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1

Comparison of the Quantum II, API Yeast Ident, and AutoMicrobic systems for identification of clinical yeast isolates.  

PubMed Central

The Quantum II Yeast Identification System (Abbott Laboratories) is a microprocessor-based spectrophotometric system for identification of clinical yeast isolates within 24 h. We compared the Quantum II system with the API Yeast Ident (Analytab Products) and the AutoMicrobic System Yeast Biochemical Card (AMS-YBC; Vitek Systems, Inc.) for the identification of 221 clinical yeast isolates, including 120 common clinical isolates (Candida albicans, C. tropicalis, C. parapsilosis, Torulopsis glabrata, and Cryptococcus neoformans) and 101 relatively uncommon clinical isolates. The API 20C (Analytab) was used as the reference system. The Quantum II and AMS-YBC systems correctly identified 181 (82%) and 184 (83%) isolates, respectively, whereas the Yeast Ident system correctly identified 132 (60%) isolates. Of the 120 common clinical isolates, 113 (94%) were correctly identified by Quantum II, 103 (86%) were correctly identified by AMS-YBC, and 83 (69%) were correctly identified by Yeast Ident. Of the 101 uncommon clinical isolates tested, 68 (67%) were correctly identified by Quantum II, 81 (80%) were correctly identified by AMS-YBC, and 49 (49%) were correctly identified by Yeast Ident. The overall accuracy of the Quantum II, AMS-YBC, and API Yeast Ident was not sufficient to recommend any of these systems for routine use in the clinical microbiology laboratory without substantial expansion of the respective data bases. PMID:3182994

Pfaller, M A; Preston, T; Bale, M; Koontz, F P; Body, B A

1988-01-01

2

Multicenter study evaluating the Vitek MS system for identification of medically important yeasts.  

PubMed

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

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; Burnham, Carey-Ann D

2013-07-01

3

Comparative study on the identification of food-borne yeasts.  

PubMed Central

Morphologically distinct yeast colonies from partially and fully processed fruits and vegetables were isolated over a 3-year period. Identification of 239 strains was achieved by using standard methods, commercial identification kits (API 20C and API YEAST-IDENT), and a simplified system for food-borne yeasts. The identified strains of fruit origin represented 36 species belonging to 19 genera. Among strains of vegetable origin, 34 species representing 17 genera were identified. The simplified identification system and the conventional method provided the same results in 80% of the cases. The commercial identification kits were easy to use but were not appropriate for food-borne yeast species. Computer-assisted identification was helpful. PMID:2059042

Torok, T; King, A D

1991-01-01

4

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

PubMed Central

Fatty acids and isoprenoids can be covalently attached to a variety of proteins. These lipid modifications regulate protein structure, localization and function. Here, we describe a yeast one-hybrid approach based on the G? recruitment system that is useful for identifying sequence motifs those influence lipid modification to recruit proteins to the plasma membrane. Our approach facilitates the isolation of yeast cells expressing lipid-modified proteins via a simple and easy growth selection assay utilizing G-protein signaling that induces diploid formation. In the current study, we selected the N-terminal sequence of G? subunits as a model case to investigate dual lipid modification, i.e., myristoylation and palmitoylation, a modification that is widely conserved from yeast to higher eukaryotes. Our results suggest that both lipid modifications are required for restoration of G-protein signaling. Although we could not differentiate between myristoylation and palmitoylation, N-terminal position 7 and 8 play some critical role. Moreover, we tested the preference for specific amino-acid residues at position 7 and 8 using library-based screening. This new approach will be useful to explore protein-lipid associations and to determine the corresponding sequence motifs. PMID:23922919

Fukuda, Nobuo; Doi, Motomichi; Honda, Shinya

2013-01-01

5

Yeast one-hybrid g? recruitment system for identification of protein lipidation motifs.  

PubMed

Fatty acids and isoprenoids can be covalently attached to a variety of proteins. These lipid modifications regulate protein structure, localization and function. Here, we describe a yeast one-hybrid approach based on the G? recruitment system that is useful for identifying sequence motifs those influence lipid modification to recruit proteins to the plasma membrane. Our approach facilitates the isolation of yeast cells expressing lipid-modified proteins via a simple and easy growth selection assay utilizing G-protein signaling that induces diploid formation. In the current study, we selected the N-terminal sequence of G? subunits as a model case to investigate dual lipid modification, i.e., myristoylation and palmitoylation, a modification that is widely conserved from yeast to higher eukaryotes. Our results suggest that both lipid modifications are required for restoration of G-protein signaling. Although we could not differentiate between myristoylation and palmitoylation, N-terminal position 7 and 8 play some critical role. Moreover, we tested the preference for specific amino-acid residues at position 7 and 8 using library-based screening. This new approach will be useful to explore protein-lipid associations and to determine the corresponding sequence motifs. PMID:23922919

Fukuda, Nobuo; Doi, Motomichi; Honda, Shinya

2013-01-01

6

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

PubMed

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

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

2014-07-01

7

[Molecular taxonomy techniques used for yeast identification].  

PubMed

Due to the major impact of yeasts in human life based on the existence of pathogen yeast species and of species with biotechnological abilities, in the last few years new molecular techniques are performed for an accurate identification of natural isolates. Our study is aimed to review some of these techniques such as electrokariotyping by PFGE (Pulsed Field Gel Electrophoresis), estimation of the molar percentage of guanine and cytosine, the applications of PCR reaction in yeast identification using RAPD (Random amplified polymorphic DNA), UP-PCR (Universally Primed Polymerase Chain Reaction), MLST (Multilocus sequence typing) techniques, mtDNA and rDNA homology studies. Such molecular techniques complete the phenotypical characterization based on classical taxonomical tests allowing thus the polyphasic identification of the microorganisms. PMID:16938931

Ghindea, Raluca; Csutak, Ortansa; Stoica, Ileana; Ionescu, Robertina; Soare, Simona; Pelinescu, Diana; Nohit, Ana-Maria; Creang?, Oana; Vassu, Tatiana

2004-01-01

8

Yeast killer systems.  

PubMed Central

The killer phenomenon in yeasts has been revealed to be a multicentric model for molecular biologists, virologists, phytopathologists, epidemiologists, industrial and medical microbiologists, mycologists, and pharmacologists. The surprisingly widespread occurrence of the killer phenomenon among taxonomically unrelated microorganisms, including prokaryotic and eukaryotic pathogens, has engendered a new interest in its biological significance as well as its theoretical and practical applications. The search for therapeutic opportunities by using yeast killer systems has conceptually opened new avenues for the prevention and control of life-threatening fungal diseases through the idiotypic network that is apparently exploited by the immune system in the course of natural infections. In this review, the biology, ecology, epidemiology, therapeutics, serology, and idiotypy of yeast killer systems are discussed. PMID:9227858

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

1997-01-01

9

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

E-print Network

Yeast Functional Genomic Screens Lead to Identification of a Role for a Bacterial Effector developed a systems biological approach using the yeast Saccharomyces cerevisiae that can expedite the viable yeast haploid deletion strain collection for mutants hypersensitive to expression of the Shigella

Starnbach, Michael

10

Yeast identification in floral nectar of Mimulus aurantiacus (Invited)  

Microsoft Academic Search

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

C. Kyauk; M. Belisle; T. Fukami

2009-01-01

11

Yeast Sequencing Report Identification of a Candida glabrata homologue of  

E-print Network

Yeast Sequencing Report Identification of a Candida glabrata homologue of the S. cerevisiae VRG4 from the pathogenic yeast, Candida glabrata, by functional complementation of an S. cerevisiae vrg4 John Wiley & Sons, Ltd. Keywords: glycosylation; Candida glabrata; nucleotide sugar transporter; GDP

Citovsky, Vitaly

12

Molecular identification of yeasts associated with traditional Egyptian dairy products.  

PubMed

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

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

2009-09-01

13

Identification of yeasts isolated from poultry meat.  

PubMed

In an assessment of the potential role of yeasts in the spoilage of poultry meat, the population and species diversity of yeasts were determined on 50 commercial raw and processed chicken and turkey product samples. Initial populations (log10 cfu/g) ranged from less than 0.1 to 2.9, and increased by the expiration date to 0.4 to 5.1, respectively. 145 of 152 isolates were identified as belonging to 12 species. Yarrowia lipolytica and Candida zeylanoides were predominant, accounting for 39% and 26% of the isolates, respectively. Six different species of basidiomycetous yeasts were determined representing 24% of the isolates. The ability of the predominant yeast species to grow at refrigeration temperatures and their proteolytic and lipolytic activies suggest that yeasts may play a more significant role than previously recognised in the spoilage of poultry products. PMID:11426853

Deák, T

2001-01-01

14

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

PubMed

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

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

2004-07-01

15

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

PubMed

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

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

2014-02-01

16

Molecular and phenotypic identification of the yeast pathogen Candida dubliniensis  

Microsoft Academic Search

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

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

2000-01-01

17

Molecular Biological Identification of Malassezia Yeasts Using Pyrosequencing  

PubMed Central

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

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

2013-01-01

18

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

PubMed Central

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

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

2013-01-01

19

Yeast On-Target Lysis (YOTL), a Procedure for Making Auxiliary Mass Spectrum Data Sets for Clinical Routine Identification of Yeasts.  

PubMed

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

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

2014-12-01

20

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

E-print Network

YEAST VOL. 14: 409­417 (1998) Identification and Analysis of Homologues of Saccharomyces cerevisiae­function relationships, we have identified and studied Spt3 homologues from three other yeasts: Kluyveromyces lactis conserved among distantly related yeasts. The new sequences have been entered in GenBank: AF005930 (K

Winston, Fred

21

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

PubMed Central

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

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

2006-01-01

22

Phenotypic and genotypic identification of yeasts from cheese.  

PubMed

Eighty-five years strains isolated from different cheeses of Austria, Denmark, France, Germany, and Italy were identified using physiological methods and genotypically using random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) analysis. Good congruence was found between the phenotypic and genotypic data for 39 of the isolates. However, 26 isolates of Geotrichum could only be identified to the species level using the genotypic methods and 7 isolates were correctly identified to the genus level only using phenotypic identification methods. The phenotypic identification did not agree with the genotypic data for 14 yeast isolates. Using ubiquinone analysis, yeast cell wall sugars and the diazonium blue B test 5 incorrectly identified isolates with phenotypic methods could be identified genotypically. In addition the 7 isolates identified only to the genus level by the phenotypic methods and the 26 Geotrichum strains were identified to the species level using the polyphasic molecular approach mentioned above. Eleven strains remained unidentified. The 76 identified yeast isolates were assigned to 39 species, the most frequent assignments were made to Debaryomyces hansenii, Geotrichum candidum, Issatchenkia orientalis, Kluyveromyces lactis, K. marxianus, Saccharomyces cerevisiae, Yarrowia lipolytica, and Candida catenulata. It is proposed that Debaryomyces hansenii (Zopf) Lodder et Kregervan Rij and Debaryomyces fabryi Ota should be reinstated. The RAPD-PCR data reinforced the view that the species Galactomyces geotrichum is heterogeneous with all of the Geotrichum isolates from cheese products being assigned G. geotrichum group A sensu M.T. Smith. It is suggested that the name Geotrichum candidum be conserved for this rather common species. PMID:10510714

Prillinger, H; Molnár, O; Eliskases-Lechner, F; Lopandic, K

1999-05-01

23

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

PubMed Central

Rapid identification of yeast isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. We present here an analysis of the utility of PCR amplification and sequence analysis of the hypervariable D1/D2 region of the 26S rRNA gene for the identification of yeast species submitted to the United Kingdom Mycology Reference Laboratory over a 2-year period. A total of 3,033 clinical isolates were received from 2004 to 2006 encompassing 50 different yeast species. While more than 90% of the isolates, corresponding to the most common Candida species, could be identified by using the AUXACOLOR2 yeast identification kit, 153 isolates (5%), comprised of 47 species, could not be identified by using this system and were subjected to molecular identification via 26S rRNA gene sequencing. These isolates included some common species that exhibited atypical biochemical and phenotypic profiles and also many rarer yeast species that are infrequently encountered in the clinical setting. All 47 species requiring molecular identification were unambiguously identified on the basis of D1/D2 sequences, and the molecular identities correlated well with the observed biochemical profiles of the various organisms. Together, our data underscore the utility of molecular techniques as a reference adjunct to conventional methods of yeast identification. Further, we show that PCR amplification and sequencing of the D1/D2 region reliably identifies more than 45 species of clinically significant yeasts and can also potentially identify new pathogenic yeast species. PMID:17251397

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

2007-01-01

24

Prospective evaluation of a matrix-assisted laser desorption ionization-time of flight mass spectrometry system in a hospital clinical microbiology laboratory for identification of bacteria and yeasts: a bench-by-bench study for assessing the impact on time to identification and cost-effectiveness.  

PubMed

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

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

2012-10-01

25

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

PubMed Central

Five different methods were used to identify yeast isolates from a variety of citrus juice sources. A total of 99 strains, including reference strains, were identified using a partial sequence of the 26S rRNA gene, restriction pattern analysis of the internal transcribed spacer region (5.8S-ITS), classical methodology, the RapID Yeast Plus system, and API 20C AUX. Twenty-three different species were identified representing 11 different genera. Distribution of the species was considerably different depending on the type of sample. Fourteen different species were identified from pasteurized single-strength orange juice that had been contaminated after pasteurization (PSOJ), while only six species were isolated from fresh-squeezed, unpasteurized orange juice (FSOJ). Among PSOJ isolates, Candida intermedia and Candida parapsilosis were the predominant species. Hanseniaspora occidentalis and Hanseniaspora uvarum represented up to 73% of total FSOJ isolates. Partial sequence of the 26S rRNA gene yielded the best results in terms of correct identification, followed by classical techniques and 5.8S-ITS analysis. The commercial identification kits RapID Yeast Plus system and API 20C AUX were able to correctly identify only 35 and 13% of the isolates, respectively. Six new 5.8S-ITS profiles were described, corresponding to Clavispora lusitaniae, Geotrichum citri-aurantii, H. occidentalis, H. vineae, Pichia fermentans, and Saccharomycopsis crataegensis. With the addition of these new profiles to the existing database, the use of 5.8S-ITS sequence became the best tool for rapid and accurate identification of yeast isolates from orange juice. PMID:11916718

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

2002-01-01

26

Identification of propulsion systems  

NASA Technical Reports Server (NTRS)

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

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

1991-01-01

27

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

PubMed

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

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

2008-11-01

28

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

PubMed Central

A simplified identification key described by Deak and Beuchat (T. Deak and L. R. Beuchat, J. Food Prot. 50:243-264, 1987) and the computer method of Barnett et al. (J. A. Barnett, R. W. Payne, and D. Yarrow, Yeast Identification Program, 1985) were used to identify 12 reference strains and 382 yeasts isolated from cultured milk products. Because the simplified key failed to account for species variability with regard to physiological, morphological, and sexual reproduction characteristics, poor agreement of the identification results was obtained. A reevaluation of the basic theoretical assumptions of the simplified key only confirmed the practical results and indicates that this identification method is unsatisfactory PMID:16348183

Rohm, Harald; Lechner, Frieda

1990-01-01

29

Use of PCR-restriction fragment length polymorphism analysis for identification of yeast species isolated from bovine intramammary infection.  

PubMed

This study reports a rapid PCR-based technique using a one-enzyme RFLP for discrimination of yeasts isolated from bovine clinical and subclinical mastitis milk samples. We analyzed a total of 1,486 milk samples collected over 1 yr in south Sardinia and northern Italy, and 142 yeast strains were preliminarily grouped based on their cultural morphology and physiological characteristics. Assimilation tests were conducted using the identification kit API ID 32C and APILAB Plus software (bioMérieux, Marcy l'Etoile, France). For PCR-RFLP analysis, the 18S-ITS1-5.8S ribosomal(r)DNA region was amplified and then digested with HaeIII, and dendrogram analysis of RFLP fragments was carried out. Furthermore, within each of the groups identified by the API or PCR-RFLP methods, the identification of isolates was confirmed by sequencing of the D1/D2 region using an ABI Prism 310 automatic sequencer (Applied Biosystems, Foster City, CA). The combined phenotypic and molecular approach enabled the identification of 17 yeast species belonging to the genera Candida (47.9%), Cryptococcus (21.1%), Trichosporon (19.7%), Geotrichum (7.1%), and Rhodotorula (4.2%). All Candida species were correctly identified by the API test and their identification confirmed by sequencing. All strains identified with the API system as Geotrichum candidum, Cryptococcus uniguttulatus, and Rhodotorula glutinis also produced characteristic restriction patterns and were confirmed as Galactomyces geotrichum (a teleomorph of G. candidum), Filobasidium uniguttulatum (teleomorph of Crypt. uniguttulatus), and R. glutinis, respectively, by D1/D2 rDNA sequencing. With regard to the genus Trichosporon, preliminary identification by API was problematic, whereas the RFLP technique used in this study gave characteristic restriction profiles for each species. Moreover, sequencing of the D1/D2 region allowed not only successful identification of Trichosporon gracile where API could not, but also correct identification of misidentified isolates. In conclusion, the 18S-ITS1-5.8S region appears to be useful in detecting genetic variability among yeast species, which is valuable for taxonomic purposes and for species identification. We have established an RFLP database for yeast species identified in milk samples using the software GelCompar II and the RFLP database constitutes an initial method for veterinary yeast identification. PMID:24119798

Fadda, M E; Pisano, M B; Scaccabarozzi, L; Mossa, V; Deplano, M; Moroni, P; Liciardi, M; Cosentino, S

2013-12-01

30

Detection and identification of wild yeast in Koumiss.  

PubMed

Koumiss is a slightly alcoholic fermented mare's milk beverage, originally obtained by using a natural mixed starter of lactic acid bacteria and yeasts. Yeast is an important component of Koumiss processing which can affect the aroma, texture, as well as the nutrients beneficial to human health, but few reports have examined the yeast ecology of local ecosystems. The purpose of this study was to isolate and identify the yeast present in Koumiss from three representative regions of China using a polyphasic method. A total of 655 yeast isolates were obtained from 96 Koumiss samples collected from three regions in China. Koumiss harbored yeast populations at 5-7 log CFU/ml. Twelve different yeast species belonging to nine genera were detected in the Koumiss samples tested, including Candida pararugosa, Dekkera anomala, Geotrichum sp., Issatchenkia orientalis, Kazachstania unispora, Kluyveromyces marxianus, Pichia deserticola, Pichia fermentans, Pichia manshurica, Pichia membranaefaciens, Saccharomyces cerevisiae and Torulaspora delbrueckii. Kluyveromyces marxianus, Kazachstania unispora and Saccharomyces cerevisiae were the dominant species present in this traditional fermented dairy product. This study is the first to identify the yeast communities associated with Koumiss in China. The results enrich our knowledge of yeast in Koumiss, give us a more complete picture of the microbial diversity in Koumiss and can be used to promote the development of the local dairy industry. PMID:22608237

Mu, Zhishen; Yang, XuJin; Yuan, Hongli

2012-09-01

31

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

PubMed

Twenty-five yeast strains isolated from sourdough samples for Panettone, Pandoro and Cornetto brioche manufactured by eight different bakeries in northern Italy were characterised. Classification was performed by the simplified identification method (SIM), Kurtzman and Fell's identification protocol, the API system from bioMérieux (France) and the MicroLog system from Biolog (USA). Genetic diversity was investigated by randomly amplified polymorphic DNA fingerprinting and mitochondrial-DNA restriction enzyme analysis. Sequences of the internal transcribed spacers between 18S and 26S rDNA genes were analysed. Candida humilis was the predominant species (56% of isolates), whereas the remaining strains (44%) were related to the Saccharomyces cerevisiae sensu stricto group. Identification systems based on phenotypic analysis proved to be unreliable to identify yeasts from sourdough. Either RAPD-PCR or mtDNA restriction analysis showed to be suitable for the identification of species, but could not be used to differentiate among the isolates at the strain level. Sequencing of the ITS region permitted a consistent classification of the sourdough yeasts. PMID:15040949

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

2004-03-01

32

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

PubMed Central

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

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

2013-01-01

33

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

E-print Network

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

Zhao, Huimin

34

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

PubMed Central

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

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

2013-01-01

35

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

PubMed Central

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

Kummerle, Michael; Scherer, Siegfried; Seiler, Herbert

1998-01-01

36

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

PubMed

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

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

2014-10-01

37

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

PubMed Central

Identification of thyroid hormone receptor (TR) co-regulators has enhanced our understanding of thyroid hormone (TH) action. However, it is likely that many other co-regulators remained unidentified, and unbiased methods are required to discover these proteins. We have previously demonstrated that the yeast Saccharomyces cerevisiae is an excellent system in which to study TR action, and that defined TR signaling complexes in a eukaryotic background devoid of complicating influences of mammalian cell co-regulators can be constructed and analyzed for endogenous yeast genes, many of which are conserved in mammals. Here, a modified synthetic genetic array analysis was performed by crossing a yeast strain that expressed TR?1 and the co-activator GRIP1/SRC2 with 384 yeast strains bearing deletions of known genes. Eight genes essential for TH action were isolated, of which 4 are conserved in mammals. Examination of one, the yeast CCR4 and its human homolog CCR4/NOT6 (hCCR4), confirmed that (i) transfected CCR4 potentiates a TH response in cultured cells more efficiently than established TR co-activators and (ii) knockdown of CCR4 expression strongly inhibited a TH response (>80%). TH treatment promoted rapid and sustained hCCR4 recruitment to the TH-responsive deiodinase 1 promoter and TR co-localizes with hCCR4 in the nucleus and interacts with hCCR4 in 2-hybrid and pull-down assays. These findings indicate that a modified yeast synthetic genetic array strategy is a feasible method for unbiased identification of conserved genes essential for TR and other nuclear receptor hormone functions in mammals. PMID:19903885

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

2009-01-01

38

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

PubMed Central

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

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

2012-01-01

39

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

PubMed Central

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

Nosek, Jozef; Tomaska, L'ubomir; Rycovska, Adriana; Fukuhara, Hiroshi

2002-01-01

40

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

PubMed

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

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

2014-10-01

41

Phenotypic and genotypic identification of yeasts from cheese  

Microsoft Academic Search

Eighty-five yeast strains isolated from different cheeses of Austria, Denmark, France, Germany, and Italy were identified using physiological methods and genotypically using random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) analysis. Good congruence was found between the phenotypic and genotypic data for 39 of the isolates. However, 26 isolates of Geotrichum could only be identified to the species level using

Hansjörg Prillinger; Orsolya Molnár; Frieda Eliskases-Lechner; Ksenija Lopandic

1999-01-01

42

Quantum identification system  

E-print Network

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

Miloslav Dusek; Ondrej Haderka; Martin Hendrych; Robert Myska

1998-09-10

43

Systems biology from a yeast omics perspective  

Microsoft Academic Search

Systems biology represents a paradigm shift from the study of individual genes, proteins or other components to that of the analysis of entire pathways, cellular, developmental, or organismal processes. Large scale studies, primarily initiated in Saccharomyces cerevisiae, have allowed the identification and characterization of components on an unprecedented level. Large scale interaction, transcription factor binding and phosphorylation data have enabled

Michael Snyder; Jennifer E. G. Gallagher

2009-01-01

44

Identification of Positive Regulators of the Yeast Fps1 Glycerol Channel  

Microsoft Academic Search

The yeast Fps1 protein is an aquaglyceroporin that functions as the major facilitator of glycerol transport in response to changes in extracellular osmolarity. Although the High Osmolarity Glycerol pathway is thought to have a function in at least basal control of Fps1 activity, its mode of regulation is not understood. We describe the identification of a pair of positive regulators

Sara E. Beese; Takahiro Negishi; David E. Levin

2009-01-01

45

Genetic Algorithms based Parameter Identification of Yeast Fed-Batch Cultivation  

E-print Network

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

Mustakerov, Ivan

46

Isolation and identification of killer yeast from fermented vegetables  

Microsoft Academic Search

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

Sunee Waema; Jaruwan Maneesri; Payap Masniyom

2009-01-01

47

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

PubMed

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

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

2014-01-01

48

Quantum System Identification  

E-print Network

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

Daniel Burgarth; Kazuya Yuasa

2011-04-04

49

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

PubMed

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

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

2014-03-01

50

Optimized System Identification  

NASA Technical Reports Server (NTRS)

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

Juang, Jer-Nan; Longman, Richard W.

1999-01-01

51

Blind system identification  

Microsoft Academic Search

Blind system identification (BSI) is a fundamental signal processing technology aimed at retrieving a system's unknown information from its output only. This technology has a wide range of possible applications such as mobile communications, speech reverberation cancellation, and blind image restoration. This paper reviews a number of recently developed concepts and techniques for BSI, which include the concept of blind

KARIM ABED-MERAIM; Wanzhi Qiu; Yingbo Hua

1997-01-01

52

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

PubMed

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

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

2014-06-13

53

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

E-print Network

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.

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

2010-01-01

54

Using a yeast inverse one-hybrid system to identify functional binding sites of transcription factors.  

PubMed

Binding of transcription factors to promoters is a necessary step to initiate transcription. From an evolutionary standpoint, the regulatory proteins and their binding sites are considered to have molecularly coevolved. We developed an efficient yeast strategy, an "inverse one-hybrid system", to identify binding targets of transcription factors globally in a genome of interest. The technique consists of a yeast strain expressing a -transcription factor of interest mated to yeast containing a library of random genomic fragments cloned upstream of a reporter gene (URA3). Positive growth on media without uracil denotes a fragment being bound by the transcription factor, e.g., zebrafish FoxI1. The bound fragments in hundreds of positive clones are sequenced and retested for their binding activities using a colony PCR and sequencing strategy. The resulting tools allow for rapid and genomic-wide identification of transcriptional binding targets. PMID:21938633

Yan, Jizhou; Burgess, Shawn M

2012-01-01

55

Quantum system identification  

E-print Network

We formulate and study, in general terms, the problem of quantum system identification, i.e., the determination (or estimation) of unknown quantum channels through their action on suitably chosen input density operators. We also present a quantitative analysis of the worst-case performance of these schemes.

Maxim Raginsky

2003-06-02

56

Automated Microbiological Detection/Identification System  

PubMed Central

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

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

1977-01-01

57

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

PubMed Central

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

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

2009-01-01

58

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

PubMed

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

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

2014-11-01

59

IMPROVED SYSTEM IDENTIFICATION FOR AEROSERVOELASTIC  

E-print Network

IMPROVED SYSTEM IDENTIFICATION FOR AEROSERVOELASTIC PREDICTIONS By CHARLES ROBERT O'NEILL Bachelor OF SCIENCE August, 2003 #12;ii IMPROVED SYSTEM IDENTIFICATION FOR AEROSERVOELASTIC PREDICTIONS Thesis......................................................................................... 28 2.6.4 Aeroservoelasticity Model

Jacob, Jamey

60

Immobilized yeast bioreactor systems for continuous beer fermentation  

PubMed

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

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

1999-01-01

61

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

PubMed Central

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

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

2013-01-01

62

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

PubMed Central

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory. PMID:20053859

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

2010-01-01

63

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

PubMed Central

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

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

2014-01-01

64

Yeast Microflora Isolated From Brazilian Cassava Roots: Taxonomical Classification Based on Molecular Identification  

Microsoft Academic Search

A rapid molecular identification technique was applied on microbial microflora isolated from Brazilian cassava roots given\\u000a a yeast profile presented in the samples analyzed. A total of 24 strain isolated from cassava were initially grouped and identified\\u000a in five groups using restriction-fragment length polymorphism (RFLPs) of 5.8S-ITS rDNA region. Sequencing analysis of the\\u000a domains D1 and D2 of the 26S

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

2010-01-01

65

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

Microsoft Academic Search

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

Zhengyu Ouyang; Z. Lewis Liu

66

System identification using transfer matrix  

Microsoft Academic Search

A new approach is proposed for multivariable system identification in the deterministic model framework. In the proposed approach, MIMO system is represented using transfer function (TF) matrix whose elements are the standard, fixed structure TFs like FOPDT, SOPDT etc. These model structures are capable of approximating well a very large class of systems found in practice. The system identification problem

Jayesh J. Barve; V. S. S. Rameshkumar Junnuri

2004-01-01

67

Yeast: A General Purpose Event-Action System  

Microsoft Academic Search

Distributed networks of personal workstations are becoming the dominant computing environment for software development organizations. Many cooperative activities that are carried out in such environments are particularly well suited for automated support. Taking the point of view that such activities are modeled most naturally as the occurrence of events requiring actions to be performed, we developed a system called Yeast

Balachander Krishnamurthy; David S. Rosenblum

1995-01-01

68

A molecular genetic system for the pathogenic yeast Candida dubliniensis  

Microsoft Academic Search

Candida dubliniensis is a recently described pathogenic yeast of the genus Candida that is closely related to Candida albicans but differs from it in several phenotypic and genotypic characteristics, including putative virulence traits, which may explain differences in the spectrum of diseases caused by the two species. In contrast to C. albicans, a molecular genetic system to study virulence of

Peter Staib; Sonja Michel; Gerwald Köhler; Joachim Morschhäuser

2000-01-01

69

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

PubMed Central

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

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

2014-01-01

70

Linear pattern identification system  

NASA Astrophysics Data System (ADS)

A novel solution for image pattern identification based on the description of linear structure is proposed. The concept is currently applied to the classification of documents such as business forms and logos. The geometric layout of objects such as lines, text and spacing is converted to a 1D string representation. A novel, generic and quantized string format is proposed for the system. Very encouraging results have been obtained and the technique can be used for a wide range of applications and extended to handle patterns including electronic circuit diagrams without obvious linear features. The use of strings facilities quick and robust measures of similarity between two patterns and a quantifiable tolerance of segmentation inconsistencies is possible. In addition, no training is required.

Ting, Antoine; Leung, Maylor K. H.

1997-08-01

71

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

PubMed

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

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

2008-09-01

72

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

PubMed Central

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

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

2011-01-01

73

Systems-level engineering of nonfermentative metabolism in yeast.  

PubMed

We designed and experimentally validated an in silico gene deletion strategy for engineering endogenous one-carbon (C1) metabolism in yeast. We used constraint-based metabolic modeling and computer-aided gene knockout simulations to identify five genes (ALT2, FDH1, FDH2, FUM1, and ZWF1), which, when deleted in combination, predicted formic acid secretion in Saccharomyces cerevisiae under aerobic growth conditions. Once constructed, the quintuple mutant strain showed the predicted increase in formic acid secretion relative to a formate dehydrogenase mutant (fdh1 fdh2), while formic acid secretion in wild-type yeast was undetectable. Gene expression and physiological data generated post hoc identified a retrograde response to mitochondrial deficiency, which was confirmed by showing Rtg1-dependent NADH accumulation in the engineered yeast strain. Formal pathway analysis combined with gene expression data suggested specific modes of regulation that govern C1 metabolic flux in yeast. Specifically, we identified coordinated transcriptional regulation of C1 pathway enzymes and a positive flux control coefficient for the branch point enzyme 3-phosphoglycerate dehydrogenase (PGDH). Together, these results demonstrate that constraint-based models can identify seemingly unrelated mutations, which interact at a systems level across subcellular compartments to modulate flux through nonfermentative metabolic pathways. PMID:19564482

Kennedy, Caleb J; Boyle, Patrick M; Waks, Zeev; Silver, Pamela A

2009-09-01

74

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

PubMed Central

Experience with a MicroSeq D2 large-subunit (LSU) ribosomal DNA (rDNA) sequencing kit for identification of yeast species commonly encountered in the mycology laboratory at Mayo Clinic is described here. A total of 131 isolates of yeasts recovered from clinical specimens were included in the study. Phenotypic methods used for initial identification included germ tube formation, urease production, microscopic morphological features on cornmeal agar, and an API 20C AUX system; all isolates were sequenced using a MicroSeq D2 LSU rDNA sequencing kit. Nucleic acid sequencing identified 93.9% of the isolates to the correct genus and species. A total of 100 of the isolates (representing 19 species of Candida) were sequenced, and 98% gave results concordant with identifications made by the API 20C AUX system; distance scores ranged from 0 to 1.88%, with an average value of 0.23%. Candida dubliniensis was not included in the MicroSeq database and was identified as Candida albicans. A total of 32 isolates representing 9 other genera (including Cryptococcus, Filobasidium, Kloeckera, Malassezia, Pichia, Sporidiobolus, Rhodotorula, Zygosaccharomyces, and Trichosporon) were included, and 81.3% showed concordant results when phenotypic and sequencing results were compared. Most discrepancies were attributed to the lack of inclusion of the species in the MicroSeq or API 20C AUX database. The MicroSeq D2 LSU rDNA sequencing kit appears to be accurate and useful for the identification of yeasts that might be seen in a clinical laboratory. PMID:14605145

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

2003-01-01

75

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

PubMed

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

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

2008-09-01

76

Multisensor fusion for system identification  

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

77

Multifunctional analysis of Chlamydia-specific genes in a yeast expression system.  

PubMed

Our understanding of how obligate intracellular pathogens co-opt eukaryotic cellular functions has been limited by their intractability to genetic manipulation and by the abundance of pathogen-specific genes with no known functional homologues. In this report we describe a gene expression system to characterize proteins of unknown function from the obligate intracellular bacterial pathogen Chlamydia trachomatis. We have devised a homologous recombination-based cloning strategy to construct an ordered array of Saccharomyces cerevisiae strains expressing all Chlamydia-specific genes. These strains were screened to identify chlamydial proteins that impaired various yeast cellular functions or that displayed tropism towards eukaryotic organelles. In addition, to identify bacterial factors that are secreted into the host cell, recombinant chlamydial proteins were screened for reactivity towards antisera raised against vacuolar membranes purified from infected mammalian cells. We report the identification of 34 C. trachomatis proteins that impact yeast cellular functions or are tropic for a range of eukaryotic organelles including mitochondria, nucleus and cytoplasmic lipid droplets, and a new family of Chlamydia-specific proteins that are exported from the parasitopherous vacuole. The versatility of molecular manipulations and protein expression in yeast allows for the rapid construction of comprehensive protein expression arrays to explore the function of pathogen-specific gene products from microorganisms that are difficult to genetically manipulate, grow in culture or too dangerous for routine analysis in the laboratory. PMID:16556220

Sisko, Jennifer L; Spaeth, Kris; Kumar, Yadunanda; Valdivia, Raphael H

2006-04-01

78

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

PubMed Central

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

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

2010-01-01

79

Development and characterization of a reconstituted yeast translation initiation system.  

PubMed Central

To provide a bridge between in vivo and in vitro studies of eukaryotic translation initiation, we have developed a reconstituted translation initiation system using components from the yeast Saccharomyces cerevisiae. We have purified a minimal set of initiation factors (elFs) that, together with yeast 80S ribosomes, GTP, and initiator methionyl-tRNA, are sufficient to assemble active initiation complexes on a minimal mRNA template. The kinetics of various steps in the pathway of initiation complex assembly and the formation of the first peptide bond in vitro have been explored. The formation of active initiation complexes in this system is dependent on ribosomes, mRNA, Met-tRNAi, GTP hydrolysis, elF1, elF1A, elF2, elF5, and elF5B. Our data indicate that elF1 and elF1A both facilitate the binding of the elF2 x GTP x Met-tRNAi complex to the 40S ribosomal subunit to form the 43S complex. elF5 stimulates a step after 43S complex formation, consistent with its proposed role in activating GTP hydrolysis by elF2 upon initiation codon recognition. The presence of elF5B is required for the joining of the 40S and 60S subunits to form the 80S initiation complex. The step at which each of these factors acts in this reconstituted system is in agreement with previous data from in vivo studies and work using reconstituted mammalian systems, indicating that the system recapitulates fundamental events in translation initiation in eukaryotic cells. This system should allow us to couple powerful yeast genetic and molecular biological experiments with in vitro kinetic and biophysical experiments, yielding a better understanding of the molecular mechanics of this central, complex process. PMID:12008673

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

2002-01-01

80

NADP Regulates the Yeast GAL Induction System  

SciTech Connect

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

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

2008-01-01

81

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

PubMed Central

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

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

1997-01-01

82

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

E-print Network

conservation to find complexes that are common to yeast S. Cerevisiae and bacteria H. pylori. Our analysis this approach on the data currently available for yeast and bacteria and detected 11 significantly conserved for a variety of uncharacterized proteins. By identifying a conserved complex whose yeast proteins function

Shamir, Ron

83

System identification. [of space structures  

NASA Technical Reports Server (NTRS)

Major issues in system identification are summarized and recent advances are reviewed. Modal testing and system identification used in control theory are examined, and the mathematical relationships and conversions of the models appropriate to modal testing and those appropriate to modern control design methods are discussed. The importance of obtaining input and output matrices in modal testing is emphasized, and the changes that may be needed in modal testing procedures to meet the needs of the control system designer are addressed. Directions for future research are considered.

Juang, Jer-Nan

1993-01-01

84

Systems identification - reprise and projections  

NASA Technical Reports Server (NTRS)

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

Taylor, L. W., Jr.

1974-01-01

85

System identification using Kautz models  

Microsoft Academic Search

In this paper, the problem of approximating a linear time-invariant stable system by a finite weighted sum of given exponentials is considered. System identification schemes using Laguerre models are extended and generalized to Kautz models, which correspond to representations using several different possible complex exponentials. In particular, linear regression methods to estimate this sort of model from measured data are

B. Wahlberg

1994-01-01

86

System identification for multivariable control  

Microsoft Academic Search

System identification methods and modern control theory are applied to industrial processes. These processes must often be controlled in order to meet certain requirements with respect to the product quality, safety, energy consumption, and environmental load. Modern control system design methods which take the occurring interaction phenomena and stochastic disturbances into account are used. An accurate dynamic mathematical model of

G. A. Vanzee

1981-01-01

87

Yeast Systems Biology: Our Best Shot at Modeling a Cell  

PubMed Central

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

Boone, Charles

2014-01-01

88

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

PubMed

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

Inoue, Yoshiharu; Maeta, Kazuhiro; Nomura, Wataru

2011-05-01

89

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

PubMed

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

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

2012-10-01

90

New and emerging yeast pathogens.  

PubMed Central

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

Hazen, K C

1995-01-01

91

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

PubMed

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

Koh, Yvonne Y; Wickens, Marvin

2014-01-01

92

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

PubMed Central

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

Thornton, Mark A.; Thornton, Roy J.

2013-01-01

93

Open quantum system identification  

E-print Network

Engineering quantum systems offers great opportunities both technologically and scientifically for communication, computation, and simulation. The construction and operation of large scale quantum information devices presents a grand challenge and a major issue is the effective control of coherent dynamics. This is often in the presence of decoherence which further complicates the task of determining the behaviour of the system. Here, we show how to determine open system Markovian dynamics of a quantum system with restricted initialisation and partial output state information.

Sophie G. Schirmer; Daniel K. L. Oi; Weiwei Zhou; Erling Gong; Ming Zhang

2012-05-28

94

A comparison and optimization of yeast two-hybrid systems.  

PubMed

Two-hybrid (Y2H) assays are available in a variety of different versions, including bacterial, yeast, and mammalian systems. However, even when done exclusively in yeast, multiple different host strains, vectors, reporter genes, or protocols can be used. Here we systematically compare protein-protein interactions (PPIs) from several previously published Y2H datasets. PPIs of a human gold-standard dataset were generated by Y2H assays as well as other methods such as LUMIER or protein fragment complementation assays (PCAs). Different Y2H methods detect substantially different subsets of these PPIs, even when protocols are standardized. In order to maximize the number of interactions found and to minimize the number of false positive interactions we recommend to combine multiple vectors and protocols. While the combined results of all 18 methods detected about 92% of a gold-standard interaction set, a combination of just three Y2H assays detected up to 78% of these protein pairs, or up to 83% when a fourth assay was included. These findings indicate that three or four separate assays may be sufficient to detect the majority of protein-protein interactions in many systems. PMID:23231818

Caufield, J H; Sakhawalkar, Neha; Uetz, Peter

2012-12-01

95

Neural networks for system identification  

Microsoft Academic Search

Two approaches are presented for utilization of neural networks in identification of dynamical systems. In the first approach, a Hopfield network is used to implement a least-squares estimation for time-varying and time-invariant systems. The second approach, which is in the frequency domain, utilizes a set of orthogonal basis functions and Fourier analysis to construct a dynamic system in terms of

S. Reynold Chu; Rahmat Shoureshi; Manoel Tenorio

1990-01-01

96

System Identification for Robust Control  

Microsoft Academic Search

This paper presents a robust-control-oriented system identification method aiming to minimize the normalized coprime factor uncertainty of the performance-weighted system. The nominal model and the normalized coprime factor uncertainty bound are estimated employing a filter bank approach, which approximately calculates the chordal distance between the identified model and the true system in the frequency range of interest. An iterative LMI

Charles Q. Zhan; Kostas Tsakalis

2007-01-01

97

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

Microsoft Academic Search

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

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

98

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

Microsoft Academic Search

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

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

2011-01-01

99

Automated drug identification system  

NASA Technical Reports Server (NTRS)

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

Campen, C. F., Jr.

1974-01-01

100

Comparison of Equivalent System Mass of Yeast and Flat Bread Systems  

Microsoft Academic Search

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

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

2003-01-01

101

Development of An ECG Identification System.  

National Technical Information Service (NTIS)

The purpose of this paper is to present a new identification engine for an ECG identification system. The system identifies subjects based on a comparison of a patient's ECG with previously registered ECG feature parameters. These feature parameters are s...

M. Kyoso, A. Uchiyama

2001-01-01

102

Mitochondrial assembly in yeast.  

PubMed

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 of the electron transport chain. Translation and respiratory complex assembly are particularly expensive processes, together requiring around 150 of the proteins so far known. Recent developments in both areas are reviewed and approaches to the identification of novel mitochondrial proteins are discussed. PMID:10376678

Grivell, L A; Artal-Sanz, M; Hakkaart, G; de Jong, L; Nijtmans, L G; van Oosterum, K; Siep, M; van der Spek, H

1999-06-01

103

Identification of a gene conferring resistance to zinc and cadmium ions in the yeast Saccharomyces cerevisiae  

Microsoft Academic Search

A DNA fragment conferring resistance to zinc and cadmium ions in the yeast Saccharomyces cerevisiae was isolated from a library of yeast genomic DNA. Its nucleotide sequence revealed the presence of a single open reading frame (ORF; 1326 bp) having the potential to encode a protein of 442 amino acid residues (molecular mass of 48.3 kDa). A frameshift mutation introduced

Akihito Kamizono; Masafumi Nishizawa; Yutaka Teranishi; Kousaku Murata; Akira Kimura

1989-01-01

104

A bimodal biometric identification system  

NASA Astrophysics Data System (ADS)

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

Laghari, Mohammad S.; Khuwaja, Gulzar A.

2013-03-01

105

Molecular identification of marine yeast and its spectroscopic analysis establishes unsaturated fatty acid accumulation.  

PubMed

Marine microbes are competent organisms, some of which can accumulate large amounts of lipids. A yeast strain, Rhodotorula mucilaginosa AMCQ8A was isolated from the marine water of the Queenscliff region, Victoria, Australia. The yeast isolate was identified by sequencing 18s rDNA genes. Scanning electron microscopy images revealed scars on the surface of the yeast cells. The Fourier transform infrared spectroscopy microspectroscopy studies demonstrated the presence of unsaturated fatty acids by differential microscopic analysis. The sharp band at 1745 cm?¹ was represented by ?(C=O) stretches of ester functional groups from lipids and fats, and therefore indicated the presence of total lipids produced by the cells. Over 65% of the fatty acids from the yeast strain were analyzed as C?? and C??:? with omega-3 content from about 6% to 7%. Thus, this marine-derived yeast could be a potential source of lipids, including omega-3 fatty acids. PMID:22727444

Gupta, Adarsha; Vongsvivut, Jitraporn; Barrow, Colin J; Puri, Munish

2012-10-01

106

Practical Attacks on Proximity Identification Systems  

E-print Network

Practical Attacks on Proximity Identification Systems Gerhard P. Hancke May 26, 2006 Practical Attacks on Proximity Identification Systems ­ p. #12;RFID Devices Applications Logistics Access control on Proximity Identification Systems ­ p. #12;Security Concerns Various attacks proposed Kfir and Wool (2005

Hancke, Gerhard

107

Lightning discharge identification system  

NASA Technical Reports Server (NTRS)

A system for differentiating between cloud to cloud and cloud to ground lightning discharges is described which includes an electric field antenna that senses the rate of charge of an electric field produced by a lightning discharge. When the signal produced by the electric field exceeds a predetermined threshold, it is fed to a coincidence detector. A VHF antenna is also provided and generates a video signal responsive to a cloud to cloud lightning discharge, and this signal is fed through a level sensor, an inverter, to the coincidence detector simultaneously with the signal from the field detector. When signals from the electric field antenna and the VHF antenna appear at the coincidence detector simultaneously, such indicates that there is a cloud to cloud lightning discharge; whereas, when there is not a signal produced on the VHF antenna simultaneously with a signal produced by the field sensor, then a strike indicator connected to the coincidence detector indicates a cloud to ground lightning discharge.

Lennon, C. L. (inventor)

1981-01-01

108

Sex-determination system in the diploid yeast Zygosaccharomyces sapae.  

PubMed

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

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

2014-06-01

109

Occurrence and identification of yeast species in fermented liquid feed for piglets.  

PubMed

The major objective of the present study was to investigate the occurrence and identity of yeast species in fermented liquid feed (FLF) used for feeding piglets. In total, 40 different Danish farms were included in the analysis. The preparation and composition of FLF was found to be very heterogeneous with high variations in both yeast counts and yeast species composition. The yeast population varied between 6.0 × 10(3) and 4.2 × 10(7) cfug(-1) with an average yeast count of 8.7 × 10(6) ± 1.1 × 10(7) cfug(-1). A total of 766 yeasts were isolated and identified by conventional and/or molecular typing techniques. The predominant yeast species in the FLF samples were found to be Candida milleri (58.4%), Kazachstania exigua (17.5%), Candida pararugosa (6.40%) and Kazachstania bulderi (5.09%). No clear separation between isolates of C. milleri and Candida humilis could be obtained based on sequencing of the D1/D2 region of the 26S rRNA gene. The combined use of ITS-RFLP analysis and phenotypic criteria did meanwhile suggest a closer relationship with C. milleri than C. humilis. PMID:20574824

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

2011-01-01

110

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

PubMed Central

Pyrosequencing was used to identify 133 isolates of clinically relevant non-dematiaceous yeasts. These included 97 ATCC strains (42 type strains), 7 UAMH strains, and 29 clinical isolates. Isolates belonged to the following genera: Candida (18 species), Trichosporon (10), Cryptococcus (7), Malassezia (3), Rhodotorula (2), Geotrichum (1), Blastoschizomyces (1) and Kodamaea (1). Amplicons were obtained of a hypervariable ITS region and analyzed using Pyrosequencing technology. The data were evaluated by a BLAST search against the GenBank database and correlated with data obtained by conventional cycle sequencing of the ITS1-5.8S-ITS2 region. Cycle sequencing identified (78.9%) if the isolates to the species level. Pyrosequencing technology identified 69.1%. In 90.1% of all the strains tested, identification results of both sequencing methods were identical. Most Candida isolates can be identified to the species level by pyrosequencing. Trichosporon species and some Cryptococcus cannot be differentiated at the species level. Pyrosequencing can be used for the reliable identification of most commonly isolated non-dematiaceous yeasts, with a reduction of cost per identification compared to conventional sequencing. PMID:18421488

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

2008-01-01

111

Automated systems for identification of microorganisms.  

PubMed Central

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

Stager, C E; Davis, J R

1992-01-01

112

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

PubMed Central

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

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

2010-01-01

113

Identification of the C. elegansanaphase promoting complex subunit Cdc26 by phenotypic profiling and functional rescue in yeast  

E-print Network

ral ssBioMed CentBMC Developmental Biology Open AcceResearch article Identification of the C. elegans anaphase promoting complex subunit Cdc26 by phenotypic profiling and functional rescue in yeast Yan Dong1, Aliona Bogdanova2, Bianca Habermann2... of RNAi feeding arrested as a single cell (Table 1). At intermediate time points, both types of terminal arrest embryos were seen (Table 1). To investigate the arrest stage of the embryos after strong RNAi of B0511.9 we examined the pattern of DNA con...

Dong, Yan; Bogdanova, Aliona; Habermann, Bianca; Zachariae, Wolfgang; Ahringer, Julie

2007-03-20

114

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

Microsoft Academic Search

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

Mogens Jakobsen; Judy Narvhus

1996-01-01

115

Quantum identification system Miloslav Dusek,1  

E-print Network

identification system combining a classical identification procedure and quantum key distribution is proposed only once and the distribution of a common secret string is achieved by means of quantum keyQuantum identification system Miloslav Dusek,1 Ondrej Haderka,2,1 Martin Hendrych,2,1 and Robert

Dusek, Miloslav

116

Identification of She3 as an SCFGrr1 Substrate in Budding Yeast  

PubMed Central

The highly orchestrated progression of the cell cycle depends on the degradation of many regulatory proteins at different cell cycle stages. One of the key cell cycle ubiquitin ligases is the Skp1-cullin-F-box (SCF) complex. Acting in concert with the substrate-binding F-box protein Grr1, SCFGrr1 promotes the degradation of cell cycle regulators as well as various metabolic enzymes. Using a yeast two-hybrid assay with a Grr1 derivative as the bait, we identified She3, which is an adaptor protein in the asymmetric mRNA transport system, as a novel Grr1 substrate. We generated stabilized She3 mutants, which no longer bound to Grr1, and found that the degradation of She3 is not required for regulating asymmetric mRNA transport. However, She3 stabilization leads to slower growth compared to wild-type cells in a co-culture assay, demonstrating that the degradation of She3 by Grr1 is required for optimal cell growth. PMID:23144720

Wang, Ruiwen; Solomon, Mark J.

2012-01-01

117

Identifiability and algebraic identification of time delay systems  

E-print Network

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

Boyer, Edmond

118

Substructure system identification and synthesis  

NASA Technical Reports Server (NTRS)

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

Su, Tzu-Jeng; Juang, Jer-Nan

1993-01-01

119

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

PubMed

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

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

2006-04-01

120

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

PubMed

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

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

1997-02-01

121

Isolation and identification of a yeast strain capable of degrading four and five ring aromatic hydrocarbons  

Microsoft Academic Search

A yeast strain AEH was isolated from oil contaminated soil and identified by analysis of 18S and 26S ribosomal DNA sequences\\u000a asPichia anomala. Strain AEH was capable of degrading naphthalene, phenanthrene and chrysene, singly, and benzo(a)pyrene in combination. The\\u000a yeast degraded 5.36 mg naphthalene l?1 within 2 days, and 5.04 mg phenanthrene l?1 and 1.54 mg chrysene 1?1 within 10

Abd El-Latif Hesham; Zhenyu Wang; Yu Zhang; Jing Zhang; Wenzhou Lv; Min Yang

2006-01-01

122

Evolutionary systems biology of amino acid biosynthetic cost in yeast.  

PubMed

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

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

2010-01-01

123

Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast  

PubMed Central

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

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

2010-01-01

124

Rapid fermentation of beer using an immobilized yeast multistage bioreactor system  

Microsoft Academic Search

A multistage bioreactor system for rapid beer fermentation was developed. The main fermentation process, which conventionally\\u000a requires 7 d, could be shortened to 2 d by this system. The concentration of esters and higher alcohols are major factors\\u000a in brewery fermentation, their production being closely related to the yeast growth phase. Yeast metabolism was successfully\\u000a subdivided into a growth and

Yoshihiro Yamauchi; Takanori Okamoto; Hiroshi Murayama; Akira Nagara; Tadashi Kashihara; Masasi Yoshida; Koichi Nakanishp

1995-01-01

125

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

E-print Network

IMPROVING THE YEAST THREE-HYBRID SYSTEM FOR HIGH-THROUGHPUT TARGET DISCOVERY By Kyle D. Bailey Submitted to the graduate degree program in Medicinal Chemistry and the Graduate Faculty of the University of Kansas in partial fulfillment.... Jeff Krise Date Defended: April 14, 2011 ii The Thesis Committee for Kyle D. Bailey certifies that this is the approved version of the following dissertation: IMPROVING THE YEAST THREE-HYBRID SYSTEM FOR HIGH-THROUGHPUT TARGET...

Bailey, Kyle

2011-05-27

126

Current status of system identification methodology  

NASA Technical Reports Server (NTRS)

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

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

1983-01-01

127

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

Microsoft Academic Search

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

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

2002-01-01

128

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

PubMed

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

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

2014-06-01

129

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

PubMed Central

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

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

2003-01-01

130

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

Microsoft Academic Search

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

Benoît van Hille; Bridget T. Hill

1998-01-01

131

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

PubMed

The yeast Saccharomyces cerevisiae has proved to be an excellent model organism to study the function of proteins. One of the many advantages of yeast is the many genetic tools available to manipulate gene expression, but there are still limitations. To complement the many methods used to control gene expression in yeast, we have established a conditional gene deletion system by using the FLP/FRT system on yeast vectors to conditionally delete specific yeast genes. Expression of Flp recombinase, which is under the control of the GAL1 promoter, was induced by galactose, which in turn excised FRT sites flanked genes. The efficacy of this system was examined using the FRT site-flanked genes HSP104, URA3 and GFP. The pre-excision frequency of this system, which might be caused by the basal activity of the GAL1 promoter or by spontaneous recombination between FRT sites, was detected ca. 2% under the non-selecting condition. After inducing expression of Flp recombinase, the deletion efficiency achieved ca. 96% of cells in a population within 9 h. After conditional deletion of the specific gene, protein degradation and cell division then diluted out protein that was expressed from this gene prior to its excision. Most importantly, the specific protein to be deleted could be expressed under its own promoter, so that endogenous levels of protein expression were maintained prior to excision by the Flp recombinase. Therefore, this system provides a useful tool for the conditional deletion of genes in yeast. PMID:21823166

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

2011-09-01

132

System identification for passive linear quantum systems  

E-print Network

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

Madalin Guta; Naoki Yamamoto

2013-03-15

133

Phenotypic and molecular identification of yeast species associated with Spanish blue-veined Cabrales cheese  

Microsoft Academic Search

Classification of 74 yeasts isolated during manufacture and ripening of Cabrales cheese was attemped by phenotypic and molecular methods. Phenotypic classification included the use of commercial kits and classical biochemical analyses. Molecular classification was performed by restriction fragment length polymorphism (RFLP) of the ITS1-5.8S-ITS2 region, sequencing and comparison of the sequences in databases. Forty-one isolates were identified by phenotypic tests,

Pablo Álvarez-Martín; Ana Belén Flórez; Teresa María López-Díaz; Baltasar Mayo

2007-01-01

134

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

SciTech Connect

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

Holmes, R.L.

1982-04-01

135

System identification of an open water channel  

Microsoft Academic Search

In this paper, models of the water level in an irrigation channel are derived from system identification experiments. We present the complete system identification procedure from experiment design to model validation, taking into account prior physical information and that the intended use of the models is prediction and control. It is shown that first and second order models capture the

Erik Weyer

2001-01-01

136

Binding of rat brain hexokinase to recombinant yeast mitochondria: identification of necessary physico-chemical determinants.  

PubMed

The association of rat brain hexokinase with heterologous recombinant yeast mitochondria harboring human porin (Yh) is comparable to that with rat liver mitochondria in terms of cation requirements, cooperativity in binding, and the effect of amphipathic compounds. Mg2+, which is required for hexokinase binding to all mitochondria, can be replaced by other cations. The efficiency of hexokinases, however, depends on the valence of hydrophilic cations, or the partition of hydrophobic cations in the membrane, implying that these act by reducing a prohibitive negative surface charge density on the outer membrane rather than fulfilling a specific structural requirement. Macromolecular crowding (using dextran) has dual effects. Dextran added in excess increases hexokinase binding to yeast mitochondria, according to the porin molecule they harbor. This effect, significant with wild-type yeast mitochondria, is only marginal with Yh as well as rat mitochondria. On the other hand, an increase in the number of hexokinase binding sites on mitochondria is also observed. This increase, moderate in wild-type organelles, is more pronounced with Yh. Finally, dextran, which has no effect on the modulation of hexokinase binding by cations, abolishes the inhibitory effect of amphipathic compounds. Thus, while hexokinase binding to mitochondria is predetermined by the porin molecule, the organization of the latter in the membrane plays a critical role as well, indicative that porin must associate with other mitochondrial components to form competent binding sites on the outer membrane. PMID:10806396

Azoulay-Zohar, H; Aflalo, C

2000-05-01

137

Stochastic system identification in structural dynamics  

USGS Publications Warehouse

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

Safak, Erdal

1988-01-01

138

Covert electronic battlefield identification system  

SciTech Connect

An electronic identification system is described for use by vehicles on a battlefield, said system comprising: an interrogator circuit in one of said vehicles and a transponder circuit in the remaining vehicles; each of said interrogator and transponder circuits including a code generating means which generates the same sequence of chip signals and timing means which generate synchronized reference timing signals; said interrogator circuit further including: (1) a range finding means which determines the propagation time for a radio signal to travel from said interrogator circuit to a selectable one of said remaining vehicles, and, (2) a transmitting means which transmits via radio said sequence of chip signals advanced in time relative to said reference timing signals by said propagation time; said transponder circuit further including: (1) a correlator means for receiving the transmitted chip signals in synchronization with said reference timing signals and correlating same with said sequence of chip signals from its own code generating means, and (2) a response circuit for transmitting via radio a response only if the result of said correlating exceeds a certain threshold.

Mouldin, R.B.; Saggio, R.J.

1993-07-27

139

System Identification: Time Varying and Nonlinear Methods  

E-print Network

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...

Majji, Manoranjan

2010-07-14

140

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

PubMed Central

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

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

2013-01-01

141

Learning Dynamics: System Identification for Perceptually Challenged Agents  

E-print Network

Learning Dynamics: System Identification for Perceptually Challenged Agents Kenneth Basye available to the agent in particular states of the environment. We view dynamical system identification efficient, high�probability learning algorithms for a number of system identification problems involving

Kaelbling, Leslie Pack

142

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

PubMed

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

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

2011-01-01

143

Heat Capacity Identification Method Using MT System  

NASA Astrophysics Data System (ADS)

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.

Suzuki, Arata; Sugimoto, Kenji

144

Automated multivariable system identification and industrial applications  

Microsoft Academic Search

A technology for automatic identification or modeling of multivariable systems from observational input\\/output data has been applied to a number of difficult industrial applications resulting in major improvements. A tutorial presentation is made of the primary elements of this technology, followed by a discussion of significant applications. This technology involves the identification of linear, time invariant dynamical processes with noise

W. E. Larimore; California June

1999-01-01

145

Favored isolation and rapid identification of the astaxanthin-producing yeast Xanthophyllomyces dendrorhous(Phaffia rhodozyma) from environmental samples.  

PubMed

Xanthophyllomyces dendrorhous (Phaffia rhodozyma) yeasts are biotechnologically exploited as a natural source of astaxanthin for aquaculture. Based on results of recent studies, it has become clear that this species possesses a greater genetic variability generating the necessity to uncover it and assess its potential for the astaxanthin industry. However, difficulties for the isolation of the X. dendrorhous hinder extensive environmental surveys which need to be carried out to better understand the habitat, distribution and genetic diversity of this species. We extensively searched for distinctive physiological traits of X. dendrorhours by testing phenotypic properties simultaneously with a panel of common sympatric fungi. As a result we obtained a new and innovative strategy for improving X. dendrorhous recovery rate and identification from environmental samples. This strategy involved the use of trehalose-based media, and a rapid X. dendrorhous identification method based on the simultaneous spectrophotometric detection of astaxanthin and UV-absorbing compounds (mycosporines). The proposed procedures proved effective in field trials conducted in natural environments of Patagonia (Argentina) and thus represent an important tool for the discovery of new astaxanthin-producing strains of X. dendrorhous useful for the aquaculture industry. PMID:23417292

Tognetti, Celia; Moliné, Martín; van Broock, María; Libkind, Diego

2013-09-01

146

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

PubMed

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

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

2013-06-01

147

Efficient least squares FIR system identification  

Microsoft Academic Search

If finite impulse response (FIR) system identification is performed by minimizing the squared error between the measured system output and an estimate from an FIR system output, a set of least squares normal equations to be solved for the FIR system coefficients is obtained. If the assumed FIR system is of duration M samples, the usual solution for the M

1981-01-01

148

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

PubMed

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

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

2014-01-01

149

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

PubMed Central

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

Morawska, Magdalena; Ulrich, Helle D

2013-01-01

150

Study of amyloids using yeast  

PubMed Central

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

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

2012-01-01

151

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

PubMed Central

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

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

2010-01-01

152

Identification of Information in Decision Systems  

E-print Network

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

Datta, Shoumen

2007-01-01

153

Security approaches for Radio Frequency Identification systems  

E-print Network

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

Foley, Joseph Timothy, 1976-

2007-01-01

154

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

Microsoft Academic Search

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

Joaquin Panadero; Francisca Randez-Gil; Jose Antonio Prieto

2005-01-01

155

Key distribution system based on identification information  

Microsoft Academic Search

A key distribution system (KDS) based on identification information (ID-based KDS) is presented. The system is founded on the Diffie-Hellman public key distribution scheme and has an identity authentication function. It uses an individual user's identification information instead of the public file used in the Diffie-Hellman scheme. It does not require any services of a center to distribute work keys

EIJI OKAMOTO; KAZUE TANAKA

1989-01-01

156

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

PubMed

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

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

2013-08-01

157

On model structure testing in system identification  

Microsoft Academic Search

In system identification it is assumed in many cases that the order of the system is known. Thus it is important to perform tests for determining the correct model order. For a single-input, single-output system the order is the only structural parameter, but for multivariable systems there are several structural parameters. It is in such cases not enough to test

T. Soderstrom

1977-01-01

158

Norovirus capsid protein expressed in yeast forms virus-like particles and stimulates systemic and mucosal immunity in mice following an oral administration of raw yeast extracts.  

PubMed

Norovirus (NV) gastroenteritis is a widespread disease affecting people of all ages worldwide. A simple, safe, and easily deliverable vaccine may be the key for the control and prevention of NV gastroenteritis. In this study, we demonstrated that a NV recombinant capsid protein (strain VA387, genogroup II.4) expressed in yeast (Pichia pastoris) spontaneously formed virus-like particles (VLPs) like those expressed in other in vitro systems. Oral administration of raw material from the yeast cell lysates containing 0.1 mg of VLPs without an adjuvant resulted in systemic and mucosal immune responses in mice. Significantly higher and earlier responses were observed in mice receiving a higher dose (1 mg per dose) of the antigen. Both the serum and fecal antibodies blocked VA387 VLP binding to its histo-blood group antigen receptors. The animals did not reveal any side effect following the administration of the yeast lysates. Our results indicated that yeast is a simple, effective alternative for NV VLP production. The mice immunization study also indicated that the oral administration of raw yeast extracts without an adjuvant is a safe and simple way which is worth to be studied for vaccine delivery in humans. PMID:17133551

Xia, Ming; Farkas, Tibor; Jiang, Xi

2007-01-01

159

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

PubMed

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

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

2013-02-01

160

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

PubMed Central

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

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

2011-01-01

161

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

PubMed Central

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

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

2013-01-01

162

[Genotoxicity of herbicide 83-1 in yeast assay system].  

PubMed

The genotoxicity of Herbicide 83-1 (Dichloronitrophenolamide, DCNPA) was detected by the yeast D61.M and D7 assay with multi-endpoint. We noted that the frequency of cyhR (resistance to cycloheximide) colonies of D61.M treated with DCNPA on cycloheximide medium was much higher than that of the control (P < 0.01) and that there was a dose-response relationship. These showed that the positivity responsed to the mitotic crossing-over endpoint. To the remaining endpoints in the D61.M and D7 assay, however, the negative response was obtained. The results have demonstrated that Herbicide 83-1 is a DNA damage agent. PMID:8340103

Heng, Z; Wu, D; Tang, X

1993-03-01

163

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

NASA Astrophysics Data System (ADS)

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

Parra-Belky, Karlett

2002-11-01

164

On Markov parameters in system identification  

NASA Technical Reports Server (NTRS)

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

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

1991-01-01

165

Protein expression-yeast.  

PubMed

Yeast is an excellent system for the expression of recombinant eukaryotic proteins. Both endogenous and heterologous proteins can be overexpressed in yeast (Phan et al., 2001; Ton and Rao, 2004). Because yeast is easy to manipulate genetically, a strain can be optimized for the expression of a specific protein. Many eukaryotic proteins contain posttranslational modifications that can be performed in yeast but not in bacterial expression systems. In comparison with mammalian cell culture expression systems, growing yeast is both faster and less expensive, and large-scale cultures can be performed using fermentation. While several different yeast expression systems exist, this chapter focuses on the budding yeast Saccharomyces cerevisiae and will briefly describe some options to consider when selecting vectors and tags to be used for protein expression. Throughout this chapter, the expression and purification of yeast eIF3 is shown as an example alongside a general scheme outline. PMID:24423273

Nielsen, Klaus H

2014-01-01

166

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

Microsoft Academic Search

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

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

2001-01-01

167

Identifying proteins that bind a known RNA sequence using the yeast three-hybrid system.  

PubMed

The yeast three-hybrid system can be used to identify a protein partner of a known RNA sequence by screening a cDNA library fused to a transcription activation domain, with a hybrid RNA as 'bait.' Most commonly, such screens are performed to identify proteins that interact with a given RNA in vivo. PMID:24581445

Koh, Yvonne Y; Wickens, Marvin

2014-01-01

168

RNAprotein interactions in the yeast three-hybrid system: Affinity, sensitivity, and enhanced library screening  

E-print Network

METHOD RNA­protein interactions in the yeast three-hybrid system: Affinity, sensitivity. However, the relationship between reporter gene activation and in vitro affinity of an RNA reporter genes as a function of the in vitro affinity of the interaction. HIS3 and LacZ expression levels

Wickens, Marv

169

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

PubMed

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

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

2013-01-01

170

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

PubMed Central

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

Simner, Patricia J.; Buckwalter, Seanne P.; Uhl, James R.; Wengenack, Nancy L.

2013-01-01

171

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

PubMed

By using a yeast two-hybrid system, a yeast two-hybrid bait vector was constructed and identified for screening of the HPV18 E6-interacting proteins, and its effects on the growth of yeast cells and the activation of reporter genes were investigated. Total mRNA extracted from Hela cells was reversely transcribed into cDNA. Fragment of HPV18 E6 cDNA was amplified using RT-PCR and directly ligated to the pGBKT7 vector. The recombinant plasmid was confirmed by restriction endonuclease analysis and DNA sequencing. The recombinant pGBKT7-HPV18 E6 plasmid and empty pGBKT7 vector were transformed into the yeast cell AH109, respectively. After they were cultured respectively in YPDA liquid medium and nutrition-deficient culture medium, their toxicity and transcriptional activation were tested by both the phenotype assay and the color assay. The bait plasmid HPV18 E6 was successfully obtained. After being cultured in YPDA liquid medium for 16h, the A (600 nm) values of two yeast fluids were 0.98+/-0.03 and 0.99+/-0.02, respectively. The recombinant pGBKT7-HPV18 E6 plasmid and empty pGBKT7 vector could grow to white colonies on SD/-Trp/X-alpha-gal plates, while no colony could survive on SD/-His/-Trp/X-alpha-gal, SD/-Ade/-Trp/X-alpha-gal plates, indicating that the bait plasmid pGBKT7-HPV18 E6 was constructed successfully and expressed correctly, and could not activate the transcription of reporter gene alone. The yeast two-hybrid GAL4 system 3 can be utilized to find HPV18 E6 interacting proteins. PMID:20155448

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

2010-02-01

172

Subcritical flutter testing and system identification  

NASA Technical Reports Server (NTRS)

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

Houbolt, J. C.

1974-01-01

173

INPUT-OUTPUT IDENTIFICATION OF CONTROLLED DISCRETE MANUFACTURING SYSTEMS  

E-print Network

INPUT-OUTPUT IDENTIFICATION OF CONTROLLED DISCRETE MANUFACTURING SYSTEMS Ana Paula Estrada-Vargas1 identification, allows obtaining models of ill-known (or even unknown) systems. In this article an identification DESs. The proposed technique allows the identification of actual complex systems because

Boyer, Edmond

174

Frequency domain system identification using arbitrary signals  

Microsoft Academic Search

It is the common conviction that frequency domain system identification suffers from the drawback that it cannot handle arbitrary signals without introducing systematic errors. This paper shows that it is possible to deal with nonperiodic signals without any approximation and under the same assumptions as in the time domain, by estimating simultaneously some initial conditions and the system model parameters

R. Pintelon; J. Schoukens; G. Vandersteen

1997-01-01

175

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

PubMed

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

Emam, M M

2013-03-01

176

Continuous-Time Bilinear System Identification  

NASA Technical Reports Server (NTRS)

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

Juang, Jer-Nan

2003-01-01

177

Nonlinear system identification and control with delayed cellular neural network  

Microsoft Academic Search

Online identification of nonlinear systems is still an important while difficult task in practice. A general and simple online identification method, by delayed cellular neural networks, is proposed for multi-input-multi-output (MIMO) nonlinear systems. The online identification framework is first formulated by delayed cellular neural networks, and the weights of the neural network are updated by the identification error by adaptive

Yanling Gao; Deying Zhang; Shuli Chen

2010-01-01

178

Examining protein-protein interactions using endogenously tagged yeast arrays: The Cross-and-Capture system  

PubMed Central

Comprehensive approaches to detect protein–protein interactions (PPIs) have been most successful in the yeast model system. Here we present “Cross-and-Capture,” a novel assay for rapid, sensitive assessment of PPIs via pulldown of differently tagged yeast strain arrays. About 500 yeast genes that function in DNA replication, repair, and recombination and nuclear proteins of unknown function were chromosomally tagged with six histidine residues or triple VSV epitopes. We demonstrate that the assay can interrogate a wide range of previously known protein complexes with increased resolution and sensitivity. Furthermore, we use “Cross-and-Capture” to identify two novel protein complexes: Rtt101p–Mms1p and Sae2p–Mre11p. The Rtt101p–Mms1p interaction was subsequently characterized by genetic and functional analyses. Our studies establish the “Cross-and-Capture” assay as a novel, versatile tool that provides a valuable complement for the next generation of yeast proteomic studies. PMID:17989249

Suter, Bernhard; Fetchko, Michael J.; Imhof, Ralph; Graham, Christopher I.; Stoffel-Studer, Ingrid; Zbinden, Caroline; Raghavan, Maanasa; Lopez, Lianet; Beneti, Lucija; Hort, Jacqueline; Fillingham, Jeffrey; Greenblatt, Jack F.; Giaever, Guri; Nislow, Corey; Stagljar, Igor

2007-01-01

179

Trk1 and Trk2 Define the Major K+ Transport System in Fission Yeast  

PubMed Central

The trk1+ gene has been proposed as a component of the K+ influx system in the fission yeast Schizosaccharomyces pombe. Previous work from our laboratories revealed that trk1 mutants do not show significantly altered content or influx of K+, although they are more sensitive to Na+. Genome database searches revealed that S. pombe encodes a putative gene (designated here trk2+) that shows significant identity to trk1+. We have analyzed the characteristics of potassium influx in S. pombe by using trk1 trk2 mutants. Unlike budding yeast, fission yeast displays a biphasic transport kinetics. trk2 mutants do not show altered K+ transport and exhibit only a slightly reduced Na+ tolerance. However, trk1 trk2 double mutants fail to grow at low K+ concentrations and show a dramatic decrease in Rb+ influx, as a result of loss of the high-affinity transport component. Furthermore, trk1 trk2 cells are very sensitive to Na+, as would be expected for a strain showing defective potassium transport. When trk1 trk2 cells are maintained in K+-free medium, the potassium content remains higher than that of the wild type or trk single mutants. In addition, the trk1 trk2 strain displays increased sensitivity to hygromycin B. These results are consistent with a hyperpolarized state of the plasma membrane. An additional phenotype of cells lacking both Trk components is a failure to grow at acidic pH. In conclusion, the Trk1 and Trk2 proteins define the major K+ transport system in fission yeast, and in contrast to what is known for budding yeast, the presence of any of these two proteins is sufficient to allow growth at normal potassium levels. PMID:10629185

Calero, Fernando; Gomez, Nestor; Arino, Joaquin; Ramos, Jose

2000-01-01

180

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

PubMed Central

We evaluated the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the rapid identification of yeast species. Using Bruker Daltonics MALDI BioTyper software, we created a spectral database library with m/z ratios of 2,000 to 20,000 Da for 109 type and reference strains of yeast (44 species in 8 genera). The database was tested for accuracy by use of 194 clinical isolates (23 species in 6 genera). A total of 192 (99.0%) of the clinical isolates were identified accurately by MALDI-TOF MS. The MALDI-TOF MS-based method was found to be reproducible and accurate, with low consumable costs and minimal preparation time. PMID:20668126

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

2010-01-01

181

Molecular identification of yeasts from soils of the alluvial forest national park along the river Danube downstream of Vienna, Austria ("Nationalpark Donauauen").  

PubMed

We analysed the diversity of yeasts from different soils in a river-floodplain landscape at the river Danube downstream of Vienna, Austria ("Nationalpark Donauauen"). 136 strains were isolated, identification of species was done with molecular methods. Partial sequencing of the 26S rRNA gene resulted in 36 different sequences, they could be assigned to 16 genera, apart from two sequence types (from three isolates), which were not clearly assigned to any genus. 18 species were identified and confirmed by means of PCR fingerprinting. The most frequently isolated genus was Cryptococcus (61 isolates and 12 sequence types). Basidiomycetes dominated with about 60% above the members of the Ascomycetes. About half the yeasts was isolated from the litter, the quantity decreased with soil depth. PMID:15462526

Wuczkowski, Michael; Prillinger, Hansjörg

2004-01-01

182

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

PubMed

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

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

1998-03-20

183

Stability evaluation and system identification of flexible multibody systems  

Microsoft Academic Search

This paper is concerned with the linearized stability analysis and system identification of flexible multibody systems. Two\\u000a closely related stability analysis approaches are summarized. Next, these approaches are extended to provide robust system\\u000a identification procedures that combine least squares techniques and Kalman filters. The singular value decomposition, a numerically\\u000a stable mathematical tool, is used to improve the robustness of the

Olivier A. Bauchau; Jielong Wang

2007-01-01

184

Identification of Structural Model for Chaotic Systems  

E-print Network

This article is talking about the study constructive method of structural identification systems with chaotic dynamics. It is shown that the reconstructed attractors are a source of information not only about the dynamics but also on the basis of the attractors which can be identified and the mere sight of models. It is known that the knowledge of the symmetry group allows you to specify the form of a minimal system. Forming a group transformation can be found in the recon-structed attractor. The affine system as the basic model is selected. Type of a nonlinear system is the subject of calcula-tions. A theoretical analysis is performed and proof of the possibility of constructing models in the central invariant manifold reduced. This developed algorithm for determining the observed symmetry in the attractor. The results of identification used in real systems are an application.

Evgeny Nikulchev; Oleg Kozlov

2014-02-28

185

TUTORIAL ON SYSTEM IDENTIFICATION USING FRACTIONAL DIFFERENTIATION  

E-print Network

fractional models is presented. Both equation-error and output-error-based models are detailed. Copyright c, output error models, equation error models, state variable filter. 1. INTRODUCTION Although fractionalTUTORIAL ON SYSTEM IDENTIFICATION USING FRACTIONAL DIFFERENTIATION MODELS Rachid Malti, Mohamed

Boyer, Edmond

186

Dynamical identification of open quantum systems  

E-print Network

I propose a quantum trajectories approach to parametric identification of the effective Hamiltonian for a Markovian open quantum system, and discuss an application motivated by recent experiments in cavity quantum electrodynamics. This example illustrates a strategy for quantum parameter estimation that efficiently utilizes the information carried by correlations between measurements distributed in time.

Hideo Mabuchi

1996-08-13

187

System identification techniques for adaptive signal processing  

Microsoft Academic Search

Many problems in adaptive filtering can be approached from the point of view of system identification. The close interconnection between these two disciplines is explored in some detail. This approach makes it possible to apply recursive parameter estimation algorithms to adaptive signal processing. Several examples are discussed including: adaptive line enhancement, generalized adaptive noise cancelling, adaptive deconvolution and adaptive TDOA

Benjamin Friedlander

1982-01-01

188

DIRC, the Particle Identification System for BABAR  

E-print Network

The DIRC, a novel type of Cherenkov ring imaging device, is the primary hadronic particle identification system for the BABAR detector at the asymmetric B-factory, PEP-II at SLAC. BABAR began taking data with colliding beams mode in late spring 1999. This paper describes the performance of the DIRC during the first 16 months of operation.

Jochen Schwiening; representing the BABAR-DIRC Collaboration

2000-10-26

189

Neural Networks in System Identification  

Microsoft Academic Search

. Neural Networks are non-linear black-box model structures, to be used with conventionalparameter estimation methods. They have good general approximation capabilities for reasonablenon-linear systems. When estimating the parameters in these structures, there is also good adaptabilityto concentrate on those parameters that have the most importance for the particular data set.Key Words. Neural Networks, Parameter estimation, Model Structures, Non-Linear Systems.1. EXECUTIVE

J. Sjöberg; H. Hjalmarsson; L. Ljung

1994-01-01

190

Formation of Hydroxamates during Proteolysis by an Enzyme System from Yeast  

Microsoft Academic Search

DURING re-investigation of an enzyme system, from yeast previously reported to form `activated' peptides1 extensive proteolysis was noted and enzyme-catalysed hydroxylaminolysis of protein was suspected as the source of hydroxamate formation2. Acyl-enzyme complexes were visualized as intermediates rather than some form of `activated' peptide originally suggested by Cooper et al.1. The main evidence for the latter hypothesis had been the

D. E. Briggs; D. J. Millin

1965-01-01

191

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

PubMed Central

Background The number of patients with yeast infection has increased during the last years. Also the variety of species of clinical importance has increased. Correct species identification is often important for efficient therapy, but is currently mostly based on phenotypic features and is sometimes time-consuming and depends largely on the expertise of technicians. Therefore, we evaluated the feasibility of PCR-based amplification of the internally transcribed spacer region 2 (ITS2), followed by fragment size analysis on the ABI Prism 310 for the identification of clinically important yeasts. Results A rapid DNA-extraction method, based on simple boiling-freezing was introduced. Of the 26 species tested, 22 could be identified unambiguously by scoring the length of the ITS2-region. No distinction could be made between the species Trichosporon asteroides and T. inkin or between T. mucoides and T. ovoides. The two varieties of Cryptococcus neoformans (var. neoformans and var. gattii) could be differentiated from each other due to a one bp length difference of the ITS2 fragment. The three Cryptococcus laurentii isolates were split into two groups according to their ITS2-fragment lengths, in correspondence with the phylogenetic groups described previously. Since the obtained fragment lengths compare well to those described previously and could be exchanged between two laboratories, an internationally usable library of ITS2 fragment lengths can be constructed. Conclusions The existing ITS2 size based library enables identification of most of the clinically important yeast species within 6 hours starting from a single colony and can be easily updated when new species are described. Data can be exchanged between laboratories. PMID:12139769

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

2002-01-01

192

New features of mitochondrial DNA replication system in yeast and man.  

PubMed

In this review, we sum up the research carried out over two decades on mitochondrial DNA (mtDNA) replication, primarily by comparing this system in Saccharomyces cerevisiae and Homo sapiens. Brief incursions into systems of other organisms have also been achieved when they provide new information.S. cerevisiae and H. sapiens mitochondrial DNA (mtDNA) have been thought for a long time to share closely related architecture and replication mechanisms. However, recent studies suggest that mitochondrial genome of S. cerevisiae may be formed, at least partially, from linear multimeric molecules, while human mtDNA is circular. Although several proteins involved in the replication of these two genomes are very similar, divergences are also now increasingly evident. As an example, the recently cloned human mitochondrial DNA polymerase beta-subunit has no counterpart in yeast. Yet, yeast Abf2p and human mtTFA are probably not as closely functionally related as thought previously. Some mtDNA metabolism factors, like DNA ligases, were until recently largely uncharacterized, and have been found to be derived from alternative nuclear products. Many factors involved in the metabolism of mitochondrial DNA are linked through genetic or biochemical interconnections. These links are presented on a map. Finally, we discuss recent studies suggesting that the yeast mtDNA replication system diverges from that observed in man, and may involve recombination, possibly coupled to alternative replication mechanisms like rolling circle replication. PMID:10767525

Lecrenier, N; Foury, F

2000-04-01

193

Computer Automated Control System Design and System Identification  

Microsoft Academic Search

A major issue in the application of control methods has been the availability of suitably accurate models of the system for the design of an appropriate con­ trol system. This has been a particular problem in multivariable systems in the past. Recent methods in automated system identification now make it pos­ sible to automatically and reliably identify large scale multivariable

Wallace E. Larimore

1995-01-01

194

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

Code of Federal Regulations, 2011 CFR

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

2011-04-01

195

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

Code of Federal Regulations, 2012 CFR

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

2012-04-01

196

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

Code of Federal Regulations, 2010 CFR

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

2010-04-01

197

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

Code of Federal Regulations, 2013 CFR

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

2013-04-01

198

33 CFR 164.46 - Automatic Identification System (AIS).  

...2014-07-01 2014-07-01 false Automatic Identification System (AIS). 164.46 Section 164.46 Navigation...NAVIGATION SAFETY REGULATIONS § 164.46 Automatic Identification System (AIS). (a) The following vessels...

2014-07-01

199

Structural system identification: Structural dynamics model validation  

SciTech Connect

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

Red-Horse, J.R.

1997-04-01

200

Parameter identification for nonlinear aerodynamic systems  

NASA Technical Reports Server (NTRS)

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

Pearson, Allan E.

1990-01-01

201

System identification using Laguerre models  

Microsoft Academic Search

The traditional approach of expanding transfer functions and noise models in the delay operator to obtain linear-in-the-parameters predictor models leads to approximations of very high order in cases of rapid sampling and\\/or dispersion in time constants. By using prior information about the time constants of the system more appropriate expansions, related to Laguerre networks, are introduced and analyzed. It is

BO Wahlberg

1991-01-01

202

A program for identification of linear systems  

NASA Technical Reports Server (NTRS)

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

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

1971-01-01

203

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

PubMed

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

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

2014-09-01

204

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

PubMed Central

Genomic data now allow the large-scale manual or semi-automated reconstruction of metabolic networks. A network reconstruction represents a highly curated organism-specific knowledge base. A few genome-scale network reconstructions have appeared for metabolism in the baker’s yeast Saccharomyces cerevisiae. These alternative network reconstructions differ in scope and content, and further have used different terminologies to describe the same chemical entities, thus making comparisons between them difficult. The formulation of a ‘community consensus’ network that collects and formalizes the ‘community knowledge’ of yeast metabolism is thus highly desirable. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. Special emphasis is laid on referencing molecules to persistent databases or using database-independent forms such as SMILES or InChI strings, since this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language, and we describe the manner in which it can be maintained as a community resource. It should serve as a common denominator for system biology studies of yeast. Similar strategies will be of benefit to communities studying genome-scale metabolic networks of other organisms. PMID:18846089

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

2014-01-01

205

Artificial Intelligence 119 (2000) 103140 Semi-quantitative system identification  

E-print Network

Artificial Intelligence 119 (2000) 103­140 Semi-quantitative system identification Herbert Kay 1 78712, USA Received 9 March 1999 Abstract System identification takes a space of possible models of the model best matches the observations. We present SQUID, a method for system identification in which

Kuipers, Benjamin

206

Genetic Programming-Based Approach for System Identification  

E-print Network

Genetic Programming-Based Approach for System Identification Jose Aguilar, Mariela Cerrada Programming is proposed for the input- output systems identification problem. Laguerre's functions and the ARX method have been commonly used to solve the systems identification problem. Recently, approaches based

Fernandez, Thomas

207

A HIERARCHICAL GENETIC SYSTEM FOR SYMBOLIC FUNCTION IDENTIFICATION  

E-print Network

A HIERARCHICAL GENETIC SYSTEM FOR SYMBOLIC FUNCTION IDENTIFICATION Mingda Jiang (cs the data. This paper describes a system for solution of symbolic function identification problems. The function identification problem is to find a functional model of an experimental system, in symbolic form

Wright, Alden H.

208

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

PubMed Central

Background Scheffersomyces stipitis is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as Saccharomyces cerevisiae, the onset of fermentation in S. stipitis is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though S. stipitis has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of S. stipitis during aerobic growth on glucose under batch and chemostat cultivations. Results Starting from the analysis of physiological data, we confirmed through 13C-based flux analysis the fully respiratory metabolism of S. stipitis when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for S. cerevisiae under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with S. cerevisiae. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through in silico transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways. Conclusions The work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for S. stipitis under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for S. cerevisiae under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, in silico analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of S. stiptis is investigated in details and is compared to S. cerevisiae. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of S. stipitis as cell factory. PMID:23043429

2012-01-01

209

Structural system identification: Structural dynamics model validation  

Microsoft Academic Search

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

Red-Horse

1997-01-01

210

Reconfigurable control and fault identification system  

Microsoft Academic Search

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

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

2004-01-01

211

Identification of dynamic systems, theory and formulation  

NASA Technical Reports Server (NTRS)

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

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

1985-01-01

212

Construction of a beta-glucosidase expression system using the multistress-tolerant yeast Issatchenkia orientalis.  

PubMed

We demonstrate the value of the thermotolerant yeast Issatchenkia orientalis as a candidate microorganism for bioethanol production from lignocellulosic biomass with the goal of consolidated bioprocessing. The I. orientalis MF-121 strain is acid tolerant, ethanol tolerant, and thermotolerant, and is thus a multistress-tolerant yeast. To express heterologous proteins in I. orientalis, we constructed a transformation system for the MF-121 strain and then isolated the promoters of TDH1 and PGK1, two genes that were found to be strongly expressed during ethanol fermentation. As a result, expression of beta-glucosidase from Aspergillus aculeatus could be achieved with I. orientalis, demonstrating successful heterologous gene expression in I. orientalis for the first time. The transformant could convert cellobiose to ethanol under acidic conditions and at high temperature. Simultaneous saccharification and fermentation (SSF) was performed with the transformant, which produced 29 g l(-1) of ethanol in 72 h at 40 degrees C even without addition of beta-glucosidase when SSF was carried out in medium containing 100 g l(-1) of microcrystalline cellulose and a commercial cellulase preparation. These results suggest that using a genetically engineered thermotolerant yeast such as I. orientalis in SSF could lead to cost reduction because less saccharification enzymes are required. PMID:20467739

Kitagawa, Takao; Tokuhiro, Kenro; Sugiyama, Hidehiko; Kohda, Katsuhiro; Isono, Naoto; Hisamatsu, Makoto; Takahashi, Haruo; Imaeda, Takao

2010-08-01

213

Implementation of the CRISPR-Cas9 system in fission yeast.  

PubMed

Application of the CRISPR-Cas9 genome editing system in the model organism Schizosaccharomyces pombe has been hampered by the lack of constructs to express RNA of arbitrary sequence. Here we present expression constructs that use the promoter/leader RNA of K RNA (rrk1) and a ribozyme to produce the targeting guide RNA. Together with constitutive expression of Cas9, this system achieves selection-free specific mutagenesis with efficiencies approaching 100%. The rrk1 CRISPR-Cas9 method enables rapid and efficient genome manipulation and unlocks the CRISPR toolset for use in fission yeast. PMID:25352017

Jacobs, Jake Z; Ciccaglione, Keith M; Tournier, Vincent; Zaratiegui, Mikel

2014-01-01

214

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2013 CFR

...1) Personnel identification media that— (i) Convey a full-face image, full name, employer, and...individual to whom the identification medium is issued; (ii) Indicate...displays the identification medium issued to that individual...

2013-10-01

215

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2012 CFR

...1) Personnel identification media that— (i) Convey a full-face image, full name, employer, and...individual to whom the identification medium is issued; (ii) Indicate...displays the identification medium issued to that individual...

2012-10-01

216

Real-time System Identification using Intelligent Algorithms  

Microsoft Academic Search

This research presents an investigation into the development of real time system identification using intelligent algorithms. A simulation platform of a flexible beam vibration using finite difference (FD) method is used to demonstrate the real time capabilities of the identification algorithms. A number of approaches and algorithms for on line system identifications are explored and evaluated to demonstrate the merits

A. A. M. Madkour; M. A. Hossain; K. P. Dahal; H. Yu

2004-01-01

217

Power system identification toolbox: Phase two progress  

SciTech Connect

This report describes current progress on a project funded by the Bonneville Power Administration (BPA) to develop a set of state-of-the-art analysis software (termed the Power System Identification [PSI] Toolbox) for fitting dynamic models to measured data. The project is being conducted as a three-phase effort. The first phase, completed in late 1992, involved investigating the characteristics of the analysis techniques by evaluating existing software and developing guidelines for best use. Phase Two includes extending current software, developing new analysis algorithms and software, and demonstrating and developing applications. The final phase will focus on reorganizing the software into a modular collection of documented computer programs and developing user manuals with instruction and application guidelines. Phase Two is approximately 50% complete; progress to date and a vision for the final product of the PSI Toolbox are described. The needs of the power industry for specialized system identification methods are particularly acute. The industry is currently pushing to operate transmission systems much closer to theoretical limits by using real-time, large-scale control systems to dictate power flows and maintain dynamic stability. Reliably maintaining stability requires extensive system-dynamic modeling and analysis capability, including measurement-based methods. To serve this need, the BPA has developed specialized system-identification computer codes through in-house efforts and university contract research over the last several years. To make full integrated use of the codes, as well as other techniques, the BPA has commissioned Pacific Northwest Laboratory (PNL) to further develop the codes and techniques into the PSI Toolbox.

Trudnowski, D.J.

1994-08-01

218

Intellectual system of identification of Arabic graphics  

NASA Astrophysics Data System (ADS)

The studies made by using the domain of graphic images allowed creating facilities of the artificial intelligence for letters, letter combinations etc. for various graphics and prints. The work proposes a system of recognition and identification of symbols of the Arabic graphics, which has its own specificity as compared to Latin and Cyrillic ones. The starting stage of the recognition and the identification is coding with further entry of information into a computer. Here the problem of entry is one of the essentials. For entry of a large volume of information in the unit of time a scanner is usually employed. Along with the scanner the authors suggest their elaboration of technical facilities for effective input and coding of the information. For refinement of symbols not identified from the scanner mostly for a small bulk of information the developed coding devices are used directly in the process of writing. The functional design of the software is elaborated on the basis of the heuristic model of the creative activity of a researcher and experts in the description and estimation of states of the weakly formalizable systems on the strength of the methods of identification and of selection of geometric features.

Abdoullayeva, Gulchin G.; Aliyev, Telman A.; Gurbanova, Nazakat G.

2001-08-01

219

Topological identification in networks of dynamical systems  

E-print Network

The paper deals with the problem of reconstructing the topological structure of a network of dynamical systems. A distance function is defined in order to evaluate the "closeness" of two processes and a few useful mathematical properties are derived. Theoretical results to guarantee the correctness of the identification procedure for networked linear systems with tree topology are provided as well. Finally, the application of the techniques to the analysis of an actual complex network, i.e. to high frequency time series of the stock market, is illustrated.

Donatello W. Materassi; Giacomo W. Innocenti

2008-04-15

220

SYSTEM IDENTIFICATION OF PHOTOSENSITISER UPTAKE KINETICS IN PHOTODYNAMIC THERAPY  

E-print Network

SYSTEM IDENTIFICATION OF PHOTOSENSITISER UPTAKE KINETICS IN PHOTODYNAMIC THERAPY T. Bastogne L to the experimental modelling of photosensitiser uptake kinetics in photodynamic therapy. The experimental framework identification, pharmacokinetics, drug delivery, photodynamic therapy 1. INTRODUCTION Photodynamic therapy (PDT

Paris-Sud XI, Université de

221

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

PubMed Central

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

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

2013-01-01

222

Parameter identification for nonlinear aerodynamic systems  

NASA Technical Reports Server (NTRS)

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

Pearson, Allan E.

1993-01-01

223

The identification of continuous, spatiotemporal systems  

E-print Network

We present a method for the identification of continuous, spatiotemporal dynamics from experimental data. We use a model in the form of a partial differential equation and formulate an optimization problem for its estimation from data. The solution is found as a multivariate nonlinear regression problem using the ACE-algorithm. The procedure is successfully applied to data, obtained by simulation of the Swift-Hohenberg equation. There are no restrictions on the dimensionality of the investigated system, allowing for the analysis of high-dimensional chaotic as well as transient dynamics. The demands on the experimental data are discussed as well as the sensitivity of the method towards noise.

H. Voss; M. J. Bünner; M. Abel

1999-06-30

224

Autonomous Frequency-Domain System-Identification Program  

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

225

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

PubMed Central

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

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

2005-01-01

226

A switchable light-input, light-output system modelled and constructed in yeast  

PubMed Central

Background Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidopsis proteins PHYTOCHROME A and FAR-RED ELONGATED HYPOCOTYL 1-LIKE. Light input to this regulatory module allows dynamic control of a light-emitting LUCIFERASE reporter gene, which we detect by real-time imaging of yeast colonies on solid media. Results The reversible activation of the phytochrome by red light, and its inactivation by far-red light, is retained. We use this quantitative readout to construct a mathematical model that matches the system's behaviour and predicts the molecular targets for future manipulation. Conclusion Our model, methods and materials together constitute a novel system for a eukaryotic host with the potential to convert a dynamic pattern of light input into a predictable gene expression response. This system could be applied for the regulation of genetic networks - both known and synthetic. PMID:19761615

Sorokina, Oxana; Kapus, Anita; Terecskei, Kata; Dixon, Laura E; Kozma-Bognar, Laszlo; Nagy, Ferenc; Millar, Andrew J

2009-01-01

227

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

Microsoft Academic Search

We report the use of a yeast one-hybrid system to isolate a transcriptional regulator of the sea urchin embryo hatching enzyme gene, SpHE. This gene is asymmetrically expressed along the animal-vegetal axis of sea urchin embryos under the cell-autonomous control of maternal regulatory activities and therefore provides an excellent entry point for understanding the mechanism that establishes animal-vegetal developmental polarity.

ZHENG WEI; ROBERT C. ANGERER; LYNNE M. ANGERER

1999-01-01

228

MIMO system identification using frequency response data  

NASA Technical Reports Server (NTRS)

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

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

1992-01-01

229

Experimental studies of a phase identification system for distribution systems  

Microsoft Academic Search

This paper presents the design and development of experimental set-ups for the purpose of testing phase identification systems for power distribution networks. A series of hardware experiments and procedures were created within a laboratory environment at Drexel University to represent actual, distribution components and multiple operating conditions. These tests included multiple transformer connection types including Wye, Delta and Scott-T, distribution

Thomas Dunmore; Eric Jaffe; Sean Kennedy; Dhruv M. Patel; Preet Soni; Michael Kleinberg; Karen Miu

2010-01-01

230

System identification for essential oil extraction system: An overview  

Microsoft Academic Search

This paper introduces a new avenue for research by presenting the gap between the essential oil extraction technique studies and the system identification studies. In the essential oil extraction research, temperature plays an important role in producing the essential oils. Numerous published articles in this area have highlighted several temperature settings and their effects on the extraction. In spite of

Mohd Hezri Fazalul Rahiman; Mohd Nasir Taib

2009-01-01

231

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

PubMed Central

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

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

2014-01-01

232

Identification of Candidate Substrates for the Golgi Tul1 E3 Ligase Using Quantitative diGly Proteomics in Yeast.  

PubMed

Maintenance of protein homeostasis is essential for cellular survival. Central to this regulation are mechanisms of protein quality control in which misfolded proteins are recognized and degraded by the ubiquitin-proteasome system. One well-studied protein quality control pathway requires endoplasmic reticulum (ER)-resident, multi-subunit E3 ubiquitin ligases that function in ER-associated degradation. Using fission yeast, our lab identified the Golgi Dsc E3 ligase as required for proteolytic activation of fungal sterol regulatory element-binding protein transcription factors. The Dsc E3 ligase contains five integral membrane subunits and structurally resembles ER-associated degradation E3 ligases. Saccharomyces cerevisiae codes for homologs of Dsc E3 ligase subunits, including the Dsc1 E3 ligase homolog Tul1 that functions in Golgi protein quality control. Interestingly, S. cerevisiae lacks sterol regulatory element-binding protein homologs, indicating that novel Tul1 E3 ligase substrates exist. Here, we show that the S. cerevisiae Tul1 E3 ligase consists of Tul1, Dsc2, Dsc3, and Ubx3 and define Tul1 complex architecture. Tul1 E3 ligase function required each subunit as judged by vacuolar sorting of the artificial substrate Pep12D. Genetic studies demonstrated that Tul1 E3 ligase was required in cells lacking the multivesicular body pathway and under conditions of ubiquitin depletion. To identify candidate substrates, we performed quantitative diGly proteomics using stable isotope labeling by amino acids in cell culture to survey ubiquitylation in wild-type and tul1? cells. We identified 3116 non-redundant ubiquitylation sites, including 10 sites in candidate substrates. Quantitative proteomics found 4.5% of quantified proteins (53/1172) to be differentially expressed in tul1? cells. Correcting the diGly dataset for these differences increased the number of Tul1-dependent ubiquitylation sites. Together, our data demonstrate that the Tul1 E3 ligase functions in protein homeostasis under non-stress conditions and support a role in protein quality control. This quantitative diGly proteomics methodology will serve as a robust platform for screening for stress conditions that require Tul1 E3 ligase activity. PMID:25078903

Tong, Zongtian; Kim, Min-Sik; Pandey, Akhilesh; Espenshade, Peter J

2014-11-01

233

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

PubMed

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

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

2014-01-01

234

System Identification of X-33 Neural Network  

NASA Technical Reports Server (NTRS)

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

Aggarwal, Shiv

2003-01-01

235

Introduction to Automatic Data Identification Systems  

NSDL National Science Digital Library

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

Jones, Jeff

2010-02-17

236

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

PubMed

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

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

2014-10-15

237

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

PubMed Central

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

Phang, James M.

2008-01-01

238

Heat Capacity Identification Method Using MT System  

Microsoft Academic Search

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

Arata Suzuki; Kenji Sugimoto

2007-01-01

239

Heat capacity identification via Mahalanobis Taguchi System  

Microsoft Academic Search

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

Arata Suzuki; Kenji Sugimoto

2008-01-01

240

Effects of Distillation System and Yeast Strain on the Aroma Profile of Albariño (Vitis vinifera L.) Grape Pomace Spirits.  

PubMed

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

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

2014-10-29

241

Time-Delay System Identification Using Genetic Algorithm -Part Two  

E-print Network

Time-Delay System Identification Using Genetic Algorithm - Part Two: FOPDT/SOPDT Model-Order-Plus-Dead-Time (FOPDT) or Second-Order-Plus-Dead-Time (SOPDT) model approximation to a complicated process system can be carried out through either a kind of model reduction approach or a kind of system identification approach

Yang, Zhenyu

242

Fractional System Identification: An Approach Using Continuous Order-Distributions  

NASA Technical Reports Server (NTRS)

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

Hartley, Tom T.; Lorenzo, Carl F.

1999-01-01

243

Implementing GIS in Bus Identification and Monitoring System  

Microsoft Academic Search

GIS is a system that analyses and displays geographic information. This paper focuses on the GIS application for Bus Identification and Monitoring System. GIS is used to map out the bus location and movement in the system. The results show that the bus operation in terms of time schedule, driver's and bus' identification, and bus' location can be monitored and

Aishah Mahani Mustapha; MA Hannan; Aini Hussain; Hassan Basri

2011-01-01

244

Mitochondrial assembly in yeast  

Microsoft Academic Search

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

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

245

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

PubMed

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

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

2014-01-01

246

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

PubMed Central

Potentially immeasurable heterodimer combinations of human G-protein-coupled receptors (GPCRs) result in a great deal of physiological diversity and provide a new opportunity for drug discovery. However, due to the existence of numerous combinations, the sets of GPCR dimers are almost entirely unknown and thus their dominant roles are still poorly understood. Thus, the identification of GPCR dimer pairs has been a major challenge. Here, we established a specialized method to screen potential heterodimer partners of human GPCRs based on the split-ubiquitin membrane yeast two-hybrid system. We demonstrate that the mitogen-activated protein kinase (MAPK) signal-independent method can detect ligand-induced conformational changes and rapidly identify heterodimer partners for target GPCRs. Our data present the abilities to apply for the intermolecular mapping of interactions among GPCRs and to uncover potential GPCR targets for the development of new therapeutic agents. PMID:23805278

Nakamura, Yasuyuki; Ishii, Jun; Kondo, Akihiko

2013-01-01

247

An overview of recent advances in system identification  

NASA Technical Reports Server (NTRS)

This paper presents an overview of the recent advances in system identification for modal testing and control of large flexible structures. Several techniques are discussed including the Observer/Kalman Filter Identification, the Observer/Controller Identification, and the State-Space System Identification in the Frequency Domain. The System/Observer/Controller Toolbox developed at NASA Langley Research Center is used to show the applications of these techniques to real aerospace structures such as the Hubble spacecraft telescope and the active flexible aircraft wing.

Juang, Jer-Nan

1994-01-01

248

An overview of recent advances in system identification  

NASA Technical Reports Server (NTRS)

This paper presents an overview of the recent advances in system identification for modal testing and control of large flexible structures. Several techniques are discussed including the Observer/Kalman Filter Identification, the Observer/Controller Identification and the State-Space System Identification in the Frequency Domain. The System/Observer/Controller Toolbox developed at NASA Langley Research Center is used to show the applications of these techniques to real aerospace structures such as the Hubble spacecraft telescope and the active flexible aircraft wing.

Juang, Jer-Nan

1993-01-01

249

Elman Network with Embedded Memory for System Identification  

Microsoft Academic Search

This paper presents a new recurrent neural network (RNN) structure called ENEM for dynamic system identification. ENEM structure is based on Elman network and NARX neural network. In order to show the performance of ENEM for system identifi- cation, the results were also compared to the results of Elman network, Jordan network and their modified models. The identification results of

Adem Kalinli; Seref Sagiroglu

2006-01-01

250

Orthogonal approaches to time-series analysis and system identification  

Microsoft Academic Search

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

M. J. Korenberg; L. D. Paarmann

1991-01-01

251

Lightweight autonomous chemical identification system (LACIS)  

NASA Astrophysics Data System (ADS)

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

Lozos, George; Lin, Hai; Burch, Timothy

2012-06-01

252

Identification and characterization of the rlp1+, the novel Rad51 paralog in the fission yeast Schizosaccharomyces pombe.  

PubMed

A new DNA repair gene from fission yeast Schizosaccharomyces pombe rlp1+ (RecA-like protein) has been identified. Rlp1 shows homology to RecA-like proteins, and is the third S. pombe Rad51 paralog besides Rhp55 and Rhp57. The new gene encodes a 363 aa protein with predicted Mr of 41,700 and has NTP-binding motif. The rlp1Delta mutant is sensitive to methyl methanesulfonate (MMS), ionizing radiation (IR), and camptothecin (CPT), although to a lesser extent than the deletion mutants of rhp55+ and rhp51+ genes. In contrast to other recombinational repair mutants, the rlp1Delta mutant does not exhibit sensitivity to UV light and mitomycin C (MMC). Mitotic recombination is moderately reduced in rlp1 mutant. Epistatic analysis of MMS and IR-sensitivity of rlp1Delta mutant indicates that rlp1+ acts in the recombinational pathway of double-strand break (DSB) repair together with rhp51+, rhp55+, and rad22+ genes. Yeast two-hybrid analysis suggests that Rlp1 may interact with Rhp57 protein. We propose that Rlp1 have an accessory role in repair of a subset of DNA damage induced by MMS and IR, and is required for the full extent of DNA recombination and cell survival under condition of a replication fork collapse. PMID:15336631

Khasanov, Fuat K; Salakhova, Albina F; Chepurnaja, Olga V; Korolev, Vladimir G; Bashkirov, Vladimir I

2004-10-01

253

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

PubMed Central

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

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

2013-01-01

254

Identification of yeast and acetic acid bacteria isolated from the fermentation and acetification of persimmon (Diospyros kaki).  

PubMed

Persimmon (Diospyros kaki) is a seasonal fruit with important health benefits. In this study, persimmon use in wine and condiment production was investigated using molecular methods to identify the yeast and acetic acid bacteria (AAB) isolated from the alcoholic fermentation and acetification of the fruit. Alcoholic fermentation was allowed to occur either spontaneously, or by inoculation with a commercial Saccharomyces cerevisiae wine strain, while acetification was always spontaneous; all these processes were performed in triplicates. Non-Saccharomyces yeast species were particularly abundant during the initial and mid-alcoholic fermentation stages, but S. cerevisiae became dominant toward the end of these processes. During spontaneous fermentation, S. cerevisiae Sc1 was the predominant strain isolated throughout, while the commercial strain of S. cerevisiae was the most common strain isolated from the inoculated fermentations. The main non-Saccharomyces strains isolated included Pichia guilliermondii, Hanseniaspora uvarum, Zygosaccharomyces florentinus and Cryptococcus sp. A distinct succession of AAB was observed during the acetification process. Acetobacter malorun was abundant during the initial and mid-stages, while Gluconacetobacter saccharivorans was the main species during the final stages of these acetifications. Four additional AAB species, Acetobacter pasteurianus, Acetobacter syzygii, Gluconacetobacter intermedius and Gluconacetobacter europaeus, were also detected. We observed 28 different AAB genotypes, though only 6 of these were present in high numbers (between 25%-60%), resulting in a high biodiversity index. PMID:22265289

Hidalgo, C; Mateo, E; Mas, A; Torija, M J

2012-05-01

255

A system identification model for adaptive nonlinear control  

NASA Technical Reports Server (NTRS)

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

Linse, Dennis J.; Stengel, Robert F.

1991-01-01

256

Linear system identification - The application of Lion's identification scheme to a third order system with noisy input-output measurements  

NASA Technical Reports Server (NTRS)

A linear system identification technique developed by Lion is adapted for use on a third-order system with six unknown parameters and noisy input-output measurements. A digital computer is employed so that rapid identification takes place with only two state variable filters. Bias in the parameter estimates is partially eliminated by a signal-to-noise ratio testing procedure.

Brown, C. M., Jr.; Monopoli, R. V.

1974-01-01

257

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

Federal Register 2010, 2011, 2012, 2013

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

2013-01-31

258

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

NASA Astrophysics Data System (ADS)

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

Pisman, T.; Somova, L.

259

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

NASA Astrophysics Data System (ADS)

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

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

260

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

PubMed Central

We have characterized the posttranslational methylation of Rps2, Rps3, and Rps27a, three small ribosomal subunit proteins in the yeast Saccharomyces cerevisiae, using mass spectrometry and amino acid analysis. We found that Rps2 is substoichiometrically modified at arginine-10 by the Rmt1 methyltransferase. We demonstrated that Rps3 is stoichiometrically modified by ?-monomethylation at arginine-146 by mass spectrometric and site-directed mutagenic analyses. Substitution of alanine for arginine at position 146 is associated with slow cell growth, suggesting that the amino acid identity at this site may influence ribosomal function and/or biogenesis. Analysis of the three-dimensional structure of Rps3 in S. cerevisiae shows that arginine-146 makes contacts with the small subunit rRNA. Screening of deletion mutants encoding potential yeast methyltransferases revealed that the loss of the YOR021C gene results in the absence of methylation on Rps3. We demonstrated that recombinant Yor021c catalyzes ?-monomethylarginine formation when incubated with S-adenosylmethionine and hypomethylated ribosomes prepared from a YOR021C deletion strain. Interestingly, Yor021c belongs to the family of SPOUT methyltransferases that, to date, have only been shown to modify RNA substrates. Our findings suggest a wider role for SPOUT methyltransferases in nature. Finally, we have demonstrated the presence of a stoichiometrically methylated cysteine residue at position 39 of Rps27a in a zinc-cysteine cluster. The discovery of these three novel sites of protein modification within the small ribosomal subunit will now allow for an analysis of their functional roles in translation and possibly other cellular processes. PMID:22650761

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

2012-01-01

261

Application of identification techniques to remote manipulator system flight data  

NASA Technical Reports Server (NTRS)

This paper addresses the application of identification techniques to flight data from the Space Shuttle Remote Manipulator System (RMS). A description of the remote manipulator, including structural and control system characteristics, sensors, and actuators is given. A brief overview of system identification procedures is presented, and the practical aspects of implementing system identification algorithms are discussed. In particular, the problems posed by desampling rate, numerical error, and system nonlinearities are considered. Simulation predictions of damping, frequency, and system order are compared with values identified from flight data to support an evaluation of RMS structural and control system models. Finally, conclusions are drawn regarding the application of identification techniques to flight data obtained from a flexible space structure.

Shepard, G. D.; Lepanto, J. A.; Metzinger, R. W.; Fogel, E.

1983-01-01

262

A New Approach to System Identification Based on the Generalised Structural Subband Decomposition  

E-print Network

A New Approach to System Identification Based on the Generalised Structural Subband Decomposition Abstract: The System Identification (SI) problem is addressed from the viewpoint of the Generalised Structural Subband Decomposition (GSSD). We present a System Identification Structure (SIS

Haddadi, Hamed

263

A NEW METHODOLOGY FOR EMERGENT SYSTEM IDENTIFICATION USING PARTICLE SWARM OPTIMIZATION  

E-print Network

A NEW METHODOLOGY FOR EMERGENT SYSTEM IDENTIFICATION USING PARTICLE SWARM OPTIMIZATION (PSO. Section 2 describes traditional System Identification and introduces the use of Particle Swarm from the results. A new methodology for Emergent System Identification is proposed in this paper

Fernandez, Thomas

264

Evaluation of the Microbact-24E bacterial identification system.  

PubMed Central

The Microbact 24E (MB24E) system is a commercial microsystem for the identification of common clinical isolates of Enterobacteriaceae and non-fermenting Gram negative bacilli, and consists of dehydrated substrates distributed in the wells of microtitre trays. This system was compared with the API20E for the identification of 386 bacterial isolates, which included 284 clinical and 102 environmental organisms. There was 97% and 91% agreement for the identification of clinical isolates of Enterobacteriaceae and other Gram negative bacilli, respectively. The identification of environmental isolates by both systems was less satisfactory. The API20E has a more extensive database than the MB24E and is thus more reliable for the identification of rare or unusual organisms, but the MB24E is cheaper, is easy and convenient to use, and is suitable for a routine microbiology laboratory. PMID:3049684

Ling, J M; Hui, Y W; French, G L

1988-01-01

265

Yeast Proteome Analysis  

NASA Astrophysics Data System (ADS)

Yeast organisms, and specifically Saccharomyces cerevisiae, have become model systems for many aspects in fundamental and applied research. Consistently, many papers have been published applying proteome techniques to study these organisms. The review will give an overview on the proteome research performed on yeast systems so far; however, due to the large number of publications, only selected reports can be cited neglecting many more interesting ones in the interest of space. The review will focus on research involving mass spectrom-etry as a basic proteome technique, although many more approaches are relevant for the functional characterization of proteins in the cell, e.g. the yeast two-hybrid system. We will provide an overview on yeasts as models in the context of pro-teome analysis, and explain the basic techniques currently applied in proteome approaches. The main part of the review will deal with a survey on the current status of proteomic studies in yeasts. In a first part of this chapter, we will deal with the currently available proteome maps of yeasts, and in the following part we will discuss studies dealing with fundamental aspects, but also mention proteome studies related to applied microbiology. Finally, we will envisage future perspectives of the proteome technology for studying yeasts, and draw major conclusion on the current status reached in this field of functional genomics.

Matros, Andrea; Mock, Hans-Peter

266

Requirements for Biological Threat Identification Systems  

Microsoft Academic Search

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

Erik A. Henchal; George V. Ludwig

267

Detecting Protein-Protein Interactions in Vesicular Stomatitis Virus Using a Cytoplasmic Yeast Two Hybrid System  

PubMed Central

Summary Protein-protein interactions play an important role in many virus-encoded functions and in virus-host interactions. While a “classical” yeast two-hybrid system (Y2H) is one of the most common techniques to detect such interactions, it has a number of limitations, including a requirement for the proteins of interest to be relocated to the nucleus. Modified Y2H, such as the Sos recruitment system (SRS), which detect interactions occurring in the cytoplasm rather than the nucleus, allow proteins from viruses replicating in the cytoplasm to be tested in a more natural context. In this study, a SRS was used to detect interactions involving proteins from vesicular stomatitis virus (VSV), a prototypic non-segmented negative strand RNA (NNS) virus. All five full-length VSV proteins, as well as several truncated proteins, were screened against each other. Using the SRS, most interactions demonstrated previously involving VSV phosphoprotein, nucleocapsid (N) and large polymerase proteins were confirmed independently, while difficulties were encountered using the membrane associated matrix and glycoproteins. A human cDNA library was also screened against VSV N protein and one cellular protein, SFRS18, was identified which interacted with N in this context. The system presented can be redesigned easily for studies in other less tractable NNS viruses. PMID:21320532

Moerdyk-Schauwecker, Megan; DeStephanis, Darla; Hastie, Eric; Grdzelishvili, Valery Z.

2011-01-01

268

Substructure System Identification for Finite Element Model Updating  

NASA Technical Reports Server (NTRS)

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

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

1997-01-01

269

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

NASA Astrophysics Data System (ADS)

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

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

270

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

Code of Federal Regulations, 2011 CFR

... Technical Requirements for Class A Automatic Identification System (AIS) equipment. 80.275 Section 80... Technical Requirements for Class A Automatic Identification System (AIS) equipment. (a) Prior to...

2011-10-01

271

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

Code of Federal Regulations, 2013 CFR

... Technical Requirements for Class A Automatic Identification System (AIS) equipment. 80.275 Section 80... Technical Requirements for Class A Automatic Identification System (AIS) equipment. (a) Prior to...

2013-10-01

272

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

Code of Federal Regulations, 2012 CFR

... Technical Requirements for Class A Automatic Identification System (AIS) equipment. 80.275 Section 80... Technical Requirements for Class A Automatic Identification System (AIS) equipment. (a) Prior to...

2012-10-01

273

Linear system identification from nonstationary cross-sectional data  

Microsoft Academic Search

The identification of time-invariant linear stochastic systems from cross-sectional data on nonstationary system behavior is considered. A strong consistency and asymptotic normality result for maximum likelihood and prediction error estimates of the system parameters, system and measurement noise covariances, and the initial state covariance is proven. A new tdentifiability property for the system model is defined and appears in the

ROBERT L. GOODRICH; PETER E. CAINES

1979-01-01

274

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

Microsoft Academic Search

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

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

2002-01-01

275

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

PubMed Central

Yeast mutants that are defective in acidification of the lysosome-like vacuole are able to grow at pH 5.5, but not at pH 7. Here, we present evidence that endocytosis is required for this low pH-dependent growth and use this observation to develop a screen for mutants defective in endocytosis. By isolating mutants that cannot grow when they lack the 60-kD vacuolar ATPase subunit (encoded by the VAT2 gene), we isolated a number of vat2-synthetic lethal (Vsl-) mutant strains. Seven of the Vsl- mutants are defective in endocytosis. Four of these mutant strains (end8-1, end9-1, end10-1, and end11-1) show altered uptake of the endocytosed ligand, alpha-factor, and three (end12-1, end12-2, and end13-1) are probably defective in transfer of internalized material to the vacuole. Most of the mutations also confer a strong Ts- growth defect. The mutants defective in uptake of alpha-factor sort newly synthesized vacuolar proteins correctly, while those which may be defective in subsequent transport steps secrete at least a fraction of the newly synthesized soluble vacuolar proteins. The mutations that result in a defect in alpha-factor uptake are not allelic to any of the genes previously shown to encode endocytic functions. PMID:7929582

1994-01-01

276

Identification of act2, an essential gene in the fission yeast Schizosaccharomyces pombe that encodes a protein related to actin.  

PubMed

Actins are a family of highly conserved proteins that are ubiquitously found among eukaryotic organisms. All actins that have previously been identified, including those of animals, plants, fungi, and protozoa, are 374-376 amino acids long and exhibit at least 70% amino acid sequence identity when compared with one another. We have cloned a gene from the fission yeast Schizosaccharomyces pombe that encodes a distantly related member of the actin protein family, herein referred to as act2. In contrast to all other actins, the derived amino acid sequence reveals that act2 is 427 residues long and exhibits only 35-40% identity to actins, including act1 from Sch. pombe. Comparison to the known x-ray crystallographic structure of rabbit skeletal muscle actin indicates that the ATP and divalent metal ion binding sites are largely conserved in act2, while regions involved in actin-actin and actin-myosin interactions are relatively divergent. Disruption of the act2 gene demonstrated that this gene encodes a function essential for germination of haploid spores. These findings indicate that while act2 and act1 are related proteins, they appear to have distinct functions. In addition, they demonstrate that the actin protein family is more diverse than was previously thought. PMID:1729722

Lees-Miller, J P; Henry, G; Helfman, D M

1992-01-01

277

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

PubMed Central

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

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

2014-01-01

278

Identification of act2, an essential gene in the fission yeast Schizosaccharomyces pombe that encodes a protein related to actin.  

PubMed Central

Actins are a family of highly conserved proteins that are ubiquitously found among eukaryotic organisms. All actins that have previously been identified, including those of animals, plants, fungi, and protozoa, are 374-376 amino acids long and exhibit at least 70% amino acid sequence identity when compared with one another. We have cloned a gene from the fission yeast Schizosaccharomyces pombe that encodes a distantly related member of the actin protein family, herein referred to as act2. In contrast to all other actins, the derived amino acid sequence reveals that act2 is 427 residues long and exhibits only 35-40% identity to actins, including act1 from Sch. pombe. Comparison to the known x-ray crystallographic structure of rabbit skeletal muscle actin indicates that the ATP and divalent metal ion binding sites are largely conserved in act2, while regions involved in actin-actin and actin-myosin interactions are relatively divergent. Disruption of the act2 gene demonstrated that this gene encodes a function essential for germination of haploid spores. These findings indicate that while act2 and act1 are related proteins, they appear to have distinct functions. In addition, they demonstrate that the actin protein family is more diverse than was previously thought. Images PMID:1729722

Lees-Miller, J P; Henry, G; Helfman, D M

1992-01-01

279

System Identification and Active Control of a Turbulent Boundary Layer  

E-print Network

An experimental investigation is made into the active control of the near-wall region of a turbulent boundary layer using a linear control scheme. System identification in the boundary layer provides optimal transfer ...

Rathnasingham, Ruben

280

System Identification And Control Using SVD's On Systolic Arrays  

NASA Astrophysics Data System (ADS)

A new class of algorithms based upon a generalized singular value decomposition (SVD) is considered for system identification, statistical model order determination, model order reduction, and predictive control. Currently available algorithms for system identification and control are not completely reliable for automatic implementation on microprocessors in real time. In the generalized SVD approach, the algorithms are computationally stable and numerically accurate and can be implemented on systolic array processors using recently developed algorithms resulting in a considerable speedup. The method is based upon a recent generalized canonical variate analysis (CVA) method for determining the optimal state of a restricted order in system identification, reduced order stochastic filtering, and model predictive control. This permits a unified approach to the solution of these problems from the viewpoints of a prediction problem as well as an approximation problem. Algorithms for online computation in identification, filtering, and control of high order linear multivariable systems are developed. Implementing these algorithms on systolic array processors are discussed.

Larimore, Wallace E.; Luk, Franklin T.

1988-04-01

281

PARAMETER AND SYSTEM IDENTIFICATION FOR FLUID FLOW IN UNDERGROUND RESERVOIRS  

E-print Network

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

Ewing, Richard E.

282

Nonlinear stochastic system identification techniques for biological tissues/  

E-print Network

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

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

2010-01-01

283

Multi-channel blind system identification for central hemodynamic monitoring  

E-print Network

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

Zhang, Yi, 1973-

2002-01-01

284

Planning, Execution, and Analysis of the Meridian UAS Flight Test Program Including System and Parameter Identification  

E-print Network

The purpose of this Master Thesis is to present the flight test procedures, planning, and analysis including system identification, parameter identification, and drag calculations of the Meridian UAS. The system identification is performed using...

Tom, Jonathan

2010-04-27

285

Mapping Yeast Transcriptional Networks  

PubMed Central

The term “transcriptional network” refers to the mechanism(s) that underlies coordinated expression of genes, typically involving transcription factors (TFs) binding to the promoters of multiple genes, and individual genes controlled by multiple TFs. A multitude of studies in the last two decades have aimed to map and characterize transcriptional networks in the yeast Saccharomyces cerevisiae. We review the methodologies and accomplishments of these studies, as well as challenges we now face. For most yeast TFs, data have been collected on their sequence preferences, in vivo promoter occupancy, and gene expression profiles in deletion mutants. These systematic studies have led to the identification of new regulators of numerous cellular functions and shed light on the overall organization of yeast gene regulation. However, many yeast TFs appear to be inactive under standard laboratory growth conditions, and many of the available data were collected using techniques that have since been improved. Perhaps as a consequence, comprehensive and accurate mapping among TF sequence preferences, promoter binding, and gene expression remains an open challenge. We propose that the time is ripe for renewed systematic efforts toward a complete mapping of yeast transcriptional regulatory mechanisms. PMID:24018767

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

2013-01-01

286

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

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

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

2014-05-01

287

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

PubMed Central

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

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

2014-01-01

288

System identification of suspension bridge from ambient vibration response  

Microsoft Academic Search

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

Dionysius M. Siringoringo; Yozo Fujino

2008-01-01

289

Neural network based system for script identification in Indian documents  

Microsoft Academic Search

The paper describes a neural network-based script identification system which can be used in the machine reading of documents\\u000a written in English, Hindi and Kannada language scripts. Script identification is a basic requirement in automation of document\\u000a processing, in multi-script, multi-lingual environments. The system developed includes a feature extractor and a modular neural\\u000a network. The feature extractor consists of two

S. Basavaraj Patil; N. V. Subbareddy

2002-01-01

290

On the time complexity of worst-case system identification  

Microsoft Academic Search

In this paper we treat a general worst-case system identification problem. This problem is worst-case with respect to both noise and system modeling uncertainty. We consider this problem under various a priori information structures. We determine bounds on the minimum duration identification experiment that must be run to identify the plant to within a specified guaranteed worst-case error bound. Our

Kameshwar Poolla; Ashok Tikku

1994-01-01

291

Training and Analysis of Mobile Robot Behaviour Through System Identification  

Microsoft Academic Search

In this paper we describe a new procedure to obtain the control code for a mobile robot, based on system identification: Initially,\\u000a the robot is controlled by a human operator, who manually guides it through a desired sensor-motor task. The robot’s motion\\u000a is then “identified” using the NARMAX system identification technique. The resulting transparent model can subsequently be\\u000a used to

Roberto Iglesias; Ulrich Nehmzow; Theocharis Kyriacou; Steve Billings

2005-01-01

292

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

PubMed Central

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

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

2013-01-01

293

49 CFR 1542.211 - Identification systems.  

Code of Federal Regulations, 2011 CFR

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

2011-10-01

294

System identification with generalized orthonormal basis functions  

Microsoft Academic Search

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

Peter S. C. Heuberger; József Bokor

1995-01-01

295

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

PubMed Central

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

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

2012-01-01

296

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

PubMed

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

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

2012-01-01

297

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

E-print Network

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

Botstein, David

298

System identification methods for aircraft flight control development and validation  

NASA Technical Reports Server (NTRS)

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

Tischler, Mark B.

1995-01-01

299

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

E-print Network

Fuzzy membership function optimization for system identification using an extended Kalman filter an extended Kalman filter to optimize the membership functions for system modeling, or system identification identification. The ideas described in this paper are illustrated for system identification of a nonlinear

Simon, Dan

300

Optimized behavioral interventions: what does system identification and control  

E-print Network

counseling visits to families with at-risk children. Keywords: social and behavioral sciences, systemOptimized behavioral interventions: what does system identification and control engineering have.rivera@asu.edu Abstract: The last decade has witnessed an increasing interest in applying systems science concepts

Contractor, Anis

301

Automatic vehicle identification with sensor-integrated RFID system  

Microsoft Academic Search

Sensor is one of the popular devices used in many applications nowadays including the intelligent transportation system (ITS) which is widely utilized in the automatic vehicle identification (AVI) system. In this research, we propose an implementation of photoelectric sensors as a vehicle detection tool in an RFID-based poultry traceability system to detect poultry transport vehicle entering and leaving an animal

J. Wisanmongkol; T. Sanpechuda; U. Ketprom

2008-01-01

302

Evaluation of the Quantum II and Rapid E identification systems.  

PubMed Central

A total of 492 clinical isolates from the family Enterobacteriaceae were tested in the API 20E, Rapid E, and Quantum II identification systems. Discrepant identifications among these three systems were resolved by repeat testing in the identification systems or use of conventional biochemical tests. Of these isolates, 94.1% were correctly identified with the API 20E and Rapid E systems, and 97.0% were correctly identified with the Quantum II system. An additional 48 non-Enterobacteriaceae isolates were tested with the Quantum II system, and 83.3% were correctly identified. The majority of incorrect identifications with the Rapid E and Quantum II systems were caused by a single aberrant biochemical reaction. Reproducibility of the biochemical reactions obtained with these two systems was evaluated by testing 40 organisms in triplicate. Identical biocodes for all three tests were obtained for 10 organisms with the Quantum II system and for 19 organisms with the Rapid E system. Reproducibility of the Quantum II test results was improved with a subsequent modification of the photometer of this system. Both the Rapid E and Quantum II systems were inexpensive and were technically easy to inoculate and interpret. PMID:6386866

Murray, P R; Gauthier, A; Niles, A

1984-01-01

303

Systems identification technology development for large space systems  

NASA Technical Reports Server (NTRS)

A methodology for synthesizinng systems identification, both parameter and state, estimation and related control schemes for flexible aerospace structures is developed with emphasis on the Maypole hoop column antenna as a real world application. Modeling studies of the Maypole cable hoop membrane type antenna are conducted using a transfer matrix numerical analysis approach. This methodology was chosen as particularly well suited for handling a large number of antenna configurations of a generic type. A dedicated transfer matrix analysis, both by virtue of its specialization and the inherently easy compartmentalization of the formulation and numerical procedures, is significantly more efficient not only in computer time required but, more importantly, in the time needed to review and interpret the results.

Armstrong, E. S.

1982-01-01

304

Authentication Without Identification using Anonymous Credential System  

Microsoft Academic Search

Privacy and security are often intertwined. For example, identity theft is\\u000arampant because we have become accustomed to authentication by identification.\\u000aTo obtain some service, we provide enough information about our identity for an\\u000aunscrupulous person to steal it (for example, we give our credit card number to\\u000aAmazon.com). One of the consequences is that many people avoid e-commerce\\u000aentirely

A. Damodaram; H. Jayasri

2009-01-01

305

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

NASA Astrophysics Data System (ADS)

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

Serrão, Carlos

306

Identification of nonlinear hysteretic systems by artificial neural network  

NASA Astrophysics Data System (ADS)

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

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

2013-01-01

307

Agent Architecture for Criminal Mobile Devices Identification Systems  

Microsoft Academic Search

Current techniques of language identification are based on a method that assigns one or more textual documents into a set\\u000a of predefined languages that are relevant to page contents. In this paper, we proposed an agent architecture that is used\\u000a in criminal mobile devices identification systems. It is based on the usage of a software agent to process at least

Ali Selamat; Choon-Ching Ng; Siti Dianah Abdul Bujang

2009-01-01

308

System Identification of Small-Size Unmanned Helicopter Dynamics  

Microsoft Academic Search

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

Bernard Mettler; Mark B. Tischler; Takeo Kanade

309

Modeling of single phase inverter of photovoltaic system using Hammerstein–Wiener nonlinear system identification  

Microsoft Academic Search

This paper proposes a new method to modeling a power inverter of grid-connected photovoltaic system by using a nonlinear system identification technique based on the Hammerstein–Weiner model. In this method, the system is considered as a black box of which it is not necessary to know structures and parameters inside. A nonlinear system identification, which is composed of nonlinear blocks

Nopporn Patcharaprakiti; Krissanapong Kirtikara; Veerapol Monyakul; Dhirayut Chenvidhya; Jatturit Thongpron; Anawach Sangswang; Ballang Muenpinij

2010-01-01

310

Improved tools for efficient mapping of fission yeast genes: identification of microtubule nucleation modifier mod22-1 as an allele of chromatin- remodelling factor gene swr1  

PubMed Central

Fission yeast genes identified in genetic screens are usually cloned by transformation of mutants with plasmid libraries. However, for some genes this can be difficult, and positional cloning approaches are required. The mutation swi5-39 reduces recombination frequency in homozygous crosses and has been used as a tool in mapping gene position (Schmidt, 1993). However, strain construction in swi5-39-based mapping is significantly more laborious than is desirable. Here we describe a set of strains designed to make swi5-based mapping more efficient and more powerful. The first improvement is the use of a swi5? strain marked with kanamycin (G418) resistance, which greatly facilitates identification of swi5 mutants. The second improvement, which follows directly from the first, is the introduction of a large number of auxotrophic markers into mapping strains, increasing the likelihood of finding close linkage between a marker and the mutation of interest. We combine these new mapping strains with a rec12?-based approach for initial mapping of a mutation to an individual chromosome. Together, the two methods allow an approximate determination of map position in only a small number of crosses. We used these to determine that mod22-1, a modifier of microtubule nucleation phenotypes, encodes a truncation allele of Swr1, a chromatin-remodelling factor involved in nucleosomal deposition of H2A.Z histone variant Pht1. Expression microarray analysis of mod22-1, swr1? and pht1? cells suggests that the modifier phenotype of mod22-1 mutants may be due to small changes in expression of one or more genes involved in tubulin function. Copyright © 2009 John Wiley & Sons, Ltd. PMID:19160458

Anders, Andreas; Watt, Stephen; Bahler, Jurg; Sawin, Kenneth E

2008-01-01

311

Application of unsymmetric block Lanczos vectors in system identification  

NASA Technical Reports Server (NTRS)

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

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

1992-01-01

312

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

SciTech Connect

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

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

2010-10-01

313

Nitrile Metabolizing Yeasts  

NASA Astrophysics Data System (ADS)

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

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

314

Time-Delay System Identification Using Genetic Algorithm -Part One: Precise  

E-print Network

Time-Delay System Identification Using Genetic Algorithm - Part One: Precise FOPDT Model Estimation, parameter identification, genetic algorithms, FOPDT 1. INTRODUCTION The identification of time-delay system-Order-Plus-Dead-Time (FOPDT) system. Due to the unknown dead-time coefficient, this type of identification problem often turns

Yang, Zhenyu

315

A contribution to the identification of switched dynamical systems over finite fields  

E-print Network

A contribution to the identification of switched dynamical systems over finite fields Phuoc Vo Tan the identification for switched linear systems over finite fields. It is inspired from the procedure suggested in [4 of the identification procedure for the class of switched linear systems. Batch identification is considered

Boyer, Edmond

316

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, ...

317

Kinetochore Structure: Pulling Answers from Yeast  

E-print Network

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

Cheeseman, Iain M.

318

A yeast surface display system for the discovery of ligands that trigger cell activation  

Microsoft Academic Search

Opposing cells often communicate signalling events using multivalent interactions between receptors present on their cell surface. For example, T cells are typically activated when the T cell receptor (TCR) and its associated costimulatory molecules are multivalently engaged by the appropriate ligands present on an antigen presenting cell. In this report, yeast expressing high cell-surface levels of a TCR ligand (a

Bryan K. Cho; Michele C. Kieke; Eric T. Boder; K. Dane Wittrup; David M. Kranz

1998-01-01

319

RBFNN-Based Hole Identification System in Conducting Plates  

Microsoft Academic Search

We propose a radial basis function neural network (RBFNN) approach to the identification of holes in conducting plates, in the context of an eddy current testing (ECT) signal processing system. The system aims to localise holes in the specimen under inspection by using a two-stage approach, namely, a RBFNN followed by a least squares post-processing block. The RBFNN stage estimates

G. Simone; Francesco Carlo Morabito

2000-01-01

320

Identification system for smart homes using footstep sounds  

Microsoft Academic Search

This work proposes an identification system for smart buildings using footstep information. Basically, the system has three modules: pre-processing, feature extraction and selection, and classification of the information. Gait frequency, spectral envelope, cepstral and mel-cepstral analysis and loudness compose the set of parameters used to identify subjects in the smart building. In order to select features, the Fisher's criterion was

Rafael Lima de Carvalho; Paulo Fernando Ferreira Rosa

2010-01-01

321

Comparison of presenilin 1 and presenilin 2 ?-secretase activities using a yeast reconstitution system.  

PubMed

?-Secretase is composed of at least four proteins, presenilin (PS), nicastrin (NCT), Aph1, and Pen2. PS is the catalytic subunit of the ?-secretase complex, having aspartic protease activity. PS has two homologs, namely, PS1 and PS2. To compare the activity of these complexes containing different PSs, we reconstituted them in yeast, which lacks ?-secretase homologs. Yeast cells were transformed with PS1 or PS2, NCT, Pen2, Aph1, and artificial substrate C55-Gal4p. After substrate cleavage, Gal4p translocates to the nucleus and activates transcription of the reporter genes ADE2, HIS3, and lacZ. ?-Secretase activity was measured based on yeast growth on selective media and ?-galactosidase activity. PS1 ?-secretase was ?24-fold more active than PS2 ?-secretase in the ?-galactosidase assay. Using yeast microsomes containing ?-secretase and C55, we compared the concentration of A? generated by PS1 or PS2 ?-secretase. PS1 ?-secretase produced ?24-fold more A? than PS2 ?-secretase. We found the optimal pH of A? production by PS2 to be 7.0, as for PS1, and that the PS2 complex included immature NCT, unlike the PS1 complex, which included mature NCT. In this study, we compared the activity of PS1 or PS2 per one ?-secretase complex. Co-immunoprecipitation experiments using yeast microsomes showed that PS1 concentrations in the ?-secretase complex were ?28 times higher than that of PS2. Our data suggest that the PS1 complex is only marginally less active than the PS2 complex in A? production. PMID:22074918

Yonemura, Yoji; Futai, Eugene; Yagishita, Sosuke; Suo, Satoshi; Tomita, Taisuke; Iwatsubo, Takeshi; Ishiura, Shoichi

2011-12-30

322

Numerical studies of identification in nonlinear distributed parameter systems  

NASA Technical Reports Server (NTRS)

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

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

1989-01-01

323

Evaluation on antagonist activities of polycyclic aromatic hydrocarbons using the yeast two-hybrid detection system for endocrine disruptors.  

PubMed

We constructed an efficient and reliable yeast two-hybrid detection system to evaluate the estrogenic activity of endocrine disruptors (EDs) (Lee et al., Journal of Biochemistry, 131, 2002). This system employs the interaction between the human estrogen receptor beta (hERbeta) ligand binding domain and the co-activator SRC1. The extent of transcriptional activation by those chemicals correlated with estrogenic activities as measured by other assay systems. We applied this assay system to evaluate anti-estrogenic activities and found that known antagonistic compounds, 4-hydroxytamoxifen (OHT) and ICI 182,780, effectively inhibited reporter gene induction by 17beta-estradiol. We then tested the estrogenic and anti-estrogenic activities of polycyclic aromatic hydrocarbons (PAHs) using this assay system. PAHs only weakly induced the lacZ reporter gene at higher concentrations, but clearly showed an inhibitory effect on reporter gene induction by 10(-9) M 17beta-estradiol. These results suggest that PAHs are potentially anti-estrogenic and that the employed yeast detection system could be applicable to primary screening for effectors on estrogen receptor functions. PMID:17057947

Lee, Haeng-Seog; Cho, Eun-Min; Jung, Jae Hak; Ohta, Akinori

2007-06-01

324

Neural networks for nonlinear dynamic system modelling and identification  

Microsoft Academic Search

Many real-world systems exhibit complex nonlinear characteristics and cannot be treated satisfactorily using linear systems theory. A neural network which has the ability to learn sophisticated nonlinear relationships provides an ideal means of modelling complicated nonlinear systems. This paper addresses the issues related to the identification of nonlinear discrete-time dynamic systems using neural networks. Three network architectures, namely the multi-layer

S. CHEN; S. A. BILLINGS

1992-01-01

325

Release of Ca2+ and Mg2+ from yeast mitochondria is stimulated by increased ionic strength  

Microsoft Academic Search

BACKGROUND: Divalent cations are required for many essential functions of mitochondrial metabolism. Yet the transporters that mediate the flux of these molecules into and out of the mitochondrion remain largely unknown. Previous studies in yeast have led to the molecular identification of a component of the major mitochondrial electrophoretic Mg2+ uptake system in this organism as well as a functional

Patrick C Bradshaw; Douglas R Pfeiffer

2006-01-01

326

Failure detection and identification for a reconfigurable flight control system  

NASA Technical Reports Server (NTRS)

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.

Dallery, Francois

1987-01-01

327

Modeling emotional content of music using system identification.  

PubMed

Research was conducted to develop a methodology to model the emotional content of music as a function of time and musical features. Emotion is quantified using the dimensions valence and arousal, and system-identification techniques are used to create the models. Results demonstrate that system identification provides a means to generalize the emotional content for a genre of music. The average R2 statistic of a valid linear model structure is 21.9% for valence and 78.4% for arousal. The proposed method of constructing models of emotional content generalizes previous time-series models and removes ambiguity from classifiers of emotion. PMID:16761812

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

2006-06-01

328

Chaotic system identification based on Kalman filter  

Microsoft Academic Search

Presents a method to predict chaotic time series, including long-term prediction, and demonstrates the possibilities of constructing governing system equations based on the behavior of observed time series. First, a general system structure is assumed. Second, typical chaotic equations as reference system equations that show similar features with those of the observed time series are defined. Then the general system

Min Han; Jianhui Xi; Shiguo Xu

2002-01-01

329

New Regulators of a High Affinity Ca2+ Influx System Revealed through a Genome-wide Screen in Yeast*  

PubMed Central

The bakers' yeast Saccharomyces cerevisiae utilizes a high affinity Ca2+ influx system (HACS) to survive assaults by mating pheromones, tunicamycin, and azole-class antifungal agents. HACS consists of two known subunits, Cch1 and Mid1, that are homologous and analogous to the catalytic ?-subunits and regulatory ?2?-subunits of mammalian voltage-gated calcium channels, respectively. To search for additional subunits and regulators of HACS, a collection of gene knock-out mutants was screened for abnormal uptake of Ca2+ after exposure to mating pheromone or to tunicamycin. The screen revealed that Ecm7 is required for HACS function in most conditions. Cycloheximide chase experiments showed that Ecm7 was stabilized by Mid1, and Mid1 was stabilized by Cch1 in non-signaling conditions, suggesting they all interact. Ecm7 is a member of the PMP-22/EMP/MP20/Claudin superfamily of transmembrane proteins that includes ?-subunits of voltage-gated calcium channels. Eleven additional members of this superfamily were identified in yeast, but none was required for HACS activity in response to the stimuli. Remarkably, many dozens of genes involved in vesicle-mediated trafficking and protein secretion were required to prevent spontaneous activation of HACS. Taken together, the findings suggest that HACS and calcineurin monitor performance of the membrane trafficking system in yeasts and coordinate compensatory processes. Conservation of this quality control system in Candida glabrata suggests that many pathogenic species of fungi may utilize HACS and calcineurin to resist azoles and other compounds that target membrane biosynthesis. PMID:21252230

Martin, D. Christian; Kim, Hyemin; Mackin, Nancy A.; Maldonado-Baez, Lymarie; Evangelista, Carlos C.; Beaudry, Veronica G.; Dudgeon, Drew D.; Naiman, Daniel Q.; Erdman, Scott E.; Cunningham, Kyle W.

2011-01-01

330

Music identification system using MPEG-7 audio signature descriptors.  

PubMed

This paper describes a multiresolution system based on MPEG-7 audio signature descriptors for music identification. Such an identification system may be used to detect illegally copied music circulated over the Internet. In the proposed system, low-resolution descriptors are used to search likely candidates, and then full-resolution descriptors are used to identify the unknown (query) audio. With this arrangement, the proposed system achieves both high speed and high accuracy. To deal with the problem that a piece of query audio may not be inside the system's database, we suggest two different methods to find the decision threshold. Simulation results show that the proposed method II can achieve an accuracy of 99.4% for query inputs both inside and outside the database. Overall, it is highly possible to use the proposed system for copyright control. PMID:23533359

You, Shingchern D; Chen, Wei-Hwa; Chen, Woei-Kae

2013-01-01

331

Music Identification System Using MPEG-7 Audio Signature Descriptors  

PubMed Central

This paper describes a multiresolution system based on MPEG-7 audio signature descriptors for music identification. Such an identification system may be used to detect illegally copied music circulated over the Internet. In the proposed system, low-resolution descriptors are used to search likely candidates, and then full-resolution descriptors are used to identify the unknown (query) audio. With this arrangement, the proposed system achieves both high speed and high accuracy. To deal with the problem that a piece of query audio may not be inside the system's database, we suggest two different methods to find the decision threshold. Simulation results show that the proposed method II can achieve an accuracy of 99.4% for query inputs both inside and outside the database. Overall, it is highly possible to use the proposed system for copyright control. PMID:23533359

You, Shingchern D.; Chen, Wei-Hwa; Chen, Woei-Kae

2013-01-01

332

A network identity authentication system based on Fingerprint identification technology  

NASA Astrophysics Data System (ADS)

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

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

2005-10-01

333

5?TRU: Identification and Analysis of Translationally Regulative 5?Untranslated Regions in Amino Acid Starved Yeast Cells*  

PubMed Central

We describe a method to identify and analyze translationally regulative 5?UTRs (5?TRU) in Saccharomyces cerevisiae. Two-dimensional analyses of 35S-methionine metabolically labeled cells revealed 13 genes and proteins, whose protein biosynthesis is post-transcriptionally up-regulated on amino acid starvation. The 5?UTRs of the respective mRNAs were further investigated. A plasmid-based reporter-testing system was developed to analyze their capability to influence translation dependent on amino acid availability. Most of the 13 candidate 5?UTRs are able to enhance translation independently of amino acids. Two 5?UTRs generally repressed translation, and the 5?UTRs of ENO1, FBA1, and TPI1 specifically up-regulated translation when cells were starved for amino acids. The TPI1-5?UTR exhibited the strongest effect in the testing system, which is consistent with elevated Tpi1p-levels in amino acid starved cells. Bioinformatical analyses support that an unstructured A-rich 5? leader is beneficial for efficient translation when amino acids are scarce. Accordingly, the TPI1-5?UTR was shown to contain an A-rich tract in proximity to the mRNA-initiation codon, required for its amino acid dependent regulatory function. PMID:21444828

Rachfall, Nicole; Heinemeyer, Isabelle; Morgenstern, Burkhard; Valerius, Oliver; Braus, Gerhard H.

2011-01-01

334

5'TRU: identification and analysis of translationally regulative 5'untranslated regions in amino acid starved yeast cells.  

PubMed

We describe a method to identify and analyze translationally regulative 5'UTRs (5'TRU) in Saccharomyces cerevisiae. Two-dimensional analyses of (35)S-methionine metabolically labeled cells revealed 13 genes and proteins, whose protein biosynthesis is post-transcriptionally up-regulated on amino acid starvation. The 5'UTRs of the respective mRNAs were further investigated. A plasmid-based reporter-testing system was developed to analyze their capability to influence translation dependent on amino acid availability. Most of the 13 candidate 5'UTRs are able to enhance translation independently of amino acids. Two 5'UTRs generally repressed translation, and the 5'UTRs of ENO1, FBA1, and TPI1 specifically up-regulated translation when cells were starved for amino acids. The TPI1-5'UTR exhibited the strongest effect in the testing system, which is consistent with elevated Tpi1p-levels in amino acid starved cells. Bioinformatical analyses support that an unstructured A-rich 5' leader is beneficial for efficient translation when amino acids are scarce. Accordingly, the TPI1-5'UTR was shown to contain an A-rich tract in proximity to the mRNA-initiation codon, required for its amino acid dependent regulatory function. PMID:21444828

Rachfall, Nicole; Heinemeyer, Isabelle; Morgenstern, Burkhard; Valerius, Oliver; Braus, Gerhard H

2011-06-01

335

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

E-print Network

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

Thomson, Ty M.

336

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

PubMed

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

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

2008-04-01

337

American Institute of Aeronautics and Astronautics Active System Identification of a DC-DC Converter Using  

E-print Network

American Institute of Aeronautics and Astronautics 1 Active System Identification of a DC and interactions among modules may cause system instabilities. System identification is generally divided about the system model, and the identification is used to directly compute the system frequency

338

Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering.  

PubMed

Reduction of endogenous gene expression is a fundamental operation of metabolic engineering, yet current methods for gene knockdown (i.e., genome editing) remain laborious and slow, especially in yeast. In contrast, RNA interference allows facile and tunable gene knockdown via a simple plasmid transformation step, enabling metabolic engineers to rapidly prototype knockdown strategies in multiple strains before expending significant cost to undertake genome editing. Although RNAi is naturally present in a myriad of eukaryotes, it has only been recently implemented in Saccharomyces cerevisiae as a heterologous pathway and so has not yet been optimized as a metabolic engineering tool. In this study, we elucidate a set of design principles for the construction of hairpin RNA expression cassettes in yeast and implement RNA interference to quickly identify routes for improvement of itaconic acid production in this organism. The approach developed here enables rapid prototyping of knockdown strategies and thus accelerates and reduces the cost of the design-build-test cycle in yeast. PMID:24328131

Crook, Nathan C; Schmitz, Alexander C; Alper, Hal S

2014-05-16

339

System identification requirements for high-bandwidth rotorcraft flight control system design  

NASA Technical Reports Server (NTRS)

The application of system identification methods to high-bandwidth rotorcraft flight control system design is examined. Flight test and modeling requirements are illustrated using flight test data from a BO-105 hingeless rotor helicopter. The proposed approach involves the identification of nonparametric (transfer function and state space) model identification. Results for the BO-105 show the need for including coupled body/rotor flapping and lead-lag dynamics in the identification model structure to allow the accurate prediction of control ssytem bandwidth limitations.

Tischler, Mark B.

1991-01-01

340

On neural networks in identification and control of dynamic systems  

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

341

Effects of yeast stress and pH on 3-monochloropropanediol (3-MCPD)-producing reactions in model dough systems  

Microsoft Academic Search

A major precursor of 3-monochloropropanediol (3-MCPD) in leavened cereal products is glycerol, which is formed as a natural by-product of yeast fermentation. However, yeast metabolism is affected by stresses such as low osmotic pressure from, for example, the incorporation of sugar or salt in the dough recipe. Tests with model doughs have shown that glycerol production was proportional to yeast

C. G. Hamlet; P. A. Sadd

2005-01-01

342

Battery status identification of battery management system with asynchronous sampling  

Microsoft Academic Search

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

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

2011-01-01

343

FORENSIC IDENTIFICATION REPORTING USING AUTOMATIC SPEAKER RECOGNITION SYSTEMS  

E-print Network

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

Autonoma de Madrid, Universidad

344

Genetic Algorithms applications to optimization and system identification  

E-print Network

and it can determine solutions in a very short time. According to these characteristics, GA is a very powerful method for optimal design and system identification. In this thesis, we will apply GA to two main topics. Chapter II is about optimal designing...

Lin, Yun-Jeng

2012-06-07

345

System identification of photosensitiser uptake kinetics in photodynamic therapy  

E-print Network

System identification of photosensitiser uptake kinetics in photodynamic therapy T. Bastogne1 , L delivery, pho- todynamic therapy. 1 Introduction Photodynamic therapy (PDT) (Moser (1998)) is an emerging apoptotic and necrotic death of tumour. In current clinical practice, photodynamic therapy is carried out

Paris-Sud XI, Université de

346

System Identification of Post Stall Aerodynamics for UAV Perching  

E-print Network

System Identification of Post Stall Aerodynamics for UAV Perching Warren Hoburg and Russ Tedrake. The relevant transient aerodynamics at high angle of attack are not addressed today by control-accessible aerodynamic models. In this work, we present a set of physically-inspired basis functions which have enabled

Tedrake, Russ

347

Backlash phenomenon observation and identification in electromechanical system  

Microsoft Academic Search

In this paper a second order sliding mode observer with finite time convergence is developed for an electromechanical system with backlash. As a consequence of finite time convergence the sliding mode equivalent control is used to apply identification algorithms in order to characterize the backlash phenomenon. The dead zone amplitude and the disturbing torque are identified asymptotically. Simulation and experimental

Paul Langevin

348

Using ECG as a measure in biometric identification systems  

Microsoft Academic Search

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

Babak Nasri; Mouhcine Guennoun; Khalil El-Khatib

2009-01-01

349

Copyright 1997 Carnegie Mellon University Gas Identification System using  

E-print Network

multi-element thick film gas sensor. A temperature gradient maintained along the sensor surface inducesCopyright © 1997 Carnegie Mellon University Gas Identification System using Graded Temperature temperature gradient along a linear sensor array. In fact, the "array" is a continuous film on a ceramic

Siegel, Mel

350

A unifying construction of orthonormal bases for system identification  

Microsoft Academic Search

In this paper we develop a general and very simple construction for complete orthonormal bases for system identification. This construction provides a unifying formulation of all known orthonormal bases since the FIR, Laguerre and Kautz model structures are restrictive special cases of our construction as is another construction method based on balanced realisations of all-pass functions. However, in contrast to

Brett Martin Ninness; F. Gustafsson

1994-01-01

351

Time-varying system identification and model validation using wavelets  

Microsoft Academic Search

Parametric identification of time-varying (TV) systems is possible if each TV coefficient can be expanded onto a finite set of basis sequences. The problem then becomes time invariant with respect to the parameters of the expansion. The authors address the question of selecting this set of basis sequences. They advocate the use of a wavelet basis because of its flexibility

Michail K. Tsatsanis; Georgios B. Giannakis

1993-01-01

352

A unifying theorem for three subspace system identification algorithms  

Microsoft Academic Search

The aim of this paper is to indicate and explore the similarities between three different subspace algorithms for the identification of combined deterministic-stochastic systems. The similarities between these algorithms have been obscured, due to different notations and backgrounds. It is shown that all three algorithms are special cases of one unifying theorem. The comparison also reveals that the three algorithms

Peter Van Overschee; Bart De Moor

1995-01-01

353

Non-linear systems identification using radial basis functions  

Microsoft Academic Search

This paper investigates the identification of discrete-time non-linear systems using radial basis functions. A forward regression algorithm based on an orthogonal decomposition of the regression matrix is employed to select a suitable set of radial basis function centers from a large number of possible candidates and this provides, for the first time, fully automatic selection procedure for identifying parsimonious radial

S. CHEN; S. A. BILLINGS; C. F. N. COWAN; P. M. GRANT

1990-01-01

354

A unifying construction of orthonormal bases for system identification  

Microsoft Academic Search

This paper develops a general and very simple construction for complete orthonormal bases for system identification. This construction provides a unifying formulation of many previously studied orthonormal bases since the common FIR and recently popular Laguerre and two-parameter Kautz model structures are restrictive special cases of the construction presented here. However, in contrast to these special cases, the basis vectors

B. Ninness; F. Gustafsson

1997-01-01

355

A recurrent fuzzy-neural model for dynamic system identification  

Microsoft Academic Search

This paper presents a fuzzy modeling approach for identification of dynamic systems. In particular, a new fuzzy model, the Dynamic Fuzzy Neural Network (DFNN), consisting of recurrent TSK rules, is developed. The premise and defuzzification parts are static while the consequent parts of the fuzzy rules are recurrent neural networks with internal feedback and time delay synapses. The network is

Ioannis B. Theocharis

2002-01-01

356

System identification and control synthesis for a benchmark problem  

Microsoft Academic Search

In this paper we apply the integrated system identification\\/H? control synthesis approach to the IFAC 1993 benchmark problem using the minimal amount of process information revealed. The resulting performance compares favorably to those using time-invariant control design techniques, and achieves prescribed performance for small and medium levels of plant uncertainties. For strong plant variations, the performance is inferior to most

Ka-Lun Tung; Yeung Yam

1998-01-01

357

Rapid Color Test Identification System for Screening of Counterfeit Fluoroquinolone  

Microsoft Academic Search

The protocol of rapid identification system consists of three chemical color reactions; two group tests for fluoroquinolone class and a compound specific test each for norfloxacin, ciprofloxacin, gatifloxacin, ofloxacin, levofloxacin and sparfloxacin. The group color reactions are based on (a) Oxidizing behavior of quinolone and (b) Fluorine functional groups, both of which are characteristic of fluoroquinolone class. The compound specific

B K. SINGH; D V. PARWATE; S K. SHUKLA

358

Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme.  

PubMed Central

Several genes encoding putative RNA:5-methylcytidine-transferases (m5C-transferases) from different organisms, including yeast, have been identified by sequence homology with the recently identified 16S rRNA:m5C967-methyltransferase (gene SUN) from Escherichia coli. One of the yeast ORFs (YBL024w) was amplified by PCR, inserted in the expression vector pET28b, and the corresponding protein was hyperexpressed in E. coli BL21 (DE3). The resulting N-terminally His6-tagged recombinant Ybl024p was purified to apparent homogeneity by one-step affinity chromatography on Ni2+-NTA-agarose column. The activity and substrate specificity of the purified Ybl024p were tested in vitro using T7 transcripts of different yeast tRNAs as substrates and S-adenosyl-L-methionine as a donor of the methyl groups. The results indicate that yeast ORF YBL024w encodes S-adenosyl-L-methionine-dependent tRNA: m5C-methyltransferase that is capable of methylating cytosine to m5C at several positions in different yeast tRNAs and pre-tRNAs containing intron. Modification of tRNA occurs at all four positions (34, 40, 48, and 49) at which m5C has been found in yeast tRNAs sequenced so far. Disruption of the ORF YBL024w leads to the complete absence of m5C in total yeast tRNA. Moreover no tRNA:m5C-methyltransferase activity towards all potential m5C methylation sites was detected in the extract of the disrupted yeast strain. These results demonstrate that the protein product of a single gene is responsible for complete m5C methylation of yeast tRNA. Because this newly characterized multisite-specific modification enzyme Ybl024p is the fourth tRNA-specific methyltransferase identified in yeast, we suggest designating it as TRM4, the gene corresponding to ORF YBL024w. PMID:10445884

Motorin, Y; Grosjean, H

1999-01-01

359

Identification of Protective Antigens for Vaccination against Systemic Salmonellosis  

PubMed Central

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

Bumann, Dirk

2014-01-01

360

Variance and bias computation for enhanced system identification  

NASA Technical Reports Server (NTRS)

A study is made of the use of a series of variance and bias confidence criteria recently developed for the eigensystem realization algorithm (ERA) identification technique. The criteria are shown to be very effective, not only for indicating the accuracy of the identification results (especially in terms of confidence intervals), but also for helping the ERA user to obtain better results. They help determine the best sample interval, the true system order, how much data to use and whether to introduce gaps in the data used, what dimension Hankel matrix to use, and how to limit the bias or correct for bias in the estimates.

Bergmann, Martin; Longman, Richard W.; Juang, Jer-Nan

1989-01-01

361

DNA barcode-based molecular identification system for fish species.  

PubMed

In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp . PMID:21110132

Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

2010-12-01

362

Early identification systems for emerging foodborne hazards.  

PubMed

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

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

2009-05-01

363

Biometric identification systems: the science of transaction facilitation  

NASA Astrophysics Data System (ADS)

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

Rogers, Robert R.

1994-10-01

364

Numerical Experimentation with Maximum Likelihood Identification in Static Distributed Systems  

NASA Technical Reports Server (NTRS)

Many important issues in the control of large space structures are intimately related to the fundamental problem of parameter identification. One might also ask how well this identification process can be carried out in the presence of noisy data since no sensor system is perfect. With these considerations in mind the algorithms herein are designed to treat both the case of uncertainties in the modeling and uncertainties in the data. The analytical aspects of maximum likelihood identification are considered in some detail in another paper. The questions relevant to the implementation of these schemes are dealt with, particularly as they apply to models of large space structures. The emphasis is on the influence of the infinite dimensional character of the problem on finite dimensional implementations of the algorithms. Those areas of current and future analysis are highlighted which indicate the interplay between error analysis and possible truncations of the state and parameter spaces.

Scheid, R. E., Jr.; Rodriguez, G.

1985-01-01

365

The primary structure of rat ribosomal protein L23a. The application of homology search to the identification of genes for mammalian and yeast ribosomal proteins and a correlation of rat and yeast ribosomal proteins.  

PubMed

The amino acid sequence of the rat 60 S ribosomal subunit protein L23a was deduced from the sequence of nucleotides in a recombinant cDNA. Ribosomal protein L23a has 156 amino acids and a molecular weight of 17,684. Hybridization of the L23a cDNA to digests of nuclear DNA suggests that there are 18-20 copies of the L23a gene. The mRNA for the protein is about 600 nucleotides in length. Rat L23a is related to the yeast Saccharomyces cerevisiae L25, to the archaebacterial Methanococcus vannielii L23, to eubacterial Escherichia coli L23, and to other members of the L23 family of ribosomal proteins. A novel application of a routine homology search procedure was employed to identify a nucleotide sequence that could be used to design an oligodeoxynucleotide probe to screen a library for a cDNA that encodes rat L23a; this same procedure uncovered a number of previously unidentified genes for yeast ribosomal proteins in the GenBank DNA data base. In a correlation of rat and yeast ribosomal proteins 48 pairs are shown to be related. PMID:8428950

Suzuki, K; Wool, I G

1993-02-01

366

Los Alamos Scientific Laboratory electronic vehicle identification system  

SciTech Connect

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

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

1980-01-01

367

An Internet-Based Expert System for Reptile Identification Ralph F. Grove  

E-print Network

An Internet-Based Expert System for Reptile Identification Ralph F. Grove Computer Science The Reptile Identification Helper (RIH) is an Internet-based expert system, i.e., a system that embodies or to confirm identifications made in the field. In order to make the system useful in the capacity of an online

Grove, Ralph

368

Identification of Backlash Type Hysteretic Systems Based on Particle Filter  

NASA Astrophysics Data System (ADS)

This paper considers the system identification problem for hysteresis systems. This problem plays an important role in achieving better control performance, because many actuators have hysteresis property. This paper proposes a method to identify linear dynamical systems having input hysteresis property of backlash type. The method is based on particle filter, which is known for its applicability to a wide class of nonlinear systems. Numerical examples are given to demonstrate the effectiveness of the proposed method in detail. Furthermore, experimental validation is performed for a DC servo motor system.

Masuda, Tetsuya; Sugie, Toshiharu

369

Non-linear system identification using neural networks  

Microsoft Academic Search

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

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

1990-01-01

370

A new class of wavelet networks for nonlinear system identification  

Microsoft Academic Search

A new class of wavelet networks (WNs) is proposed for nonlinear system identification. In the new networks, the model structure for a high-dimensional system is chosen to be a superimposition of a number of functions with fewer variables. By expanding each function using truncated wavelet decompositions, the multivariate nonlinear networks can be converted into linear-in-the-parameter regressions, which can be solved

Stephen A. Billings; Hua-Liang Wei

2005-01-01

371

ARMA bispectrum approach to nonminimum phase system identification  

Microsoft Academic Search

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.

C. L. Nikias

1988-01-01

372

Identification of nonminimum phase systems using higher order statistics  

Microsoft Academic Search

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,

G. B. Giannakis; J. M. Mendel

1989-01-01

373

Identification of linear parameter-varying systems via LFTs  

Microsoft Academic Search

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

Lawton H. Lee; Kameshwar Poolla

1996-01-01

374

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

PubMed

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

Ikushima, Shigehito; Fujii, Toshio; Kobayashi, Osamu

2009-04-23

375

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

PubMed

Despite extensive research carried out in the last few decades, continuous beer fermentation has not yet managed to outperform the traditional batch technology. An industrial breakthrough in favour of continuous brewing using immobilized yeast could be expected only on achievement of the following process characteristics: simple design, low investment costs, flexible operation, effective process control and good product quality. The application of cheap carrier materials of by-product origin could significantly lower the investment costs of continuous fermentation systems. This work deals with a complete continuous beer fermentation system consisting of a main fermentation reactor (gas-lift) and a maturation reactor (packed-bed) containing yeast immobilized on spent grains and corncobs, respectively. The suitability of cheap carrier materials for long-term continuous brewing was proved. It was found that by fine tuning of process parameters (residence time, aeration) it was possible to adjust the flavour profile of the final product. Consumers considered the continuously fermented beer to be of a regular quality. Analytical and sensorial profiles of both continuously and batch fermented beers were compared. PMID:16835782

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

2006-12-01

376

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

PubMed Central

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

Jahn, Michael; Molle, Annett; Rodel, Gerhard; Ostermann, Kai

2013-01-01

377

In situ simulation: identification of systems issues.  

PubMed

The Institute of Medicine's report, To Err is Human, concluded that "medical errors are not a result of isolated individual actions but rather faulty systems, processes, and conditions that lead people to make mistakes." In situ simulation offers the unique opportunity to train the teams of people who deliver healthcare while enhancing policies, evaluating new technologies, and improving the systems that support the delivery of safe healthcare. For this reason, the Institute of Medicine, the Joint Commission, and the Agency for Healthcare Research and Quality recommend medical simulation as one of the most important safe practice interventions to reduce errors and risks associated with the process of care. This review builds on other reports in this issue and discusses the application of in situ simulation to identify, address, and test systems improvements. PMID:23721772

Guise, Jeanne-Marie; Mladenovic, Jeanette

2013-06-01

378

System and Method for Automatic Singer Identification  

NSDL National Science Digital Library

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

Zhang, Tong

379

Biodegradation of Oil Pollutants by Yeasts and Yeast-Like Fungi.  

National Technical Information Service (NTIS)

In exploring the feasibility of the use of microbial systems for the facilitated biodegradation of waste oils, yeasts and yeast-like fungi from marine, freshwater and terrestrial sources were screened for their ability to utilize hydrocarbons. Mixed cultu...

D. G. Ahearn, N. H. Berner

1978-01-01

380

Parametric Identification of Nonlinear Dynamical Systems  

NASA Technical Reports Server (NTRS)

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.

Feeny, Brian

2002-01-01

381

A system identification approach to non-invasive central cardiovascular monitoring  

E-print Network

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

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

2008-01-01

382

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

Code of Federal Regulations, 2010 CFR

...2010-10-01 false Technical Requirements for Class A Automatic Identification System (AIS) equipment. ...Compulsory Ships § 80.275 Technical Requirements for Class A Automatic Identification System (AIS)...

2010-10-01

383

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

E-print Network

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

Bond, Bradley N.

384

Frequency domain state-space system identification  

NASA Technical Reports Server (NTRS)

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

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

1992-01-01

385

Nonlinear system identification and control using state transition algorithm  

E-print Network

This paper presents a novel optimization method named state transition algorithm (STA) to solve the problem of identification and control for nonlinear system. In the proposed algorithm, a solution to optimization problem is considered as a state, and the updating of a solution equates to the process of state transition, which makes the STA easy to understand and convenient to be implemented. First, the STA is applied to identify the optimal parameters of the estimated system with previously known structure. With the accurate estimated model, an off-line PID controller is then designed optimally by using the STA as well. Experimental results demonstrate the validity of the methodology, and comparison to STA with other optimization algorithms confirms that STA is a promising alternative method for system identification and control due to its stronger search ability, faster convergence speed and more stable performance.

Yang, Chunhua; Gui, Weihua

2012-01-01

386

Asymptotic inference in system identification for the atom maser  

E-print Network

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

Catalin Catana; Merlijn van Horssen; Madalin Guta

2011-12-09

387

Closed Loop System Identification with Genetic Algorithms  

NASA Technical Reports Server (NTRS)

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

Whorton, Mark S.

2004-01-01

388

Multivariable feedback relevant system identification of a wafer stepper system  

Microsoft Academic Search

This paper discusses the approximation and feedback relevant parametric identification of a positioning mechanism present in a wafer stepper. The positioning mechanism in a wafer stepper is used in chip manufacturing processes for accurate positioning of the silicon wafer on which the chips are to be produced. The accurate positioning requires a robust and high-performance feedback controller that enables a

Raymond A. de Callafon; Paul M. J. Van den Hof

2001-01-01

389

System Identification for Nonlinear Control Using Neural Networks  

NASA Technical Reports Server (NTRS)

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

Stengel, Robert F.; Linse, Dennis J.

1990-01-01

390

Efficient System Identification for Model Predictive Control with the ISIAC Software  

Microsoft Academic Search

ISIAC (as Industrial System Identification for Advanced Control) is a new software package geared to meet the requirements of system identification for model predictive control and the needs of practicing advanced process control (APC) engineers. It has been designed to naturally lead the user through the different steps of system identification, from experiment planning to ready-to-use models. Each phase can

Paolino Tona; Jean-marc Bader

2004-01-01

391

Integration of Chroma and Rhythm Histogram Features in a Music Identification System  

E-print Network

Integration of Chroma and Rhythm Histogram Features in a Music Identification System Riccardo {riccardo.miotto,nicola.montecchio}@dei.unipd.it Abstract--A system for Music Identification is presented of different tempo with alignment techniques. Efficiency becomes then a key issue if an identification system

Miotto, Riccardo

392

Performance Analysis of Identification System Based on Order Statistics List Decoder  

E-print Network

Performance Analysis of Identification System Based on Order Statistics List Decoder Farzad of an identification system. The statistical performance analysis is accomplished for the corre- sponding probability it noisy. Therefore, the identification system should be able to cope with data variations. The decoders

Genève, Université de

393

Predicting Identification Errors in a Multibiometric System Based on Ranks and Scores  

E-print Network

Predicting Identification Errors in a Multibiometric System Based on Ranks and Scores Emanuela Marasco, Arun Ross, Carlo Sansone Abstract-- The goal of a biometric identification system is to determine the effectiveness of our framework in improving identification performance of biometric systems. I. INTRODUCTION

Ross, Arun Abraham

394

An Optical/Digital Identification/Verification System based on Digital Watermarking Technology  

E-print Network

An Optical/Digital Identification/Verification System based on Digital Watermarking Technology A integrity verification of driver licenses, passports or other analogue identification documents. The system the weaknesses of the current passport or other identification systems, since it is not hard for professionals

Genève, Université de

395

Linear and nonlinear system identification of autonomic heart-rate modulation  

Microsoft Academic Search

The authors' findings show that system identification provides a useful, noninvasive, and quantitative means for evaluating cardiovascular regulatory mechanisms. With combinations of linear and nonlinear identification, new insights about the cardiovascular regulatory dynamics were obtained. System identification provides a new way of studying and monitoring cardiovascular function. Instead of just studying the signals generated by the cardiovascular regulatory system, the

Ki. H. Chon; Ramakrishna Mukkamala; Karin Toska; Thomas J. Mullen; A. A. Armoundas; R. J. Cohen

1997-01-01

396

Material Outgassing, Identification and Deposition, MOLIDEP System  

NASA Technical Reports Server (NTRS)

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

Scialdone, John J.; Montoya, Alex F.

2002-01-01

397

Prefire identification for pulse power systems  

DOEpatents

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

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

1985-01-01

398

Prefire identification for pulse-power systems  

DOEpatents

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

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

1982-08-23

399

[Search for protein-protein interaction partners of peroxiredoxin 6 with the yeast two-hybrid system].  

PubMed

Peroxiredoxins (Prx) are a family of nonselenium peroxidases that are involved in cell defense against oxidative stress and in redox regulation of intracellular signaling. Mammalian peroxiredoxin 6 (Prx6) belongs to the 1-Cys Prx subfamily. The protein--protein interactions of human Prx6 were studied using a yeast two-hybrid system. Hybrid plasmid pHybLex/Zeo/Prx6, which directed synthesis of a chimeric protein consisting of the DNA-binding domain (BD) of LexA and a Prx6 sequence, was used to screen a two-hybrid cDNA library Hybrid Hunter (Invitrogen). The screening identified two potential interaction partners of Prx6: the calcium-activated cysteine endopeptidase calpain and the p50RhoGAP protein of the family of Sec14-like proteins. The possibility for the interactions observed in the two-hybrid system to occur in oxidative stress in vivo is discussed. PMID:18619034

Budanova, E N; Bystrova, M F

2008-02-01

400

System identification methods for metal rubber devices  

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

401

Identification of linear stochastic systems through projection filters  

NASA Technical Reports Server (NTRS)

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.

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

1992-01-01

402

Terahertz imaging system performance model for concealed-weapon identification  

Microsoft Academic Search

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

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

2008-01-01

403

Terahertz imaging system performance model for concealed weapon identification  

Microsoft Academic Search

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

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

2005-01-01

404

Advanced terahertz imaging system performance model for concealed weapon identification  

Microsoft Academic Search

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

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

2007-01-01

405

The use of frequency methods in rotorcraft system identification  

NASA Technical Reports Server (NTRS)

A new approach to model structure determination is examined. Flight data from the Rotor Systems Research Aircraft (RSRA) are transformed into the frequency domain and truncated to provide band limiting. The stepwise regression technique is then used to identify a quasistatic state-space model from the transformed data. The data processing requirements for both time domain and frequency domain identification are discussed and the results of the two techniques are compared.

Duval, R. W.

1981-01-01

406

Gunshot identification system by integration of open source consumer electronics  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

407

Observer-based Hamiltonian identification for quantum systems  

E-print Network

An observer-based Hamiltonian identification algorithm for quantum systems is proposed. For the 2-level case an exponential convergence result based on averaging arguments and some relevant transformations is provided. The convergence for multi-level cases is discussed using some heuristic arguments and the relevance of the method is tested via simulations. Finally, the robustness issue with respect to non-negligible uncertainties and experimental noises is also addressed on simulations.

Mazyar Mirrahimi; Pierre Rouchon

2007-03-07

408

Subspace-based multivariable system identification from frequency response data  

Microsoft Academic Search

Two noniterative subspace-based algorithms which identify linear, time-invariant MIMO (multi-input\\/multioutput) systems from frequency response data are presented. The algorithms are related to the recent time-domain subspace identification techniques. The first algorithm uses equidistantly, in frequency, spaced data and is strongly consistent under weak noise assumptions. The second algorithm uses arbitrary frequency spacing and is strongly consistent under more restrictive noise

Tomas McKelvey; H. Akcay; L. Ljung

1996-01-01

409

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

PubMed Central

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

Lin, Jing-Yi

2013-01-01

410

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 ...

411

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...

412

Development of a transformation system for gene knock-out in the flavinogenic yeast Pichia guilliermondii.  

PubMed

Pichia guilliermondii is a representative of a yeast species, all of which over-synthesize riboflavin in response to iron deprivation. Molecular genetic studies in this yeast species have been hampered by a lack of strain-specific tools for gene manipulation. Stable P. guilliermondii ura3 mutants were selected on the basis of 5'-fluoroorotic acid resistance. Plasmid carrying Saccharomyces cerevisiae URA3 gene transformed the mutant strains to prototrophy with a low efficiency. Substitution of a single leucine codon CUG by another leucine codon CUC in the URA3 gene increased the efficiency of transformation 100 fold. Deletion cassettes for the RIB1 and RIB7 genes, coding for GTP cyclohydrolase and riboflavin synthase, respectively, were constructed using the modified URA3 gene and subsequently introduced into a P. guilliermondii ura3 strain. Site-specific integrants were identified by selection for the Rib(-) Ura(+) phenotype and confirmed by PCR analysis. Transformation of the P. guilliermondii ura3 strain was performed using electroporation, spheroplasting or lithium acetate treatment. Only the lithium acetate transformation procedure provided selection of uracil prototrophic, riboflavin deficient recombinant strains. Depending on the type of cassette, efficiency of site-specific integration was 0.1% and 3-12% in the case of the RIB1 and RIB7 genes, respectively. We suggest that the presence of the ARS element adjacent to the 3' end of the RIB1 gene significantly reduced the frequency of homologous recombination. Efficient gene deletion in P. guilliermondii can be achieved using the modified URA3 gene of S. cerevisiae flanked by 0.8-0.9 kb sequences homologous to the target gene. PMID:17467833

Boretsky, Yuriy R; Pynyaha, Yuriy V; Boretsky, Volodymyr Y; Kutsyaba, Vasyl I; Protchenko, Olga V; Philpott, Caroline C; Sibirny, Andriy A

2007-07-01

413

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

SciTech Connect

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

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

1986-01-01

414

Local identification analyses of soils and soil-structure systems  

NASA Astrophysics Data System (ADS)

Geotechnical structures and natural deposits are massive multi-phase particulate systems characterized by the development of localized response mechanisms under extreme loading conditions. A thorough monitoring of the whole response of such massive and distributed soil-systems commonly constitutes a significant challenge and would be prohibitively expensive. Identification and analysis of these systems based on inverse boundary value problem formulations and sparse measurements are generally overly indeterminate. This study presents an alternative inverse problem algorithm to evaluate the local response mechanisms of soil-systems. Point-wise identification analyses of the constitutive behavior of water-saturated geotechnical and geophysical systems are performed using acceleration and pore pressure records provided by a cluster of closely spaced instruments. The developed algorithm consists of: (1) estimation of strain-time histories using the motions recorded by the cluster, (2) evaluation of stress-time histories corresponding to the estimated strains employing a pre-selected class of constitutive models of soil response, (3) computation of accelerations associated with the estimated stresses and recorded pore-water pressures utilizing the equilibrium equations, and (4) evaluation and calibration of an optimal model of soil response by minimizing the discrepancies between recorded and computed accelerations. The developed novel algorithm does not require the availability of boundary condition measurements, or solution of an associated boundary value problem. The constitutive behavior at a specific location of a soil-system is analyzed independently of adjacent response mechanisms or properties. Computer simulations and downhole array records of Lotung (Taiwan) site were used to assess the validity of the proposed technique for level sites and infinite slopes, under conditions of vertical seismic wave propagation. Numerical simulations and centrifuge test data of a quay wall-soil system were employed to demonstrate the capabilities of the developed algorithm in multi-dimensional situations. Results of the identification analyses showed that the proposed technique provides an effective tool to identify local dynamic soil characteristics and properties.

Oskay, Caglar

415

Measurement-based Coherency Identification and Aggregation for Power Systems  

SciTech Connect

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.

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

2012-07-26

416

The yeasts of cheese brines.  

PubMed

A total of 365 yeasts were isolated from the brines of soft, semihard and hard cheeses from different manufacturers. Identification was based on 131 characteristics, primarily employing a method with microtitration plates. Most brines exhibited a characteristic yeast flora. The predominant strains proved to be mainly Debaryomyces hansenii and Candida versatilis. In a few brines Trichosporon beigelii, C. rugosa, C. intermedia, Kluyveromyces marxianus, Saccharomyces sp. and C. tenuis/polymorpha were predominant. Also of importance were C. tropicalis, C. parapsilosis, C. zeylanoides, Issatchenkia orientalis and Geotrichum klebahnii. Not all strains could be clearly identified. Lists of characters are provided for subdividing D. hansenii and T. beigelii. The specificity of the yeast flora of brines is assumed to contribute to the sensory variety of cheeses. PMID:2282287

Seiler, H; Busse, M

1990-12-01

417

Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation.  

PubMed

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

Mihalik, Ágoston; Csermely, Peter

2011-10-01

418

Application of a FIB-STEM system for 3D observation of a resin-embedded yeast cell.  

PubMed

The combination of a focused ion beam (FIB) system and a scanning transmission electron microscope (STEM) has been applied to the three-dimensional (3D) observation of a resin-embedded yeast cell. Using a FIB microsampling technique, a sample with a thickness of tens of micrometres was extracted from a resin-embedded block sample. The extracted sample was transferred to a FIB-STEM-compatible specimen rotation holder and trimmed by FIB milling for 3D STEM observation. Although the FIB milling was carried out at an operating voltage of 40 KV, the sample was cross sectioned without forming a harmful damage layer on its surface. Cell structures, such as cell wall, cell membrane, mitochondria, peroxisomes, endoplasmic reticulum and vacuoles, were observed clearly in a pillar-shaped sample of 20 microm long, 4 microm wide and 3 microm deep. PMID:15582966

Kamino, Takeo; Yaguchi, Toshie; Ohnishi, Tsuyoshi; Ishitani, Tohru; Osumi, Masako

2004-01-01

419

System Identification of Mistuned Bladed Disks from Traveling Wave Response Measurements  

NASA Technical Reports Server (NTRS)

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

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

2003-01-01

420

A Decision Theoretic Framework for Analyzing Binary Hash-based Content Identification Systems  

E-print Network

A Decision Theoretic Framework for Analyzing Binary Hash-based Content Identification Systems-based identification systems is that a large volume of legacy multimedia content does not have any embedded watermarks University of Maryland College Park, MD, USA minwu@umd.edu ABSTRACT Content identification has many

Wu, Min

421

Development of a Decentralized Control System for Operation of Yeast Fermentation in Semi-Continuous Reactors. Control Through Respiration Rate and Role of the Metabolites.  

National Technical Information Service (NTIS)

The objective of this work was to develop a control structure for the operation of a semi-continuous digester used for production fo (baker's) yeast by substrate supply: the system is composed of classical analogical controls when the algorithm is simple ...

M. N. Pons

1984-01-01

422

[Groundwater organic pollution source identification technology system research and application].  

PubMed

Groundwater organic pollutions are found in large amount of locations, and the pollutions are widely spread once onset; which is hard to identify and control. The key process to control and govern groundwater pollution is how to control the sources of pollution and reduce the danger to groundwater. This paper introduced typical contaminated sites as an example; then carried out the source identification studies and established groundwater organic pollution source identification system, finally applied the system to the identification of typical contaminated sites. First, grasp the basis of the contaminated sites of geological and hydrogeological conditions; determine the contaminated sites characteristics of pollutants as carbon tetrachloride, from the large numbers of groundwater analysis and test data; then find the solute transport model of contaminated sites and compound-specific isotope techniques. At last, through groundwater solute transport model and compound-specific isotope technology, determine the distribution of the typical site of organic sources of pollution and pollution status; invest identified potential sources of pollution and sample the soil to analysis. It turns out that the results of two identified historical pollution sources and pollutant concentration distribution are reliable. The results provided the basis for treatment of groundwater pollution. PMID:23668138

Wang, Xiao-Hong; Wei, Jia-Hua; Cheng, Zhi-Neng; Liu, Pei-Bin; Ji, Yi-Qun; Zhang, Gan

2013-02-01

423

System identification for modeling for control of flexible structures  

NASA Technical Reports Server (NTRS)

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

Mettler, Edward; Milman, Mark

1986-01-01

424

Biological tissue identification using a multispectral imaging system  

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

425

An approximation theory for the identification of linear thermoelastic systems  

NASA Technical Reports Server (NTRS)

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

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

1990-01-01

426

A dynamic interface between vacuoles and mitochondria in yeast.  

PubMed

Cellular life depends on continuous transport of lipids and small molecules between mitochondria and the endomembrane system. Recently, endoplasmic reticulum-mitochondrial encounter structure (ERMES) was identified as an important yet nonessential contact for such transport. Using a high-content screen in yeast, we found a contact site, marked by Vam6/Vps39, between vacuoles (the yeast lysosomal compartment) and mitochondria, named vCLAMP (vacuole and mitochondria patch). vCLAMP is enriched with ion and amino-acid transporters and has a role in lipid relay between the endomembrane system and mitochondria. Critically, we show that mitochondria are dependent on having one of two contact sites, ERMES or vCLAMP. The absence of one causes expansion of the other, and elimination of both is lethal. Identification of vCLAMP adds to our ability to understand the complexity of interorganellar crosstalk. PMID:25026036

Elbaz-Alon, Yael; Rosenfeld-Gur, Eden; Shinder, Vera; Futerman, Anthony H; Geiger, Tamar; Schuldiner, Maya

2014-07-14

427

Modal Parameter Identification of a Flexible Arm System  

NASA Technical Reports Server (NTRS)

In this paper an experiment is designed for the modal parameter identification of a flexible arm system. This experiment uses a function generator to provide input signal and an oscilloscope to save input and output response data. For each vibrational mode, many sets of sine-wave inputs with frequencies close to the natural frequency of the arm system are used to excite the vibration of this mode. Then a least-squares technique is used to analyze the experimental input/output data to obtain the identified parameters for this mode. The identified results are compared with the analytical model obtained by applying finite element analysis.

Barrington, Jason; Lew, Jiann-Shiun; Korbieh, Edward; Wade, Montanez; Tantaris, Richard

1998-01-01

428

Yeast 14, 14531469 (1998) Expanding Yeast Knowledge Online  

E-print Network

YEAST Yeast 14, 1453­1469 (1998) Expanding Yeast Knowledge Online KARA DOLINSKI1 , CATHERINE A in the amount of new yeast genetics and molecular biology data. Efficient organization, presentation Sequences; Yeast Protein Database CONTENTS Introduction

Botstein, David

429

Linear system identification via backward-time observer models  

NASA Technical Reports Server (NTRS)

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.

Juang, Jer-Nan; Phan, Minh Q.

1992-01-01

430

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

PubMed Central

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

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

2011-01-01

431

Alu-primed polymerase chain reaction for regional assignment of 110 yeast artificial chromosome clones from the human X chromosome: Identification of clones associated with a disease locus  

SciTech Connect

Over 400 yeast artificial chromosome (YAC) clones were isolated from the human X chromosome, and 110 of these were assigned to regions defined by chromosome translocation and deletion breakpoints. Polymerase chain reaction using Alu primers was applied to YAC clones in order to generate probes, to identify overlapping clones, and to derive fingerprints and sequence data directly from total yeast DNA. Several clones were identified in regions of medical interest. One set of three overlapping clones was found to cross a chromsomal translocation implicated in Lowe syndrome. The regional assignment of groups of YAC clones provides initiation points for further attempts to develop large cloned contiguous sequences, as well as material for investigation of regions involved in genetic diseases.

Nelson, D.L.; Ballabio, A.; Victoria, M.F.; Pieretti, M.; Bies, R.D.; Gibbs, R.A.; Maley, J.A.; Chinault, A.C.; Webster, T.D.; Caskey, C.T. (Baylor College of Medicine, Houston, TX (United States))

1991-07-15

432

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

Microsoft Academic Search

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

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

2001-01-01

433

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

PubMed Central

A series of yeast shuttle vectors and host strains has been created to allow more efficient manipulation of DNA in Saccharomyces cerevisiae. Transplacement vectors were constructed and used to derive yeast strains containing nonreverting his3, trp1, leu2 and ura3 mutations. A set of YCp and YIp vectors (pRS series) was then made based on the backbone of the multipurpose plasmid pBLUESCRIPT. These pRS vectors are all uniform in structure and differ only in the yeast selectable marker gene used (HIS3, TRP1, LEU2 and URA3). They possess all of the attributes of pBLUESCRIPT and several yeast-specific features as well. Using a pRS vector, one can perform most standard DNA manipulations in the same plasmid that is introduced into yeast. PMID:2659436

Sikorski, R. S.; Hieter, P.

1989-01-01