects in astral microtubule formation and anchoring, suggesting that these proteins have specific roles in astral microtubule function. This study expands the known roles of gamma-tubulin complex components in organizing different types of microtubule structures in S. pombe. PMID:15004232

  5. Generation of an isogenic collection of yeast actin mutants and identification of three interrelated phenotypes.

    PubMed

    Whitacre, J; Davis, D; Toenjes, K; Brower, S; Adams, A

    2001-02-01

    A large collection of yeast actin mutations has been previously isolated and used in numerous studies of actin cytoskeletal function. However, the various mutations have been in congenic, rather than isogenic, backgrounds, making it difficult to compare the subtle phenotypes that are characteristic of these mutants. We have therefore placed 27 mutations in an isogenic background. We used a subset of these mutants to compare the degree to which different actin alleles are defective in sporulation, endocytosis, and growth on NaCl-containing media. We found that the three phenotypes are highly correlated. The correlations are specific and not merely a reflection of general growth defects, because the phenotypes are not correlated with growth rates under normal conditions. Significantly, those actin mutants exhibiting the most severe phenotypes in all three processes have altered residues that cluster to a small region of the actin crystal structure previously defined as the fimbrin (Sac6p)-binding site. We examined the relationship between endocytosis and growth on salt and found that shifting wild-type or actin mutant cells to high salt reduces the rate of alpha-factor internalization. These results suggest that actin mutants may be unable to grow on salt because of additive endocytic defects (due to mutation and salt). PMID:11156976

  6. Generation of an isogenic collection of yeast actin mutants and identification of three interrelated phenotypes.

    PubMed Central

    Whitacre, J; Davis, D; Toenjes, K; Brower, S; Adams, A

    2001-01-01

    A large collection of yeast actin mutations has been previously isolated and used in numerous studies of actin cytoskeletal function. However, the various mutations have been in congenic, rather than isogenic, backgrounds, making it difficult to compare the subtle phenotypes that are characteristic of these mutants. We have therefore placed 27 mutations in an isogenic background. We used a subset of these mutants to compare the degree to which different actin alleles are defective in sporulation, endocytosis, and growth on NaCl-containing media. We found that the three phenotypes are highly correlated. The correlations are specific and not merely a reflection of general growth defects, because the phenotypes are not correlated with growth rates under normal conditions. Significantly, those actin mutants exhibiting the most severe phenotypes in all three processes have altered residues that cluster to a small region of the actin crystal structure previously defined as the fimbrin (Sac6p)-binding site. We examined the relationship between endocytosis and growth on salt and found that shifting wild-type or actin mutant cells to high salt reduces the rate of alpha-factor internalization. These results suggest that actin mutants may be unable to grow on salt because of additive endocytic defects (due to mutation and salt). PMID:11156976

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

    PubMed Central

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

    2013-01-01

    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

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

    PubMed

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

    1992-12-15

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

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

    PubMed Central

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

    1992-01-01

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

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

    PubMed

    Kaneko, Takamasa

    2011-01-01

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

  11. System identification and control using genetic algorithms

    Microsoft Academic Search

    Kristinn Kristinsson; Guy A. Dumont

    1992-01-01

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

  12. 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...

  13. [Development of a detection system (APC yeast color assay) of APC mutations by color change of yeast].

    PubMed

    Furuuchi, K

    2000-11-01

    The author developed a sensitive yeast-based color assay which expresses APC-ADE2 (reporter) fusion protein in yeast and can screen almost the entire coding region of the APC gene. In this assay, the wild-type APC coding sequence of 8.5 kb is divided into 5 overlapping regions which are respectively ligated in-frame with an ADE2 open reading frame. The resulting five constructs containing a part of wild-type APC gene preserve the ADE2(+) phenotype (white yeast colony) when introduced into the yeast, whereas the yeast transfected with plasmids containing frameshift mutations of the APC gene shows an ADE2(-) phenotype (red yeast colony). Six human colon cancer cell lines were analyzed by this yeast color assay. HCT116 cells with wild-type APC and normal colonic mucosa gave low percentages of red colonies (0-9.9%) in all the regions. On the other hand, more than 96% red colonies were observed in one of the five regions in SW480, Colo201 and Colo320DM cells. Sequence analysis demonstrated the clonal APC mutations at codon 1,338 in SW480, 1,554 in Colo201 and 811 in Colo320DM. Moreover, the assay detected a germline mutation of the APC gene in polyps of a familial adenomatous polyposis (FAP) patient which gave about 50% red colonies. For testing the assay for clinical utilization, 18 colon cancer tissues were subjected to the assay. Eleven cancers (61%) gave more than 10% red colonies (17-57%) and clonal mutations were detected in all these samples. The same mutations were demonstrated in both DNA and RNA samples derived from idendical tissues. These results suggest that this APC yeast color assay is powerful means for detection of APC mutations in clinical samples. PMID:11193931

  14. Parameter Identification Using -Decisions for Biological Hybrid Systems

    E-print Network

    Parameter Identification Using -Decisions for Biological Hybrid Systems Bing Liu Soonho Kong Sicun other entity. #12;Keywords: systems biology, hybrid systems, decision procedures, parameter identification #12;Abstract Biological systems can possess multiple operational modes with specific nonlinear

  15. Gaussian process based recursive system identification

    NASA Astrophysics Data System (ADS)

    Prüher, Jakub; Šimandl, Miroslav

    2014-12-01

    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.

  16. 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...

  17. Model-driven system identification of transcritical vapor compression systems

    Microsoft Academic Search

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

    2005-01-01

    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

  18. Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies

    PubMed Central

    Lasserre, Jean-Paul; Dautant, Alain; Aiyar, Raeka S.; Kucharczyk, Roza; Glatigny, Annie; Tribouillard-Tanvier, Déborah; Rytka, Joanna; Blondel, Marc; Skoczen, Natalia; Reynier, Pascal; Pitayu, Laras; Rötig, Agnčs; Delahodde, Agnčs; Steinmetz, Lars M.; Dujardin, Genevičve; Procaccio, Vincent; di Rago, Jean-Paul

    2015-01-01

    ABSTRACT Mitochondrial diseases are severe and largely untreatable. Owing to the many essential processes carried out by mitochondria and the complex cellular systems that support these processes, these diseases are diverse, pleiotropic, and challenging to study. Much of our current understanding of mitochondrial function and dysfunction comes from studies in the baker's yeast Saccharomyces cerevisiae. Because of its good fermenting capacity, S. cerevisiae can survive mutations that inactivate oxidative phosphorylation, has the ability to tolerate the complete loss of mitochondrial DNA (a property referred to as ‘petite-positivity’), and is amenable to mitochondrial and nuclear genome manipulation. These attributes make it an excellent model system for studying and resolving the molecular basis of numerous mitochondrial diseases. Here, we review the invaluable insights this model organism has yielded about diseases caused by mitochondrial dysfunction, which ranges from primary defects in oxidative phosphorylation to metabolic disorders, as well as dysfunctions in maintaining the genome or in the dynamics of mitochondria. Owing to the high level of functional conservation between yeast and human mitochondrial genes, several yeast species have been instrumental in revealing the molecular mechanisms of pathogenic human mitochondrial gene mutations. Importantly, such insights have pointed to potential therapeutic targets, as have genetic and chemical screens using yeast. PMID:26035862

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

    PubMed

    Emam, M M

    2013-03-01

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

  20. Educational Virtual Instrumentation Application for System Identification

    Microsoft Academic Search

    Mircea Popa; Raul Ionel; Voicu Groza; Marius Marcu

    2006-01-01

    The PC based virtual instrumentation is a dynamic and attractive alternative to the classic instrumentation. Its main advantages are: flexibility and adaptability, low cost, wide development of extension PC boards with measurements features, attractive representation of measurement results, in different forms, on the PC's monitor. The paper presents a system identification application with PC based (virtual) instrumentation. The virtual system

  1. Choosing Between Yeast and Bacterial Expression Systems: Yield Dependent

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

    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.

  2. A practical approach to rotorcraft systems identification

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

    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.

  3. System Identification through Model Composition and Stochastic Search

    Microsoft Academic Search

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

    2005-01-01

    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

  4. An expanded tool kit for the auxin-inducible degron system in budding yeast.

    PubMed

    Morawska, Magdalena; Ulrich, Helle D

    2013-09-01

    Fusion of inducible degradation signals, so-called degrons, to cellular proteins is an elegant method of controlling protein levels in vivo. Recently, a degron system relying on the plant hormone auxin has been described for use in yeast and vertebrate cells. We now report the construction of a series of vectors that significantly enhance the versatility of this auxin-inducible degron (AID) system in Saccharomyces cerevisiae. We have minimized the size of the degron and appended a series of additional epitope tags, allowing detection by commercial antibodies or fluorescence microscopy. The vectors are compatible with PCR-based genomic tagging strategies, allow for C- or N-terminal fusion of the degron, and provide a range of selection markers. Application to a series of yeast proteins, including essential replication factors, provides evidence for a general usefulness of the system. PMID:23836714

  5. Contributions to helicopter frequency domain system identification

    NASA Astrophysics Data System (ADS)

    Jones, Christopher Tyler

    The objective of this dissertation is to develop a series of mathematical tools that simplify planning, execution, and interpretation of a state-space, frequency-domain based system identification procedure. These tools start from the recognition that the identification is an unconstrained optimization problem. Therefore, a variety of tools of optimization theory can be usefully applied to the identification. The identification was carried out on simulated flight test data. The study showed that it is possible to identify directly individual elements of the state and control matrices of a state-space model of the helicopter. The sensitivity to noise and inaccuracies of the initial guesses were quantified for some representative examples. The resistance to noise is generally good. The identification is rather insensitive to inaccuracies in the initial guesses, but is still important to start from the best possible estimates. A frequency response sensitivity function, which describes the sensitivity of the frequency responses of a linear system to changes in elements of the state and control matrices, was defined in this study. Variants of this function were found to be useful in determining which types of inputs and outputs, and over which frequency bands, are the best for the identification of given elements of the state or the control matrices. These functions provided quantitative results consistent with engineering judgment, and thus can help automate some critical phases of the system identification. A technique was developed to determine which elements of the state-space model are important over given frequency bands, and to identify the elements in each frequency band independently. The accuracy of this "frequency-banded" procedure is comparable to that obtained from a simultaneous identification of all the unknown elements, and the computational cost is lower. This dissertation presents a method for the calculation of the sensitivity of eigenvalues to changes in elements of the state matrix of the system. Using this method it was possible to determine which elements of the state matrix most affected the accuracy of a given pole, and therefore the identification could be focused on precisely those elements.

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

    PubMed Central

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

    2014-01-01

    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

  7. Authentication Without Identification using Anonymous Credential System

    E-print Network

    Damodaram, A

    2009-01-01

    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.

  8. The CSU Face Identification Evaluation System

    Microsoft Academic Search

    J. Ross Beveridge; David S. Bolme; Bruce A. Draper; Marcio Teixeira

    2005-01-01

    The CSU Face Identification Evaluation System includes standardized image preprocessing software, four distinct face recognition algorithms, analysis tools to study algorithm performance, and Unix shell scripts to run standard experiments. All code is written in ANSII C. The four algorithms provided are principle components analysis (PCA), a.k.a eigenfaces, a combined principle components analysis and linear discriminant analysis algorithm (PCA +

  9. Voice identification system based on server

    Microsoft Academic Search

    Wang Zhongwei; Wang Hongbo

    2010-01-01

    Voice identification system is a great breakthrough in computer automation technology. In recent years, it has developed with rapid speed and will be popularized to many different fields, especially in logistics. The paper is aimed at discussing the integration of radio frequency technology and voice technology. Through the comprehensive analysis on the structure and basic principle and operation method of

  10. Aircraft System Identification Using Artificial Neural Networks

    E-print Network

    Valasek, John

    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

  11. Practical reactor systems for yeast cell immobilization using biomass support particles.

    PubMed

    Black, G M; Webb, C; Matthews, T M; Atkinson, B

    1984-02-01

    The technique of cell immobilization using porous support particles (biomass support particles) has been successfully applied to yeast cells. Two reactor configurations exploiting the use of these particles have been developed and assessed for use in aseptic yeast fermentations. A liquid-fluidized bed fermenter has been devised for use with particles denser than the fermentation liquor whilst a gas-stirred circulating bed fermenter proved suitable for particles of essentially neutral buoyancy. Both systems have been operated successfully for extended periods of continuous operation. The utilization of biomass support particle technology in such reactors provides a practical and robust system for immobilized cell reactors. This technology offers significant opportunities for further development. PMID:18551699

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

    Microsoft Academic Search

    Yewang Zhang; Ruijiang Liu; Xiaoyu Wu

    2007-01-01

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

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

    Microsoft Academic Search

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

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

  14. Analysis of a Peptide Hormone-Receptor Interaction in the Yeast Two-Hybrid System

    Microsoft Academic Search

    Jianwei Zhu; C. Ronald Kahn

    1997-01-01

    Interaction between a peptide hormone and extracellular domains of its receptor is a crucial step for initiation of hormone action. We have developed a modification of the yeast two-hybrid system to study this interaction and have used it to characterize the interaction of insulin-like growth factor 1 (IGF-1) with its receptor by using GAL4 transcriptional regulation with a beta -galactosidase

  15. Stabilization of the yeast desaturase system by low levels of oxygen

    NASA Technical Reports Server (NTRS)

    Volkmann, C. M.; Klein, H. P.

    1983-01-01

    The stability of particulate palmitoyl-CoA desaturase preparations from anaerobically grown yeast cells was increased by exposure to low levels of oxygen. The stabilizing effect of oxygen may be based upon the increased amounts of palmitoleic acid and ergosterol that become available to the cells. These results suggest the evolutinary appearance of this system at a time when atmospheric oxygen was at a low level.

  16. Development of an integrative DNA transformation system for the yeast Candida utilis

    Microsoft Academic Search

    Luis Rodr??guez; Francisco P. Chávez; Liliana Basabe; Tanilo Rivero; Julio M. Delgado

    1998-01-01

    We report here the development of an auxotrophic transformation system for the food yeast Candida utilis. To facilitate molecular studies in Candida utilis, we isolated auxotrophic strains for uracil biosynthesis by the combination of NTG-mutagenesis and 5-fluorotic acid (FOA) selection. The ura? mutation could be functionally complemented by the homologous URA3 gene. We used both, LiAc and electroporation methods to

  17. Comparison of three different systems used for flux enhancement: application to crossflow filtration of yeast suspensions

    Microsoft Academic Search

    Omar Al-akoum; Muriel Mercier-Bonin; Luhui Ding; Christian Fonade; Philippe Aptel; Michel Jaffrin

    2002-01-01

    The aim of this work is to characterize more accurately, through experimental or theoretical approaches, the hydrodynamics of three particular systems usually used for flux enhancement: shear-enhanced filtration with a vibrating membrane module, gas\\/liquid two-phase flows and Dean vortices. The correlation between local hydrodynamics and permeate flux obtained during crossflow filtration of a yeast suspension under different operating conditions confirmed

  18. 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 164.46 Navigation...46 Automatic Identification System (AIS). (a) The following vessels must...properly installed, operational, type approved AIS as of the date specified: (1)...

  19. 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 164.46 Navigation...46 Automatic Identification System (AIS). (a) The following vessels must...properly installed, operational, type approved AIS as of the date specified: (1)...

  20. 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 164.46 Navigation...46 Automatic Identification System (AIS). (a) The following vessels must...properly installed, operational, type approved AIS as of the date specified: (1)...

  1. 33 CFR 164.46 - Automatic Identification System (AIS).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...false Automatic Identification System (AIS). 164.46 Section 164.46 Navigation...46 Automatic Identification System (AIS). (a) The following vessels must...properly installed, operational, type approved AIS as of the date specified: (1)...

  2. Identification of oleaginous yeast strains able to accumulate high intracellular lipids when cultivated in alkaline pretreated corn stover.

    PubMed

    Sitepu, Irnayuli R; Jin, Mingjie; Fernandez, J Enrique; da Costa Sousa, Leonardo; Balan, Venkatesh; Boundy-Mills, Kyria L

    2014-09-01

    Microbial oil is a potential alternative to food/plant-derived biodiesel fuel. Our previous screening studies identified a wide range of oleaginous yeast species, using a defined laboratory medium known to stimulate lipid accumulation. In this study, the ability of these yeasts to grow and accumulate lipids was further investigated in synthetic hydrolysate (SynH) and authentic ammonia fiber expansion (AFEX™)-pretreated corn stover hydrolysate (ACSH). Most yeast strains tested were able to accumulate lipids in SynH, but only a few were able to grow and accumulate lipids in ACSH medium. Cryptococcus humicola UCDFST 10-1004 was able to accumulate as high as 15.5 g/L lipids, out of a total of 36 g/L cellular biomass when grown in ACSH, with a cellular lipid content of 40 % of cell dry weight. This lipid production is among the highest reported values for oleaginous yeasts grown in authentic hydrolysate. Preculturing in SynH media with xylose as sole carbon source enabled yeasts to assimilate both glucose and xylose more efficiently in the subsequent hydrolysate medium. This study demonstrates that ACSH is a suitable medium for certain oleaginous yeasts to convert lignocellullosic sugars to triacylglycerols for production of biodiesel and other valuable oleochemicals. PMID:25052467

  3. Tandem-yeast expression system for engineering and producing unspecific peroxygenase.

    PubMed

    Molina-Espeja, Patricia; Ma, Su; Mate, Diana M; Ludwig, Roland; Alcalde, Miguel

    2015-06-01

    Unspecific peroxygenase (UPO) is a highly efficient biocatalyst with a peroxide dependent monooxygenase activity and many biotechnological applications, but the absence of suitable heterologous expression systems has precluded its use in different industrial settings. Recently, the UPO from Agrocybe aegerita was evolved for secretion and activity in Saccharomyces cerevisiae [8]. In the current work, we describe a tandem-yeast expression system for UPO engineering and large scale production. By harnessing the directed evolution process in S. cerevisiae, the beneficial mutations for secretion enabled Pichia pastoris to express the evolved UPO under the control of the methanol inducible alcohol oxidase 1 promoter. Whilst secretion levels were found similar for both yeasts in flask fermentation (?8mg/L), the recombinant UPO from P. pastoris showed a 27-fold enhanced production in fed-batch fermentation (217mg/L). The P. pastoris UPO variant maintained similar biochemical properties of the S. cerevisiae counterpart in terms of catalytic constants, pH activity profiles and thermostability. Thus, this tandem-yeast expression system ensures the engineering of UPOs to use them in future industrial applications as well as large scale production. PMID:26002501

  4. Blind identification of co-channel systems

    Microsoft Academic Search

    M. I. Gurelli; C. L. Nikas

    1994-01-01

    One of the major impediments of reliable communication in systems employing frequency reusage is co-channel interference. In many cases, neither a training signal nor a priori measurements of the channel transfer functions are available. Hence, the receiver has to start up blindly. In this paper, we propose a new method for the blind identification of co-channel systems using higher-order statistics.

  5. Parameter identification for nonlinear aerodynamic systems

    NASA Technical Reports Server (NTRS)

    Pearson, Allan E.

    1990-01-01

    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.

  6. Structural system identification: Structural dynamics model validation

    SciTech Connect

    Red-Horse, J.R.

    1997-04-01

    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.

  7. Antifungal properties of the immunosuppressant FK-506: identification of an FK-506-responsive yeast gene distinct from FKB1.

    PubMed Central

    Brizuela, L; Chrebet, G; Bostian, K A; Parent, S A

    1991-01-01

    FK-506 is a novel and potent antagonist of T-cell activation and an inhibitor of fungal growth. Its immunosuppressive activity can be antagonized by the structurally related antibiotic rapamycin, and both compounds interact with cytoplasmic FK-506-binding proteins (FKBPs) in T cells and yeast cells. In this paper, we show that FK-506 and two analogs inhibit vegetative growth of Saccharomyces cerevisiae in a fashion that parallels the immunosuppressive activity of these compounds. Yeast mutants resistant to FK-506 were isolated, and at least three complementation groups (fkr1, fkr2, and fkr3) were defined. These fkr mutants show no alteration in their levels of FK-506-binding activity. Likewise, strains carrying null alleles of FKB1 (the yeast gene coding for the FKBP) remain FK-506 sensitive, indicating that depletion of yeast FKBP is not sufficient to confer an FK-506 resistance phenotype, although fkb1 null mutants are resistant to rapamycin. FKB1 does not map to the three fkr loci defined here. These results suggest that yeast FKBP mediates the inhibitory effect of rapamycin but that at least one other protein is directly involved in mediating the activity of FK-506. Interestingly, the ability of FK-506 to rescue a temperature-sensitive growth defect of the fkr3 mutant suggests that the FKR3 gene may define such a protein. Images PMID:1715022

  8. Unique device identification system. Final rule.

    PubMed

    2013-09-24

    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

  9. Sorting in the endosomal system in yeast and animal cells

    Microsoft Academic Search

    Sandra K Lemmon; Linton M Traub

    2000-01-01

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

  10. Protein Kinase Activity and Identification of a Toxic Effector Domain of the Target of Rapamycin TOR Proteins in Yeast

    PubMed Central

    Alarcon, Clara M.; Heitman, Joseph; Cardenas, Maria E.

    1999-01-01

    In complex with FKBP12, the immunosuppressant rapamycin binds to and inhibits the yeast TOR1 and TOR2 proteins and the mammalian homologue mTOR/FRAP/RAFT1. The TOR proteins promote cell cycle progression in yeast and human cells by regulating translation and polarization of the actin cytoskeleton. A C-terminal domain of the TOR proteins shares identity with protein and lipid kinases, but only one substrate (PHAS-I), and no regulators of the TOR-signaling cascade have been identified. We report here that yeast TOR1 has an intrinsic protein kinase activity capable of phosphorylating PHAS-1, and this activity is abolished by an active site mutation and inhibited by FKBP12-rapamycin or wortmannin. We find that an intact TOR1 kinase domain is essential for TOR1 functions in yeast. Overexpression of a TOR1 kinase-inactive mutant, or of a central region of the TOR proteins distinct from the FRB and kinase domains, was toxic in yeast, and overexpression of wild-type TOR1 suppressed this toxic effect. Expression of the TOR-toxic domain leads to a G1 cell cycle arrest, consistent with an inhibition of TOR function in translation. Overexpression of the PLC1 gene, which encodes the yeast phospholipase C homologue, suppressed growth inhibition by the TOR-toxic domains. In conclusion, our findings identify a toxic effector domain of the TOR proteins that may interact with substrates or regulators of the TOR kinase cascade and that shares sequence identity with other PIK family members, including ATR, Rad3, Mei-41, and ATM. PMID:10436010

  11. Selective systems for obtaining recessive ribosomal suppressors in Saccharomyces yeast

    SciTech Connect

    Inge-Vechtomov, S.G.; Tichodeev, O.N.; Karpova, T.S.

    1989-01-01

    The absolute selectivity of the system used for the selection of recessive mutations in only two genes (ribosomal suppressors sup1 and sup2) is based on the obtaining of simultaneous reversions to prototrophy for adenine and histidine in Saccharomyces cerevisiae haploids carrying two different nonsense mutations: his7-1 (UAA) and adel-14 (UGA, identified in this study). The selectivity of the system is determined not only by the use of different types of nonsense but also by the selection of actual nonsense alleles, and also by the genotypic background of the culture. The lys2 mutants were induced by UV irradiation (dose 300 J/m/sup 2/) of the strains on the AAA medium, selective for the growth of these mutants.

  12. Identification of dynamic systems, theory and formulation

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

    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.

  13. System identification of Drosophila olfactory sensory neurons

    PubMed Central

    Kim, Anmo J.; Slutskiy, Yevgeniy B.

    2013-01-01

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

  14. Screening of hepatocyte proteins binding to F protein of hepatitis C virus by yeast two-hybrid system

    PubMed Central

    Huang, Yan-Ping; Cheng, Jun; Zhang, Shu-Lin; Wang, Lin; Guo, Jiang; Liu, Yan; Yang, Yuan; Zhang, Li-Ying; Bai, Gui-Qin; Gao, Xue-Song; Ji, Dong; Lin, Shu-Mei; Shao, Qing

    2005-01-01

    AIM: To investigate the biological function of F protein by yeast two-hybrid system. METHODS: We constructed F protein bait plasmid by cloning the gene of F protein into pGBKT7, then recombinant plasmid DNA was transformed into yeast AH109 (a type). The transformed yeast AH109 was mated with yeast Y187 (? type) containing liver cDNA library plasmid in 2×YPDA medium. Diploid yeast was plated on synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) containing X-?-gal for selection and screening. After extracting and sequencing plasmids from positive (blue) colonies, we underwent sequence analysis by bioinformatics. RESULTS: Thirty-six colonies were selected and sequenced. Among them, 11 colonies were zymogen granule protein, 5 colonies were zinc finger protein, 4 colonies were zinc-?-2-glycoprotein, 1 colony was sialyltransferase, 1 colony was complement control protein factor I, 1 colony was vitronectin, and 2 colonies were new genes with unknown function. CONCLUSION: The yeast two-hybrid system is an effective method for identifying hepatocyte proteins interacting with F protein of hepatitis C virus. F protein may bind to different proteins. PMID:16237761

  15. Realization-Based System Identification with Applications

    NASA Astrophysics Data System (ADS)

    Miller, Daniel N.

    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.

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

    E-print Network

    Citovsky, Vitaly

    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

  17. Identification of Wiener systems with known noninvertible nonlinearities

    Microsoft Academic Search

    Seth L. Lacy; R. Scott Erwin; Dennis S. Bernstein

    2001-01-01

    In this paper we develop a method for identifying Wiener-type nonlinear systems, that is, systems consisting of a linear dynamic system followed by a static nonlinearity. Unlike previous techniques developed for Wiener system identification, our approach allows the identification of systems with noninvertible, but known, nonlinearities

  18. An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast.

    PubMed Central

    Bellí, G; Garí, E; Piedrafita, L; Aldea, M; Herrero, E

    1998-01-01

    We have developed an activator/repressor expression system for budding yeast in which tetracyclines control in opposite ways the ability of tetR-based activator and repressor molecules to bind tetO promoters. This combination allows tight expression of tetO- driven genes, both in a direct (tetracycline-repressible) and reverse (tetracycline-inducible) dual system. Ssn6 and Tup1, that are components of a general repressor complex in yeast, have been tested for their repressing properties in the dual system, using lacZ and CLN2 as reporter genes. Ssn6 gives better results and allows complete switching-off of the regulated genes, although increasing the levels of the Tup1-based repressor by expressing it from a stronger promoter improves repressing efficiency of the latter. Effector-mediated shifts between expression and non-expression conditions are rapid. The dual system here described may be useful for the functional analysis of essential genes whose conditional expression can be tightly controlled by tetracyclines. PMID:9461451

  19. Incremental closed-loop identification of linear parameter varying systems

    Microsoft Academic Search

    Jan Bendtsen; Klaus Trangbaek

    2011-01-01

    This paper deals with system identification for control of linear parameter varying systems. In practical applications, it is often important to be able to identify small plant changes in an incremental manner without shutting down the system and\\/or disconnecting the controller; unfortunately, closed-loop system identification is more difficult than open- loop identification. In this paper we prove that the so-called

  20. SUPPORT VECTOR MACHINE BASED SPEAKER IDENTIFICATION SYSTEMS USING GMM PARAMETERS

    E-print Network

    De Leon, Phillip

    . INTRODUCTION The objective of speaker identification (SI) is to determine which voice sample from a setSUPPORT VECTOR MACHINE BASED SPEAKER IDENTIFICATION SYSTEMS USING GMM PARAMETERS Vijendra Raj Engineering Las Cruces, New Mexico USA 88003 {vijendra, pdeleon}@nmsu.edu ABSTRACT Speaker identification

  1. The identification of nonlinear biological systems: LNL cascade models

    Microsoft Academic Search

    M. J. Korenberg; I. W. Hunter

    1986-01-01

    Systems that can be represented by a cascade of a dynamic linear (L), a static nonlinear (N) and a dynamic linear (L) subsystem are considered. Various identification schemes that have been proposed for these LNL systems are critically reviewed with reference to the special problems that arise in the identification of nonlinear biological systems. A simulated LNL system is identified

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

    PubMed

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

    2014-07-01

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

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

    PubMed Central

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

    2014-01-01

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

  4. Parameter identification for nonlinear aerodynamic systems

    NASA Technical Reports Server (NTRS)

    Pearson, Allan E.

    1993-01-01

    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.

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

    Microsoft Academic Search

    Cristina Giusto; Dagmara Medrala; Giuseppe Comi; Marisa Manzano

    2007-01-01

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

  6. Networked Dynamic Systems: Identification, Controllability, and Randomness

    NASA Astrophysics Data System (ADS)

    Nabi-Abdolyousefi, Marzieh

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

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

    PubMed Central

    Kolb, Alexander R.; Buck, Teresa M.

    2011-01-01

    Ion channels, solute transporters, aquaporins, and factors required for signal transduction are vital for kidney function. Because mutations in these proteins or in associated regulatory factors can lead to disease, an investigation into their biogenesis, activities, and interplay with other proteins is essential. To this end, the yeast, Saccharomyces cerevisiae, represents a powerful experimental system. Proteins expressed in yeast include the following: 1) ion channels, including the epithelial sodium channel, members of the inward rectifying potassium channel family, and cystic fibrosis transmembrane conductance regulator; 2) plasma membrane transporters, such as the Na+-K+-ATPase, the Na+-phosphate cotransporter, and the Na+-H+ ATPase; 3) aquaporins 1–4; and 4) proteins such as serum/glucocorticoid-induced kinase 1, phosphoinositide-dependent kinase 1, Rh glycoprotein kidney, and trehalase. The variety of proteins expressed and studied emphasizes the versatility of yeast, and, because of the many available tools in this organism, results can be obtained rapidly and economically. In most cases, data gathered using yeast have been substantiated in higher cell types. These attributes validate yeast as a model system to explore renal physiology and suggest that research initiated using this system may lead to novel therapeutics. PMID:21490136

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

    PubMed

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

    2014-10-15

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

  9. The GCD10 subunit of yeast eIF-3 binds the methyltransferase-like domain of the 126 and 183 kDa replicase proteins of tobacco mosaic virus in the yeast two-hybrid system.

    PubMed

    Taylor, D N; Carr, J P

    2000-06-01

    The tobacco mosaic virus (TMV) replicase complex contains virus- and host-encoded proteins. In tomato, one of these host proteins was reported previously to be related serologically to the GCD10 subunit of yeast eIF-3. The yeast two-hybrid system has now been used to show that yeast GCD10 interacts selectively with the methyltransferase domain shared by the 126 and 183 kDa TMV replicase proteins. These findings are consistent with a role for a GCD10-like protein in the TMV replicase complex and suggest that, in TMV-infected cells, the machinery of virus replication and protein synthesis may be closely connected. PMID:10811942

  10. Whole Pichia pastoris yeast expressing measles virus nucleoprotein as a production and delivery system to multimerize Plasmodium antigens.

    PubMed

    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

    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

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

    PubMed Central

    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

    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

  12. Mitochondrial assembly in yeast

    Microsoft Academic Search

    Les A Grivell; Marta Artal-Sanz; Gertjan Hakkaart; Liesbeth de Jong; Leo G. J Nijtmans; Katinka van Oosterum; Michel Siep; Hans van der Spek

    1999-01-01

    The yeast Saccharomyces cerevisiae is likely to be the first organism for which a complete inventory of mitochondrial proteins and their functions can be drawn up. A survey of the 340 or so proteins currently known to be localised in yeast mitochondria reveals the considerable investment required to maintain the organelle’s own genetic system, which itself contributes seven key components

  13. MIMO system identification using frequency response data

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  14. System Identification of Civil Engineering Structures through Wireless Structural Monitoring and Subspace System Identification Methods

    E-print Network

    Lynch, Jerome P.

    System Identification of Civil Engineering Structures through Wireless Structural Monitoring of the requirements for the degree of Doctor of Philosophy (Civil Engineering) in The University of Michigan 2011 engineers; amazingly, there were many keys which unlocked many civil engineering problems. All achievements

  15. 47 CFR 25.281 - Automatic Transmitter Identification System (ATIS).

    Code of Federal Regulations, 2013 CFR

    2013-10-01

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

  16. 47 CFR 25.281 - Automatic Transmitter Identification System (ATIS).

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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

  17. 47 CFR 25.281 - Automatic Transmitter Identification System (ATIS).

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  18. 47 CFR 25.281 - Automatic Transmitter Identification System (ATIS).

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

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

    PubMed

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

    2014-10-29

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

  20. CRJ Aircraft Flight Simulation: A Lateral System Identification Study

    E-print Network

    Liu, Hugh H.T.

    CRJ Aircraft Flight Simulation: A Lateral System Identification Study Prof. Hugh H.T. Liu 30-Jul-2007 The "Flight Systems and Control" research laboratory at the UTIAS is in- terested in aircraft integrated modeling and simulation. Our previous work [1] investigated system identification for longitudinal

  1. System Identification and Modelling of a High Performance Hydraulic Actuator

    E-print Network

    Hayward, Vincent

    System Identification and Modelling of a High Performance Hydraulic Actuator Benoit Boulet, Laeeque hydraulic systems on the part of robot designers in the research community. Hydraulic actuation is often on the modelling and system identification of one particular high performance hydraulic actuator built by ASI

  2. Introduction to Automatic Data Identification Systems

    NSDL National Science Digital Library

    Jones, Jeff

    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

  3. Abstract: In this paper, one of models which describe dynamics of budding yeasts is verified based on simulations using SIMULINK. By analyzing parameter sensitivity of the model, in view of the system

    E-print Network

    E-7 Abstract: In this paper, one of models which describe dynamics of budding yeasts is verified of the system theory. Key Words: Systems Biology, Cell Cycle, Budding Yeast, Sensitivity Analysis 1 [1, 2

  4. Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.

    PubMed

    Canelas, André B; Harrison, Nicola; Fazio, Alessandro; Zhang, Jie; Pitkänen, Juha-Pekka; van den Brink, Joost; Bakker, Barbara M; Bogner, Lara; Bouwman, Jildau; Castrillo, Juan I; Cankorur, Ayca; Chumnanpuen, Pramote; Daran-Lapujade, Pascale; Dikicioglu, Duygu; van Eunen, Karen; Ewald, Jennifer C; Heijnen, Joseph J; Kirdar, Betul; Mattila, Ismo; Mensonides, Femke I C; Niebel, Anja; Penttilä, Merja; Pronk, Jack T; Reuss, Matthias; Salusjärvi, Laura; Sauer, Uwe; Sherman, David; Siemann-Herzberg, Martin; Westerhoff, Hans; de Winde, Johannes; Petranovic, Dina; Oliver, Stephen G; Workman, Christopher T; Zamboni, Nicola; Nielsen, Jens

    2010-01-01

    The field of systems biology is often held back by difficulties in obtaining comprehensive, high-quality, quantitative data sets. In this paper, we undertook an interlaboratory effort to generate such a data set for a very large number of cellular components in the yeast Saccharomyces cerevisiae, a widely used model organism that is also used in the production of fuels, chemicals, food ingredients and pharmaceuticals. With the current focus on biofuels and sustainability, there is much interest in harnessing this species as a general cell factory. In this study, we characterized two yeast strains, under two standard growth conditions. We ensured the high quality of the experimental data by evaluating a wide range of sampling and analytical techniques. Here we show significant differences in the maximum specific growth rate and biomass yield between the two strains. On the basis of the integrated analysis of the high-throughput data, we hypothesize that differences in phenotype are due to differences in protein metabolism. PMID:21266995

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

    PubMed Central

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

    2012-01-01

    The CapitalBio Mycobacterium identification microarray system is a rapid system for the detection of Mycobacterium tuberculosis. The performance of this system was assessed with 24 reference strains, 486 Mycobacterium tuberculosis clinical isolates, and 40 clinical samples and then compared to the “gold standard” of DNA sequencing. The CapitalBio Mycobacterium identification microarray system showed highly concordant identification results of 100% and 98.4% for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM), respectively. The sensitivity and specificity of the CapitalBio Mycobacterium identification array for identification of Mycobacterium tuberculosis isolates were 99.6% and 100%, respectively, for direct detection and identification of clinical samples, and the overall sensitivity was 52.5%. It was 100% for sputum, 16.7% for pleural fluid, and 10% for bronchoalveolar lavage fluid, respectively. The total assay was completed in 6 h, including DNA extraction, PCR, and hybridization. The results of this study confirm the utility of this system for the rapid identification of mycobacteria and suggest that the CapitalBio Mycobacterium identification array is a molecular diagnostic technique with high sensitivity and specificity that has the capacity to quickly identify most mycobacteria. PMID:22090408

  6. Heat capacity identification via Mahalanobis Taguchi System

    Microsoft Academic Search

    Arata Suzuki; Kenji Sugimoto

    2008-01-01

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

  7. Heat Capacity Identification Method Using MT System

    Microsoft Academic Search

    Arata Suzuki; Kenji Sugimoto

    2007-01-01

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

  8. Screening of APP interaction proteins by DUALmembrane yeast two-hybrid system

    PubMed Central

    Yu, You; Li, Yinan; Zhang, Yan

    2015-01-01

    Alzheimer’s disease (AD) is one of the most common forms of neurodegenerative disease. There is a growing interest in the amyloid precursor protein (APP) over the years due to its involvement in AD. Besides its role in pathological mechanisms of AD, APP participates in many signaling pathways as well. APP functions through protein-protein interactions, and in this report staufen 1 (STAU1) is demonstrated to have interaction with APP, using yeast two-hybrid screening and co-immunoprecipitation in mammalian system. STAU1 belongs to the double-stranded RNA binding protein family and can mediate mRNA degradation in mammalian system, implicating that APP may be involved in the regulation of mRNA as well.

  9. Source options for nuclear weapons identification system

    SciTech Connect

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

    1995-07-01

    This report briefly presents the advantages and disadvantages of two timed sources of neutrons that can be used with the source-driven noise analysis method: (1) {sup 252}Cf in an ionization chamber and (2) an associated-particle sealed tube neutron generator (APSTNG). These sources can be used with frequency and time analysis methods for nuclear weapons identification, quality assurance in production, special nuclear materials assay, criticality safety, and provision of measured data for verification of neutron and gamma ray transport calculational methods. The advantages of {sup 252}Cf for a nuclear materials identification system are that it is simple, reliable, and small and that all source events are detected. The disadvantages are that it cannot be turned off, leads to small radiation doses in handling, and produces more than one neutron per fission event. The advantages of APSTNG are that it is directional, can be turned off, and has one particle per deuterium-tritium reaction. The disadvantages are that it is large and complicated compared to {sup 252}Cf.

  10. p68 RNA helicase: identification of a nucleolar form and cloning of related genes containing a conserved intron in yeasts.

    PubMed Central

    Iggo, R D; Jamieson, D J; MacNeill, S A; Southgate, J; McPheat, J; Lane, D P

    1991-01-01

    The human p68 protein is an RNA-dependent ATPase and RNA helicase which was first identified because of its immunological cross-reaction with a viral RNA helicase, simian virus 40 large T antigen. It belongs to a recently discovered family of proteins (DEAD box proteins) that share extensive regions of amino acid sequence homology, are ubiquitous in living organisms, and are involved in many aspects of RNA metabolism, including splicing, translation, and ribosome assembly. We have shown by immunofluorescent microscopy that mammalian p68, which is excluded from the nucleoli during interphase, translocates to prenucleolar bodies during telophase. We have cloned 55% identical genes from both Schizosaccharomyces pombe and Saccharomyces cerevisiae and shown that they are essential in both yeasts. The human and yeast genes contain a large intron whose position has been precisely conserved. In S. cerevisiae, the intron is unusual both because of its size and because of its location near the 3' end of the gene. We discuss possible functional roles for such an unusual intron in an RNA helicase gene. Images PMID:1996094

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

    Microsoft Academic Search

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

    2002-01-01

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

  12. State space modeling and identification of stochastic linear structural systems

    Microsoft Academic Search

    Brad A Pridham

    2005-01-01

    This thesis presents techniques for the modeling and identification of linear state space models of structural response to stochastic dynamic input. Two approaches to stochastic system identification are investigated and further developed within the state space modeling framework. These methods require only measurements of the response of the system for estimation of modal parameters. ^ In the first part of

  13. Design of a Vein Based Personal Identification System

    Microsoft Academic Search

    Madhumita Kathuria

    2010-01-01

    A wide variety of real world systems require reliable personal recognition schemes to either confirm or determine the identity of an individual requesting their services. Biometric recognition scheme refers to the automatic recognition\\/identification of individuals based on their physiological and\\/or behavioral characteristics. We have proposed a Vein Based Personal Identification System (VBPIS), which overcomes the deficiencies usually found in commercially

  14. Feature Selection Using Stochastic Search: An Application to System Identification

    Microsoft Academic Search

    Sandro Saitta; Prakash Kripakaran; Benny Raphael; Ian F. C. Smith

    2010-01-01

    System identification using multiple-model strategies may involve thousands of models with several parameters. However, only a few models are close to the correct model. A key task involves finding which parameters are important for explaining candidate models. The application of feature selection to system identification is studied in this paper. A new feature selection algorithm is proposed. It is based

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

    Microsoft Academic Search

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

    1996-01-01

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

  16. VSS theory-based parameter identification scheme for MIMO systems

    Microsoft Academic Search

    Jian-Xin Xu; Hideki Hashimoto

    1996-01-01

    A new identification methodology, the variable structure system-based identification method, is proposed for multi-input multi-output systems. The developed identifier can successfully estimate unknown system parameters for both linear and some kinds of nonlinear systems that may not be linear in parametric space. The new identifier is essentially a closed-loop system with variable structure control. One major advantage of the proposed

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

    PubMed Central

    2014-01-01

    Introduction Invasive fungal infections are alarmingly common in intensive care unit patients; invasive fungal infections are associated with increased morbidity and mortality. Risk factors are the increased use of indwelling central venous catheters, the use of broad spectrum antibiotics, parenteral nutrition, renal replacement therapy and immunosuppression. Diagnosis of these infections might be complicated, requiring tissue cultures. In addition, therapy of invasive fungal infections might be difficult, given the rising resistance of fungi to antifungal agents. Case presentation We describe the case of a 28-year-old Greek man with yeast central nervous system infection. Conclusions Difficult-to-treat fungal infections may complicate the clinical course of critically ill patients and render their prognosis unfavorable. This report presents a case that was rare and difficult to treat, along with a thorough review of the investigation and treatment of these kinds of fungal infections in critically ill patients. PMID:25026870

  18. 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)

    Pisman, T.; Somova, L.

    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.

  19. 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)

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

    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.

  20. System Identification of Physiological Systems Using Short Data Segments

    PubMed Central

    Perreault, Eric J.

    2013-01-01

    System identification of physiological systems poses unique challenges, especially when the structure of the system under study is uncertain. Non-parametric techniques can be useful for identifying system structure, but these typically assume stationarity, and require large amounts of data. Both of these requirements are often not easily obtained in the study of physiological systems. Ensemble methods for time-varying, non-parametric estimation have been developed to address the issue of stationarity, but these require an amount of data that can be prohibitive for many experimental systems. To address this issue, we developed a novel algorithm that uses multiple short data segments. Using simulation studies, we showed that this algorithm produces system estimates with lower variability than previous methods when limited data are present. Furthermore we showed that the new algorithm generates time-varying system estimates with lower total error than an ensemble method. Thus, this algorithm is well suited for the identification of physiological systems that vary with time or from which only short segments of stationary data can be collected. PMID:23033429

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

    PubMed Central

    Wang, R; Jin, Y; Norris, D

    1997-01-01

    Mating type switching in Saccharomyces cerevisiae initiates when Ho endonuclease makes a site-specific double-stranded break at MAT, the yeast mating type locus. To identify other proteins involved in this process, we examined whether extracts prepared from ho- mutants contain additional factors that bind near the recognition sequence for Ho. Using an electrophoretic mobility shift assay, we isolated a chromatographic fraction that contains an activity, named YZbp, which binds to two sequences flanking the recognition sequence at MATalpha and to one sequence overlapping it at MATa. MAT plasmids carrying mutations in the YZbp recognition sequence are cleaved by purified Ho at wild-type efficiencies in an in vitro assay. These same plasmids, however, are not cleaved by Ho inside cells, demonstrating that YZbp acts as a positive activator of in vivo cleavage. YZbp is present in all cell types, even those not undergoing mating type switching, suggesting that it has additional cellular functions. PMID:9001231

  2. 47 CFR 80.231 - Technical Requirements for Class B Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...Class B Automatic Identification System (AIS) equipment. 80.231 Section 80...Class B Automatic Identification System (AIS) equipment. (a) Class B Automatic Identification System (AIS) equipment must meet the technical...

  3. 47 CFR 80.231 - Technical Requirements for Class B Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...Class B Automatic Identification System (AIS) equipment. 80.231 Section 80...Class B Automatic Identification System (AIS) equipment. (a) Class B Automatic Identification System (AIS) equipment must meet the technical...

  4. 47 CFR 80.231 - Technical Requirements for Class B Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...Class B Automatic Identification System (AIS) equipment. 80.231 Section 80...Class B Automatic Identification System (AIS) equipment. (a) Class B Automatic Identification System (AIS) equipment must meet the technical...

  5. 47 CFR 80.231 - Technical Requirements for Class B Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...Class B Automatic Identification System (AIS) equipment. 80.231 Section 80...Class B Automatic Identification System (AIS) equipment. (a) Class B Automatic Identification System (AIS) equipment must meet the...

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

    Microsoft Academic Search

    Lidia Pérez-Pérez; Manuel Pereiro; Jaime Toribio

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

  7. Computer-assisted skull identification system using video superimposition

    Microsoft Academic Search

    Mineo Yoshino; Hideaki Matsuda; Satoshi Kubota; Kazuhiko Imaizumi; Sachio Miyasaka; Sueshige Seta

    1997-01-01

    This system consists of two main units, namely a video superimposition system and a computer-assisted skull identification system. The video superimposition system is comprised of the following five parts: a skull-positioning box having a monochrome CCD camera, a photo-stand having a color CCD camera, a video image mixing device, a TV monitor and a videotape recorder. The computer-assisted skull identification

  8. Characterization of ?-amyloid peptide precursor processing by the yeast Yap3 and Mkc7 proteases

    Microsoft Academic Search

    Wei Zhang; Daniel Espinoza; Victoria Hines; Michael Innis; Pankaj Mehta; David L Miller

    1997-01-01

    Two proteases, denoted ?- and ?-secretase, process the ?-amyloid peptide precursor (APP) to yield the A? peptides involved in Alzheimer's disease. A third protein, ?-secretase, cleaves APP near the middle of the A? sequence and thus prevents A? formation. These enzymes have defied identification. Because of its similarity to the systems of mammalian cells the yeast secretory system has provided

  9. 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

    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

    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

  10. Identification and control of dynamical systems using neural networks

    Microsoft Academic Search

    KUMPATI S. NARENDRA; KANNAN PARTHASARATHY

    1990-01-01

    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

  11. The Green Card Protocol: An Identification Protocol for Decentralized Systems

    Microsoft Academic Search

    Stefano Campadello

    2006-01-01

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

  12. How Nonlinear Parametric Wiener System Identification is Under Gaussian Inputs?

    Microsoft Academic Search

    Zhijun Cai; Er-Wei Bai

    2012-01-01

    A number of methods exist for identifying nonlinear Wiener systems. However, there is no attempt to address the fundamental question of how nonlinear these identification problems really are? In this technical note, we try to address this question by investigating the average squared error cost function used in identification. By a proper normalization and a clever characterization of the cost

  13. Support vector method for robust ARMA system identification

    Microsoft Academic Search

    José Luis Rojo-Álvarez; Manel Martínez-Ramón; Mario de Prado-Cumplido; Antonio Artés-Rodríguez; Aníbal R. Figueiras-Vidal

    2004-01-01

    This paper presents a new approach to auto-regressive and moving average (ARMA) modeling based on the support vector method (SVM) for identification applications. A statistical analysis of the characteristics of the proposed method is carried out. An analytical relationship between residuals and SVM-ARMA coefficients allows the linking of the fundamentals of SVM with several classical system identification methods. Additionally, the

  14. 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

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

    2014-01-01

    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

  15. Development of Identification System of cans And Bottle

    NASA Astrophysics Data System (ADS)

    Yani, Irsyadi; Budiman, Ihsan

    2015-06-01

    The objectives of this research was developed an integrated simulation model of an intelligent sorting system based on machine vision, which is focused on object detection, identification and automatic sorting system of cans and bottle. In this research we used 60 cans and 40 bottles for database with five direction of each sample (upper, bottom, diagonal left and right side). Performance of the identification system for correct cans and bottles are 91.33% with estimated amount of 21,600 items per hour. The success of the identification depends on the size and type of the objects.

  16. Substructure System Identification for Finite Element Model Updating

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

    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.

  17. Identification of high gamma-aminobutyric acid producing marine yeast strains by physiological and biochemical characteristics and gene sequence analyses.

    PubMed

    Guo, Xiao-feng; Aoki, Hitoshi; Hagiwara, Toshihiko; Masuda, Kazuaki; Watabe, Shugo

    2009-07-01

    Four marine yeasts isolated from the Pacific Ocean off Japan (Siki No. 4, Siki No. 15, Hach No. 6, and Inub No. 11), which showed high gamma-aminobutyric acid (GABA) producing abilities, were identified and classified by physiological and biochemical characteristics and gene sequence analyses. Analysis of biochemical data suggested that while Siki No. 15 was identical to Candida, the remaining three isolates belonged to the genus Pichia. However, these data were insufficient to resolve their identity at the species level. Subsequently, analysis of the 5.8S rRNA genes and the two internal transcribed spacer regions (ITS) sequences revealed that Siki No. 15 belongs to Pichia guilliermondii, while the remaining three isolates corresponded to Pichia anomala. Since Siki No. 4 showed slightly different biochemical properties than the other two isolates, which were otherwise identical, we sought to investigate the sequences of the intergenic spacer region 1 (IGS1). We observed few nucleotide changes, suggesting that the Hach No. 6 and Inub No. 11 isolates belong to different but new strains for which we propose the names P. anomola MR-1 and MR-2 respectively. PMID:19584549

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

    PubMed Central

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

    2014-01-01

    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

  19. Yeast proteome map (update 2006).

    PubMed

    Perrot, Michel; Guieysse-Peugeot, Anne-Laure; Massoni, Aurélie; Espagne, Christelle; Claverol, Stéphane; Silva, Raquel Monteiro; Jenö, Paul; Santos, Manuel; Bonneu, Marc; Boucherie, Hélian

    2007-04-01

    To improve the potential of two-dimensional gel electrophoresis for proteomic investigations in yeast we have undertaken the systematic identification of Saccharomyces cerevisiae proteins separated on 2-D gels. We report here the identification of 187 novel protein spots. They were identified by two methods, mass spectrometry and gene inactivation. These identifications extend the number of protein spots identified on our yeast 2-D proteome map to 602, i.e. nearly half the detectable spots of the proteome map. These spots correspond to 417 different proteins. The reference map and the list of identified proteins can be accessed on the Yeast Protein Map server (www.ibgc.u-bordeaux2.fr/YPM). PMID:17351888

  20. 280 EXPRESSION IN YEAST [23] [23] Manipulating Yeast Genome Using Plasmid Vectors

    E-print Network

    Botstein, David

    280 EXPRESSION IN YEAST [23] [23] Manipulating Yeast Genome Using Plasmid Vectors By TIM STEARNS, HONG MA, and DAVID BOTSTEIN The yeast Saccharomyces cerevisiae has proved to be a popular high status of yeast as an experimental system is in large part due to the work of the many geneticists

  1. 49 CFR 1542.211 - Identification systems.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...individual in the secured area or SIDA continuously displays the identification medium issued to that individual on the outermost garment above waist level, or is under escort. (3) Procedures to ensure accountability through the following: (i)...

  2. 49 CFR 1542.211 - Identification systems.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...individual in the secured area or SIDA continuously displays the identification medium issued to that individual on the outermost garment above waist level, or is under escort. (3) Procedures to ensure accountability through the following: (i)...

  3. 49 CFR 1542.211 - Identification systems.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...individual in the secured area or SIDA continuously displays the identification medium issued to that individual on the outermost garment above waist level, or is under escort. (3) Procedures to ensure accountability through the following: (i)...

  4. CERTIFIED SYSTEM IDENTIFICATION Marco C. Campi

    E-print Network

    Campi, Marco

    IDENTIFICATION TOWARDS DISTRIBUTION-FREE RESULTS Marco C. Campi University of Brescia Italy #12;Simone Garatti - Algo Care' - Sangho Ko - Su Ki Ooi - Bernardo Pagnoncelli - Maria Prandini - Daniel Reich #12;Preamble

  5. Patulin biodegradation by marine yeast Kodameae ohmeri.

    PubMed

    Dong, Xiaoyan; Jiang, Wei; Li, Chunsheng; Ma, Ning; Xu, Ying; Meng, Xianghong

    2015-01-01

    Patulin contamination of fruit- and vegetable-based products had become a major challenge for the food industry. Biological methods of patulin control can play an important role due to their safety and high efficiency. In this study, a strain of marine yeast with high patulin degradation ability was screened. The yeast was identified as Kodameae ohmeri by the BioLog identification system and partial 26S rRNA gene sequencing. The degradation products of patulin were identified as (E)- and (Z)-ascladiol through HPLC and LC-TOF/MS. High patulin tolerance at 100 ?g ml(-1) and a high degradation rate at 35°C at a pH between 3 and 6 indicates the potential application of K. ohmeri for patulin detoxification of apple-derived products. PMID:25585640

  6. The genetic control of growth rate: a systems biology study in yeast.

    E-print Network

    Pir, Pinar; Gutteridge, Alex; Wu, Jian; Rash, Bharat; Kell, Douglas B; Zhang, Nianshu; Oliver, Stephen G

    2012-01-13

    HFC genes were identified in competition experiments in which a population of hemizygous diploid yeast deletants were grown at, or close to, the maximum specific growth rate in either nutrient-limiting or nutrient-sufficient conditions. A hemizygous...

  7. Fuzzy System Identification Takagi-Sugeno Modelling and Identification

    E-print Network

    Rostock, Universität

    System as Basis Function Approximator Singleton model : Ri : IF x is Ai, THEN y is bi, i = 1, 2 as Basis Function Approximator . . . . 5 1.3 Takagi-Sugeno Model . . . . . . . . . . . . . . . . . . . 7 1 #12;Section 1: Model Structures 3 1. Model Structures NARX model structure : Ri : IF y(k) is Ai1

  8. 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

    Microsoft Academic Search

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

    Triacylglycerols (TAG) and steryl esters (SE) are the principal storage lipids in all eukaryotic cells. In yeasts, these storage\\u000a lipids accumulate within special organelles known as lipid bodies (LB). In the lipid accumulation-oriented metabolism of the\\u000a oleaginous yeast Yarrowia lipolytica, storage lipids are mostly found in the form of TAG, and only small amounts of SE accumulate. We report here

  9. Dry yeast

    NSDL National Science Digital Library

    Ranveig Thattai (None; )

    2005-09-27

    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.

  10. Yeast virology

    Microsoft Academic Search

    REED B. WICKNER

    The three families of double-stranded RNA (dsRNA) viruses and two families of retroviruses (retrotranspo- sons) of the yeast Sacc\\/zaromyces cerevisiaeare all trans- mitted between cells only by cell fusion, probably re- flecting the high frequency of mating of yeast cells in nature. One dsRNA virus and two retroviruses appar- ently use ribosomal \\

  11. Multi-channel blind system identification for central hemodynamic monitoring

    E-print Network

    Zhang, Yi, 1973-

    2002-01-01

    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 ...

  12. Modeling of Biometric Identification System Using the Colored Petri Nets

    NASA Astrophysics Data System (ADS)

    Petrosyan, G. R.; Ter-Vardanyan, L. A.; Gaboutchian, A. V.

    2015-05-01

    In this paper we present a model of biometric identification system transformed into Petri Nets. Petri Nets, as a graphical and mathematical tool, provide a uniform environment for modelling, formal analysis, and design of discrete event systems. The main objective of this paper is to introduce the fundamental concepts of Petri Nets to the researchers and practitioners, both from identification systems, who are involved in the work in the areas of modelling and analysis of biometric identification types of systems, as well as those who may potentially be involved in these areas. In addition, the paper introduces high-level Petri Nets, as Colored Petri Nets (CPN). In this paper the model of Colored Petri Net describes the identification process much simpler.

  13. Frequency-based structural damage identification and dynamic system characterisation 

    E-print Network

    Mao, Lei

    2012-11-29

    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 ...

  14. 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...

  15. Research of Uncertainty Reasoning in Pineapple Disease Identification System

    NASA Astrophysics Data System (ADS)

    Liu, Liqun; Fan, Haifeng

    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.

  16. Cumulant-based parametric multichannel FIR system identification methods

    Microsoft Academic Search

    S. A. Alshebeili; M. T. Ozgen; A. E. Cetin; A. N. Venetsanopoulos

    1993-01-01

    The least squares and recursive methods for simultaneous identification of four nonminimum phase linear, time-invariant FIR systems are presented. The methods utilize the second- and fourth-order cumulants of outputs of the four FIR systems whose common input is an independent, identically distributed (i.i.d.) non-Gaussian process. The new methods can be extended to the general problem of simultaneous identification of three

  17. Parameter identification of a vibratory system with a clearance

    E-print Network

    Franck, Charles Graves

    1987-01-01

    PARAMETER IDENTIFICATION OF A VIBRATORY SYSTEM WITH A CLEARANCE A Thesis by CHARLES GRAVES FRANCK Submitted to the Graduate College of Texas AkM University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE... August 1987 Major Subject: Mechanical Engineering PARAMETER IDENTIFICATION OF A VIBRATORY SYSTEM WITH A CLEARANCE A Thesis by CHARLES GRAVES FRANCK Approved as to style and content by: FCEz ~i. -. ~wgc s R. M. Alexander (Co-Chairman of Committee...

  18. Parameter estimation techniques for LTP system identification

    NASA Astrophysics Data System (ADS)

    Nofrarias Serra, Miquel

    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.

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

    PubMed Central

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

    2013-01-01

    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

  20. Structural parameter identification of distributed systems using finite element approximation

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

    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.

  1. Kinetochore Structure: Pulling Answers from Yeast

    E-print Network

    Cheeseman, Iain M.

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

  2. Contribution to the knowledge of the enzymatic activity of yeasts of clinical interest

    Microsoft Academic Search

    Pedro Garcia-Martos; Jose Mira-Gutierrez

    1995-01-01

    The determination of the enzymatic activity of the yeasts has been applied to the identification of species, specially that ofCandida albicans. In order to know its usefulness in species of clinical interest, we have tested the commercial system API ZYM (Bio Mérieux) on 500 isolated strains of different organic samples, belonging to eight genera and twenty species. All the strains

  3. Structural damage identification using system dynamic properties

    Microsoft Academic Search

    Ma Ge; Eric M. Lui

    2005-01-01

    A damage detection method is presented for the identification and quantification of damage that leads to a change in the structure’s mass and\\/or stiffness properties. The proposed method requires the use of finite element to model the structure in its undamaged state as well as information on the dynamic properties such as frequencies and mode shapes of the structure in

  4. Nitrile Metabolizing Yeasts

    NASA Astrophysics Data System (ADS)

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

    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.

  5. Attack Detection and Identification in Cyber-Physical Systems

    E-print Network

    Bullo, Francesco

    Attack Detection and Identification in Cyber-Physical Systems Fabio Pasqualetti, Florian D for cyber- physical systems, attacks, and monitors; (ii) we characterize fundamental monitoring limitations-physical systems are prone to failures and attacks on their physical infrastructure, and cyber attacks

  6. DESIGN AND SYSTEM IDENTIFICATION OF A NANOSATELLITE STRUCTURE

    E-print Network

    Hall, Christopher D.

    that define the satellite structural and mass properties. SYSTEM DESIGN Satellites typically have unique and mass optimization. Integration compatibility of the multiple spacecraft system is an integral partAAS 01-352 DESIGN AND SYSTEM IDENTIFICATION OF A NANOSATELLITE STRUCTURE Craig L. Stevens , Jana L

  7. Identification of Wiener systems based on fixed point theory

    Microsoft Academic Search

    Guoqi Li; Changyun Wen

    2010-01-01

    In this paper, we propose a new method for the identification of Wiener systems based on fixed point theory. The linear part of the system is an infinite impulse response (IIR) system and the nonlinear static function is allowed to be non-continuous or non-smooth. Our proposed technique transforms the estimation of parameters to finding a fixed point of a nonlinear

  8. Nonlinear identification of the PCO2 control system in man.

    PubMed

    Noshiro, M; Furuya, M; Linkens, D; Goode, K

    1993-07-01

    Two approaches to identification of the PCO2 system in man are described. The first uses a nonlinear 'black box' NARMAX identification package, while the second method uses a structured two-compartment Belville model. The data were obtained from volunteers breathing either room air or a controlled gas mixture, controlled via a pseudorandom M-sequence. Measurements were made of respiratory gas flow and PCO2 content of inspired and expired gases. The identification results indicate that a low-order dynamic model with nonlinear polynomial expansion gave the best fit to the data. In contrast, the Belville model gave best results with a two-compartment linear model, mainly because of difficulties in the optimisation routines when the Belville model was not linear. Thus, modern systemic methods of excitation and identification appear to be appropriate for modelling this respiratory subsystem of humans. PMID:8243076

  9. A modular and hybrid connectionist system for speaker identification.

    PubMed

    Bennani, Y

    1995-07-01

    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

  10. Identification of nonlinear hysteretic systems by artificial neural network

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  11. Neuro-fuzzy methods for nonlinear system identification

    Microsoft Academic Search

    Robert Babuška; Henk Verbruggen

    2003-01-01

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

  12. System Identification of Small-Size Unmanned Helicopter Dynamics

    Microsoft Academic Search

    Bernard Mettler; Mark B. Tischler; Takeo Kanade

    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

  13. Yeast screening system for the detection of mutation, recombination, and aneuploidy

    SciTech Connect

    Dixon, M.L.

    1983-09-01

    Two strains of the yeast Saccharomyces cerevisiae were constructed to detect genetic damage. Strain XD99 can detect chromosome loss, important in the induction of teratogenesis, aneuploidy, and possibly carcinogenesis. Two positive selection techniques were developed which select for the simultaneous loss of both arms of chromosome X. Confirmation of chromosome loss using a centromere-linked marker was found to be essential for distinguishing chromosome loss from coincident crossing-over. The high selectivity of strain XD99 allowed the development of a spot test for chromosome loss. Methyl benzimidazole-2-yl-carbamate and ethyl methanesulfonate induced chromosome loss in the spot test. The two carcinogens 4-nitroquinoline-N-oxide and N-methyl-N'-nitro-N-nitrosoguanidine also induced chromosome loss. Chromosome X monosomics were found to be unstable and were restored to euploidy. This restoration of euploidy may have important implications regarding chromosome loss as a mechanism of promotion. Strain XD83 can detect multiple genetic changes: nuclear frameshift and base pair substitution mutations, nuclear mitotic crossing-over and gene conversion and mitochondrial large deletions and forward point mutations. Ethyl methanesulfonate, ICR-170, N-methyl-N'-nitro-N-nitrosoguanidine, 4-nitroquinoline-N-oxide, ultraviolet light and ethidium bromide were tested. None of the carcinogens were specific in their induced spectrum of damage. Only ethidium bromide induced a highly specific spectrum of damage: petite induction. The variety of endpoints monitored here may allow the detection of certain carcinogens and other genetically toxic agents which have escaped detection in other systems. This system may be useful in the study of possible mechanisms of carcinogenesis and aneuploidy.

  14. Counting Yeast.

    ERIC Educational Resources Information Center

    Bealer, Jonathan; Welton, Briana

    1998-01-01

    Describes changes to a traditional study of population in yeast colonies. Changes to the procedures include: (1) only one culture per student team; (2) cultures are inoculated only once; and (3) the same tube is sampled daily. (DDR)

  15. Yeast Infections

    MedlinePLUS

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

  16. Relative quantitation of protein-protein interaction strength within the yeast two-hybrid system via fluorescence beta-galactosidase activity detection in a high-throughput and low-cost manner.

    PubMed

    Oender, K; Niedermayr, P; Hintner, H; Richter, K; Koller, L; Trost, A; Bauer, J W; Hundsberger, H

    2006-12-01

    The yeast two-hybrid (Y2H) method is capable of delivering vast amounts of interacting positive yeast colonies from a single library screen, particularly if a multifunctional protein is used as bait. However, the selection of definitive colonies for further molecular analysis is limited by both technical practicality and high costs. Here we demonstrate a cost-effective and simple method for the rapid selection and ranking of those Y2H-positive interaction clones that are suitable for further analysis. We performed a Y2H screen for the identification of human transforming growth factor beta2- interacting proteins in a human skin keratinocyte library. The identified clones were ranked by the amount of beta-galactosidase enzyme produced, as well as by the interaction strength of the positive colonies. The combination of high-throughput microplate fluorescence readers and specific fluorescence assays can be utilized for relative quantitation of protein-protein interaction strength of Y2H-positive colonies in crude yeast-cell lysates. We demonstrate here that the high sensitivity of the fluorescence approach can bypass cumbersome conventional methods of cell lysis used in beta-galactosidase assays, and still deliver accurate values for analysis of protein interaction data. Finally, we also achieved a better understanding of general aspects of beta-galactosidase measurements in the Y2H system, such as protein normalization, the influence of yeast culture incubation time on optimal beta-galactosidase detection, and the linearity of beta-galactosidase detection in crude cell lysates. PMID:17199509

  17. A GATA-type transcription factor regulates expression of the high-affinity iron uptake system in the methylotrophic yeast Pichia pastoris

    Microsoft Academic Search

    Rossella Miele; Donatella Barra; Maria Carmela Bonaccorsi di Patti

    2007-01-01

    The ferroxidase Fet3 and the permease Ftr1 constitute a well-conserved high-affinity iron uptake system in yeast. We have investigated the mechanism of transcriptional regulation of Fet3 in the methylotrophic yeast Pichia pastoris. Isolation and functional analysis of the Fet3 promoter indicate that a GATA sequence element plays a role in iron-dependent expression of Fet3. A GATA-type transcription factor, which we

  18. Quality assessment of lager brewery yeast samples and strains using barley malt extracts with anti-yeast activity.

    PubMed

    van Nierop, Sandra N E; Axcell, Barry C; Cantrell, Ian C; Rautenbach, Marina

    2009-04-01

    Membrane active anti-yeast compounds, such as antimicrobial peptides and proteins, cause yeast membrane damage which is likely to affect yeast vitality and fermentation performance, parameters which are notoriously difficult to analyse. In this work the sensitivity of lager brewery yeast strains towards barley malt extracts with anti-yeast activity was assessed with an optimised assay. It was found that yeast, obtained directly from a brewery, was much more sensitive towards the malt extracts than the same yeast strain propagated in the laboratory. Sensitivity to the malt extracts increased during the course of a laboratory scale fermentation when inoculated with brewery yeast. As the assay was able to differentiate yeast samples with different histories, it shows promise as a yeast quality assay measuring the yeast's ability to withstand stress which can be equated to vitality. The assay was also able to differentiate between different lager yeast strains of Saccharomyces cerevisiae propagated in the laboratory when challenged with a number of malt extracts of varying anti-yeast activity. The assessment of yeast strains in the presence of malt extracts will lead to the identification of yeast strains with improved quality/vitality that can withstand malt-associated anti-yeast activity during brewery fermentations. PMID:19171262

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

    SciTech Connect

    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

    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.

  20. Identification and robust control of linear parameter-varying systems

    Microsoft Academic Search

    Lawton Hubert Lee

    1997-01-01

    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).

  1. Decentralized System Identification Using Stochastic Subspace Identification for Wireless Sensor Networks

    PubMed Central

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

    2015-01-01

    Wireless sensor networks (WSNs) facilitate a new paradigm to structural identification and monitoring for civil infrastructure. Conventional structural monitoring systems based on wired sensors and centralized data acquisition systems are costly for installation as well as maintenance. WSNs 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, WSNs require decentralized computing algorithms to reduce data transmission due to the limitation associated with wireless communication. In this paper, the stochastic subspace identification (SSI) technique is selected for system identification, and SSI-based decentralized system identification (SDSI) is proposed to be implemented in a WSN composed of Imote2 wireless sensors that measure acceleration. The SDSI is tightly scheduled in the hierarchical WSN, and its performance is experimentally verified in a laboratory test using a 5-story shear building model. PMID:25856325

  2. Malassezia Baillon, emerging clinical yeasts

    Microsoft Academic Search

    Roma Batra; Teun Boekhout; Eveline Guého; F. Javier Cabańes; Thomas L. Dawson; Aditya K. Gupta

    2005-01-01

    The human and animal pathogenic yeast genus Malassezia has received considerable attention in recent years from dermatologists, other clinicians, veterinarians and mycologists. Some points highlighted in this review include recent advances in the technological developments related to detection, identification, and classification of Malassezia species. The clinical association of Malassezia species with a number of mammalian dermatological diseases including dandruff, seborrhoeic

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

    Microsoft Academic Search

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

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

  4. Recent developments in damage detection based on system identification methods

    Microsoft Academic Search

    P. Hajela; F. J. Soeiro

    1990-01-01

    The output error and equation error methods of system identification are compared for their effectiveness in assessing damage in structural systems. Damage is modeled on an element-by-element basis as changes in sectional properties, which then contribute to variations in the terms of the structural stiffness matrix. Both static displacements and eigenmodes of the structure are used in the damage detection

  5. Evaluation of the BBL Crystal Anaerobe Identification System

    Microsoft Academic Search

    JOSEPH J. CAVALLARO; LOIS S. WIGGS; J. MICHAEL MILLER

    1997-01-01

    The BBL Crystal Anaerobe (ANR) identification system was evaluated, and the results were compared with those from conventional anaerobic methods. We tested 322 clinically significant anaerobic bacteria according to the manufacturer's instructions. The system identified correctly 286 of 322 (88.8%) of the anaerobic bacteria tested. Of these, 263 of 322 (81.7%) were identified correctly on initial testing and 49 were

  6. Subspace identification of multivariable linear parameter-varying systems

    Microsoft Academic Search

    Vincent Verdult; Michel Verhaegen

    2002-01-01

    A subspace identification method is discussed that deals with multivariable linear parameter-varying state-space systems with affine parameter dependence. It is shown that a major problem with subspace methods for this kind of system is the enormous dimension of the data matrices involved. To overcome the curse of dimensionality, we suggest using only the most dominant rows of the data matrices

  7. Real-time FEXT crosstalk identification in ADSL systems

    Microsoft Academic Search

    Nikolaos Papandreou; Theodore Antonakopoulos

    2003-01-01

    FEXT crosstalk identification results in improved frequency spectrum utilization in ADSL systems. The accurate determination of the crosstalk transfer function is a demanding task that is affected by various system impairments. We investigate the performance of a real-time method that exploits the exchange of signaling information of a new activated ADSL line in order to determine the crosstalk function between

  8. System Identification for the Berkeley Lower Extremity Exoskeleton (BLEEX)

    Microsoft Academic Search

    Justin Ghan; Hami Kazerooni

    2006-01-01

    The exoskeleton is an autonomous robotic device whose function is to increase the strength and endurance of a human pilot. In order to achieve an exoskeleton controller which reacts compliantly to external forces, an accurate model of the dynamics of the system is required. In this report, a series of system identification experiments are designed and carried out for the

  9. Performance of an optical identification and interrogation system

    NASA Astrophysics Data System (ADS)

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

    2008-04-01

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

  10. Automatic vehicle identification to support driver information systems

    Microsoft Academic Search

    P. Davies; C. Hill; N. Emmott

    1989-01-01

    The authors describe how research in automatic vehicle identification (AVI) technology can be transferred to practical transportation engineering situations. They focus on the development and implementation, for the Virginia Department of Transportation, of an AVI-based electronic toll collection system known as Fastoll. One of the most promising areas where the Fastoll system could be enhanced relatively easily is through the

  11. Trust and Reliance on an Automated Combat Identification System

    Microsoft Academic Search

    Lu Wang; Greg A. Jamieson; Justin G. Hollands

    2009-01-01

    Objective: We examined the effects of aid reliability and reliability disclosure on human trust in and reliance on a combat identification (CID) aid. We tested whether trust acts as a mediating factor between belief in and reliance on a CID aid. Background: Individual CID systems have been developed to reduce friendly fire incidents. However, these systems cannot positively identify a

  12. ARMA system identification based on second-order cyclostationarity

    Microsoft Academic Search

    Geoffrey Ye Li; Zhi Ding

    1994-01-01

    Previous work has presented novel techniques that exploit cyclostationarity for channel identification in data communication systems. The present authors investigate the identifiability of linear time-invariant (LTI) ARMA systems based on second-order cyclic statistics. They present a parametric and a nonparametric method. The parametric method directly identifies the zeros and poles of ARMA channels with a mixed phase. The nonparametric method

  13. A discrete ARMA model for nonlinear system identification

    Microsoft Academic Search

    SYDNEY R. PARKER; FRANCIS A. PERRY

    1981-01-01

    A nonlinear extension of the discrete linear autoregressive moving average (ARMA) model is presented for the identification of nonlinear systems from measurements of input and output signals. This model is linear In the parameters and is shown to be applicable to a broad class of interconnected inear and memoryless nonlinear subsystems. Conditions for identifiability of nonlinear systems and memory requirements

  14. Reconstructing Chemical Reaction Networks: Data Mining meets System Identification

    E-print Network

    Ramakrishnan, Naren

    Reconstructing Chemical Reaction Networks: Data Mining meets System Identification Yong Ju Cho typically begins with a chemical reaction network (CRN), which is then converted to a set of simul- taneous in any domain where chemical reaction systems form the origins of the underlying numerical model (ODE

  15. PARTY IDENTIFICATION AND SYSTEM LEGITIMACY IN ESTABLISHED AND NEW DEMOCRACIES

    Microsoft Academic Search

    Aida Paskeviciute

    Although students of democratic politics believe that party identification is directly related to the legitimacy of democratic political systems, we know very little about the causal mechanisms underlying this relationship. Drawing on public opinion survey data collected as part of the Comparative Study of Electoral Systems (CSES) along with the Manifestos Research Group (MRG) project data my study examines the

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

    Microsoft Academic Search

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

    1992-01-01

    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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  18. Numerical studies of identification in nonlinear distributed parameter systems

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    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.

  19. YEASTBOOK PERSPECTIVES Yeast: An Experimental Organism

    E-print Network

    Botstein, David

    YEASTBOOK PERSPECTIVES Yeast: An Experimental Organism for 21st Century Biology David Botstein*,1, Cambridge, Massachusetts 02139 ABSTRACT In this essay, we revisit the status of yeast as a model system for biology. We first summarize important contributions of yeast to eukaryotic biology that we anticipated

  20. Yeast: A Research Organism for Teaching Genetics.

    ERIC Educational Resources Information Center

    Manney, Thomas R.; Manney, Monta L.

    1992-01-01

    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)

  1. Failure detection and identification for a reconfigurable flight control system

    NASA Technical Reports Server (NTRS)

    Dallery, Francois

    1987-01-01

    Failure detection and identification logic for a fault-tolerant longitudinal control system were investigated. Aircraft dynamics were based upon the cruise condition for a hypothetical transonic business jet transport configuration. The fault-tolerant control system consists of conventional control and estimation plus a new outer loop containing failure detection, identification, and reconfiguration (FDIR) logic. It is assumed that the additional logic has access to all measurements, as well as to the outputs of the control and estimation logic. The pilot may also command the FDIR logic to perform special tests.

  2. Identification of a human cDNA encoding a protein that is structurally and functionally related to the yeast adenylyl cyclase-associated CAP proteins

    SciTech Connect

    Matviw, Yu, G.; Young, D. (Univ. of Calgary Health Science Centre, Alberta (Canada))

    1992-11-01

    The adenylyl cyclases of both Saccharomyces cerevisiae and Schizosaccharomyces pombe are associated with related proteins named CAP. In S. cerevisiae, CAP is required for cellular responses mediated by the RAS/cyclic AMP pathway. Both yeast CAPs appear to be bifunctional proteins: The N-terminal domains are required for the proper function of adenylyl cyclase, while loss of the C-terminal domains results in morphological and nutritional defects that appear to be unrelated to the cAMP pathways. Expression of either yeast CAP in the heterologous yeast suppresses phenotypes associated with loss of the C-terminal domain of the endogenous CAP but does not suppress loss of the N-terminal domain. On the basis of the homology between the two yeast CAP proteins, we have designed degenerate oligonucleotides that we used to detect, by the polymerase chain reaction method, a human cDNA fragment encoding a CAP-related peptide. Using the polymerase chain reaction fragment as a probe, we isolated a human cDNA clone encoding a 475-amino-acid protein that is homologous to the yeast CAP proteins. Expressions of the human CAP protein in S. cerevisiae suppresses the phenotypes associated with loss of the C-terminal domain of CAP but does not suppress phenotypes associated with loss of the N-terminal domain. Thus, CAP proteins have been structurally and, to some extent, functionally conserved in evolution between yeasts and mammals. 42 refs., 5 figs.

  3. 78 FR 58785 - Unique Device Identification System

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-24

    ...upon the GMDN classification system for this program will foreclose...alternative classification systems in other contexts. Accordingly...competition among classification systems should not be adversely affected...Federal Government, FDA is immune from antitrust...

  4. Mathematical modeling, system identification, and controller design of a two tank system

    Microsoft Academic Search

    J. A. Ramos; P. L. dos Santos

    2007-01-01

    In this paper we present a case study involving mathematical modeling, system identification, and controller design of a two tank fluid level system. The case study is motivated by a realistic application of a two tank problem. We address some fundamental control oriented issues such as physical plant design and identification, transformation from discrete-time to continuous-time, and finally the controller

  5. Investigation of an expert systems approach to bacterial identification.

    PubMed

    Brammer, R J; Bryant, T N; May, J H

    1991-10-01

    An investigation was carried out to assess the feasibility of using an expert systems approach to assist in the identification of unknown isolates of bacteria. A system was developed using Lisp which utilized the knowledge stored in standard bacteriological texts. A comparison of the expert systems approach and the probabilistic approach based on Bayes Theorem was made together with the advantages and disadvantages of each approach. PMID:1747777

  6. On-line identification of interacting two-tank system

    Microsoft Academic Search

    Sea Cheon Oh; Yeong-Koo Yeo

    1996-01-01

    In order to demonstrate the effectiveness of the process identification algorithm, on-line parameter estimator is evaluated\\u000a experimentally by using two-tank system with interaction. On-line parameter estimator used in this paper is based on a recursive\\u000a parameter estimation algorithm. MIMO linear, bilinear and quadratic models based on ARMA model are used to identify two-tank\\u000a system. A quadratic model for two-tank system

  7. A Global-local Approach to Nonlinear System Identification

    Microsoft Academic Search

    Young S. Lee; Alexander Vakakis; D. Michael McFarland; Lawrence Bergman

    \\u000a We present the basic components of a time-domain nonlinear system identification (NSI) method with promise of applicability\\u000a to a broad class of smooth and non-smooth dynamical systems. The proposed NSI method is based on the close correspondence\\u000a between analytical and empirical slow-flow dynamics, and relies on direct analysis of measured time series without any a priori\\u000a assumptions on the system

  8. Animal voice recognition for identification (ID) detection system

    Microsoft Academic Search

    Che Yong Yeo; S. A. R. Al-Haddad; Chee Kyun Ng

    2011-01-01

    Voice recognition systems have become the important applications for speech recognition technology. In this paper, an animal identification (ID) detection system based on animal voice pattern recognition algorithm has been developed. The developed animal voice recognition system uses the zero-cross-rate (ZCR), Mel-Frequency Cepstral Coefficients (MFCC) and Dynamic Time Warping (DTW) joint algorithms as the tools for recognizing the voice of

  9. Linear system identification via backward-time observer models

    Microsoft Academic Search

    Jer-Nan Juang; Minh Q. Phan

    1992-01-01

    Presented here is an algorithm to compute the Markov parameters of a backward-time observer for a backward-time model from experimental input and output data. The backward-time observer Markov parameters are decomposed to obtain the backward-time system Markov parameters (backward-time pulse response samples) for the backward-time system identification. The identified backward-time system Markov parameters are used in the Eigensystem Realization Algorithm

  10. Online identification of a nonlinear mechatronic system

    Microsoft Academic Search

    Bernhard T Angerer; Christian Hintz; Dierk Schröder

    2004-01-01

    In this paper, a method to identify all physically relevant parameters and nonlinear characteristics of a mechatronic system is presented. For this purpose, the a priori known system structure is used. As an example, a nonlinear two-mass system with friction and backlash is identified. This approach is enhanced to identify systems with a partially unknown structure, which will be outlined

  11. WAVELET TRANSFORMS FOR SYSTEM IDENTIFICATION AND ASSOCIATED PROCESSING CONCERNS

    E-print Network

    Kareem, Ahsan

    WAVELET TRANSFORMS FOR SYSTEM IDENTIFICATION AND ASSOCIATED PROCESSING CONCERNS Tracy L. Kijewski1 , Student Member ASCE and Ahsan Kareem2 , Member ASCE ABSTRACT The time-frequency character of wavelet-domain transform, particularly for the popular Morlet wavelet. Unfortunately, in prior applications of wavelet

  12. A Numerical Approach to Genetic Programming for System Identification

    Microsoft Academic Search

    Hitoshi Iba; Hugo De Garis; Taisuke Sato

    1995-01-01

    This paper introduces a new approach to genetic programming (GP), based on a numerical technique, which integrates a GP-based adaptive search of tree structures, and a local parameter tuning mechanism employing statistical search (a system identification technique). In traditional GP, recombination can cause frequent disruption of building blocks or mutation can cause abrupt changes in the semantics. To overcome these

  13. A novel direct sequence spread spectrum automatic vehicle identification system

    Microsoft Academic Search

    Brad Hamant; B. Kamali

    1996-01-01

    Due to a world wide surge in the intelligent vehicle highway system (IVHS), the field of automatic vehicle identification (AVI) has been rapidly growing. The use of spread spectrum communications has not yet pervaded the AVI market. However, in the already cramped electromagnetic environment, spread spectrum techniques have gained significant popularity in many growing areas of wireless communication. AVI is

  14. Bayesian Nonparametric Nonlinear System Identification A quick overview

    E-print Network

    Ghahramani, Zoubin

    , ) In a nonparametric model, we perform inference on the space of functions, not parameters! Data is not condensedBayesian Nonparametric Nonlinear System Identification A quick overview Roger Frigola1 1University distributions to find distributions over predictions p(xt+1 | xt, D) = f (xt+1 | xt, ) p( | D) d 2 of 10 #12;Why

  15. Training Sessions Provide Working Knowledge of National Animal Identification System

    ERIC Educational Resources Information Center

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

    2010-01-01

    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…

  16. A HIERARCHICAL GENETIC SYSTEM FOR SYMBOLIC FUNCTION IDENTIFICATION

    E-print Network

    Wright, Alden H.

    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

  17. Addressing the issue of system identification for space manipulators

    Microsoft Academic Search

    Joy H. Kelly; R. L. Glade; Thomas M. Depkovich

    1992-01-01

    This paper discusses the use of system identification of manipulator dynamics (especially manipulator and payload mass properties) for improvement of manipulator performance. The results presented are based on realistic error bounds on the sensor data. While there are many differences between terrestrial and space robots, one aspect in particular is most important from the standpoint of the development of effective

  18. HYDROMECHANICAL COUPLED FIELD SYSTEM IDENTIFICATION - APPLICATION TO WATER RESERVOIRS

    Microsoft Academic Search

    T. Lahmer

    It is well known that the precision of the output of any model simulation strongly depends on the caliber of the model parameters. The detection of the model parameters requires generally an adaption of the mathematical model output to certain experimental data. This pro- cedure is referred to as parameter or system identification. Due to the fact that the input

  19. Refined Instrumental Variable methods for closed-loop system identification

    E-print Network

    Paris-Sud XI, Université de

    Box-Jenkins (BJ) model, where the plant and the noise models are not constrained to have common the system operates in closed-loop. Several noise models required for the design of optimal prefilters the identification of a linear (ARX) predictor combined with an ARMA noise model in a closed-loop framework

  20. An experimental study of nonlinear dynamic system identification

    Microsoft Academic Search

    Greselda I. Stry; D. Joseph Mook

    1992-01-01

    A technique for robust identification of nonlinear dynamic systems is developed and illustrated using both digital simulations and analog experiments. The technique is based on the Minimum Model Error optimal estimation approach. A detailed literature review is included in which fundamental differences between the current approach and previous work is described. The most significant feature of the current work is

  1. Evaluation of Speaker Identification System using GSMEFR speech Data

    Microsoft Academic Search

    Ahmed KROBBA; Mohamed DEBYECHE; Abederrahmane AMROUCHE

    2010-01-01

    This paper investigate the influence of GSMEFR speech Data on the performance of a text independent Speaker Identification System (SIS) based on Gaussian Mixture Models (GMM) classifiers. The performance evaluation due to the use of the GSMEFR speech Data, obtained by passing the local ARADIGIT database through the GSM coder\\/decoder. The recognition evaluation was also conducted using original ARADIGIT sampled

  2. College students򠰥rceptions of the national animal identification system 

    E-print Network

    Long, Jeanie Marie

    2009-05-15

    The purpose of this study was to determine awareness, knowledge, and perceptions of the National Animal Identification System (NAIS) among college students in the College of Agriculture and Life Sciences at Texas A&M University. Since the issue of a...

  3. Identification problem of Klein-Gordon-Schrödinger quantum system control

    NASA Astrophysics Data System (ADS)

    Wang, Quan-Fang

    2015-02-01

    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.

  4. Unsupervised Regression with applications to Nonlinear System Identification

    E-print Network

    Recht, Ben

    @media.mit.edu Abstract We derive a cost functional for estimating the inverse of the observation function in nonlinear. This is a similar problem to manifold learning, except a generative model and a prior over the latent variablesUnsupervised Regression with applications to Nonlinear System Identification Ali Rahimi Intel

  5. COMPLETE FUNCTIONAL CHARACTERIZATION OF SENSORY NEURONS BY SYSTEM IDENTIFICATION

    Microsoft Academic Search

    Michael C.-K. Wu; Stephen V. David; Jack L. Gallant

    2006-01-01

    System identification is a growing approach to sensory neurophys- iology that facilitates the development of quantitative functional models of sensory processing. This approach provides a clear set of guidelines for combining experimental data with other knowl- edge about sensory function to obtain a description that optimally predicts the way that neurons process sensory information. This pre- diction paradigm provides an

  6. Modeling and System Identification for a DC Servo

    E-print Network

    to use the DC Servo motor SRV02ET that is provided by Quanser. The motor has a transfer function that we. · 1 SRV 02ET servo DC motor. · 1 Analog sensor cable. · 1 To load Cable. · 1 To A/D Cable. · 1 From DModeling and System Identification for a DC Servo Nicanor Quijano and Kevin M. Passino The Ohio

  7. Online weighted LS-SVM for hysteretic structural system identification

    Microsoft Academic Search

    He-Sheng Tang; Song-Tao Xue; Rong Chen; Tadanobu Sato

    2006-01-01

    The identification of structural damage is an important objective of health monitoring for civil infrastructures. Frequently, damage to a structure may be reflected by a change of some system parameters, such as a degradation of the stiffness. In this paper, we propose an online sequential weighted Least Squares Support Vector Machine (LS-SVM) technique to identify the structural parameters and their

  8. MINIMAL CUT SETS IDENTIFICATION OF NUCLEAR SYSTEMS BY EVOLUTIONARY ALGORITHMS

    E-print Network

    Paris-Sud XI, Université de

    issue. In this work, we transform the search of the event sets leading to system failure the combinatorial explosion of failure sets. Then, minimal cut sets (mcs) identification is not a trivial technical Tree (FT) is a tool widely used in Probabilistic Safety Assessment (PSA) of Nuclear Power Plants (NPPs

  9. Migration-based multiobjective genetic programming for nonlinear system identification

    Microsoft Academic Search

    Lavinia Ferariu; Alina Patelli

    2009-01-01

    Nonlinear system identification is addressed by means of genetic programming. For a flexible selection of model structure and parameters, a multiobjective optimization of the tree encoded individuals is carried out, in terms of accuracy and parsimony. The paper suggests a new optimization algorithm based on the evolvement of two quasi-independent subpopulations, which makes use of a flexible migration scheme with

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

    E-print Network

    Thomson, Ty M.

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

  11. 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 ...

  12. Identification of Protective Antigens for Vaccination against Systemic Salmonellosis

    PubMed Central

    Bumann, Dirk

    2014-01-01

    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

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

    SciTech Connect

    Tugendreich, S.; Hieter, P. (Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)); Boguski, M.S. (National Institute of Health, Bethesda, MD (United States)); Seldin, M.S. (Duke Univ. Medical Center, Durham, NC (United States))

    1993-11-15

    The authors 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.

  14. Identification and chemical profiling of monacolins in red yeast rice using high-performance liquid chromatography with photodiode array detector and mass spectrometry.

    PubMed

    Li, Yong-Guo; Zhang, Fang; Wang, Zheng-Tao; Hu, Zhi-Bi

    2004-09-01

    Monascus purpureus-fermented rice (red yeast rice) was one of the food supplements that had the ability of lowering the blood-lipid levels, and monacolins have been proved to be main active constituents. In total 14 monacolin compounds such as monacolin K (mevinolin), J, L, M, X, and their hydroxy acid form, as well as dehydromonacolin K, dihydromonacolin L, compactin, 3alpha-hydroxy-3,5-dihydromonacolin L, etc. were identified in red yeast rice, using high-performance liquid chromatography with photodiode array detector and tandem mass spectrometry. A chemical fingerprint profiling method to display bioactive monacolins in red yeast rice was established and could be used for the quality control of the target material and its related products. Ten finish products labeled as red yeast rice from different manufacturers in marketing were traced using the chromatographic chemical profiling method, and the results show that only two of them were similar while the other eight were significantly different from the reference red yeast rice. All of these materials including raw material powder and finished products available were quantified and the contents of monacolins were calculated with reference of monacolin K (mevinolin) as the standard. PMID:15336357

  15. Screening of hepatocyte proteins binding with C?terminally truncated surface antigen middle protein of hepatitis B virus (MHBst167) by a yeast two?hybrid system.

    PubMed

    Li, Zhi Qun; Linghu, Enqiang; Jun, Wan; Cheng, Jun

    2014-09-01

    The function of middle hepatitis B surface protein C?terminally truncated at amino acid position 167 (MHBst167) is not currently clear. This study aimed to screen and identify the proteins that interact with MHBst167 in hepatocytes using a yeast two?hybrid system, and to explore the effects of MHBst167 in the development of hepatocellular carcinoma and precancerous diseases of the liver. The MHBst167 gene was amplified by polymerase chain reaction (PCR) and cloned into a pGEM?T vector. The target region was sequenced and the constructed bait plasmid, pGBKT7?MHBst167, was transformed into AH109 yeast cells. The transformed AH109 cells were then mated with Y187 yeast cells containing the fetal liver cDNA library plasmid using a yeast two?hybrid system. The false positives were eliminated and the true positive clones were selected by PCR and sequencing analysis. The pGBKT7?MHBst167 bait plasmid was successfully constructed and 66 clones grew in the selective synthetic defined media lacking leucine, tryptophan, histidine and adenine. Fifty?two clones were identified following X???Gal selection and segregation analysis. Seven proteins were found to be expressed that could interact with MHBst167 in hepatocytes by the yeast two?hybrid system. These results have provided novel insights into the biological functions of MHBst167. PMID:24968805

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

    E-print Network

    Bond, Bradley N.

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

  17. 47 CFR 80.275 - Technical Requirements for Class A Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...Class A Automatic Identification System (AIS) equipment. 80.275 Section 80...Class A Automatic Identification System (AIS) equipment. (a) Prior to submitting a certification application for a Class A AIS device, the following information...

  18. 47 CFR 80.275 - Technical Requirements for Class A Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...Class A Automatic Identification System (AIS) equipment. 80.275 Section 80...Class A Automatic Identification System (AIS) equipment. (a) Prior to submitting a certification application for a Class A AIS device, the following information...

  19. 47 CFR 80.275 - Technical Requirements for Class A Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...Class A Automatic Identification System (AIS) equipment. 80.275 Section 80...Class A Automatic Identification System (AIS) equipment. (a) Prior to submitting a certification application for a Class A AIS device, the following information...

  20. 47 CFR 80.275 - Technical Requirements for Class A Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...Class A Automatic Identification System (AIS) equipment. 80.275 Section 80...Class A Automatic Identification System (AIS) equipment. (a) Prior to submitting a certification application for a Class A AIS device, the following information...

  1. 47 CFR 80.275 - Technical Requirements for Class A Automatic Identification System (AIS) equipment.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...Class A Automatic Identification System (AIS) equipment. 80.275 Section 80...Class A Automatic Identification System (AIS) equipment. (a) Prior to submitting a certification application for a Class A AIS device, the following information...

  2. Use of the BioMerieux ID 32C Yeast Identification System for Identification of Aerobic Actinomycetes of Medical Importance

    Microsoft Academic Search

    D. B. MUIR; R. C. PRITCHARD

    1997-01-01

    There has been an increase in the occurrence of aerobic actinomycetes in the clinical laboratory in recent years. Infec- tions due to these organisms have become more prevalent with the use of cytotoxic agents, immunosuppression for organ transplants, and the advent of AIDS. Nocardia species have been most often considered as the agents of infection, but laboratories now need to

  3. Binary system for regulating transgene expression in mice: targeting int-2 gene expression with yeast GAL4/UAS control elements.

    PubMed Central

    Ornitz, D M; Moreadith, R W; Leder, P

    1991-01-01

    We have developed a binary transgenic system that activates an otherwise silent transgene in the progeny of a simple genetic cross. The system consists of two types of transgenic mouse strains, targets and transactivators. A target strain bears a transgene controlled by yeast regulatory sequences (UAS) that respond only to the yeast transcriptional activator GAL4. A transactivator strain expresses an active GAL4 gene that can be driven by any selected promoter. The current paradigm uses the murine growth factor int-2 cDNA as the target gene and the GAL4 gene driven by the mouse mammary tumor virus long terminal repeat as the transactivator. Both target and transactivator strains are phenotypically normal. By contrast, the bigenic offspring of these two strains express high levels of the target int-2 gene in each organ expressing the GAL4 transactivator. They also display a characteristic dominant int-2 phenotype that consists of epithelial hyperplasia in mammary and salivary glands, as well as prostatic and epididymal hypertrophy, which results in male sterility. Images PMID:1846961

  4. Efficient gene disruption in the high-ploidy yeast Candida utilis using the Cre-loxP system.

    PubMed

    Ikushima, Shigehito; Fujii, Toshio; Kobayashi, Osamu

    2009-04-23

    In order to take full advantage of the industrially important yeast Candida utilis, we developed a practical recombinant DNA tool for multiple gene disruption in C. utilis based on the Cre-loxP system, which makes possible the reuse of selection markers. For this purpose, two plasmids were constructed: one harbored a heterologous loxP-flanked selection marker cassette carrying the gene responsible for hygromycin B-resistance, and the other had an autonomous replication sequence (ARS) and a Cre-recombinase expression module. Multiple disruption of C. utilis NBRC0988 URA3 genes (CuURA3), encoding orotidine-5'-phosphate decarboxylase, validated the efficiency of the system. The fourth round of deletion yielded a null mutant, i.e., a uracil auxotroph, giving some support to the possibility that C. utilis NBRC0988 is a tetraploid. This agreed very well with the outcomes of FACS analysis, which showed that various strains of this yeast contained 3-5 times more DNA than a Saccharomyces cerevisiae haploid. PMID:19352042

  5. Identification of Clostridium difficile using the API ZYM system

    Microsoft Academic Search

    P. N. Levett

    1985-01-01

    The use of the API ZYM system for the identification ofClostridium difficile was investigated. The enzyme profiles generated by this system readily distinguished strains ofClostridium difficile from other clostridia commonly isolated from faeces. Enzyme activity ofClostridium difficile was influenced by the composition of the culture medium but appeared to be independent of the age of the culture. Given careful standardisation

  6. Identification of linear parameter-varying systems via LFTs

    Microsoft Academic Search

    Lawton H. Lee; Kameshwar Poolla

    1996-01-01

    This paper considers the identification of linear parameter-varying (LPV) systems having linear-fractional parameter dependence. We present a natural prediction error method, using gradient- and Hessian-based nonlinear optimization algorithms to minimize the cost function. Computing the gradients and (approximate) Hessians is shown to reduce to simulating LPV systems and computing inner products. Issues relating to initialization and identifiability are discussed. The

  7. Toward Automated Anomaly Identification in Large-Scale Systems

    Microsoft Academic Search

    Zhiling Lan; Ziming Zheng; Yawei Li

    2010-01-01

    When a system fails to function properly, health-related data are collected for troubleshooting. However, it is challenging to effectively identify anomalies from the voluminous amount of noisy, high-dimensional data. The traditional manual approach is time-consuming, error-prone, and even worse, not scalable. In this paper, we present an automated mechanism for node-level anomaly identification in large-scale systems. A set of techniques

  8. Identification of nonminimum phase systems using higher order statistics

    Microsoft Academic Search

    G. B. Giannakis; J. M. Mendel

    1989-01-01

    A method is presented for identification of linear, time-variant, nonminimum phase systems when only output data are available. The input sequence need not be independent, but it must be non-Gaussian, with some special properties described in the test. The authors model a finite-dimensional system as an ARMA (autoregressive moving-average) rational function of known orders, but the special cases of AR,

  9. Identification of nonlinear biological systems using laguerre expansions of kernels

    Microsoft Academic Search

    Vasilis Z. Marmarelis

    1993-01-01

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

  10. Non-linear system identification using neural networks

    Microsoft Academic Search

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

    1990-01-01

    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

  11. ARMA bispectrum approach to nonminimum phase system identification

    Microsoft Academic Search

    C. L. Nikias

    1988-01-01

    An identification procedure is proposed for a nonGaussian white-noise-driven, linear, time-invariant, nonminimum-phase FIR (finite-impulse response) system. The method is based on parametric modeling of the third moments of the output sequence and uses causal and anticausal autoregressive moving-average (ARMA) models. The magnitude and phase response of the system are expressed in terms of the AR parameters of the ARMA models.

  12. Computer assisted voice identification system (CAVIS)

    Microsoft Academic Search

    H. Nakasone; C. Melvin

    1988-01-01

    The major goal of the CAVIS project is to develop a system that is capable of dealing with transmission-independent and text-independent voice data, as well as rendering objective decisions. The need for such a system for law enforcement is discussed. The project's approach to handling different types of voice data, signal conditioning for cross channel frequency distortion, statistical processing for

  13. Towards Biological System Identification: Fast and Accurate Estimates of Parameters in Genetic Regulatory Networks

    E-print Network

    Murray, Richard M.

    Towards Biological System Identification: Fast and Accurate Estimates of Parameters in Genetic as an example of a class of interesting biological system identification problems. We compare the performance for parameter estimation. Some challenges that are unique to biological system identification problems

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

    E-print Network

    Paris-Sud XI, Université de

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

  15. Pharmacology of GPR55 in yeast and identification of GSK494581A as a mixed-activity glycine transporter subtype 1 inhibitor and GPR55 agonist.

    PubMed

    Brown, Andrew J; Daniels, Dion A; Kassim, Mumta; Brown, Sue; Haslam, Carl P; Terrell, Victoria R; Brown, Jason; Nichols, Paula L; Staton, Penny C; Wise, Alan; Dowell, Simon J

    2011-04-01

    GPR55 is a G protein-coupled receptor activated by L-?-lysophosphatidylinositol and suggested to have roles in pain signaling, bone morphogenesis, and possibly in vascular endothelial cells. It has affinity for certain cannabinoids (molecules that interact with the cannabinoid CB(1) and CB(2) receptors), but investigation of its functional role in cell-based systems and in tissue has been limited by a lack of selective pharmacological tools. Here, we present our characterization of GPR55 in the yeast Saccharomyces cerevisiae and in human embryonic kidney (HEK293) cells. We describe GSK494581A (1-{2-fluoro-4-[1-(methyloxy)ethyl]phenyl}-4-{[4'-fluoro-4-(methylsulfonyl)-2-biphenylyl]carbonyl}piperazine), a selective small-molecule ligand of GPR55 identified through diversity screening. GSK494581A is one of a series of benzoylpiperazines originally identified and patented as inhibitors of the glycine transporter subtype 1 (GlyT1). The structure-activity relationship between GPR55 and GlyT1 is divergent across this series. The most GPR55-selective example is GSK575594A (3-fluoro-4-(4-{[4'-fluoro-4-(methylsulfonyl)-2-biphenylyl]carbonyl}-1-piperazinyl)aniline), which is approximately 60-fold selective for GPR55 (pEC(50) = 6.8) over GlyT1 (pIC(50) = 5.0). Several exemplars with activity at GPR55 and GlyT1 have been profiled at a broad range of other molecular targets and are inactive at cannabinoid receptors and all other targets tested. The benzoylpiperazine agonists activate human GPR55 but not rodent GPR55, suggesting that the relatively low level of sequence identity between these orthologs (75%) translates to important functional differences in the ligand-binding site. PMID:21233197

  16. Asymptotic inference in system identification for the atom maser

    E-print Network

    Catalin Catana; Merlijn van Horssen; Madalin Guta

    2011-12-09

    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.

  17. 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 ...

  18. Neural network identification of power system transfer functions

    SciTech Connect

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

    1996-03-01

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

  19. On-orbit system identification using active members

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

    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.

  20. Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters

    Microsoft Academic Search

    Chuhu Yang; Eugene Bolotin; Tao Jiang; Frances M. Sladek; Ernest Martinez

    2007-01-01

    The core promoter of eukaryotic genes is the minimal DNA region that recruits the basal transcription machinery to direct efficient and accurate transcription initiation. The fraction of human and yeast genes that contain specific core promoter elements such as the TATA box and the initiator (INR) remains unclear and core promoter motifs specific for TATA-less genes remain to be identified.

  1. 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 ...

  2. 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...

  3. Identification of Novel Host Factors via Conserved Domain Search: Cns1 Cochaperone Is a Novel Restriction Factor of Tombusvirus Replication in Yeast

    PubMed Central

    Lin, Jing-Yi

    2013-01-01

    A large number of host-encoded proteins affect the replication of plus-stranded RNA viruses by acting as susceptibility factors. Many other cellular proteins are known to function as restriction factors of viral infections. Previous studies with tomato bushy stunt tombusvirus (TBSV) in a yeast model host have revealed the inhibitory function of TPR (tetratricopeptide repeat) domain-containing cyclophilins, which are members of the large family of host prolyl isomerases, in TBSV replication. In this paper, we tested additional TPR-containing yeast proteins in a cell-free TBSV replication assay and identified the Cns1p cochaperone for heat shock protein 70 (Hsp70) and Hsp90 chaperones as a strong inhibitor of TBSV replication. Cns1p interacted with the viral replication proteins and inhibited the assembly of the viral replicase complex and viral RNA synthesis in vitro. Overexpression of Cns1p inhibited TBSV replication in yeast. The use of a temperature-sensitive (TS) mutant of Cns1p in yeast revealed that at a semipermissive temperature, TS Cns1p could not inhibit TBSV replication. Interestingly, Cns1p and the TPR-containing Cpr7p cyclophilin have similar inhibitory functions during TBSV replication, although some of the details of their viral restriction mechanisms are different. Our observations indicate that TPR-containing cellular proteins could act as virus restriction factors. PMID:24027337

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

    DOEpatents

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

    2011-02-01

    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.

  5. Generalized Sensitivity Functions in Physiological System Identification

    Microsoft Academic Search

    Karl Thomaseth; Claudio Cobelli

    1999-01-01

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

  6. A computer-assisted cell identification system.

    PubMed

    Peet, F G; Sahota, T S

    1984-03-01

    A computer and optical microscope image processing system for the acquisition, editing and analysis of quantitative, multivariate, cell nuclear data is described. The experimental equipment and methods are discussed, the mathematics used are presented, and the additions, modifications and deletions to the TICAS 11/45 set of computer programs for the analysis of the data are outlined. PMID:6375496

  7. Development of pilot scale nanofiltration system for yeast industry wastewater treatment.

    PubMed

    Rahimpour, Ahmad; Jahanshahi, Mohsen; Peyravi, Majid

    2014-01-01

    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

  8. Development of pilot scale nanofiltration system for yeast industry wastewater treatment

    PubMed Central

    2014-01-01

    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

  9. Parametric Identification of Nonlinear Dynamical Systems

    NASA Technical Reports Server (NTRS)

    Feeny, Brian

    2002-01-01

    In this project, we looked at the application of harmonic balancing as a tool for identifying parameters (HBID) in a nonlinear dynamical systems with chaotic responses. The main idea is to balance the harmonics of periodic orbits extracted from measurements of each coordinate during a chaotic response. The periodic orbits are taken to be approximate solutions to the differential equations that model the system, the form of the differential equations being known, but with unknown parameters to be identified. Below we summarize the main points addressed in this work. The details of the work are attached as drafts of papers, and a thesis, in the appendix. Our study involved the following three parts: (1) Application of the harmonic balance to a simulation case in which the differential equation model has known form for its nonlinear terms, in contrast to a differential equation model which has either power series or interpolating functions to represent the nonlinear terms. We chose a pendulum, which has sinusoidal nonlinearities; (2) Application of the harmonic balance to an experimental system with known nonlinear forms. We chose a double pendulum, for which chaotic response were easily generated. Thus we confronted a two-degree-of-freedom system, which brought forth challenging issues; (3) A study of alternative reconstruction methods. The reconstruction of the phase space is necessary for the extraction of periodic orbits from the chaotic responses, which is needed in this work. Also, characterization of a nonlinear system is done in the reconstructed phase space. Such characterizations are needed to compare models with experiments. Finally, some nonlinear prediction methods can be applied in the reconstructed phase space. We developed two reconstruction methods that may be considered if the common method (method of delays) is not applicable.

  10. Applications of nonlinear system identification to structural health monitoring.

    SciTech Connect

    Farrar, C. R. (Charles R.); Sohn, H. (Hoon); Robertson, A. N. (Amy N.)

    2004-01-01

    The process of implementing a damage detection strategy for aerospace, civil and mechanical engineering infrastructure is referred to as structural health monitoring (SHM). In many cases damage causes a structure that initially behaves in a predominantly linear manner to exhibit nonlinear response when subject to its operating environment. The formation of cracks that subsequently open and close under operating loads is an example of such damage. The damage detection process can be significantly enhanced if one takes advantage of these nonlinear effects when extracting damage-sensitive features from measured data. This paper will provide an overview of nonlinear system identification techniques that are used for the feature extraction process. Specifically, three general approaches that apply nonlinear system identification techniques to the damage detection process are discussed. The first two approaches attempt to quantify the deviation of the system from its initial linear characteristics that is a direct result of damage. The third approach is to extract features from the data that are directly related to the specific nonlinearity associated with the damaged condition. To conclude this discussion, a summary of outstanding issues associated with the application of nonlinear system identification techniques to the SHM problem is presented.

  11. Frequency domain state-space system identification

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

    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.

  12. Continuous-Time System Identification of a Smoking Cessation Intervention.

    PubMed

    Timms, Kevin P; Rivera, Daniel E; Collins, Linda M; Piper, Megan E

    2014-01-01

    Cigarette smoking is a major global public health issue and the leading cause of preventable death in the United States. Toward a goal of designing better smoking cessation treatments, system identification techniques are applied to intervention data to describe smoking cessation as a process of behavior change. System identification problems that draw from two modeling paradigms in quantitative psychology (statistical mediation and self-regulation) are considered, consisting of a series of continuous-time estimation problems. A continuous-time dynamic modeling approach is employed to describe the response of craving and smoking rates during a quit attempt, as captured in data from a smoking cessation clinical trial. The use of continuous-time models provide benefits of parsimony, ease of interpretation, and the opportunity to work with uneven or missing data. PMID:25382865

  13. Genome and transcriptome analysis of the food-yeast Candida utilis.

    PubMed

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

    2012-01-01

    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

  14. Identification of linear stochastic systems through projection filters

    NASA Technical Reports Server (NTRS)

    Chen, Chung-Wen; Huang, Jen-Kuang; Juang, Jer-Nan

    1992-01-01

    A novel method is presented for identifying a state-space model and a state estimator for linear stochastic systems from input and output data. The method is primarily based on the relationship between the state-space model and the finite-difference model of linear stochastic systems derived through projection filters. It is proved that least-squares identification of a finite difference model converges to the model derived from the projection filters. System pulse response samples are computed from the coefficients of the finite difference model.

  15. Advanced terahertz imaging system performance model for concealed weapon identification

    Microsoft Academic Search

    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

    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,

  16. Terahertz imaging system performance model for concealed weapon identification

    Microsoft Academic Search

    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

    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

  17. Terahertz imaging system performance model for concealed-weapon identification

    Microsoft Academic Search

    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

    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.

  18. The HDA+ data set for research on fully automated re-identification systems

    E-print Network

    Instituto de Sistemas e Robotica

    The HDA+ data set for research on fully automated re-identification systems Dario Figueira, Matteo - Lisbon Abstract. There are no available datasets to evaluate integrated Pedes- trian Detectors and Re-Identification systems, and the standard evalu- ation metric for Re-Identification (Cumulative Matching Characteristic

  19. System Identification of Mistuned Bladed Disks from Traveling Wave Response Measurements

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

    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.

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

    PubMed Central

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

    2010-01-01

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

  1. Material Outgassing, Identification and Deposition, MOLIDEP System

    NASA Technical Reports Server (NTRS)

    Scialdone, John J.; Montoya, Alex F.

    2002-01-01

    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.

  2. Prefire identification for pulse power systems

    DOEpatents

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

    1985-01-01

    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.

  3. Prefire identification for pulse-power systems

    DOEpatents

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

    1982-08-23

    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.

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

    E-print Network

    Gailey, Glenn Andrew

    2001-01-01

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

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

    PubMed

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

    2004-06-01

    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

  6. Malassezia Baillon, emerging clinical yeasts.

    PubMed

    Batra, Roma; Boekhout, Teun; Guého, Eveline; Cabańes, F Javier; Dawson, Thomas L; Gupta, Aditya K

    2005-12-01

    The human and animal pathogenic yeast genus Malassezia has received considerable attention in recent years from dermatologists, other clinicians, veterinarians and mycologists. Some points highlighted in this review include recent advances in the technological developments related to detection, identification, and classification of Malassezia species. The clinical association of Malassezia species with a number of mammalian dermatological diseases including dandruff, seborrhoeic dermatitis, pityriasis versicolor, psoriasis, folliculitis and otitis is also discussed. PMID:16084129

  7. Measurement-based Coherency Identification and Aggregation for Power Systems

    SciTech Connect

    Wang, Shaobu; Lu, Shuai; Lin, Guang; Zhou, Ning

    2012-07-26

    In power system model reduction, a high reduction ratio is often desired to handle much more complex power systems. The bottleneck of traditional methods lies in: ? Coherency identification methods are conservative. Some coherency generators are not detected when system topology or operating points change, because coherency identification depends on system topology or operating points. ?There are some solitary generators in external systems. These generators do not belong to any coherency group. However, sometimes these solitary generators have little impact on tie-line power flow, and it might be possible to ignore their dynamics in model reduction. But because they do not belong to any coherency group, existing reduction methods cannot handle them well. In order to overcome the first problem, a measurement-based online coherency identification method is presented in this paper. By analyzing post-fault trajectories measured by Phasor Measurement Units (PMUs), coherency generators are identified through principal component analysis. The method can track time-varying system topology and operating points. In order to address the second problem, this paper introduces sensitivity analysis into traditional reduction methods. The sensitivity of tie-line power flow against injected active power of external system generators is derived. Those generators having loose connection with tie-line power are identified through the sensitivity analysis, and their dynamics are ignored by replacing them with negative impedances. We test if the sensitivity, based on static power flow, provides good guidance to reduce the dynamic model. Case studies show that the proposed method can handle well these solitary generators and the reduction ratio can be enhanced through this method. Future work will include generalization of the sensitivity method.

  8. Nonlinear Identification of NMR Spin Systems by Adaptive Filtering

    NASA Astrophysics Data System (ADS)

    Asfour, Aktham; Raoof, Kosai; Fournier, Jean-Marc

    2000-07-01

    In this paper, we present two new methods for identifying NMR spin systems. These methods are based on nonlinear adaptive filtering. The spin system is assumed to be time-invariant with memory. The first method uses a truncated discrete Volterra series to describe the nonlinear relationship between excitation (input) and system response (output). First-, second-, and third-order kernels of this series are estimated employing the least mean square (LMS) algorithm. Three parallel filters can then model the NMR spin system so that its output is no more than simple sum of three convolution products between combinations of the input signal and filters coefficients. It is also shown that the contribution of the Volterra second-order term to the total system response is neglected compared with the contributions of the first- and the third-order terms. In the second identification method, the output signal is related to the input signal through a recursive nonlinear difference equation with constant coefficients. The LMS algorithm is used again to estimate the equation coefficients. The two methods are validated with a simulated NMR system model based on Bloch equations. The results and the performances of these methods are analyzed and compared. It is shown that our methods permit a simple identification of NMR spin systems. The field of applications of this study is promising in the optimization of NMR signal detection, especially in the cases of low signal-to-noise ratios where optimum signal filtering and analysis must be performed.

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

    PubMed Central

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

    2011-01-01

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

  10. Effect of COD level and HRT on microbial community in a yeast-predominant activated sludge system.

    PubMed

    Han, Hui; Zhang, Yanyan; Cui, Cancan; Zheng, Shaokui

    2010-05-01

    This study was conducted to compare the effect of influent chemical oxygen demand (COD(in)) level and hydraulic retention time (HRT), two primary components of influent COD loading rate (COD(LR)), on the structure and function of sludge microbial community in a yeast-predominant activated sludge system (1m Hx0.2m D) for synthetic industrial wastewater. A combination of polymerase chain reaction-denaturing gradient gel electrophoresis with BIOLOG community-level physiological profiles was used. At higher COD(LR) and higher COD(in) and identical HRTs, more microbial species were supported and could metabolise a greater variety of carbon sources in the aerated column. Conversely, a shorter HRT at identical COD(in) supported fewer microbial species, which resulted in the metabolism of fewer carbon sources. PMID:20096563

  11. NONLINEAR MODEL EVALUATION VIA SYSTEM IDENTIFICATION OF A MOORED STRUCTURAL SYSTEM

    E-print Network

    Yim, Solomon C.

    NONLINEAR MODEL EVALUATION VIA SYSTEM IDENTIFICATION OF A MOORED STRUCTURAL SYSTEM S. Narayanan1 in various compliant ocean systems characterized by nonlinear mooring restoring force and coupled fluid-structure interaction exciting force. The design of these systems, with inherent high degree of nonlinear dynamics

  12. Identification and chemical profiling of monacolins in red yeast rice using high-performance liquid chromatography with photodiode array detector and mass spectrometry

    Microsoft Academic Search

    Yong-guo Li; Fang Zhang; Zheng-tao Wang; Zhi-bi Hu

    2004-01-01

    Monascus purpureus-fermented rice (red yeast rice) was one of the food supplements that had the ability of lowering the blood-lipid levels, and monacolins have been proved to be main active constituents. In total 14 monacolin compounds such as monacolin K (mevinolin), J, L, M, X, and their hydroxy acid form, as well as dehydromonacolin K, dihydromonacolin L, compactin, 3?-hydroxy-3,5-dihydromonacolin L,

  13. Identification and Analysis of National Airspace System Resource Constraints

    NASA Technical Reports Server (NTRS)

    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

    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.

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

    PubMed Central

    Phang, James M.

    2008-01-01

    St. John’s Wort (SJW; Hypericum perforatum L.) is commonly known for its antidepressant properties and was traditionally used to promote wound healing, but its molecular mechanism of action is not known. Here, chemical-genetic profiling in yeast was used to predict the human intracellular targets of an aqueous extract of SJW. SJW source material was authenticated by TLC, digital microscopy, and HPLC, and further characterized by colorimetric methods for antioxidant activity, protein content, and total soluble phenolic content. SJW extract contained 1.76µg/mL hyperforin, 10.14µg/mL hypericin, and 46.05µg/mL pseudohypericin. The effect of SJW extract on ~5900 barcoded heterozygous diploid deletion strains of Saccharomyces cerevisiae was investigated using high-density oligonucleotide microarrays. Seventy-eight (78) yeast genes were identified as sensitive to SJW and were primarily associated with vesicle-mediated transport and signal transduction pathways. Potential human intracellular targets were identified using sequence-based comparisons and included proteins associated with neurological disease and angiogenesis-related pathways. Selected human targets were confirmed by cell-based immunocytochemical assays. The comprehensive and systematic nature of chemical-genetic profiling in yeast makes this technique attractive for elucidating the potential molecular mechanisms of action of botanical medicines and other bioactive dietary plants. PMID:18975972

  15. An approximation theory for the identification of linear thermoelastic systems

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

    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.

  16. Sensor network based vehicle classification and license plate identification system

    SciTech Connect

    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

    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.

  17. Linear system identification via backward-time observer models

    NASA Technical Reports Server (NTRS)

    Juang, Jer-Nan; Phan, Minh Q.

    1992-01-01

    Presented here is an algorithm to compute the Markov parameters of a backward-time observer for a backward-time model from experimental input and output data. The backward-time observer Markov parameters are decomposed to obtain the backward-time system Markov parameters (backward-time pulse response samples) for the backward-time system identification. The identified backward-time system Markov parameters are used in the Eigensystem Realization Algorithm to identify a backward-time state-space model, which can be easily converted to the usual forward-time representation. If one reverses time in the model to be identified, what were damped true system modes become modes with negative damping, growing as the reversed time increases. On the other hand, the noise modes in the identification still maintain the property that they are stable. The shift from positive damping to negative damping of the true system modes allows one to distinguish these modes from noise modes. Experimental results are given to illustrate when and to what extent this concept works.

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

    PubMed Central

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

    2013-01-01

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

  19. A novel ascosporogenous yeast species, Zygosaccharomyces siamensis , and the sugar tolerant yeasts associated with raw honey collected in Thailand

    Microsoft Academic Search

    Sujinan Saksinchai; Motofumi Suzuki; Panuwan Chantawannakul; Moriya Ohkuma; Saisamorn Lumyong

    Diversity of yeasts in association with bees and their food sources has been explored during the last decade. In Thailand,\\u000a there has been no study of yeast identification in honey and bees. Hence, a total of 186 yeast strains were isolated from\\u000a 37 honey samples of 12 different bee species. On the basis of morphological and physiological characteristics, 55 representative

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

    PubMed Central

    Volkov, Vadim

    2015-01-01

    Modeling of ion transport via plasma membrane needs identification and quantitative understanding of the involved processes. Brief characterization of main ion transport systems of a yeast cell (Pma1, Ena1, TOK1, Nha1, Trk1, Trk2, non-selective cation conductance) and determining the exact number of molecules of each transporter per a typical cell allow us to predict the corresponding ion flows. In this review a comparison of ion transport in small yeast cell and several animal cell types is provided. The importance of cell volume to surface ratio is emphasized. The role of cell wall and lipid rafts is discussed in respect to 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.

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

    E-print Network

    Volkov, Vadim

    2012-01-01

    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.

  2. Terahertz imaging system performance model for concealed-weapon identification.

    PubMed

    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

    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

  3. Terahertz imaging system performance model for concealed weapon identification

    NASA Astrophysics Data System (ADS)

    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

    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.

  4. Terahertz imaging system performance model for concealed-weapon identification

    NASA Astrophysics Data System (ADS)

    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

    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.

  5. Modeling and identification of continuous-time system for RF amplifiers

    E-print Network

    Boyer, Edmond

    Modeling and identification of continuous-time system for RF amplifiers Mourad Djamai 1 , Smail present a new identification proce- dure for radio frequency Power Amplifier (PA) in the presence signals in time domain. I. INTRODUCTION Numerous approaches in Power Amplifier identification area have

  6. The CLEAR'07 LIMSI System for Acoustic Speaker Identification in Seminars

    E-print Network

    The CLEAR'07 LIMSI System for Acoustic Speaker Identification in Seminars Claude Barras, Xuan Zhu the LIMSI participation in the CLEAR 2007 acoustic speaker identification task that aims to identify acoustic speaker identi- fication task is a text-independent, closed-set identification task with far

  7. Hierarchical gradient-based identification of multivariable discrete-time systems

    Microsoft Academic Search

    Feng Ding; Tongwen Chen

    2005-01-01

    Abstract In this paper, we use a hierarchical identification principle to study identification problems for multivariable discrete-time systems. We propose a hierarchical gradient iterative algorithm and a hierarchical stochastic gradient algorithm and prove that the parameter estimation errors given by the algorithms converge to zero for any initial values under persistent excitation. The proposed,algorithms can be applied to identification of

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

    PubMed

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

    2009-06-01

    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

  9. Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast.

    PubMed

    Kainth, Pinay; Sassi, Holly Elizabeth; Peńa-Castillo, Lourdes; Chua, Gordon; Hughes, Timothy R; Andrews, Brenda

    2009-07-01

    The development and application of genomic reagents and techniques has fuelled progress in our understanding of regulatory networks that control gene expression in eukaryotic cells. However, a full description of the network of regulator-gene interactions that determine global gene expression programs remains elusive and will require systematic genetic as well as biochemical assays. Here, we describe a functional genomics approach that combines reporter technology, genome-wide array-based reagents and high-throughput imaging to discover new regulators controlling gene expression patterns in Saccharomyces cerevisiae. Our strategy utilizes the synthetic genetic array (SGA) method to systematically introduce promoter-GFP (green fluorescent protein) reporter constructs along with a control promoter-RFP (red fluorescent protein) gene into the array of approximately 4500 viable yeast deletion mutants. Fluorescence intensities from each reporter are assayed from individual colonies arrayed on solid agar plates using a scanning fluorimager and the ratio of GFP to RFP intensity reveals deletion mutants that cause differential GFP expression. We are exploiting this screening approach to construct a detailed map describing the interplay of regulators controlling the eukaryotic cell cycle. The method is extensible to any transcription factor or signalling pathway for which an appropriate reporter gene can be devised. PMID:19269327

  10. Indirect Identification of Linear Stochastic Systems with Known Feedback Dynamics

    NASA Technical Reports Server (NTRS)

    Huang, Jen-Kuang; Hsiao, Min-Hung; Cox, David E.

    1996-01-01

    An algorithm is presented for identifying a state-space model of linear stochastic systems operating under known feedback controller. In this algorithm, only the reference input and output of closed-loop data are required. No feedback signal needs to be recorded. The overall closed-loop system dynamics is first identified. Then a recursive formulation is derived to compute the open-loop plant dynamics from the identified closed-loop system dynamics and known feedback controller dynamics. The controller can be a dynamic or constant-gain full-state feedback controller. Numerical simulations and test data of a highly unstable large-gap magnetic suspension system are presented to demonstrate the feasibility of this indirect identification method.

  11. YEAST GENETICS Fred Winston

    E-print Network

    Winston, Fred

    YEAST GENETICS Fred Winston 7.1 Introduction Key Concepts · Genetic studies of the yeast. The yeast Saccharomyces cerevisiae is an ideal experimental organism. It is a microorganism that has a fast biology. Yeast has been the focus of extensive studies in many aspects of molecular biology. These areas

  12. Genital Yeast Infections

    Microsoft Academic Search

    J. D. Oriel; Betty M. Partridge; Maire J. Denny; J. C. Coleman

    1972-01-01

    Genital yeast infection was studied in 533 women seen in a department of venereology. Yeasts were recovered in culture from 138 patients (26% of the total). Candida albicans accounted for 112 (81%) of the isolates and Torulopsis glabrata for 22 (16%); other yeasts were uncommon. There was no evidence that the presence of yeasts was related to age. 32% of

  13. Translational comparison of HPV58 long and short L1 mRNAs in yeast ( Saccharomyces cerevisiae) cell-free system

    Microsoft Academic Search

    Xiao Wang; Juan Liu; Wei Ming Zhao; Kong-Nan Zhao

    2010-01-01

    Recently, we developed a yeast cell-free system for translation of human papillomavirus (HPV) 58 short L1 mRNA and VLP assembly in vitro. In the present study, we examined the translation efficiency of HPV58 long and short L1 mRNAs in our established system. Production of HPV 58 long and short L1 proteins was significantly dependent on the amounts of the L1

  14. Explosives identification model in reflection mode for THz security system

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

    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.

  15. Nonlinear damage identification of breathing cracks in Truss system

    NASA Astrophysics Data System (ADS)

    Zhao, Jie; DeSmidt, Hans

    2014-03-01

    The breathing cracks in truss system are detected by Frequency Response Function (FRF) based damage identification method. This method utilizes damage-induced changes of frequency response functions to estimate the severity and location of structural damage. This approach enables the possibility of arbitrary interrogation frequency and multiple inputs/outputs which greatly enrich the dataset for damage identification. The dynamical model of truss system is built using the finite element method and the crack model is based on fracture mechanics. Since the crack is driven by tensional and compressive forces of truss member, only one damage parameter is needed to represent the stiffness reduction of each truss member. Assuming that the crack constantly breathes with the exciting frequency, the linear damage detection algorithm is developed in frequency/time domain using Least Square and Newton Raphson methods. Then, the dynamic response of the truss system with breathing cracks is simulated in the time domain and meanwhile the crack breathing status for each member is determined by the feedback from real-time displacements of member's nodes. Harmonic Fourier Coefficients (HFCs) of dynamical response are computed by processing the data through convolution and moving average filters. Finally, the results show the effectiveness of linear damage detection algorithm in identifying the nonlinear breathing cracks using different combinations of HFCs and sensors.

  16. Studying Functions of All Yeast Genes Simultaneously

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

    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.

  17. Parametric identification of a vibratory system with a clearance

    NASA Technical Reports Server (NTRS)

    Alexander, R. M.; Noah, S. T.; Franck, C. G.

    1993-01-01

    An analytical and experimental investigation of a vibratory system with a clearance was conducted. A finite element model and an equivalent single-degree-of-freedom closed-form solution were used to determine the dynamic parameters and response of an experimental structure interacting with a gap. The closed-form solution is obtained by taking advantage of the piecewise linearity of the system. Results from these solution methods are in agreement with experimental data. The results also suggest that the closed-form solution approximates the response of the experimental structure with accuracy greater than that of the finite element model. The closed-form solution was also used to determine the gap size of the structure. The parameter identification procedure utilized in this study appears to be simple to use and can be readily extended to other types of piecewise-linear multi-degree-of-freedom systems.

  18. A Gamma Memory Neural Network for System Identification

    NASA Technical Reports Server (NTRS)

    Motter, Mark A.; Principe, Jose C.

    1992-01-01

    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.

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

    PubMed Central

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

    2000-01-01

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

  20. Advanced Techniques for Power System Identification from Measured Data

    SciTech Connect

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

    2008-11-25

    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

  1. Nonlinear System Identification for Aeroelastic Systems with Application to Experimental Data

    NASA Technical Reports Server (NTRS)

    Kukreja, Sunil L.

    2008-01-01

    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.

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

    NASA Technical Reports Server (NTRS)

    Kukreja, Sunil L.

    2008-01-01

    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.

  3. Functional adaptation between yeast actin and its cognate myosin motors.

    PubMed

    Stark, Benjamin C; Wen, Kuo-Kuang; Allingham, John S; Rubenstein, Peter A; Lord, Matthew

    2011-09-01

    We employed budding yeast and skeletal muscle actin to examine the contribution of the actin isoform to myosin motor function. While yeast and muscle actin are highly homologous, they exhibit different charge density at their N termini (a proposed myosin-binding interface). Muscle myosin-II actin-activated ATPase activity is significantly higher with muscle versus yeast actin. Whether this reflects inefficiency in the ability of yeast actin to activate myosin is not known. Here we optimized the isolation of two yeast myosins to assess actin function in a homogenous system. Yeast myosin-II (Myo1p) and myosin-V (Myo2p) accommodate the reduced N-terminal charge density of yeast actin, showing greater activity with yeast over muscle actin. Increasing the number of negative charges at the N terminus of yeast actin from two to four (as in muscle) had little effect on yeast myosin activity, while other substitutions of charged residues at the myosin interface of yeast actin reduced activity. Thus, yeast actin functions most effectively with its native myosins, which in part relies on associations mediated by its outer domain. Compared with yeast myosin-II and myosin-V, muscle myosin-II activity was very sensitive to salt. Collectively, our findings suggest differing degrees of reliance on electrostatic interactions during weak actomyosin binding in yeast versus muscle. Our study also highlights the importance of native actin isoforms when considering the function of myosins. PMID:21757693

  4. Unscented Kalman filtering for wave energy converters system identification

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  5. A Frequency-Domain Substructure System Identification Algorithm

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

    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.

  6. Detection of Bacterial and Yeast Species with the Bactec 9120 Automated System with Routine Use of Aerobic, Anaerobic, and Fungal Media?

    PubMed Central

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

    2008-01-01

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

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

    PubMed Central

    Korber, Philipp; Barbaric, Slobodan

    2014-01-01

    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

  8. Frataxin depletion in yeast triggers up-regulation of iron transport systems before affecting iron-sulfur enzyme activities.

    PubMed

    Moreno-Cermeńo, Armando; Obis, Elia; Bellí, Gemma; Cabiscol, Elisa; Ros, Joaquim; Tamarit, Jordi

    2010-12-31

    The primary function of frataxin, a mitochondrial protein involved in iron homeostasis, remains controversial. Using a yeast model of conditional expression of the frataxin homologue YFH1, we analyzed the primary effects of YFH1 depletion. The main conclusion unambiguously points to the up-regulation of iron transport systems as a primary effect of YFH1 down-regulation. We observed that inactivation of aconitase, an iron-sulfur enzyme, occurs long after the iron uptake system has been activated. Decreased aconitase activity should be considered part of a group of secondary events promoted by iron overloading, which includes decreased superoxide dismutase activity and increased protein carbonyl formation. Impaired manganese uptake, which contributes to superoxide dismutase deficiency, has also been observed in YFH1-deficient cells. This low manganese content can be attributed to the down-regulation of the metal ion transporter Smf2. Low Smf2 levels were not observed in AFT1/YFH1 double mutants, indicating that high iron levels could be responsible for the Smf2 decline. In summary, the results presented here indicate that decreased iron-sulfur enzyme activities in YFH1-deficient cells are the consequence of the oxidative stress conditions suffered by these cells. PMID:20956517

  9. The identification of nonlinear biological systems: Wiener and Hammerstein cascade models

    Microsoft Academic Search

    I. W. Hunter; M. J. Korenberg

    1986-01-01

    Systems that can be represented by a cascade of a dynamic linear subsystem preceded (Hammerstein cascade model) or followed (Wiener cascade model) by a static nonlinearity are considered. Various identification schemes that have been proposed for the Hammerstein and Wiener systems are critically reviewed with reference to the special problems that arise in the identification of nonlinear biological systems. Examples

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

    E-print Network

    Paris-Sud XI, Université de

    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

  11. The automatic identification system of maritime accident risk using rule-based reasoning

    E-print Network

    Boyer, Edmond

    The automatic identification system of maritime accident risk using rule-based reasoning IDIRI B of maritime accident risk. It is very difficult for operators responsible for monitoring traffic to identify a system for the automatic identification of maritime accident risk. The system consists of two modules

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

    Microsoft Academic Search

    Robert S. Sikorski; Philip Hieter

    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

  13. Inulinase production by a marine yeast Pichia guilliermondii and inulin hydrolysis by the crude inulinase

    Microsoft Academic Search

    Fang Gong; Jun Sheng; Zhenming Chi; Jing Li

    2007-01-01

    Marine yeast strain 1, isolated from the surface of a marine alga, was found to secrete a large amount of inulinase into the\\u000a medium. This marine yeast was identified as a strain of Pichia guilliermondii according to the results of routine yeast identification and molecular methods. The crude inulinase produced by this marine\\u000a yeast worked optimally at pH 6.0 and

  14. CFRP damage identification system based on FBG sensors and ELM method

    NASA Astrophysics Data System (ADS)

    Lu, Shizeng; Jiang, Mingshun; Jia, Lei; Sui, Qingmei; Sai, Yaozhang

    2015-02-01

    The identification of the damage state of Carbon fiber-reinforced plastic (CFRP) structure is the necessary information for ensuring the safety of CFRP structure. In this paper, the structural damage identification system using fiber Bragg grating (FBG) sensors and the damage identification method were investigated. FBG sensors were used to detect the structural dynamic response signal, which was generated by an active actuation way. Fourier transform and principal component analysis (PCA) were used to extract the damage characteristic. After that, the structural damage identification model was constructed based on extreme learning machine (ELM), whose input is the damage characteristic and output is the damage state. Finally, the damage identification system was established and verified on a CFRP plate with 160 mm160 mm experiment area. The experimental results showed that the identification accuracy was more than 90 %. This paper provided a reliable method for CFRP structural damage identification.

  15. Force-chain identification in quasi-2D granular systems

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  16. Assembly of eukaryotic algal chromosomes in yeast

    PubMed Central

    2013-01-01

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

  17. A System Identification and Change Detection Methodology for Stochastic Nonlinear Dynamic Systems

    SciTech Connect

    Yun, Hae-Bum; Masri, Sami F.; Caffrey, John P. [University of Southern California, Los Angeles, CA (United States)

    2008-07-08

    In this paper a component-level detection methodology for system identification and change detection is discussed. The methodology is based on non-parametric, data-driven, stochastic system identification classifications using statistical pattern recognition techniques. In order to validate the methodology discussed in this paper an experimental study was performed using a complex nonlinear magneto-rheological (MR) damper. The results of this study show that the proposed methodology is very promising to detect interpret changes in critical structural components such as nonlinear springs joints as well as various types of dampers.

  18. Yeast: An Experimental Organism for Modern Biology.

    ERIC Educational Resources Information Center

    Botstein, David; Fink, Gerald R.

    1988-01-01

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

  19. Phosphoinositides in yeast: genetically tractable signalling

    Microsoft Academic Search

    Stefaan Wera; Jan C. T. Bergsma; Johan M. Thevelein

    2001-01-01

    Research on signalling through phosphoinositides has made tremendous advances over the last few years. Studies with budding yeast (Saccharomyces cerevisiae) combine the advantage of a eukaryotic system with those of a rapidly growing, genetically modifiable and tractable organism of which the genome is fully sequenced. Hence, despite some differences in phosphoinositide signalling between mammals and yeast (e.g. the absence of

  20. Topical Therapy for Mucosal Yeast Infections

    Microsoft Academic Search

    Paul R. Summers

    2011-01-01

    Mucosal yeast infection is best understood as a consequence of compromised mucosal cell-mediated and innate immunity. Defense against oral candidiasis is dominantly cell mediated. The innate immune system may play the main role in regulating vulvovaginal yeast infection. Conditions that compromise cell-mediated immunity such as leukemia, severe illness and HIV infection must be considered as predisposing factors for recurrent oral

  1. Underwater electro-optical system for mine identification

    Microsoft Academic Search

    Michael P. Strand

    1995-01-01

    The Electro-Optic Identification (EOID) Sensors project is developing a Laser Visual Iidentification Sensor (LVIS) for identification of proud, partially buried, and moored mines in shallow water\\/very shallow water. LVIS will be deployed in small diameter underwater vehicles, including unmanned underwater vehicles (UUVs). Since the mission is mine identification, LVIS must: a) deliver high quality images in turbid coastal waters, while

  2. Construction of a High-Quality Yeast Two-Hybrid Library and Its Application in Identification of Interacting Proteins with Brn1 in Curvularia lunata

    PubMed Central

    Gao, Jin-Xin; Jing, Jing; Yu, Chuan-Jin; Chen, Jie

    2015-01-01

    Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China, and several key pathogenic factors have been isolated. An yeast two-hybrid (Y2H) library is a very useful platform to further unravel novel pathogenic factors in C. lunata. To construct a high-quality full length-expression cDNA library from the C. lunata for application to pathogenesis-related protein-protein interaction screening, total RNA was extracted. The SMART (Switching Mechanism At 5? end of the RNA Transcript) technique was used for cDNA synthesis. Double-stranded cDNA was ligated into the pGADT7-Rec vector with Herring Testes Carrier DNA using homologous recombination method. The ligation mixture was transformed into competent yeast AH109 cells to construct the primary cDNA library. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about 6.39 ×105 transformants/3 ?g pGADT7-Rec. The titer of the primary cDNA library was 2.5×108 cfu/mL. The numbers for the cDNA library was 2.46×105. Randomly picked clones show that the recombination rate was 88.24%. Gel electrophoresis results indicated that the fragments ranged from 0.4 kb to 3.0 kb. Melanin synthesis protein Brn1 (1,3,8-hydroxynaphthalene reductase) was used as a “bait” to test the sufficiency of the Y2H library. As a result, a cDNA clone encoding VelB protein that was known to be involved in the regulation of diverse cellular processes, including control of secondary metabolism containing melanin and toxin production in many filamentous fungi was identified. Further study on the exact role of the VelB gene is underway.

  3. Construction of a High-Quality Yeast Two-Hybrid Library and Its Application in Identification of Interacting Proteins with Brn1 in Curvularia lunata.

    PubMed

    Gao, Jin-Xin; Jing, Jing; Yu, Chuan-Jin; Chen, Jie

    2015-06-01

    Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China, and several key pathogenic factors have been isolated. An yeast two-hybrid (Y2H) library is a very useful platform to further unravel novel pathogenic factors in C. lunata. To construct a high-quality full length-expression cDNA library from the C. lunata for application to pathogenesis-related protein-protein interaction screening, total RNA was extracted. The SMART (Switching Mechanism At 5' end of the RNA Transcript) technique was used for cDNA synthesis. Double-stranded cDNA was ligated into the pGADT7-Rec vector with Herring Testes Carrier DNA using homologous recombination method. The ligation mixture was transformed into competent yeast AH109 cells to construct the primary cDNA library. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about 6.39 ×10(5) transformants/3 ?g pGADT7-Rec. The titer of the primary cDNA library was 2.5×10(8) cfu/mL. The numbers for the cDNA library was 2.46×10(5). Randomly picked clones show that the recombination rate was 88.24%. Gel electrophoresis results indicated that the fragments ranged from 0.4 kb to 3.0 kb. Melanin synthesis protein Brn1 (1,3,8-hydroxynaphthalene reductase) was used as a "bait" to test the sufficiency of the Y2H library. As a result, a cDNA clone encoding VelB protein that was known to be involved in the regulation of diverse cellular processes, including control of secondary metabolism containing melanin and toxin production in many filamentous fungi was identified. Further study on the exact role of the VelB gene is underway. PMID:26060429

  4. Modelling and system identification of active magnetic bearing systems

    Microsoft Academic Search

    Young Man Cho; Sriram Srinavasan; Jae-Hyuk Oh; Hwa Soo Kim

    2007-01-01

    Active magnetic bearing (AMB) systems have recently attracted much attention in the rotating machinery industry due to their advantages over traditional bearings such as fluid film and rolling element bearings. The AMB control system must provide robust performance over a wide range of machine operating conditions and over the machine lifetime in order to make this technology commercially viable. An

  5. Pump-free multi-well-based microfluidic system for high-throughput analysis of size-control relative genes in budding yeast.

    PubMed

    Kang, Xianjie; Jiang, Lingli; Chen, Xi; Yuan, Haiyu; Luo, Chunxiong; Ouyang, Qi

    2014-07-24

    Time-lapse single cell imaging by microscopy can provide precise cell information such as the cell size, the cell cycle duration, protein localization and protein expression level. Usually, a microfluidic system is needed for these measurements in order to provide a constant culture environment and confine the cells so that they grow in a monolayer. However, complex connections are required between the channels inside the chip and the outside media, and a complex procedure is needed for loading of cells, thereby making this type of system unsuitable for application in high-throughput single cell scanning experiments. Here we provide a novel and easily operated pump-free multi-well-based microfluidic system which enables the high-throughput loading of many different budding yeast strains into monolayer growth conditions just by use of a multi-channel pipette. Wild type budding yeast (Saccharomyces cerevisiae) and 62 different budding yeast size control relative gene deletion strains were chosen for scanning. We obtained normalized statistical results for the mother cell doubling time, daughter cell doubling time, mother cell size and daughter cell size of different gene deletion strains relative to the corresponding parameters of the wild type cells. Meanwhile, we compared the typical cell morphology of different strains and analyzed the relationship between the cell genotype and phenotype. This method which can be easily used in a normal biology lab may help researchers who need to carry out the high-throughput scanning of cell morphology and growth. PMID:24872017

  6. Analysis of osmoadaptation system in budding yeast suggests that regulated degradation of glycerol synthesis enzyme is key to near-perfect adaptation.

    PubMed

    Patel, Anilkumar K; Bhartiya, Sharad; Venkatesh, K V

    2014-06-01

    In order to maintain its turgor pressure at a desired homeostatic level, budding yeast, Saccharomyces cerevisiae responds to the external variation of the osmotic pressure by varying its internal osmotic pressure through regulation of synthesis and transport of the intracellular glycerol. Hog1PP (dually phosphorylated Hog1), a final effector in the signalling pathway of the hyper osmotic stress, regulates the glycerol synthesis both at transcriptional and non-transcriptional stages. It is known that for a step-change in salt concentration leading to moderate osmotic shock, Hog1PP activity shows a transient response before it returns to the vicinity of pre-stimulus level. It is believed that an integrating process in a negative feedback loop can be a design strategy to yield such an adaptive response. Several negative feedback loops have been identified in the osmoadaptation system in yeast. However, the precise location of the integrating process in the osmoadaptation system which includes signalling, gene regulation, metabolism and biophysical modules is unclear. To address this issue, we developed a reduced model which captures various experimental observations of the osmoadaptation behaviour of wild type and mutant strains. Dynamic simulations and steady state analysis suggested that known information about the osmoadaptation system of budding yeast does not necessarily give a perfect integrating process through the known feedback loops of Hog1PP. On the other hand, regulation of glycerol synthesising enzyme degradation can result in a near integrating process leading to a near-perfect adaptation. PMID:24799959

  7. Evaluation of the single yeast cell's adhesion to ITO substrates with various surface energies via ESEM nanorobotic manipulation system.

    PubMed

    Shen, Yajing; Ahmad, Mohd Ridzuan; Nakajima, Masahiro; Kojima, Seiji; Homma, Michio; Fukuda, Toshio

    2011-12-01

    Cell-surface adhesion force is important for cell activities and the development of bio materials. In this paper, a method for in situ single cell (W303) adhesion force measurement was proposed based on nanorobotic manipulation system inside an environment scanning electron microscope (ESEM). An end effector was fabricated from a commercial atomic force microscope (AFM) cantilever by focused ion beam (FIB) etching. The spring constant of it was calibrated by nanomanipulation approach. Three kinds of hydrophilic and hydrophobic ITO plates were prepared by using VUV-irradiation and OTS coating techniques. The shear adhesion strength of the single yeast cell to each substrate was measured based on the deflection of the end effector. The results demonstrated that the cell adhesion force was larger under the wet condition in the ESEM environment than in the aqueous condition. It also showed that the cell adhesion force to hydrophilic surface was larger than that to the hydrophobic surface. Studies of single cell's adhesion on various plate surfaces and environments could give new insights into the tissue engineering and biological field. PMID:22249767

  8. Model Identification and Control of Electro-hydraulic Position Servo System

    Microsoft Academic Search

    Junpeng Shao; Zhongwen Wang; Jianying Lin; Guihua Han

    2009-01-01

    In view of introduction of the composition and working principle of the electro-hydraulic position servo control system, the mathematical model of the system was built. In order to acquire more accuracy system mathematical model, System model identification and verification of electro-hydraulic position servo system were carried out based on hardware-in-the-loop simulation environment of Real-time Workshop (RTW) and system identification toolbox

  9. The humanization of N-glycosylation pathways in yeast

    Microsoft Academic Search

    Stefan Wildt; Tilllman U. Gerngross

    2005-01-01

    Yeast and other fungal protein-expression hosts have been extensively used to produce industrial enzymes, and are often the expression system of choice when manufacturing costs are of primary concern. However, for the production of therapeutic glycoproteins intended for use in humans, yeast have been less useful owing to their inability to modify proteins with human glycosylation structures. Yeast N-glycosylation is

  10. The long physiological reach of the yeast vacuolar H + ATPase

    Microsoft Academic Search

    Patricia M. Kane

    2007-01-01

    V-ATPases are structurally conserved and functionally versatile proton pumps found in all eukaryotes. The yeast V-ATPase has\\u000a emerged as a major model system, in part because yeast mutants lacking V-ATPase subunits (vma mutants) are viable and exhibit a distinctive Vma- phenotype. Yeast vma mutants are present in ordered collections of all non-essential yeast deletion mutants, and a number of additional

  11. Structural system identification in time domain using measured acceleration

    NASA Astrophysics Data System (ADS)

    Kang, Joo Sung; Park, Seung-Keun; Shin, Soobong; Lee, Hae Sung

    2005-11-01

    This paper presents a system identification scheme in time domain to estimate stiffness and damping parameters of a structure using measured acceleration. An error function is defined as the time integral of the least-squared errors between measured accelerations and calculated accelerations by a numerical model of a structure. To alleviate the ill-posedness of SI problems a regularization technique is employed and a new regularization function for the time-domain SI is proposed. The regularization factor is determined by the geometric mean scheme. The validity of the proposed method is demonstrated by a numerical simulation study on a two-span truss bridge and by an experimental laboratory study on a three-story shear building model.

  12. COMPARISON OF SYSTEM IDENTIFICATION TECHNIQUES FOR A SPHERICAL AIR-BEARING

    E-print Network

    Hall, Christopher D.

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

  13. Lithofacies identification using multiple adaptive resonance theory neural networks and group decision expert system

    Microsoft Academic Search

    Hsien-cheng Chang; David C. Kopaska-Merkel; Hui-Chuan Chen; S. Rocky Durrans

    2000-01-01

    Lithofacies identification supplies qualitative information about rocks. Lithofacies represent rock textures and are important components of hydrocarbon reservoir description. Traditional techniques of lithofacies identification from core data are costly and different geologists may provide different interpretations. In this paper, we present a low-cost intelligent system consisting of three adaptive resonance theory neural networks and a rule-based expert system to consistently

  14. A traceability system for beef products based on radio frequency identification technology in China

    Microsoft Academic Search

    Chuanheng Sun; Zengtao Ji; Xinting Yang; Xiao Han; Zhiling Wang

    2007-01-01

    Radio frequency identification (RFID) technology is an automatic identification and data capture (AIDC) technique and it is the representative technology for handling beef traceability. In this paper we offer a complete solution including: frequency, identifier information system, information system, data organisation, tag reclaimation and control technology, from three segments of the beef production process in China. From the farm to

  15. GLOMAP Approach for Nonlinear System Identification of Aircraft Dynamics Using Flight Data

    E-print Network

    Valasek, John

    of aircraft dynamics, a longitudinal and a lateral/directional example using nonlinear simulation data for on-line system identification of six-DOF simulated aircraft dynamics, and found it is suitableGLOMAP Approach for Nonlinear System Identification of Aircraft Dynamics Using Flight Data Monika

  16. Application of fault detection and identification (FDI) techniques in power regulating systems of nuclear reactors

    Microsoft Academic Search

    Kallol Roy; R. N. Banavar; S. Thangasamy

    1998-01-01

    Application of failure detection and identification (FDI) algorithms have essentially been limited to identification of a global fault in the system, and no further attempts have been made to locate subcomponent faults for root cause analysis. This paper presents Kalman filter-based methods for FDI in power regulating systems of nuclear reactors. The attempt here is to explain how the behavior

  17. Frequency-domain identification of linear systems using arbitrary excitations and a nonparametric noise model

    Microsoft Academic Search

    J. Schoukens; G. Vandersteen; R. Pintelon; P. Guillaume

    1999-01-01

    Presents a generalized frequency domain identification method to identify single-input\\/single-output (SISO) systems combining two previously published extensions in one method: arbitrary but persistent excitations are allowed and a nonparametric noise model is extracted from the same data that are used to identify the system. The method is directly applicable to identification in feedback if an external persistently exciting reference signal

  18. A Multistage Algorithm for Identification of Nonlinear Aggregate Power System Loads

    Microsoft Academic Search

    Pouyan Jazayeri; William Rosehart; David T. Westwick

    2007-01-01

    A multistage identification algorithm for dynamic power system load models is proposed in this paper. The multistage approach is used to address the nonconvexity of the identification problem. Initial stages are used to find good preliminary estimates for the parameters of the model. Specifically, the initial stages are as follows: Equations for dynamic power system loads are discretized using the

  19. 47 CFR 76.905 - Standards for identification of cable systems subject to effective competition.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...2014-10-01 false Standards for identification of cable systems subject...76.905 Standards for identification of cable systems subject...separately billed or billable customer will count as a household...buildings billed as a single customer. Individual units of...

  20. 47 CFR 76.905 - Standards for identification of cable systems subject to effective competition.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...2013-10-01 false Standards for identification of cable systems subject...76.905 Standards for identification of cable systems subject...separately billed or billable customer will count as a household...buildings billed as a single customer. Individual units of...

  1. 47 CFR 76.905 - Standards for identification of cable systems subject to effective competition.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...2012-10-01 false Standards for identification of cable systems subject...76.905 Standards for identification of cable systems subject...separately billed or billable customer will count as a household...buildings billed as a single customer. Individual units of...

  2. System identification and model reduction using modulating function techniques

    NASA Technical Reports Server (NTRS)

    Shen, Yan

    1993-01-01

    Weighted least squares (WLS) and adaptive weighted least squares (AWLS) algorithms are initiated for continuous-time system identification using Fourier type modulating function techniques. Two stochastic signal models are examined using the mean square properties of the stochastic calculus: an equation error signal model with white noise residuals, and a more realistic white measurement noise signal model. The covariance matrices in each model are shown to be banded and sparse, and a joint likelihood cost function is developed which links the real and imaginary parts of the modulated quantities. The superior performance of above algorithms is demonstrated by comparing them with the LS/MFT and popular predicting error method (PEM) through 200 Monte Carlo simulations. A model reduction problem is formulated with the AWLS/MFT algorithm, and comparisons are made via six examples with a variety of model reduction techniques, including the well-known balanced realization method. Here the AWLS/MFT algorithm manifests higher accuracy in almost all cases, and exhibits its unique flexibility and versatility. Armed with this model reduction, the AWLS/MFT algorithm is extended into MIMO transfer function system identification problems. The impact due to the discrepancy in bandwidths and gains among subsystem is explored through five examples. Finally, as a comprehensive application, the stability derivatives of the longitudinal and lateral dynamics of an F-18 aircraft are identified using physical flight data provided by NASA. A pole-constrained SIMO and MIMO AWLS/MFT algorithm is devised and analyzed. Monte Carlo simulations illustrate its high-noise rejecting properties. Utilizing the flight data, comparisons among different MFT algorithms are tabulated and the AWLS is found to be strongly favored in almost all facets.

  3. Yeast Education Network

    NSDL National Science Digital Library

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

  4. Vaginal Yeast Infections

    MedlinePLUS

    ... infection from your sexual partner. Condoms and dental dams may help prevent getting or passing yeast infections ... infection from your sexual partner. Condoms and dental dams may help prevent getting or passing yeast infections ...

  5. Vaginal Yeast Infection

    MedlinePLUS

    ... on. Read more information on enabling JavaScript. Vaginal Yeast Infection Skip Content Marketing Share this: Main Content Area Vaginal yeast infection, or vulvovaginal candidiasis, is a common cause ...

  6. Parameter identification of time-varying systems using neural networks

    NASA Astrophysics Data System (ADS)

    Gao, Keqin; Ahmad, M. Omair; Swamy, M. N. S.

    A neural network solution is introduced for the problem of parameter identification of time-varying systems. An autoregressive (AR) model is used to identify the unknown system. The problem is formulated to minimize the least squares (LS) error between the output of the unknown system and the output of the AR model when they are driven by a white Gaussian noise. Because of the time-varying nature of the unknown system, an exponentially weighted LS scheme is employed to attach more weight to the current data. A neural network is designated to estimate the solution of the weighted LS problem that gives the parameter of the AR model. Since this is an unconstrained quadratic optimization problem and the AR parameters can assume either + or - values, a hyperbolic tangent function is used as the nonlinear activation function for the neurons. A space iterative search technique is incorporated into the computational procedure of the neural network such that it can find solution in an open space rather than within a hypercube. In order to identify the time-varying parameters efficiently, recursive formulations are derived so that the coefficient of the neural network can be updated whenever a new observation is available. Finally, computer simulation results are presented to demonstrate the performance of the scheme.

  7. Issues in identifying germ tube positive yeasts by conventional methods.

    PubMed

    Yazdanpanah, Atta; Khaithir, Tzar Mohd Nizam

    2014-01-01

    Candida speciation is vital for epidemiology and management of candidiasis. Nonmolecular conventional methods often fail to identify closely related germ tube positive yeasts from clinical specimens. The present study was conducted to identify these yeasts and to highlight issues in conventional versus molecular methods of identification. A total of 98 germ tube positive yeasts from high vaginal swabs were studied over a 12-month period. Isolates were examined with various methods including growth at 42 °C and 45 °C on Sabouraud dextrose agar (SDA), color development on CHROMagar Candida medium, chlamydospore production on corn meal agar at 25 °C, carbohydrate assimilation using ID 32C system, and polymerase chain reaction using a single pair of primers targeting the hyphal wall protein 1 (Hwp1) gene. Of all the isolates studied, 97 were molecularly confirmed as C. albicans and one isolate was identified as C. dubliniensis. No C. africana was detected in this study. The molecular method used in our study was an accurate and useful tool for discriminating C. albicans, C. dubliniensis, and C. africana. The conventional methods, however, were less accurate and riddled with many issues that will be discussed in further details. PMID:24375729

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

  9. A unified approach to aircraft parameter identification. [considering algorithm, control input, and instrumentation system

    NASA Technical Reports Server (NTRS)

    Stepner, D. E.; Sorensen, J. A.

    1974-01-01

    The most accurate identification results are obtained when all three elements of the identification process - the identification algorithm, the control input, and the instrumentation system - are considered in a unified approach. This type of approach for the design of optimal control inputs and for determining the effect of the instrumentation system, in each case with respect to the identification process is discussed. Design of control inputs which optimize the sensitivity of the system output to the unknown parameters is given. Results using these inputs in an extensive simulation of the identification process indicate they perform measurably better than doublet type inputs. A technique is then presented for specifying an optimal instrumentation system or for determining the effect, the instrumentation system has on the accuracy of the parameter estimates.

  10. CLONTECHInnovative Yeast Protocols Handbook

    E-print Network

    Erickson, F. Les

    CLONTECHInnovative Tools to Accelerate Discovery Yeast Protocols Handbook PT3024-1 (PR13103 FOR RESEARCH USE ONLY #12;Yeast Protocols Handbook CLONTECH Laboratories, Inc. www.clontech.com Protocol # PT3024-1 2 Version # PR13103 I. Introduction 4 II. Introduction to Yeast Promoters 5 III. Culturing

  11. Construction of a Highly Active Xylanase Displaying Oleaginous Yeast: Comparison of Anchoring Systems

    PubMed Central

    Duquesne, Sophie; Bozonnet, Sophie; Bordes, Florence; Dumon, Claire; Nicaud, Jean-Marc; Marty, Alain

    2014-01-01

    Three Yarrowia lipolytica cell wall proteins (YlPir, YlCWP1 and YlCBM) were evaluated for their ability to display the xylanase TxXYN from Thermobacillus xylanilyticus on the cell surface of Y. lipolytica. The fusion proteins were produced in Y. lipolytica JMY1212, a strain engineered for mono-copy chromosomal insertion, and enabling accurate comparison of anchoring systems. The construction using YlPir enabled cell bound xylanase activity to be maximised (71.6 U/g). Although 48% of the activity was released in the supernatant, probably due to proteolysis at the fusion zone, this system is three times more efficient for the anchoring of TxXYN than the YlCWP1 system formerly developed for Y. lipolytica. As far as we know it represents the best displayed xylanase activity ever published. It could be an attractive alternative anchoring system to display enzymes in Y. lipolytica. PMID:24743311

  12. Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast

    PubMed Central

    Popelka, Hana; Uversky, Vladimir N; Klionsky, Daniel J

    2014-01-01

    The mechanism of autophagy relies on complex cell signaling and regulatory processes. Each cell contains many proteins that lack a rigid 3-dimensional structure under physiological conditions. These dynamic proteins, called intrinsically disordered proteins (IDPs) and protein regions (IDPRs), are predominantly involved in cell signaling and regulation. Yet, very little is known about their presence among proteins of the core autophagy machinery. In this work, we characterized the autophagy protein Atg3 from yeast and human along with 2 variants to show that Atg3 is an IDPRs-containing protein and that disorder/order predicted for these proteins from their amino acid sequence corresponds to their experimental characteristics. Based on this consensus, we applied the same prediction methods to all known Atg proteins from Saccharomyces cerevisiae. The data presented here provide an insight into the structural dynamics of each Atg protein. They also show that intrinsic disorder at various levels has to be taken into consideration for about half of the Atg proteins. This work should become a useful tool that will facilitate and encourage exploration of protein intrinsic disorder in autophagy. PMID:24879155

  13. Cloning and characterization of a gene encoding HMG-CoA reductase from Ganoderma lucidum and its functional identification in yeast.

    PubMed

    Shang, Chang-Hua; Zhu, Fen; Li, Na; Ou-Yang, Xiang; Shi, Liang; Zhao, Ming-Wen; Li, Yu-Xiang

    2008-05-01

    A gene encoding 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) was isolated from a triterpene-producing fungus, Ganoderma lucidum (Reishi or Lingzhi). This report provides the complete nucleotide sequence of the full-length cDNA encoding HMGR and its genomic DNA sequence. The cDNA of the HMGR (GenBank Accession no., EU263989) was found to contain an open reading frame (ORF) of 3,681 bp encoding a 1,226-amino-acid polypeptide, whereas the HMGR genomic DNA sequence (GenBank Accession no., EU263990) consisted of 4,262 bp and contained seven exons and six introns. The deduced amino acid sequence of G. lucidum HMGR showed significant homology to the known HMGRs from Ustilago maydis and Cryptococcus neoformans, and contained four conserved domains. Gene expression analysis showed that the expression level was relatively low in mycelia incubated for 10, 12, and 14 d, and reached the highest level in the primordia. Functional complementation of Gl-HMGR in a HMGR-deficient mutant yeast strain indicated that the cloned cDNA encoded a HMG-CoA reductase. PMID:18460810

  14. Analysis of the structural genes encoding M-factor in the fission yeast Schizosaccharomyces pombe: identification of a third gene, mfm3.

    PubMed Central

    Kjaerulff, S; Davey, J; Nielsen, O

    1994-01-01

    We previously identified two genes, mfm1 and mfm2, with the potential to encode the M-factor mating pheromone of the fission yeast Schizosaccharomyces pombe (J. Davey, EMBO J. 11:951-960, 1992), but further analysis revealed that a mutant strain lacking both genes still produced active M-factor. Here we describe the isolation and characterization of a third M-factor gene, mfm3. A mutant lacking all three genes fails to produce M-factor, indicating that all functional M-factor genes now have been identified. The triple mutant exhibits an absolute mating defect in M cells, a defect that is not rescued by addition of exogenous M-factor. A mutational analysis reveals that all three mfm genes contribute to the production of M-factor. Their transcription is limited to M cells and requires the mat1-Mc and ste11 gene products. Each gene is induced when the cells are starved of nitrogen and further induced by a pheromone signal. Additionally, the signal transduction machinery associated with the pheromone response is required for transcription of the mfm genes in both stimulated and unstimulated cells. Images PMID:8196631

  15. Identification of Target Genes Regulated by Homeotic Proteins in Drosophila Melanogaster through Genetic Selection of Ultrabithorax Protein-Binding Sites in Yeast

    PubMed Central

    Mastick, G. S.; McKay, R.; Oligino, T.; Donovan, K.; Lopez, A. J.

    1995-01-01

    A method based on the transcriptional activation of a selectable reporter in yeast cells was used to identify genes regulated by the Ultrabithorax homeoproteins in Drosophila melanogaster. Fifty-three DNA fragments that can mediate activation by UBX isoform Ia in this test were recovered after screening 15% of the Drosophila genome. Half of these fragments represent single-copy sequences in the genome. Six single-copy fragments were investigated in detail, and each was found to reside near a transcription unit whose expression in the embryo is segmentally modulated as expected for targets of homeotic genes. Four of these putative target genes are expressed in patterns that suggest roles in the development of regional specializations within mesoderm derivatives; in three cases these expression patterns depend on Ultrabithorax function. Extrapolation from this pilot study indicates that 85-170 candidate target genes can be identified by screening the entire Drosophila genome with UBX isoform Ia. With appropriate modifications, this approach should be applicable to other transcriptional regulators in diverse organisms. PMID:7705635

  16. Genetic analysis of regulatory mutants affecting synthesis of extracellular proteinases in the yeast Yarrowia lipolytica: identification of a RIM101/pacC homolog.

    PubMed Central

    Lambert, M; Blanchin-Roland, S; Le Louedec, F; Lepingle, A; Gaillardin, C

    1997-01-01

    Depending on the pH of the growth medium, the yeast Yarrowia lipolytica secretes both an acidic proteinase and an alkaline proteinase, the synthesis of which is also controlled by carbon, nitrogen, and sulfur availability, as well as by the presence of extracellular proteins. Recessive mutations at four unlinked loci, named PAL1 to PAL4, were isolated which prevent alkaline proteinase derepression under conditions of carbon and nitrogen limitation at pH 6.8. These mutations markedly affect mating and sporulation. A dominant suppressor of all four PAL mutations was isolated from a wild-type genomic library, which turned out to be a C-terminally truncated form of a 585-residue transcriptional factor of the His2Cys2 zinc finger family, which we propose to call YlRim101p. Another C-terminally truncated version of YlRim101p (419 residues) is encoded by the dominant RPH2 mutation previously isolated as expressing alkaline protease independently of the pH. YlRim101p is homologous to the transcriptional activators Rim101p of Saccharomyces cerevisiae, required for entry into meiosis, and PacC of Aspergillus nidulans and Penicillium chrysogenum, which were recently shown to mediate regulation by ambient pH. YlRim101p appears essential for mating and sporulation and for alkaline proteinase derepression. YlRIM101 expression is autoregulated, maximal at alkaline pH, and strongly impaired by PAL mutations. PMID:9199331

  17. RNA Cytidine Acetyltransferase of Small-Subunit Ribosomal RNA: Identification of Acetylation Sites and the Responsible Acetyltransferase in Fission Yeast, Schizosaccharomyces pombe

    PubMed Central

    Taoka, Masato; Ishikawa, Daisuke; Nobe, Yuko; Ishikawa, Hideaki; Yamauchi, Yoshio; Terukina, Goro; Nakayama, Hiroshi; Hirota, Kouji; Takahashi, Nobuhiro; Isobe, Toshiaki

    2014-01-01

    The eukaryotic small-subunit (SSU) ribosomal RNA (rRNA) has two evolutionarily conserved acetylcytidines. However, the acetylation sites and the acetyltransferase responsible for the acetylation have not been identified. We performed a comprehensive MS-based analysis covering the entire sequence of the fission yeast, Schizosaccharomyces pombe, SSU rRNA and identified two acetylcytidines at positions 1297 and 1815 in the 3? half of the rRNA. To identify the enzyme responsible for the cytidine acetylation, we searched for an S. pombe gene homologous to TmcA, a bacterial tRNA N-acetyltransferase, and found one potential candidate, Nat10. A temperature-sensitive strain of Nat10 with a mutation in the Walker A type ATP-binding motif abolished the cytidine acetylation in SSU rRNA, and the wild-type Nat10 supplemented to this strain recovered the acetylation, providing evidence that Nat10 is necessary for acetylation of SSU rRNA. The Nat10 mutant strain showed a slow-growth phenotype and was defective in forming the SSU rRNA from the precursor RNA, suggesting that cytidine acetylation is necessary for ribosome assembly. PMID:25402480

  18. Comparison of Five System Identification Algorithms for Rotorcraft Higher Harmonic Control

    NASA Technical Reports Server (NTRS)

    Jacklin, Stephen A.

    1998-01-01

    This report presents an analysis and performance comparison of five system identification algorithms. The methods are presented in the context of identifying a frequency-domain transfer matrix for the higher harmonic control (HHC) of helicopter vibration. The five system identification algorithms include three previously proposed methods: (1) the weighted-least- squares-error approach (in moving-block format), (2) the Kalman filter method, and (3) the least-mean-squares (LMS) filter method. In addition there are two new ones: (4) a generalized Kalman filter method and (5) a generalized LMS filter method. The generalized Kalman filter method and the generalized LMS filter method were derived as extensions of the classic methods to permit identification by using more than one measurement per identification cycle. Simulation results are presented for conditions ranging from the ideal case of a stationary transfer matrix and no measurement noise to the more complex cases involving both measurement noise and transfer-matrix variation. Both open-loop identification and closed- loop identification were simulated. Closed-loop mode identification was more challenging than open-loop identification because of the decreasing signal-to-noise ratio as the vibration became reduced. The closed-loop simulation considered both local-model identification, with measured vibration feedback and global-model identification with feedback of the identified uncontrolled vibration. The algorithms were evaluated in terms of their accuracy, stability, convergence properties, computation speeds, and relative ease of implementation.

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

    Microsoft Academic Search

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

    2009-01-01

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

  20. Advanced terahertz imaging system performance model for concealed weapon identification

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

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