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Sample records for time-course maldi-tof-ms serum

  1. Weak cation magnetic separation technology and MALDI-TOF-MS in screening serum protein markers in primary type I osteoporosis.

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    Shi, X L; Li, C W; Liang, B C; He, K H; Li, X Y

    2015-11-30

    We investigated weak cation magnetic separation technology and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) in screening serum protein markers of primary type I osteoporosis. We selected 16 postmenopausal women with osteoporosis and nine postmenopausal women as controls to find a new method for screening biomarkers and establishing a diagnostic model for primary type I osteoporosis. Serum samples were obtained from controls and patients. Serum protein was extracted with the WCX protein chip system; protein fingerprints were examined using MALDI-TOF-MS. The preprocessed and model construction data were handled by the ProteinChip system. The diagnostic models were established using a genetic arithmetic model combined with a support vector machine (SVM). The SVM model with the highest Youden index was selected. Combinations with the highest accuracy in distinguishing different groups of data were selected as potential biomarkers. From the two groups of serum proteins, 123 cumulative MS protein peaks were selected. Significant intensity differences in the protein peaks of 16 postmenopausal women with osteoporosis were screened. The difference in Youden index between the four groups of protein peaks showed that the highest peaks had mass-to-charge ratios of 8909.047, 8690.658, 13745.48, and 15114.52. A diagnosis model was established with these four markers as the candidates, and the model specificity and sensitivity were found to be 100%. Two groups of specimens in the SVM results on the scatterplot were distinguishable. We established a diagnosis model, and provided a new serological method for screening and diagnosis of osteoporosis with high sensitivity and specificity.

  2. Two Classifiers Based on Serum Peptide Pattern for Prediction of HBV-Induced Liver Cirrhosis Using MALDI-TOF MS

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    Yuan Cao

    2013-01-01

    Full Text Available Chronic infection with hepatitis B virus (HBV is associated with the majority of cases of liver cirrhosis (LC in China. Although liver biopsy is the reference method for evaluation of cirrhosis, it is an invasive procedure with inherent risk. The aim of this study is to discover novel noninvasive specific serum biomarkers for the diagnosis of HBV-induced LC. We performed bead fractionation/MALDI-TOF MS analysis on sera from patients with LC. Thirteen feature peaks which had optimal discriminatory performance were obtained by using support-vector-machine-(SVM- based strategy. Based on the previous results, five supervised machine learning methods were employed to construct classifiers that discriminated proteomic spectra of patients with HBV-induced LC from those of controls. Here, we describe two novel methods for prediction of HBV-induced LC, termed LC-NB and LC-MLP, respectively. We obtained a sensitivity of 90.9%, a specificity of 94.9%, and overall accuracy of 93.8% on an independent test set. Comparisons with the existing methods showed that LC-NB and LC-MLP held better accuracy. Our study suggests that potential serum biomarkers can be determined for discriminating LC and non-LC cohorts by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. These two classifiers could be used for clinical practice in HBV-induced LC assessment.

  3. Early Diagnosis of Irkut Virus Infection Using Magnetic Bead-Based Serum Peptide Profiling by MALDI-TOF MS in a Mouse Model

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    Nan Li

    2014-03-01

    Full Text Available Early diagnosis is important for the prompt post-exposure prophylaxis of lyssavirus infections. To diagnose Irkut virus (IRKV infection during incubation in mice, a novel method using magnetic bead-based serum peptide profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS has been established. For this test, serum peptides were concentrated by adsorption to and elution from the magnetic bead-based weak cation ion exchanger. Mass spectrograms obtained by MALDI-TOF MS were analyzed using ClinProTools bioinformatics software. Construction of the diagnostic model was performed using serum samples from mice infected with IRKV and rabies virus (RABV BD06, Flury-LEP, and SRV9 (as controls. The method accurately diagnosed sera 2, 4 and 8 days after IRKV and RABV infections. The sensitivity, specificity, and total accuracy of diagnosis were 86.7%, 95.2%, and 92.9%, respectively. However, IRKV could not be differentiated from RABV 1 day after infection. The results of the present study indicate that serum peptide profiling by MALDI-TOF MS is a promising technique for the early clinical diagnosis of lyssavirus infections and needs to be further tested in humans and farm animals.

  4. [Detection of serum proteins in the patients of lung adenocarcinoma by the method of magnetic bead based sample fractionation and MALDI-TOF-MS].

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    Liu, Dan; Liu, Lun-Xu; Yuan, Quan; Li, Xiao-Liang; Huang, Na; Yang, Xiao-Dong

    2010-05-01

    To screen the serum proteins related to human lung adenocarcinoma using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) technology. The blood samples were collected from 10 patients of lung adenocarcinoma before and one week after the surgery, while 10 healthy subjects were used as control. The differential protein expression between the two groups and the change of those proteins after surgery were studied by ClinProt magnetic bead enrichment and MALDI-TOF-MS. Six protein peaks were identified, 2 of them were highly expressed protein biomarkers with relative molecular weights of 2661, 2991, and increased after the surgery, 4 of them were lowly expressed protein biomarkers with relative molecular weights of 4091, 4210, 4644, 5336, which continuously decreased after the surgery. ClinProt magnetic bead enrichment and MALDI-TOF-MS is a quick, easy and sensitive method of proteomics. The differential expressed proteins may be the latent tumor marker of lung adenocarcinoma. The alteration of those proteins after surgery might be helpful to assess the therapeutic effect and prognosis.

  5. Proteomic profiling of renal allograft rejection in serum using magnetic bead-based sample fractionation and MALDI-TOF MS.

    Science.gov (United States)

    Sui, Weiguo; Huang, Liling; Dai, Yong; Chen, Jiejing; Yan, Qiang; Huang, He

    2010-12-01

    Proteomics is one of the emerging techniques for biomarker discovery. Biomarkers can be used for early noninvasive diagnosis and prognosis of diseases and treatment efficacy evaluation. In the present study, the well-established research systems of ClinProt Micro solution incorporated unique magnetic bead sample preparation technology, which, based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), have become very successful in bioinformatics due to its outstanding performance and reproducibility for discovery disease-related biomarker. We collected fasting blood samples from patients with biopsy-confirmed acute renal allograft rejection (n = 12), chronic rejection (n = 12), stable graft function (n = 12) and also from healthy volunteers (n = 13) to study serum peptidome patterns. Specimens were purified with magnetic bead-based weak cation exchange chromatography and analyzed with a MALDI-TOF mass spectrometer. The results indicated that 18 differential peptide peaks were selected as potential biomarkers of acute renal allograft rejection, and 6 differential peptide peaks were selected as potential biomarkers of chronic rejection. A Quick Classifier Algorithm was used to set up the classification models for acute and chronic renal allograft rejection. The algorithm models recognize 82.64% of acute rejection and 98.96% of chronic rejection episodes, respectively. We were able to identify serum protein fingerprints in small sample sizes of recipients with renal allograft rejection and establish the models for diagnosis of renal allograft rejection. This preliminary study demonstrated that proteomics is an emerging tool for early diagnosis of renal allograft rejection and helps us to better understand the pathogenesis of disease process.

  6. Detection of Serum Peptides in Patients with Lung Squamous Cell Carcinoma by MALDI-TOF-MS and Analysis of Their Correlation with Chemotherapy Efficacy

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    Guanhua ZHAO

    2017-05-01

    Full Text Available Background and objective Treatment options for patients with squamous cell carcinoma of the lung (SCC are limited in chemotherapy. However, not all patients could benefit form standard platinum regimen. Considering the dismal prognosis of patients with advanced SCC, a greater focus on selecting sensitive chemotherapy regimens remains of upmost importance to improve outcomes in this disease. In this study, we used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to detect pre-chemotherapy serum peptides in advanced lung squamous cell carcinoma patients accepting paclitaxel combined with platinum chemotherapy and to analyze the correlation between serum peptides and chemotherapy efficacy. Methods Patients with advanced lung squamous cell carcinoma received paclitaxel combining with platinum chemotherapy and evaluated the efficacy every two cycles. Evaluation of complete response (CR or partial response (PR patients defined as sensitive group, progressive disease (PD patients defined as resistant group. Serum samples were collected from patients with lung squamous cell carcinoma. Eighty-one patients were randomly divided into training group (sensitive group I and resistant group I and validation group (sensitive group II and resistant group II according to the ratio of 3:1. Serum samples were pretreated and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS was used to detect serum peptide fingerprints. ClinProTools software was used to analyze the differences between the sensitive group I and the resistant group I. Three kinds of biological algorithms (SNN, GA, QC built in CPT software were used to establish the curative effect prediction model respectively and the optimal algorithm was selected. The validation group was used for blind verification. Results Thirty sensitive patients and 31 resistant patients were enrolled in the training group. Ten sensitive patients and 10

  7. Proteomic profiling of occupational medicamentosa-like dermatitis induced by trichloroethylene in serum based on MALDI-TOF MS.

    Science.gov (United States)

    Liu, Wei; Hong, Wen-Xu; Zhang, Yanfang; Huang, Peiwu; Yang, Xifei; Ren, Xiaohu; Huang, Haiyan; Liu, Jianjun

    2015-11-01

    Trichloroethylene (TCE) has long been well known as a major pollutant that affects both occupational and general environments. Occupational medicamentosa-like dermatitis induced by TCE (OMLDT) is an autoimmune disease, which has become one of the critical occupational health issues in China. In this study, we analyzed 18 OMLDT patients and 29 professional TCE contact people on serum proteomic analysis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and ClinProTools bioinformatics software. The intensities of 35 protein/peptide peaks were significantly different between TCE contact controls and OMLDT patients. A pattern of six peaks (m/z 1,450.33, 1,866.16, 3,262.39, 4,109.55, 5,064.85 and 5,956.57) were selected to construct a diagnostic model to discriminate the OMLDT patients from controls with sensitivity and specificity of both 93.8 %. Our findings provide an alternative proteomic approach to differentiate the OMLDT patients from TCE contact workers with high sensitivity and high specificity, which will be of potential value in clinical diagnosis for occupational disease.

  8. The identification of anaerobic bacteria using MALDI-TOF MS

    NARCIS (Netherlands)

    Veloo, A. C. M.; Welling, G. W.; Degener, J. E.

    Matrix Assisted Laser Desorption and Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has gained more and more popularity for the identification of bacteria. Several studies show that bacterial diagnosticis is being revolutionized by the application of MALDI-TOF MS. For anaerobic bacteria,

  9. MALDI-TOF MS/MS measurements of PMMA

    NARCIS (Netherlands)

    Becer, C.R.; Baumgaertel, A.; Gottschaldt, M.; Schubert, U.S.

    2008-01-01

    The polymer poly(Me methacrylate) (PMMA) was analyzed using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique. The MALDI-TOF MS app. was coupled with a collision-induced dissocn. (CID) unit. The performance of the MALDI-TOF/TOF MS method in

  10. MALDI-TOF MS in the Microbiology Laboratory: Current Trends.

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    Schubert, Sören; Kostrzewa, Markus

    2017-01-01

    Within less than a decade matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a gold standard for microbial identification in clinical microbiology laboratories. Besides identification of microorganisms the typing of single strains as well as the antibiotic and antimycotic resistance testing has come into focus in order to speed up the microbiological diagnostic. However, the full potential of MALDI-TOF MS has not been tapped yet and future technological advancements will certainly expedite this method towards novel applications and enhancement of current practice. So, the following chapter shall be rather a brainstorming and forecast of how MALDI-TOF MS will develop to influence clinical diagnostics and microbial research in the future. It shall open up the stage for further discussions and does not claim for overall validity.

  11. [Applications of MALDI-TOF-MS in clinical microbiology laboratory].

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    Carbonnelle, Etienne; Nassif, Xavier

    2011-10-01

    For twenty years, mass spectrometry (MS) has emerged as a particularly powerful tool for analysis and characterization of proteins in research. It is only recently that this technology, especially MALDI-TOF-MS (Matrix Assisted Laser Desorption Ionization Time-Of-Flight) has entered the field of routine microbiology. This method has proven to be reliable and safe for the identification of bacteria, yeasts, filamentous fungi and dermatophytes. MALDI-TOF-MS is a rapid, precise and cost-effective method for identification, compared to conventional phenotypic techniques or molecular biology. Its ability to analyse whole microorganisms with few sample preparation has greatly reduced the time to identification (1-2 min). Furthermore, this technology can be used to identify bacteria directly from clinical samples as blood culture bottles or urines. Future applications will be developed in order to provide direct information concerning virulence or resistance protein markers. © 2011 médecine/sciences – Inserm / SRMS.

  12. Applications of MALDI-TOF MS in Microbiological identification

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    Soner Yilmaz

    2014-10-01

    Full Text Available MALDI-TOF MS (Matriks assisted laser desorption ionization time of flight mass spectrometry is a new metohod for identification of microorganisms nowadays. This method is based revealing of microorganisms protein profile with ionization of protein structure and these ionized mass pass through the electrical field. Profiles which were obtained from microorganisms compare with database of system thus identification is made by this way. Ribosomal proteins are used in identification which are less affected by enviromental conditions. Fresh culture should preferably use in MALDI-TOF MS identification. Ribosomal proteins can be deteriorate in old cultures. The correct identification rates are changing between 84,1% to 95,2% in routine bacterial isolates. The correct identification rates in yeasts are changing between 85% to 100%. It makes identification in positive blood culture bottles without the need of subculture, also makes identification on urine samples without the need of culture which has greater than 105 microorganisms in a microliter. When it compared with conventional and molecular identification methods, it is more effective on per sample costs and elapsed time on working [TAF Prev Med Bull 2014; 13(5.000: 421-426

  13. A simpler method of preprocessing MALDI-TOF MS data for differential biomarker analysis: stem cell and melanoma cancer studies

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    Tong Dong L

    2011-09-01

    Full Text Available Abstract Introduction Raw spectral data from matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF with MS profiling techniques usually contains complex information not readily providing biological insight into disease. The association of identified features within raw data to a known peptide is extremely difficult. Data preprocessing to remove uncertainty characteristics in the data is normally required before performing any further analysis. This study proposes an alternative yet simple solution to preprocess raw MALDI-TOF-MS data for identification of candidate marker ions. Two in-house MALDI-TOF-MS data sets from two different sample sources (melanoma serum and cord blood plasma are used in our study. Method Raw MS spectral profiles were preprocessed using the proposed approach to identify peak regions in the spectra. The preprocessed data was then analysed using bespoke machine learning algorithms for data reduction and ion selection. Using the selected ions, an ANN-based predictive model was constructed to examine the predictive power of these ions for classification. Results Our model identified 10 candidate marker ions for both data sets. These ion panels achieved over 90% classification accuracy on blind validation data. Receiver operating characteristics analysis was performed and the area under the curve for melanoma and cord blood classifiers was 0.991 and 0.986, respectively. Conclusion The results suggest that our data preprocessing technique removes unwanted characteristics of the raw data, while preserving the predictive components of the data. Ion identification analysis can be carried out using MALDI-TOF-MS data with the proposed data preprocessing technique coupled with bespoke algorithms for data reduction and ion selection.

  14. Application of MALDI-TOF MS for requalification of a Candida clinical isolates culture collection

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    Reginaldo Lima-Neto

    2014-06-01

    Full Text Available Microbial culture collections underpin biotechnology applications and are important resources for clinical microbiology by supplying reference strains and/or performing microbial identifications as a service. Proteomic profiles by MALDI-TOF MS have been used for Candida spp. identification in clinical laboratories and demonstrated to be a fast and reliable technique for the routine identification of pathogenic yeasts. The main aim of this study was to apply MALDI-TOF MS combined with classical phenotypic and molecular approaches to identify Candida clinical isolates preserved from 1 up to 52 years in a Brazilian culture collection and assess its value for the identification of yeasts preserved in this type of collections. Forty Candida spp. clinical isolates were identified by morphological and biochemical analyses. Identifications were also performed by the new proteomic approach based on MALDI-TOF MS. Results demonstrated 15% discordance when compared with morphological and biochemical analyses. Discordant isolates were analysed by ITS sequencing, which confirmed the MALDI-TOF MS identifications and these strains were renamed in the culture collection catalogue. In conclusion, proteomic profiles by MALDI-TOF MS represents a rapid and reliable method for identifying clinical Candida species preserved in culture collections and may present clear benefits when compared with the performance of existing daily routine methods applied at health centres and hospitals.

  15. [Utility of MALDI-TOF MS for the identification of anaerobic bacteria].

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    Zárate, Mariela S; Romano, Vanesa; Nievas, Jimena; Smayevsky, Jorgelina

    2014-01-01

    The analysis by MALDI-TOF MS (Matrix-assited laser desorption/ionization time-of-flight mass spectrometry) has become a reference method for the identification of microorganisms in Clinical Microbiology. However, data on some groups of microorganisms are still controversial. The aim of this study is to determine the utility of MALDI-TOF MS for the identification of clinical isolates of anaerobic bacteria. One-hundred and six anaerobic bacteria isolates were analyzed by MALDI-TOF MS and by conventional biochemical tests. In those cases where identification by conventional methodology was not applicable or in the face of discordance between sequencing methodologies, 16 S rRNA gene sequence analysis was performed. The conventional method and MALDI-TOF MS agreed at genus and species level by 95.3 %. Concordance in gram-negative bacilli was 91.4% and 100% among gram-positive bacilli; there was also concordance both in the 8 isolates studied in gram-positive cocci and in the single gram-negative cocci included. The data obtained in this study demonstrate that MALDI-TOF MS offers the possibility of adequate identification of anaerobic bacteria. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

  16. MALDI-TOF MS as a tool to identify foodborne yeasts and yeast-like fungi.

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    Quintilla, Raquel; Kolecka, Anna; Casaregola, Serge; Daniel, Heide M; Houbraken, Jos; Kostrzewa, Markus; Boekhout, Teun; Groenewald, Marizeth

    2018-02-02

    Since food spoilage by yeasts causes high economic losses, fast and accurate identifications of yeasts associated with food and food-related products are important for the food industry. In this study the efficiency of the matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify food related yeasts was evaluated. A CBS in-house MALDI-TOF MS database was created and later challenged with a blinded test set of 146 yeast strains obtained from food and food related products. Ninety eight percent of the strains were correctly identified with log score values>1.7. One strain, Mrakia frigida, gained a correct identification with a score value1.7. Ambiguous identifications were observed due to two incorrect reference mass spectra's found in the commercial database BDAL v.4.0, namely Candida sake DSM 70763 which was re-identified as Candida oleophila, and Candida inconspicua DSM 70631 which was re-identified as Pichia membranifaciens. MALDI-TOF MS can distinguish between most of the species, but for some species complexes, such as the Kazachstania telluris and Mrakia frigida complexes, MALDI-TOF MS showed limited resolution and identification of sibling species was sometimes problematic. Despite this, we showed that the MALDI-TOF MS is applicable for routine identification and validation of foodborne yeasts, but a further update of the commercial reference databases is needed. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Rapid and accurate identification of Streptococcus equi subspecies by MALDI-TOF MS

    DEFF Research Database (Denmark)

    Kudirkiene, Egle; Welker, Martin; Knudsen, Nanna Reumert

    2015-01-01

    phenotypic and sequence similarity between three subspecies their discrimination remains difficult. In this study, we aimed to design and validate a novel, Superspectra based, MALDI-TOF MS approach for reliable, rapid and cost-effective identification of SEE and SEZ, the most frequent S. equi subspecies.......3±7.5%). This result may be attributed to the highly clonal population structure of SEE, as opposed to the diversity of SEZ seen in horses. Importantly strains with atypical colony appearance both within SEE and SEZ did not affect correct identification of the strains by MALDI-TOF MS. Atypical colony variants...... are often associated with a higher persistence or virulence of S. equi, thus their correct identification using the current method strengthens its potential use in routine clinical diagnostics. In conclusion, reliable identification of S. equi subspecies was achieved by combining a MALDI-TOF MS method...

  18. A simple and effective method for detecting precipitated proteins in MALDI-TOF MS.

    Science.gov (United States)

    Oshikane, Hiroyuki; Watabe, Masahiko; Nakaki, Toshio

    2018-04-01

    MALDI-TOF MS has developed rapidly into an essential analytical tool for the life sciences. Cinnamic acid derivatives are generally employed in routine molecular weight determinations of intact proteins using MALDI-TOF MS. However, a protein of interest may precipitate when mixed with matrix solution, perhaps preventing MS detection. We herein provide a simple approach to enable the MS detection of such precipitated protein species by means of a "direct deposition method" -- loading the precipitant directly onto the sample plate. It is thus expected to improve routine MS analysis of intact proteins. Copyright © 2018. Published by Elsevier Inc.

  19. Characterisation of oligosaccharides in vegetables by HPLC and MALDI-TOF MS

    Czech Academy of Sciences Publication Activity Database

    Štikarovská, M.; Chmelík, Josef

    96(S), - (2002), s. S189-S191 ISSN 0009-2770. [Meeting of Chemistry & Life /2./. Brno, 10.09.2002-11.09.2002] Institutional research plan: CEZ:AV0Z4031919 Keywords : oligosaccharides * HPLC * MALDI-TOF-MS Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 0.336, year: 2002

  20. Aspergillus ibericus : a new species of section nigri characterised by MALDI-TOF MS

    OpenAIRE

    Kallow, W.; Santos, Isabel; Erhard, M.; Serra, Rita; Venâncio, Armando; Lima, Nelson

    2006-01-01

    Strains from the new described species Aspergillus ibericus were characterised using MALDI-TOF MS and the results were compared with other related species of section Nigri. Fundação para a Ciência e a Tecnologia (FCT)

  1. A sample preparation method for recovering suppressed analyte ions in MALDI TOF MS

    NARCIS (Netherlands)

    Lou, X.; Waal, de B.F.M.; Milroy, L.G.; Dongen, van J.L.J.

    2015-01-01

    In matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS), analyte signals can be substantially suppressed by other compounds in the sample. In this technical note, we describe a modified thin-layer sample preparation method that significantly reduces the analyte

  2. False results caused by solvent impurity in tetrahydrofuran for maldi tof ms analysis of amines

    NARCIS (Netherlands)

    Lou, X.; Leenders, C.M.A.; van Onzen, Thuur; Bovee, R.A.A.; Van Dongen, J.L.J.; Vekemans, J.A.J.M.; Meijer, E. W.

    Tetrahydrofuran (THF) is one of the most frequently used solvents in the MALDI TOF MS analysis of synthetic compounds. However, it should be used with caution because a trace amount of 4-hydroxybutanal (HBA) might be generated and accumulated in THF during storage. Since only a tiny amount of

  3. Detection and identification of bio-threats using MALDI-TOF-MS

    NARCIS (Netherlands)

    Paauw, A.

    2012-01-01

    MALDI-TOF-MS emerged as a new diagnostic tool in established clinical laboratories. Advantages compared to conventional techniques are that it is a fast, cost-effective, accurate method, which is suitable for high-throughput identification of bacteria by less skilled laboratory personnel because

  4. Rapid identification of clinical members of Fusarium fujikuroi complex using MALDI-TOF MS

    NARCIS (Netherlands)

    Al-Hatmi, Abdullah Ms; Normand, Anne-Cécile; van Diepeningen, Anne D; Hendrickx, Marijke; de Hoog, G Sybren; Piarroux, Renaud

    2015-01-01

    AIM: To develop the matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) method for identification of Fusarium species within Fusarium fujikuroi complex for use in clinical microbiology laboratories. MATERIALS & METHODS: A total of 24 reference and 60 clinical and

  5. Detection of Rickettsia spp in Ticks by MALDI-TOF MS

    Science.gov (United States)

    Yssouf, Amina; Almeras, Lionel; Terras, Jérôme; Socolovschi, Cristina; Raoult, Didier; Parola, Philippe

    2015-01-01

    Background Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has been shown to be an effective tool for the rapid identification of arthropods, including tick vectors of human diseases. Methodology/Principal Findings The objective of the present study was to evaluate the use of MALDI-TOF MS to identify tick species, and to determine the presence of rickettsia pathogens in the infected Ticks. Rhipicephalus sanguineus and Dermacentor marginatus Ticks infected or not by R. conorii conorii or R. slovaca, respectively, were used as experimental models. The MS profiles generated from protein extracts prepared from tick legs exhibited mass peaks that distinguished the infected and uninfected Ticks, and successfully discriminated the Rickettsia spp. A blind test was performed using Ticks that were laboratory-reared, collected in the field or removed from patients and infected or not by Rickettsia spp. A query against our in-lab arthropod MS reference database revealed that the species and infection status of all Ticks were correctly identified at the species and infection status levels. Conclusions/Significance Taken together, the present work demonstrates the utility of MALDI-TOF MS for a dual identification of tick species and intracellular bacteria. Therefore, MALDI-TOF MS is a relevant tool for the accurate detection of Rickettsia spp in Ticks for both field monitoring and entomological diagnosis. The present work offers new perspectives for the monitoring of other vector borne diseases that present public health concerns. PMID:25659152

  6. Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS

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    Lista Florigio

    2011-12-01

    Full Text Available Abstract Background The genus Brucella contains highly infectious species that are classified as biological threat agents. The timely detection and identification of the microorganism involved is essential for an effective response not only to biological warfare attacks but also to natural outbreaks. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS is a rapid method for the analysis of biological samples. The advantages of this method, compared to conventional techniques, are rapidity, cost-effectiveness, accuracy and suitability for the high-throughput identification of bacteria. Discrepancies between taxonomy and genetic relatedness on the species and biovar level complicate the development of detection and identification assays. Results In this study, the accurate identification of Brucella species using MALDI-TOF-MS was achieved by constructing a Brucella reference library based on multilocus variable-number tandem repeat analysis (MLVA data. By comparing MS-spectra from Brucella species against a custom-made MALDI-TOF-MS reference library, MALDI-TOF-MS could be used as a rapid identification method for Brucella species. In this way, 99.3% of the 152 isolates tested were identified at the species level, and B. suis biovar 1 and 2 were identified at the level of their biovar. This result demonstrates that for Brucella, even minimal genomic differences between these serovars translate to specific proteomic differences. Conclusions MALDI-TOF-MS can be developed into a fast and reliable identification method for genetically highly related species when potential taxonomic and genetic inconsistencies are taken into consideration during the generation of the reference library.

  7. Identification of Algerian Field-Caught Phlebotomine Sand Fly Vectors by MALDI-TOF MS.

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    Ismail Lafri

    2016-01-01

    Full Text Available Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Precise sand fly identification is essential to prevent phlebotomine-borne diseases. Over the past two decades, progress in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS has emerged as an accurate tool for arthropod identification. The objective of the present study was to investigate the usefulness of MALDI-TOF MS as a tool for identifying field-caught phlebotomine.Sand flies were captured in four sites in north Algeria. A subset was morphologically and genetically identified. Six species were found in these areas and a total of 28 stored frozen specimens were used for the creation of the reference spectrum database. The relevance of this original method for sand fly identification was validated by two successive blind tests including the morphological identification of 80 new specimens which were stored at -80°C, and 292 unknown specimens, including engorged specimens, which were preserved under different conditions. Intra-species reproducibility and inter-species specificity of the protein profiles were obtained, allowing us to distinguish specimens at the gender level. Querying of the sand fly database using the MS spectra from the blind test groups revealed concordant results between morphological and MALDI-TOF MS identification. However, MS identification results were less efficient for specimens which were engorged or stored in alcohol. Identification of 362 phlebotomine sand flies, captured at four Algerian sites, by MALDI-TOF MS, revealed that the subgenus Larroussius was predominant at all the study sites, except for in M'sila where P. (Phlebotomus papatasi was the only sand fly species detected.The present study highlights the application of MALDI-TOF MS for monitoring sand fly fauna captured in the field. The low cost, reliability and

  8. Identification of Algerian Field-Caught Phlebotomine Sand Fly Vectors by MALDI-TOF MS.

    Science.gov (United States)

    Lafri, Ismail; Almeras, Lionel; Bitam, Idir; Caputo, Aurelia; Yssouf, Amina; Forestier, Claire-Lise; Izri, Arezki; Raoult, Didier; Parola, Philippe

    2016-01-01

    Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Precise sand fly identification is essential to prevent phlebotomine-borne diseases. Over the past two decades, progress in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as an accurate tool for arthropod identification. The objective of the present study was to investigate the usefulness of MALDI-TOF MS as a tool for identifying field-caught phlebotomine. Sand flies were captured in four sites in north Algeria. A subset was morphologically and genetically identified. Six species were found in these areas and a total of 28 stored frozen specimens were used for the creation of the reference spectrum database. The relevance of this original method for sand fly identification was validated by two successive blind tests including the morphological identification of 80 new specimens which were stored at -80°C, and 292 unknown specimens, including engorged specimens, which were preserved under different conditions. Intra-species reproducibility and inter-species specificity of the protein profiles were obtained, allowing us to distinguish specimens at the gender level. Querying of the sand fly database using the MS spectra from the blind test groups revealed concordant results between morphological and MALDI-TOF MS identification. However, MS identification results were less efficient for specimens which were engorged or stored in alcohol. Identification of 362 phlebotomine sand flies, captured at four Algerian sites, by MALDI-TOF MS, revealed that the subgenus Larroussius was predominant at all the study sites, except for in M'sila where P. (Phlebotomus) papatasi was the only sand fly species detected. The present study highlights the application of MALDI-TOF MS for monitoring sand fly fauna captured in the field. The low cost, reliability and rapidity of MALDI-TOF

  9. [Application of MALDI-TOF-MS in gene testing for non-syndromic hearing loss].

    Science.gov (United States)

    Zeng, Yun; Jiang, Dan; Feng, Da-fei; Jin, Dong-dong; Wu, Xiao-hui; Ding, Yan-li; Zou, Jing

    2013-12-01

    To investigate the feasibility of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) , according to the genetic test of non-syndromic hearing loss (NSHL), and check using the direct sequencing. Peripheral blood was collected from 454 NSHL patients. DNA samples were extracted and 20 loci of the four common disease-causing genes were analysed by MALDI-TOF-MS, including GJB2 (35delG, 167delT, 176_191del16, 235delC, 299_300delAT ), GJB3 (538C→T, 547G→A), SLC26A4 (281C→T, 589G→A, IVS7-2A→G, 1174A→T, 1226G→A, 1229C→T, IVS15+5G→A, 1975G→C, 2027T→A, 2162C→T, 2168A→G), and mitochondrial 12S rRNA (1494C→T, 1555A→G). Direct sequencing was also used to analyse the aforementioned 20 loci in order to validate the accuracy of MALDI-TOF-MS. Among the 454 patients, 166 cases (36.56%) of disease-causing mutations were detected, which included 69 cases (21.15%) of GJB2 gene mutation, four cases (0.88%) of GJB3 gene mutation, 64 cases (14.10%) of SLC26A4 gene mutation, and three cases (0.66%) of mitochondrial 12S rRNA gene mutation. Moreover, the results obtained from direct sequencing and MALDI-TOF-MS were consistent, and the results showed that the two methods were consistent. The MALDI-TOF-MS detection method was designed based on the hearing loss-related mutation hotspots seen in the Chinese population, and it has a high detection rate for NSHL related mutations. In comparison to the conventional detection methods, MALDI-TOF-MS has the following advantages: more detection sites, greater coverage, accurate, high throughput and low cost. Therefore, this method is capable of satisfying the needs of clinical detection for hearing impairment and it is suitable for large-scale implementation.

  10. Yeast identification by sequencing, biochemical kits, MALDI-TOF MS and rep-PCR DNA fingerprinting.

    Science.gov (United States)

    Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Chan, Jasper F W; Lau, Susanna K P; Kong, Fanrong; Xu, Yingchun; Woo, Patrick C Y

    2017-12-08

    No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Identification of Apis mellifera gut microbiota with MALDI TOF MS Biotyper

    OpenAIRE

    Jaroslav Gasper; Margarita Terentjeva; Attila Kántor; Eva Ivanišová; Maciej Kluz; Miroslava Kačániová

    2017-01-01

    The honey bee, Apis mellifera, is critically important for the pollination of many economically important crops. Continued colony losses have called for a deeper understanding of both symbiotic and pathogenic microbial interactions, particularly as they relate to food storage and the pollination environment. Therefore, the aim of this study was to explore and characterize the bacteria colonizing the alimentary tract of the native honey bees using MALDI TOF MS Biotyper. Content of the intestin...

  12. [Evaluation of mass spectrometry: MALDI-TOF MS for fast and reliable yeast identification].

    Science.gov (United States)

    Relloso, María S; Nievas, Jimena; Fares Taie, Santiago; Farquharson, Victoria; Mujica, María T; Romano, Vanesa; Zarate, Mariela S; Smayevsky, Jorgelina

    2015-01-01

    The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique known as MALDI-TOF MS is a tool used for the identification of clinical pathogens by generating a protein spectrum that is unique for a given species. In this study we assessed the identification of clinical yeast isolates by MALDI-TOF MS in a university hospital from Argentina and compared two procedures for protein extraction: a rapid method and a procedure based on the manufacturer's recommendations. A short protein extraction procedure was applied in 100 isolates and the rate of correct identification at genus and species level was 98.0%. In addition, we analyzed 201 isolates, previously identified by conventional methods, using the methodology recommended by the manufacturer and there was 95.38% coincidence in the identification at species level. MALDI TOF MS showed to be a fast, simple and reliable tool for yeast identification. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  13. Assessment of heat treatment of dairy products by MALDI-TOF-MS.

    Science.gov (United States)

    Meltretter, Jasmin; Birlouez-Aragon, Inès; Becker, Cord-Michael; Pischetsrieder, Monika

    2009-12-01

    The formation of the Amadori product from lactose (protein lactosylation) is a major parameter to evaluate the quality of processed milk. Here, MALDI-TOF-MS was used for the relative quantification of lactose-adducts in heated milk. Milk was heated at a temperature of 70, 80, and 100 degrees C between 0 and 300 min, diluted, and subjected directly to MALDI-TOF-MS. The lactosylation rate of alpha-lactalbumin increased with increasing reaction temperature and time. The results correlated well with established markers for heat treatment of milk (concentration of total soluble protein, soluble alpha-lactalbumin and beta-lactoglobulin at pH 4.6, and fluorescence of advanced Maillard products and soluble tryptophan index; r=0.969-0.997). The method was also applied to examine commercially available dairy products. In severely heated products, protein pre-purification by immobilized metal affinity chromatography improved spectra quality. Relative quantification of protein lactosylation by MALDI-TOF-MS proved to be a very fast and reliable method to monitor early Maillard reaction during milk processing.

  14. Rapid Classification and Identification of Microcystis aeruginosa Strains Using MALDI-TOF MS and Polygenetic Analysis.

    Directory of Open Access Journals (Sweden)

    Li-Wei Sun

    Full Text Available Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (MALDI-TOF MS was used to establish a rapid, simple, and accurate method to differentiate among strains of Microcystis aeruginosa, one of the most prevalent types of bloom-forming cyanobacteria. M. aeruginosa NIES-843, for which a complete genome has been sequenced, was used to characterize ribosomal proteins as biomarkers and to optimize conditions for observing ribosomal proteins as major peaks in a given mass spectrum. Thirty-one of 52 ribosomal subunit proteins were detected and identified along the mass spectrum. Fifty-five strains of M. aeruginosa from different habitats were analyzed using MALDI-TOF MS; among these samples, different ribosomal protein types were observed. A polygenetic analysis was performed using an unweighted pair-group method with arithmetic means and different ribosomal protein types to classify the strains into five major clades. Two clades primarily contained toxic strains, and the other three clades contained exclusively non-toxic strains. This is the first study to differentiate cyanobacterial strains using MALDI-TOF MS.

  15. Rapid Classification and Identification of Microcystis aeruginosa Strains Using MALDI-TOF MS and Polygenetic Analysis.

    Science.gov (United States)

    Sun, Li-Wei; Jiang, Wen-Jing; Sato, Hiroaki; Kawachi, Masanobu; Lu, Xi-Wu

    2016-01-01

    Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was used to establish a rapid, simple, and accurate method to differentiate among strains of Microcystis aeruginosa, one of the most prevalent types of bloom-forming cyanobacteria. M. aeruginosa NIES-843, for which a complete genome has been sequenced, was used to characterize ribosomal proteins as biomarkers and to optimize conditions for observing ribosomal proteins as major peaks in a given mass spectrum. Thirty-one of 52 ribosomal subunit proteins were detected and identified along the mass spectrum. Fifty-five strains of M. aeruginosa from different habitats were analyzed using MALDI-TOF MS; among these samples, different ribosomal protein types were observed. A polygenetic analysis was performed using an unweighted pair-group method with arithmetic means and different ribosomal protein types to classify the strains into five major clades. Two clades primarily contained toxic strains, and the other three clades contained exclusively non-toxic strains. This is the first study to differentiate cyanobacterial strains using MALDI-TOF MS.

  16. A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS.

    Science.gov (United States)

    Veloo, A C M; Jean-Pierre, H; Justesen, U S; Morris, T; Urban, E; Wybo, I; Shah, H N; Friedrich, A W; Morris, T; Shah, H N; Jean-Pierre, H; Justesen, U S; Nagy, E; Urban, E; Kostrzewa, M; Veloo, A; Friedrich, A W

    2017-12-01

    Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Identification of Apis mellifera gut microbiota with MALDI TOF MS Biotyper

    Directory of Open Access Journals (Sweden)

    Jaroslav Gasper

    2017-05-01

    Full Text Available The honey bee, Apis mellifera, is critically important for the pollination of many economically important crops. Continued colony losses have called for a deeper understanding of both symbiotic and pathogenic microbial interactions, particularly as they relate to food storage and the pollination environment. Therefore, the aim of this study was to explore and characterize the bacteria colonizing the alimentary tract of the native honey bees using MALDI TOF MS Biotyper. Content of the intestinal tract was cultured for isolation of Gram-negative, Gram-positive microorganisms and yeasts. Then, the identification of isolates with MALDI-TOF MS Biotyper was done. Results showed that the most abundant genera in bees’ samples were Lactobacillus, Pseudomonas and Serratia. Altogether, 12 genera with 21 bacterial species and one yeast genus with two species were isolated. Bacteria were represented with Acidovorax facilis, Lactobacillus gasseri, L. amylovorus, L. kunkeei, L. fructivorans, Pseudomonas oryzihabitans, Ps. brenneri, Ps. indica, Micrococcus luteus, Serratia fonticola, Ser. marcescens, Ser. ureilytica, Hafnia alvei, Candida magnolia, Bacillus oleronius, B. horneckiae, Issatchenkia orientalis, Pantoea agglomerans, Enterobacter cloacae, Staphylococcus epidermidis, Staph. pasteuri, Shewanella profunda.  The results of the study shows that the microflora of the bees gut is heterogenic and depend of locality and resources of environment for bees.

  18. Evaluation of sample preparation protocols for spider venom profiling by MALDI-TOF MS.

    Science.gov (United States)

    Bočánek, Ondřej; Šedo, Ondrej; Pekár, Stano; Zdráhal, Zbyněk

    2017-07-01

    Spider venoms are highly complex mixtures containing biologically active substances with potential for use in biotechnology or pharmacology. Fingerprinting of venoms by Matrix-Assisted Laser Desorption-Ionization - Time of Flight Mass Spectrometry (MALDI-TOF MS) is a thriving technology, enabling the rapid detection of peptide/protein components that can provide comparative information. In this study, we evaluated the effects of sample preparation procedures on MALDI-TOF mass spectral quality to establish a protocol providing the most reliable analytical outputs. We adopted initial sample preparation conditions from studies already published in this field. Three different MALDI matrixes, three matrix solvents, two sample deposition methods, and different acid concentrations were tested. As a model sample, venom from Brachypelma albopilosa was used. The mass spectra were evaluated on the basis of absolute and relative signal intensities, and signal resolution. By conducting three series of analyses at three weekly intervals, the reproducibility of the mass spectra were assessed as a crucial factor in the selection for optimum conditions. A sample preparation protocol based on the use of an HCCA matrix dissolved in 50% acetonitrile with 2.5% TFA deposited onto the target by the dried-droplet method was found to provide the best results in terms of information yield and repeatability. We propose that this protocol should be followed as a standard procedure, enabling the comparative assessment of MALDI-TOF MS spider venom fingerprints. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Ellagitannin composition of blackberry as determined by HPLC-ESI-MS and MALDI-TOF-MS.

    Science.gov (United States)

    Hager, Tiffany J; Howard, Luke R; Liyanage, Rohana; Lay, Jackson O; Prior, Ronald L

    2008-02-13

    Blackberries ( Rubus sp.) were evaluated by high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) to identify the ellagitannins present in flesh, torus (receptacle tissue), and seeds. Most ellagitannins were present (or detectable) only in seed tissues. Ellagitannins identified by HPLC-ESI-MS in the seeds included pedunculagin, casuarictin/potentillin, castalagin/vescalagin, lambertianin A/sanguiin H-6, lambertianin C, and lambertianin D. For several of the ellagitannins, isomeric separation was also obtained. The MALDI-TOF-MS analysis was primarily utilized to evaluate and identify high molecular mass (>1000 Da) ellagitannins. The MALDI analysis verified the presence of the ellagitannins identified by HPLC-ESI-MS including lambertianin A/sanguiin H-6, lambertianin C, and lambertianin D, but the analysis also indicated the presence of several other compounds that were most likely ellagitannins based on the patterns observed in the masses (i.e., loss or addition of a gallic acid moiety to a known ellagitannin). This study determined the presence of several possible isomeric forms of ellagitannins previously unidentified in fruit and presents a possible analytical HPLC method for the analysis of the major ellagitannins present in the fruit.

  20. New Insights for Diagnosis of Pineapple Fusariosis by MALDI-TOF MS Technique.

    Science.gov (United States)

    Santos, Cledir; Ventura, José Aires; Lima, Nelson

    2016-08-01

    Fusarium is one of the most economically important fungal genus, since it includes many pathogenic species which cause a wide range of plant diseases. Morphological or molecular biology identification of Fusarium species is a limiting step in the fast diagnosis and treatment of plant disease caused by these fungi. Mass spectrometry by matrix-assisted laser/desorption ionisation-time-of-flight (MALDI-TOF)-based fingerprinting approach was applied to the fungal growth monitoring and direct detection of strain Fusarium guttiforme E-480 inoculated in both pineapple cultivars Pérola and Imperial side shoots, that are susceptible and resistant, respectively, to this fungal strain. MALDI-TOF MS technique was capable to detect fungal molecular mass peaks in the susceptible pineapple stem side shoot tissue. It is assumed that these molecular masses are mainly constituted by ribosomal proteins. MALDI-TOF-based fingerprinting approach has herein been demonstrated to be sensitive and accurate for the direct detection of F. guttiforme E-480 molecular masses on both susceptible and resistant pineapple side stem free of any pre-treatment. According to the results obtained, the changing on molecular mass peaks of infected susceptible pineapple tissue together with the possibility of fungal molecular masses analysis into this pineapple tissue can be a good indication for an early diagnosis by MALDI-TOF MS of pineapple fusariosis.

  1. Enhanced MALDI-TOF MS Analysis of Phosphopeptides Using an Optimized DHAP/DAHC Matrix

    Science.gov (United States)

    Hou, Junjie; Xie, Zhensheng; Xue, Peng; Cui, Ziyou; Chen, Xiulan; Li, Jing; Cai, Tanxi; Wu, Peng; Yang, Fuquan

    2010-01-01

    Selecting an appropriate matrix solution is one of the most effective means of increasing the ionization efficiency of phosphopeptides in matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In this study, we systematically assessed matrix combinations of 2, 6-dihydroxyacetophenone (DHAP) and diammonium hydrogen citrate (DAHC), and demonstrated that the low ratio DHAP/DAHC matrix was more effective in enhancing the ionization of phosphopeptides. Low femtomole level of phosphopeptides from the tryptic digests of α-casein and β-casein was readily detected by MALDI-TOF-MS in both positive and negative ion mode without desalination or phosphopeptide enrichment. Compared with the DHB/PA matrix, the optimized DHAP/DAHC matrix yielded superior sample homogeneity and higher phosphopeptide measurement sensitivity, particularly when multiple phosphorylated peptides were assessed. Finally, the DHAP/DAHC matrix was applied to identify phosphorylation sites from α-casein and β-casein and to characterize two phosphorylation sites from the human histone H1 treated with Cyclin-Dependent Kinase-1 (CDK1) by MALDI-TOF/TOF MS. PMID:20339515

  2. Enhanced MALDI-TOF MS Analysis of Phosphopeptides Using an Optimized DHAP/DAHC Matrix

    Directory of Open Access Journals (Sweden)

    Junjie Hou

    2010-01-01

    Full Text Available Selecting an appropriate matrix solution is one of the most effective means of increasing the ionization efficiency of phosphopeptides in matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS. In this study, we systematically assessed matrix combinations of 2, 6-dihydroxyacetophenone (DHAP and diammonium hydrogen citrate (DAHC, and demonstrated that the low ratio DHAP/DAHC matrix was more effective in enhancing the ionization of phosphopeptides. Low femtomole level of phosphopeptides from the tryptic digests of α-casein and β-casein was readily detected by MALDI-TOF-MS in both positive and negative ion mode without desalination or phosphopeptide enrichment. Compared with the DHB/PA matrix, the optimized DHAP/DAHC matrix yielded superior sample homogeneity and higher phosphopeptide measurement sensitivity, particularly when multiple phosphorylated peptides were assessed. Finally, the DHAP/DAHC matrix was applied to identify phosphorylation sites from α-casein and β-casein and to characterize two phosphorylation sites from the human histone H1 treated with Cyclin-Dependent Kinase-1 (CDK1 by MALDI-TOF/TOF MS.

  3. DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS.

    Science.gov (United States)

    Ling, Ling; Li, Ying; Wang, Sheng; Guo, Liming; Xiao, Chunsheng; Chen, Xuesi; Guo, Xinhua

    2018-04-01

    Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H] - ) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. Graphical Abstract ᅟ.

  4. MALDI-TOF MS typing of a nosocomial methicillin-resistant Staphylococcus aureus outbreak in a neonatal intensive care unit.

    Science.gov (United States)

    Steensels, Deborah; Deplano, Ariane; Denis, Olivier; Simon, Anne; Verroken, Alexia

    2017-08-01

    The early detection of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak is decisive to control its spread and rapidly initiate adequate infection control measures. Therefore, prompt determination of epidemiologic relatedness of clinical MRSA isolates is essential. Genetic typing methods have a high discriminatory power but their availability remains restricted. In this study, we aimed to challenge matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a typing tool of a nosocomial MRSA outbreak in a neonatal intensive care unit. Over a 2-year period, 15 MRSA isolates were recovered from patients (n = 14) and health care workers (n = 1) at the neonatal intensive care unit. Five reference strains were included for comparison. Identification was performed by MALDI-TOF MS and susceptibility profiles determined by automated broth microdilution. Typing analysis by MALDI-TOF MS included mean spectrum profiles and subsequent dendrogram creation using BioNumerics software. Results were compared with spa typing and pulsed-field gel electrophoresis (PFGE). Our study showed good concordance (93%) between PFGE, spa typing, and MALDI-TOF MS for the outbreak-related MRSA strains. MALDI-TOF MS typing showed excellent typeability and discriminatory power but showed poor reproducibility. This study is one of the first to document the potential usefulness of MALDI-TOF MS with standardized data analysis as a typing tool for investigating a nosocomial MRSA outbreak. A concordance of 93% compared to reference typing techniques was observed. However, because of poor reproducibility, long-term follow-up of prospective isolated strains is not practical for routine use. Further studies are needed to confirm our observations.

  5. Rapid first-line discrimination of methicillin resistant Staphylococcus aureus strains using MALDI-TOF MS

    DEFF Research Database (Denmark)

    Østergaard, Claus; Grønvall Kjær Hansen, Sanne; Møller, Jens K

    2015-01-01

    /z-values (peaks) and used a concept of arranging these peaks into pairs or small clusters within a small mass range, allowing for quality control of the spectra obtained. Using this concept we could reproducibly characterise and arrange the isolates into 26 MALDI-TOF groups, which strongly correlated with spa...... used for this purpose. These methods are all relatively time-consuming and not performed routinely in all laboratories. The aim of this study is to examine whether MALDI-TOF MS can be used as a fast, simple and easily implemented method for first-line discrimination of MRSA isolates. Mass spectra from...... 600 clinical MRSA isolates were included in the study, representing 89 spa types, associated with 16 different known clonal complexes. All spectra were obtained directly from colony material obtained from overnight cultures without prior protein extraction. We identified 43 useful discriminatory m...

  6. MALDI-TOF MS Profiling-Advances in Species Identification of Pests, Parasites, and Vectors

    Directory of Open Access Journals (Sweden)

    Jayaseelan Murugaiyan

    2017-05-01

    Full Text Available Invertebrate pests and parasites of humans, animals, and plants continue to cause serious diseases and remain as a high treat to agricultural productivity and storage. The rapid and accurate species identification of the pests and parasites are needed for understanding epidemiology, monitoring outbreaks, and designing control measures. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS profiling has emerged as a rapid, cost effective, and high throughput technique of microbial species identification in modern diagnostic laboratories. The development of soft ionization techniques and the release of commercial pattern matching software platforms has resulted in the exponential growth of applications in higher organisms including parasitology. The present review discusses the proof-of-principle experiments and various methods of MALDI MS profiling in rapid species identification of both laboratory and field isolates of pests, parasites and vectors.

  7. MALDI-TOF MS Profiling-Advances in Species Identification of Pests, Parasites, and Vectors.

    Science.gov (United States)

    Murugaiyan, Jayaseelan; Roesler, Uwe

    2017-01-01

    Invertebrate pests and parasites of humans, animals, and plants continue to cause serious diseases and remain as a high treat to agricultural productivity and storage. The rapid and accurate species identification of the pests and parasites are needed for understanding epidemiology, monitoring outbreaks, and designing control measures. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as a rapid, cost effective, and high throughput technique of microbial species identification in modern diagnostic laboratories. The development of soft ionization techniques and the release of commercial pattern matching software platforms has resulted in the exponential growth of applications in higher organisms including parasitology. The present review discusses the proof-of-principle experiments and various methods of MALDI MS profiling in rapid species identification of both laboratory and field isolates of pests, parasites and vectors.

  8. Isolation and Identification of Spoilage Yeasts in Wine Samples by MALDI-TOF MS Biotyper

    Directory of Open Access Journals (Sweden)

    Attila Kántor

    2015-05-01

    Full Text Available Many genera and species of microorganisms can be found in grape musts and wines at various times during the winemaking process. For instance, Saccharomyces, Brettanomyces, and Pediococcus can be found together in wine. There are many species of yeast involved in wine spoilage during storage. Aim of this study was to isolate the spoilage yeasts from wine samples with using special selective agar media and identified on species level by Matrix-Assisted Laser Desorption/Ionization-Time of Fly Mass Spectrometry (MALDI-TOF MS. Six red wines used in this study. We identified 10 yeast species from 152 isolates. The most common species in wine samples was Saccharomyces cerevisiae. We also identified four Candida species, two Zygosaccharomyces species and one species from genus Rhodotorula, Saccharomycodes and Dekkera.

  9. Mapping the dark space of chemical reactions with extended nanomole synthesis and MALDI-TOF MS.

    Science.gov (United States)

    Lin, Shishi; Dikler, Sergei; Blincoe, William D; Ferguson, Ronald D; Sheridan, Robert P; Peng, Zhengwei; Conway, Donald V; Zawatzky, Kerstin; Wang, Heather; Cernak, Tim; Davies, Ian W; DiRocco, Daniel A; Sheng, Huaming; Welch, Christopher J; Dreher, Spencer D

    2018-05-24

    Understanding the practical limitations of chemical reactions is critically important for efficiently planning the synthesis of compounds in pharmaceutical, agrochemical and specialty chemical research and development. However, literature reports of the scope of new reactions are often cursory and biased toward successful results, severely limiting the ability to predict reaction outcomes for untested substrates. We herein illustrate strategies for carrying out large scale surveys of chemical reactivity using a material-sparing nanomole-scale automated synthesis platform with greatly expanded synthetic scope combined with ultra-high throughput (uHT) matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Copyright © 2018, American Association for the Advancement of Science.

  10. Simplifying the Preparation of Pollen Grains for MALDI-TOF MS Classification

    Directory of Open Access Journals (Sweden)

    Franziska Lauer

    2017-03-01

    Full Text Available Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS is a well-implemented analytical technique for the investigation of complex biological samples. In MS, the sample preparation strategy is decisive for the success of the measurements. Here, sample preparation processes and target materials for the investigation of different pollen grains are compared. A reduced and optimized sample preparation process prior to MALDI-TOF measurement is presented using conductive carbon tape as target. The application of conductive tape yields in enhanced absolute signal intensities and mass spectral pattern information, which leads to a clear separation in subsequent pattern analysis. The results will be used to improve the taxonomic differentiation and identification, and might be useful for the development of a simple routine method to identify pollen based on mass spectrometry.

  11. Discrimination of Aspergillus lentulus from Aspergillus fumigatus by Raman spectroscopy and MALDI-TOF MS.

    Science.gov (United States)

    Verwer, P E B; van Leeuwen, W B; Girard, V; Monnin, V; van Belkum, A; Staab, J F; Verbrugh, H A; Bakker-Woudenberg, I A J M; van de Sande, W W J

    2014-02-01

    In 2005, a new sibling species of Aspergillus fumigatus was discovered: Aspergillus lentulus. Both species can cause invasive fungal disease in immune-compromised patients. The species are morphologically very similar. Current techniques for identification are PCR-based or morphology-based. These techniques are labour-intense and not sufficiently discriminatory. Since A. lentulus is less susceptible to several antifungal agents, it is important to correctly identify the causative infectious agent in order to optimize antifungal therapy. In this study we determined whether Raman spectroscopy and/or MALDI-TOF MS were able to differentiate between A. lentulus and A. fumigatus. For 16 isolates of A. lentulus and 16 isolates of A. fumigatus, Raman spectra and peptide profiles were obtained using the Spectracell and MALDI-TOF MS (VITEK MS RUO, bioMérieux) respectively. In order to obtain reliable Raman spectra for A. fumigatus and A. lentulus, the culture medium needed to be adjusted to obtain colourless conidia. Only Raman spectra obtained from colourless conidia were reproducible and correctly identified 25 out of 32 (78 %) of the Aspergillus strains. For VITEK MS RUO, no medium adjustments were necessary. Pigmented conidia resulted in reproducible peptide profiles as well in this case. VITEK MS RUO correctly identified 100 % of the Aspergillus isolates, within a timeframe of approximately 54 h including culture. Of the two techniques studied here, VITEK MS RUO was superior to Raman spectroscopy in the discrimination of A. lentulus from A. fumigatus. VITEK MS RUO seems to be a successful technique in the daily identification of Aspergillus spp. within a limited timeframe.

  12. MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria.

    Science.gov (United States)

    Li, Yang; Gu, Bing; Liu, Genyan; Xia, Wenying; Fan, Kun; Mei, Yaning; Huang, Peijun; Pan, Shiyang

    2014-05-01

    Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an accurate, rapid and inexpensive technique that has initiated a revolution in the clinical microbiology laboratory for identification of pathogens. The Vitek 2 anaerobe and Corynebacterium (ANC) identification card is a newly developed method for identification of corynebacteria and anaerobic species. The aim of this study was to evaluate the effectiveness of the ANC card and MALDI-TOF MS techniques for identification of clinical anaerobic isolates. Five reference strains and a total of 50 anaerobic bacteria clinical isolates comprising ten different genera and 14 species were identified and analyzed by the ANC card together with Vitek 2 identification system and Vitek MS together with version 2.0 database respectively. 16S rRNA gene sequencing was used as reference method for accuracy in the identification. Vitek 2 ANC card and Vitek MS provided comparable results at species level for the five reference strains. Of 50 clinical strains, the Vitek MS provided identification for 46 strains (92%) to the species level, 47 (94%) to genus level, one (2%) low discrimination, two (4%) no identification and one (2%) misidentification. The Vitek 2 ANC card provided identification for 43 strains (86%) correct to the species level, 47 (94%) correct to the genus level, three (6%) low discrimination, three (6%) no identification and one (2%) misidentification. Both Vitek MS and Vitek 2 ANC card can be used for accurate routine clinical anaerobe identification. Comparing to the Vitek 2 ANC card, Vitek MS is easier, faster and more economic for each test. The databases currently available for both systems should be updated and further developed to enhance performance.

  13. MALDI-TOF MS analysis of labile Lolium perenne major allergens in mixes.

    Science.gov (United States)

    Irañeta, S G; Acosta, D M; Duran, R; Apicella, C; Orlando, U D; Seoane, M A; Alonso, A; Duschak, V G

    2008-08-01

    It is well known that allergen extracts used for specific therapy of allergic disorders are commonly stored as mixtures, causing an alteration of its stability. The aim of this report is to identify pollen allergens susceptible to degradation during storage of mixtures containing different sources of proteases in the absence of glycerol as a preserving agent. Mixes containing Lolium perenne (Lol p) pollen extract with either Aspergillus fumigatus or Periplaneta americana extracts were prepared and co-incubated for 90 days at 4 degrees C. Samples were taken off at fixed times and comparatively tested by in vitro and in vivo assays with atopic patients. Selected pollinic allergens were subjected to MALDI-TOF MS analysis. ELISA inhibition evidenced the loss of potency from ryegrass extract, and immunoblotting assays showed the degradation of specific pollinic allergens during storage of mixtures containing protease-rich sources. An in vivo intradermal skin assay confirmed the gradual loss of the biological activity of L. perenne pollen extract co-incubated with non-related protease-rich extracts in comparison with that of the control pollen extract. MALDI-TOF MS analysis allowed us to determine that Lol p 1 and Lol p 5 are susceptible to proteolysis whereas Lol p 4 was found to be resistant to degradation during storage. Lol p 1 and Lol p 5 degradation is responsible for the loss of the biological activity of L. perenne pollen extract when co-incubated with protease-rich fungal and cockroach extracts in the same vial for months in the absence of glycerol as a preserving agent. The integrity of these major allergens must be preserved to increase the vaccine stability and to assure efficacy when mixes are used for immunotherapy.

  14. MALDI-TOF MS coupled with collision-induced dissociation (CID) measurements of poly(methyl methacrylate)

    NARCIS (Netherlands)

    Baumgaertel, A.; Becer, C.R.; Gottschaldt, M.; Schubert, U.S.

    2008-01-01

    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was chosen for an in-detail analysis of poly(methyl methacrylate) (PMMA) in order to determine the possible fragmentation mechanism with the help of collision-induced dissociation (CID). All experiments were

  15. Capillary and gel electromigration techniques and MALDI-TOF MS – Suitable tools for identification of filamentous fungi

    Czech Academy of Sciences Publication Activity Database

    Horká, Marie; Kubesová, Anna; Šalplachta, Jiří; Zapletalová, E.; Horký, J.; Šlais, Karel

    2012-01-01

    Roč. 716, - (2012), s. 155-162 ISSN 0003-2670 R&D Projects: GA MV VG20102015023; GA AV ČR IAAX00310701 Institutional research plan: CEZ:AV0Z40310501 Keywords : electormigration techniques * MALDI - TOF MS * Monilinia spp. Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.387, year: 2012

  16. ATR-FTIR Spectroscopy Highlights the Problem of Distinguishing Between Exophiala dermatitidis and E. phaeomuriformis Using MALDI-TOF MS

    NARCIS (Netherlands)

    Ergin, C.; Gok, Y.; Baygu, Y.; Gumral, R.; Ozhak-Baysan, B.; Dogen, A.; Ogunc, D.; Ilkit, M.; Seyedmousavi, S.

    2016-01-01

    The present study compared two chemical-based methods, namely, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, to understand the misidentification of Exophiala

  17. A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS

    DEFF Research Database (Denmark)

    Veloo, A; Jean-Pierre, H; Justesen, U S

    2017-01-01

    Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network...

  18. MALDI-TOF MS Andromas strategy for the routine identification of bacteria, mycobacteria, yeasts, Aspergillus spp. and positive blood cultures.

    Science.gov (United States)

    Bille, E; Dauphin, B; Leto, J; Bougnoux, M-E; Beretti, J-L; Lotz, A; Suarez, S; Meyer, J; Join-Lambert, O; Descamps, P; Grall, N; Mory, F; Dubreuil, L; Berche, P; Nassif, X; Ferroni, A

    2012-11-01

    All organisms usually isolated in our laboratory are now routinely identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using the Andromas software. The aim of this study was to describe the use of this strategy in a routine clinical microbiology laboratory. The microorganisms identified included bacteria, mycobacteria, yeasts and Aspergillus spp. isolated on solid media or extracted directly from blood cultures. MALDI-TOF MS was performed on 2665 bacteria isolated on solid media, corresponding to all bacteria isolated during this period except Escherichia coli grown on chromogenic media. All acquisitions were performed without extraction. After a single acquisition, 93.1% of bacteria grown on solid media were correctly identified. When the first acquisition was not contributory, a second acquisition was performed either the same day or the next day. After two acquisitions, the rate of bacteria identified increased to 99.2%. The failures reported on 21 strains were due to an unknown profile attributed to new species (9) or an insufficient quality of the spectrum (12). MALDI-TOF MS has been applied to 162 positive blood cultures. The identification rate was 91.4%. All mycobacteria isolated during this period (22) were correctly identified by MALDI-TOF MS without any extraction. For 96.3% and 92.2% of yeasts and Aspergillus spp., respectively, the identification was obtained with a single acquisition. After a second acquisition, the overall identification rate was 98.8% for yeasts (160/162) and 98.4% (63/64) for Aspergillus spp. In conclusion, the MALDI-TOF MS strategy used in this work allows a rapid and efficient identification of all microorganisms isolated routinely. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

  19. Exploring MALDI-TOF MS approach for a rapid identification of Mycobacterium avium ssp. paratuberculosis field isolates.

    Science.gov (United States)

    Ricchi, M; Mazzarelli, A; Piscini, A; Di Caro, A; Cannas, A; Leo, S; Russo, S; Arrigoni, N

    2017-03-01

    The aim of the study was to explore the suitability of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for a rapid and correct identification of Mycobacterium avium ssp. paratuberculosis (MAP) field isolates. MALDI-TOF MS approach is becoming one of the most popular tests for the identification of intact bacterial cells which has been shown to be fast and reliable. For this purpose, 36 MAP field isolates were analysed through MALDI-TOF MS and the spectra compared with two different databases: one provided by the vendor of the system employed (Biotyper ver. 3·0; Bruker Daltonics) and a homemade database containing spectra from both tuberculous and nontuberculous Mycobacteria. Moreover, principal component analysis procedure was employed to confirm the ability of MALDI-TOF MS to discriminate between very closely related subspecies. Our results suggest MAP can be differentiated from other Mycobacterium species, both when the species are very close (M. intracellulare) and when belonging to different subspecies (M. avium ssp. avium and M. avium ssp. silvaticum). The procedure applied is fast, easy to perform, and achieves an earlier accurate species identification of MAP and nontuberculous Mycobacteria in comparison to other procedures. The gold standard test for the diagnosis of paratuberculosis is still isolation of MAP by cultural methods, but additional assays, such as qPCR and subculturing for determination of mycobactin dependency are required to confirm its identification. We have provided here evidence pertaining to the usefulness of MALDI-TOF MS approach for a rapid identification of this mycobacterium among other members of M. avium complex. © 2016 The Society for Applied Microbiology.

  20. Validation of a for anaerobic bacteria optimized MALDI-TOF MS biotyper database: The ENRIA project.

    Science.gov (United States)

    Veloo, A C M; Jean-Pierre, H; Justesen, U S; Morris, T; Urban, E; Wybo, I; Kostrzewa, M; Friedrich, A W

    2018-03-12

    Within the ENRIA project, several 'expertise laboratories' collaborated in order to optimize the identification of clinical anaerobic isolates by using a widely available platform, the Biotyper Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Main Spectral Profiles (MSPs) of well characterized anaerobic strains were added to one of the latest updates of the Biotyper database db6903; (V6 database) for common use. MSPs of anaerobic strains nominated for addition to the Biotyper database are included in this validation. In this study, we validated the optimized database (db5989 [V5 database] + ENRIA MSPs) using 6309 anaerobic isolates. Using the V5 database 71.1% of the isolates could be identified with high confidence, 16.9% with low confidence and 12.0% could not be identified. Including the MSPs added to the V6 database and all MSPs created within the ENRIA project, the amount of strains identified with high confidence increased to 74.8% and 79.2%, respectively. Strains that could not be identified using MALDI-TOF MS decreased to 10.4% and 7.3%, respectively. The observed increase in high confidence identifications differed per genus. For Bilophila wadsworthia, Prevotella spp., gram-positive anaerobic cocci and other less commonly encountered species more strains were identified with higher confidence. A subset of the non-identified strains (42.1%) were identified using 16S rDNA gene sequencing. The obtained identities demonstrated that strains could not be identified either due to the generation of spectra of insufficient quality or due to the fact that no MSP of the encountered species was present in the database. Undoubtedly, the ENRIA project has successfully increased the number of anaerobic isolates that can be identified with high confidence. We therefore recommend further expansion of the database to include less frequently isolated species as this would also allow us to gain valuable insight into the clinical

  1. Evaluation of the Biotyper MALDI-TOF MS system for identification of Staphylococcus species.

    Science.gov (United States)

    Zhu, Wenming; Sieradzki, Krzysztof; Albrecht, Valerie; McAllister, Sigrid; Lin, Wen; Stuchlik, Olga; Limbago, Brandi; Pohl, Jan; Kamile Rasheed, J

    2015-10-01

    The Bruker Biotyper MALDI-TOF MS (Biotyper) system, with a modified 30 minute formic acid extraction method, was evaluated by its ability to identify 216 clinical Staphylococcus isolates from the CDC reference collection comprising 23 species previously identified by conventional biochemical tests. 16S rDNA sequence analysis was used to resolve discrepancies. Of these, 209 (96.8%) isolates were correctly identified: 177 (84.7%) isolates had scores ≥2.0, while 32 (15.3%) had scores between 1.70 and 1.99. The Biotyper identification was inconsistent with the biochemical identification for seven (3.2%) isolates, but the Biotyper identifications were confirmed by 16S rDNA analysis. The distribution of low scores was strongly species-dependent, e.g. only 5% of Staphylococcus epidermidis and 4.8% of Staphylococcus aureus isolates scored below 2.0, while 100% of Staphylococcus cohnii, 75% of Staphylococcus sciuri, and 60% of Staphylococcus caprae produced low but accurate Biotyper scores. Our results demonstrate that the Biotyper can reliably identify Staphylococcus species with greater accuracy than conventional biochemicals. Broadening of the reference database by inclusion of additional examples of under-represented species could further optimize Biotyper results. Published by Elsevier B.V.

  2. A Novel Rapid MALDI-TOF-MS-Based Method for Measuring Urinary Globotriaosylceramide in Fabry Patients

    Science.gov (United States)

    Alharbi, Fahad J.; Geberhiwot, Tarekegn; Hughes, Derralynn A.; Ward, Douglas G.

    2016-04-01

    Fabry disease is an X-linked lysosomal storage disorder caused by deficiency of α-galactosidase A, resulting in the accumulation of glycosphingolipids in various organs. Globotriaosylceramide (Gb3) and its isoforms and analogues have been identified and quantified as biomarkers of disease severity and treatment efficacy. The current study aimed to establish rapid methods for urinary Gb3 extraction and quantitation. Urine samples from 15 Fabry patients and 21 healthy control subjects were processed to extract Gb3 by mixing equal volumes of urine, methanol containing an internal standard, and chloroform followed by sonication and centrifugation. Thereafter, the lower phase was analyzed by MALDI-TOF MS and the relative peak areas of the internal standard and four major species of Gb3 determined. The results showed high reproducibility with intra- and inter-assay coefficients variation of 9.9% and 13.7%, respectively. The limit of detection was 0.15 ng/μL and the limit of quantitation was 0.30 ng/μL. Total urinary Gb3 levels in both genders of classic Fabry patients were significantly higher than in healthy controls (p < 0.0001). Gb3 levels in Fabry males were higher than in Fabry females (p = 0.08). We have established a novel assay for urinary total Gb3 that takes less than 15 min from start to finish.

  3. Towards Spectral Library-free MALDI-TOF MS Bacterial Identification.

    Science.gov (United States)

    Cheng, Ding; Qiao, Liang; Horvatovich, Péter

    2018-05-11

    Bacterial identification is of great importance in clinical diagnosis, environmental monitoring and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interests, and has been clinically used. Nevertheless, current bioinformatics solutions use spectral libraries for the identification of bacterial strains. Spectral library generation requires acquisition of MALDI-TOF spectra from monoculture bacterial colonies, which is time-consuming and not possible for many species and strains. We propose a strategy for bacterial typing by MALDI-TOF using protein sequences from public database, i.e. UniProt. Ten genes were identified to encode proteins most often observed by MALD-TOF from bacteria through 500 times repeated a 10-fold double cross-validation procedure, using 403 MALDI-TOF spectra corresponding to 14 genera, 81 species and 403 strains, and the protein sequences of 1276 species in UniProt. The 10 genes were then used to annotate peaks on MALDI-TOF spectra of bacteria for bacterial identification. With the approach, bacteria can be identified at the genus level by searching against a database containing the protein sequences of 42 genera of bacteria from UniProt. Our approach identified 84.1% of the 403 spectra correctly at the genus level. Source code of the algorithm is available at https://github.com/dipcarbon/BacteriaMSLF.

  4. Experimental design for optimizing MALDI-TOF-MS analysis of palladium complexes

    Directory of Open Access Journals (Sweden)

    Rakić-Kostić Tijana M.

    2017-01-01

    Full Text Available This paper presents optimization of matrix-assisted laser desorption/ionization (MALDI time-of-flight (TOF mass spectrometer (MS instrumental parameters for the analysis of chloro(2,2'',2"-terpyridinepalladium(II chloride dihydrate complex applying design of experiments methodology (DoE. This complex is of interest for potential use in the cancer therapy. DoE methodology was proved to succeed in optimization of many complex analytical problems. However, it has been poorly used for MALDI-TOF-MS optimization up to now. The theoretical mathematical relationships which explain the influence of important experimental factors (laser energy, grid voltage and number of laser shots on the selected responses (signal to noise – S/N ratio and the resolution – R of the leading peak is established. The optimal instrumental settings providing maximal S/N and R are identified and experimentally verified. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. 172052 and Grant no. 172011

  5. Comparison among four proposed direct blood culture microbial identification methods using MALDI-TOF MS

    Directory of Open Access Journals (Sweden)

    Ali M. Bazzi

    2017-05-01

    Full Text Available Summary: Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF mass spectrometry facilitates rapid and accurate identification of pathogens, which is critical for sepsis patients.In this study, we assessed the accuracy in identification of both Gram-negative and Gram-positive bacteria, except for Streptococcus viridans, using four rapid blood culture methods with Vitek MALDI-TOF-MS. We compared our proposed lysis centrifugation followed by washing and 30% acetic acid treatment method (method 2 with two other lysis centrifugation methods (washing and 30% formic acid treatment (method 1; 100% ethanol treatment (method 3, and picking colonies from 90 to 180 min subculture plates (method 4. Methods 1 and 2 identified all organisms down to species level with 100% accuracy, except for Streptococcus viridans, Streptococcus pyogenes, Enterobacter cloacae and Proteus vulgaris. The latter two were identified to genus level with 100% accuracy. Each method exhibited excellent accuracy and precision in terms of identification to genus level with certain limitations. Keywords: MALDI-TOF, Gram-negative, Gram-positive, Sepsis, Blood culture

  6. Comparison among four proposed direct blood culture microbial identification methods using MALDI-TOF MS.

    Science.gov (United States)

    Bazzi, Ali M; Rabaan, Ali A; El Edaily, Zeyad; John, Susan; Fawarah, Mahmoud M; Al-Tawfiq, Jaffar A

    Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry facilitates rapid and accurate identification of pathogens, which is critical for sepsis patients. In this study, we assessed the accuracy in identification of both Gram-negative and Gram-positive bacteria, except for Streptococcus viridans, using four rapid blood culture methods with Vitek MALDI-TOF-MS. We compared our proposed lysis centrifugation followed by washing and 30% acetic acid treatment method (method 2) with two other lysis centrifugation methods (washing and 30% formic acid treatment (method 1); 100% ethanol treatment (method 3)), and picking colonies from 90 to 180min subculture plates (method 4). Methods 1 and 2 identified all organisms down to species level with 100% accuracy, except for Streptococcus viridans, Streptococcus pyogenes, Enterobacter cloacae and Proteus vulgaris. The latter two were identified to genus level with 100% accuracy. Each method exhibited excellent accuracy and precision in terms of identification to genus level with certain limitations. Copyright © 2016 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

  7. Applications of MALDI-TOF MS to large-scale human mtDNA population-based studies

    Czech Academy of Sciences Publication Activity Database

    Cerezo, M.; Černý, Viktor; Carracedo, Á.; Salas, A.

    2009-01-01

    Roč. 30, č. 21 (2009), s. 3665-3673 ISSN 0173-0835 R&D Projects: GA ČR GA206/08/1587 Institutional research plan: CEZ:AV0Z80020508 Keywords : Haplogroup * High-throughput SNP genotyping * MALDI-TOF MS * Mitochondrial DNA * Multiplex assay Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 3.077, year: 2009 http://www3.interscience.wiley.com/journal/122665008/abstract?CRETRY=1&SRETRY=0

  8. A rapid MALDI-TOF MS identification database at genospecies level for clinical and environmental Aeromonas strains.

    Directory of Open Access Journals (Sweden)

    Cinzia Benagli

    Full Text Available The genus Aeromonas has undergone a number of taxonomic and nomenclature revisions over the past 20 years, and new (subspecies and biogroups are continuously described. Standard identification methods such as biochemical characterization have deficiencies and do not allow clarification of the taxonomic position. This report describes the development of a matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS identification database for a rapid identification of clinical and environmental Aeromonas isolates.

  9. The influence of culture conditions on the identification of Mycobacterium species by MALDI-TOF MS profiling.

    Science.gov (United States)

    Balážová, Tereza; Makovcová, Jitka; Šedo, Ondrej; Slaný, Michal; Faldyna, Martin; Zdráhal, Zbyněk

    2014-04-01

    Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) represents a simple reliable approach for rapid bacterial identification based on specific peptide/protein fingerprints. However, cell-wall characteristics of mycobacterial species, and their well known stability, complicate MALDI-TOF MS profiling analysis. In this study, we tested two recently published protocols for inactivation and disruption of mycobacteria, and we also examined the influence of different culture conditions (four culture media and five cultivation times) on mass spectral quality and the discriminatory power of the method. We found a significant influence of sample pretreatment method and culture medium on species identification and differentiation for a total of 10 strains belonging to Mycobacterium phlei and Mycobacterium smegmatis. Optimum culture conditions yielding the highest identification success rate against the BioTyper database (Bruker Daltonics) and permitting the possibility of automatic acquisition of mass spectra were found to be distinct for the two mycobacterial species examined. Similarly, individual changes in growth conditions had diverse effects on the two species. For these reasons, thorough control over cultivation conditions should always be employed to maximize the performance and discriminatory power of MALDI-TOF MS profiling, and cultivation conditions must be optimized separately for individual groups of mycobacterial species/strains. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  10. MALDI-TOF-MS with PLS Modeling Enables Strain Typing of the Bacterial Plant Pathogen Xanthomonas axonopodis

    Science.gov (United States)

    Sindt, Nathan M.; Robison, Faith; Brick, Mark A.; Schwartz, Howard F.; Heuberger, Adam L.; Prenni, Jessica E.

    2018-02-01

    Matrix-assisted desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) is a fast and effective tool for microbial species identification. However, current approaches are limited to species-level identification even when genetic differences are known. Here, we present a novel workflow that applies the statistical method of partial least squares discriminant analysis (PLS-DA) to MALDI-TOF-MS protein fingerprint data of Xanthomonas axonopodis, an important bacterial plant pathogen of fruit and vegetable crops. Mass spectra of 32 X. axonopodis strains were used to create a mass spectral library and PLS-DA was employed to model the closely related strains. A robust workflow was designed to optimize the PLS-DA model by assessing the model performance over a range of signal-to-noise ratios (s/n) and mass filter (MF) thresholds. The optimized parameters were observed to be s/n = 3 and MF = 0.7. The model correctly classified 83% of spectra withheld from the model as a test set. A new decision rule was developed, termed the rolled-up Maximum Decision Rule (ruMDR), and this method improved identification rates to 92%. These results demonstrate that MALDI-TOF-MS protein fingerprints of bacterial isolates can be utilized to enable identification at the strain level. Furthermore, the open-source framework of this workflow allows for broad implementation across various instrument platforms as well as integration with alternative modeling and classification algorithms.

  11. MALDI-TOF MS identification of anaerobic bacteria: assessment of pre-analytical variables and specimen preparation techniques.

    Science.gov (United States)

    Hsu, Yen-Michael S; Burnham, Carey-Ann D

    2014-06-01

    Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a tool for identifying clinically relevant anaerobes. We evaluated the analytical performance characteristics of the Bruker Microflex with Biotyper 3.0 software system for identification of anaerobes and examined the impact of direct formic acid (FA) treatment and other pre-analytical factors on MALDI-TOF MS performance. A collection of 101 anaerobic bacteria were evaluated, including Clostridium spp., Propionibacterium spp., Fusobacterium spp., Bacteroides spp., and other anaerobic bacterial of clinical relevance. The results of our study indicate that an on-target extraction with 100% FA improves the rate of accurate identification without introducing misidentification (Panaerobes grown in suboptimal conditions, such as on selective culture media and following oxygen exposure. In conclusion, we report on a number of simple and cost-effective pre- and post-analytical modifications could enhance MALDI-TOF MS identification for anaerobic bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Enterococcus genus identification isolated from gastrointestinal tract of chickens after bees products application using MALDI TOF MS Biotyper

    Directory of Open Access Journals (Sweden)

    Miroslava Kačániová

    2013-10-01

    Full Text Available The general objective of this study was to examine the effect of bee product on the Enterococci colonization of chickens. Bee products were administered to both feed mixtures in various amounts in addition to the control group. First experimental group was with propolis in feed mixture with the addition of 200 mg propolis per 1 kg of compound and second group was with pollen with the addition of 250 mg pollen per 1 kg of compound. In this experiment, quantitative counts of Enterococci in ceca of 49-day-old chicken (Ross 308 using classical and MALDI TOF MS Biotyper method were investigated. Counts of Enterococci on Slanetz-Bartley agar were monitored. Enterococcus cells, isolated from gastrointestinal tract, were detected using MALDI TOF MS Biotyper. Counts of CFU of Enterococci were compared in experimental and control treatments, respectively. The lowest count was detected in the control experimental group. The highest count was detected in the first experimental group where was 200 mg of propolis added to 1 kg of feed mixture. Using MALDI TOF MS Biotyper, we identified the species range of the genera Enterococcus in the intestinal tract of broiler. Detected species from the genus Enterococcus were:      E. avium, E. casseliflavus, E cecorum, E. faecalis, E. faecium, E. gallinarum, E. hirae and E. malodoratus. In the experimental groups (caecal samples were most frequent species of E. avium E. faecium and E. gallinarum.

  13. Comparison between MALDI-TOF MS and FilmArray Blood Culture Identification panel for rapid identification of yeast from positive blood culture.

    Science.gov (United States)

    Paolucci, M; Foschi, C; Tamburini, M V; Ambretti, S; Lazzarotto, T; Landini, M P

    2014-09-01

    In this study we evaluated MALDI-TOF MS and FilmArray methods for the rapid identification of yeast from positive blood cultures. FilmArray correctly identified 20/22 of yeast species, while MALDI-TOF MS identified 9/22. FilmArray is a reliable and rapid identification system for the direct identification of yeasts from positive blood cultures. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. A comparison of Api 20A vs MALDI-TOF MS for routine identification of clinically significant anaerobic bacterial strains to the species level.

    Science.gov (United States)

    Kierzkowska, Marta; Majewska, Anna; Kuthan, Robert T; Sawicka-Grzelak, Anna; Młynarczyk, Grażyna

    2013-02-15

    Adequate identification of anaerobic bacteria still presents a challenge for laboratories conducting microbiological diagnostics. The aim of this study was to compare the use of Api 20A and MALDI-TOF MS techniques for identification of obligate anaerobes. The results indicate that MALDI-TOF MS ensures a rapid and accurate identification of the species isolated from patients. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Optimization of analytical and pre-analytical conditions for MALDI-TOF-MS human urine protein profiles.

    Science.gov (United States)

    Calvano, C D; Aresta, A; Iacovone, M; De Benedetto, G E; Zambonin, C G; Battaglia, M; Ditonno, P; Rutigliano, M; Bettocchi, C

    2010-03-11

    Protein analysis in biological fluids, such as urine, by means of mass spectrometry (MS) still suffers for insufficient standardization in protocols for sample collection, storage and preparation. In this work, the influence of these variables on healthy donors human urine protein profiling performed by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was studied. A screening of various urine sample pre-treatment procedures and different sample deposition approaches on the MALDI target was performed. The influence of urine samples storage time and temperature on spectral profiles was evaluated by means of principal component analysis (PCA). The whole optimized procedure was eventually applied to the MALDI-TOF-MS analysis of human urine samples taken from prostate cancer patients. The best results in terms of detected ions number and abundance in the MS spectra were obtained by using home-made microcolumns packed with hydrophilic-lipophilic balance (HLB) resin as sample pre-treatment method; this procedure was also less expensive and suitable for high throughput analyses. Afterwards, the spin coating approach for sample deposition on the MALDI target plate was optimized, obtaining homogenous and reproducible spots. Then, PCA indicated that low storage temperatures of acidified and centrifuged samples, together with short handling time, allowed to obtain reproducible profiles without artifacts contribution due to experimental conditions. Finally, interesting differences were found by comparing the MALDI-TOF-MS protein profiles of pooled urine samples of healthy donors and prostate cancer patients. The results showed that analytical and pre-analytical variables are crucial for the success of urine analysis, to obtain meaningful and reproducible data, even if the intra-patient variability is very difficult to avoid. It has been proven how pooled urine samples can be an interesting way to make easier the comparison between

  16. Reducing time to identification of positive blood cultures with MALDI-TOF MS analysis after a 5-h subculture.

    Science.gov (United States)

    Verroken, A; Defourny, L; Lechgar, L; Magnette, A; Delmée, M; Glupczynski, Y

    2015-02-01

    Speeding up the turn-around time of positive blood culture identifications is essential in order to optimize the treatment of septic patients. Several sample preparation techniques have been developed allowing direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification of positive blood cultures. Yet, the hands-on time restrains their routine workflow. In this study, we evaluated an approach whereby MALDI-TOF MS identification without any additional steps was carried out on short subcultured colonies from positive blood bottles with the objective of allowing results reporting on the day of positivity detection. Over a 7-month period in 2012, positive blood cultures detected by 9 am with an automated system were inoculated onto a Columbia blood agar and processed after a 5-h incubation on a MALDI-TOF MicroFlex platform (Bruker Daltonik GmbH). Single-spotted colonies were covered with 1 μl formic acid and 1 μl matrix solution. The results were compared to the validated identification techniques. A total of 925 positive blood culture bottles (representing 470 bacteremic episodes) were included. Concordant identification was obtained in 727 (81.1 %) of the 896 monomicrobial blood cultures, with failure being mostly observed with anaerobes and yeasts. In 17 episodes of polymicrobic bacteremia, the identification of one of the two isolates was achieved in 24/29 (82.7 %) positive cultures. Routine implementation of MALDI-TOF MS identification on young positive blood subcultures provides correct results to the clinician in more than 80 % of the bacteremic episodes and allows access to identification results on the day of blood culture positivity detection, potentially accelerating the implementation of targeted clinical treatments.

  17. MALDI-TOF MS contribution to the diagnosis of Campylobacter rectus multiple skull base and brain abscesses

    Directory of Open Access Journals (Sweden)

    D. Martiny

    2017-09-01

    Full Text Available Campylobacter rectus is rarely associated with invasive infection. Both the isolation and the identification requirements of C. rectus are fastidious, probably contributing to an underestimation of its burden. We report the case of a 66-year-old man who developed several skull base and intracerebral abscesses after dental intervention. Campylobacter rectus was isolated from the brain biopsy. Within 45 minutes of reading the bacterial plate, the strain was accurately identified by MALDI-TOF MS. This rapid identification avoided the extra costs and delays present with 16S rRNA gene sequencing and allowed for a rapid confirmation of the adequacy of the empirical antibiotic treatment.

  18. The optimization and validation of the Biotyper MALDI-TOF MS database for the identification of Gram-positive anaerobic cocci

    DEFF Research Database (Denmark)

    Veloo, A C M; de Vries, E D; Jean-Pierre, H

    2016-01-01

    Gram-positive anaerobic cocci (GPAC) account for 24%-31% of the anaerobic bacteria isolated from human clinical specimens. At present, GPAC are under-represented in the Biotyper MALDI-TOF MS database. Profiles of new species have yet to be added. We present the optimization of the matrix-assisted......Gram-positive anaerobic cocci (GPAC) account for 24%-31% of the anaerobic bacteria isolated from human clinical specimens. At present, GPAC are under-represented in the Biotyper MALDI-TOF MS database. Profiles of new species have yet to be added. We present the optimization of the matrix......-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) database for the identification of GPAC. Main spectral profiles (MSPs) were created for 108 clinical GPAC isolates. Identity was confirmed using 16S rRNA gene sequencing. Species identification was considered to be reliable...... if the sequence similarity with its closest relative was ≥98.7%. The optimized database was validated using 140 clinical isolates. The 16S rRNA sequencing identity was compared with the MALDI-TOF MS result. MSPs were added from 17 species that were not yet represented in the MALDI-TOF MS database or were under...

  19. Direct identification of microorganisms from positive blood cultures by MALDI-TOF MS using an in-house saponin method.

    Science.gov (United States)

    Yonetani, Shota; Ohnishi, Hiroaki; Ohkusu, Kiyofumi; Matsumoto, Tetsuya; Watanabe, Takashi

    2016-11-01

    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast and reliable method for the identification of bacteria. A MALDI Sepsityper kit is generally used to prepare samples obtained directly from culture bottles. However, the relatively high cost of this kit is a major obstacle to introducing this method into routine clinical use. In this study, the accuracies of three different preparation methods for rapid direct identification of bacteria from positive blood culture bottles by MALDI-TOF MS analysis were compared. In total, 195 positive bottles were included in this study. Overall, 78.5%, 68.7%, and 76.4% of bacteria were correctly identified to the genus level (score ≥1.7) directly from positive blood cultures using the Sepsityper, centrifugation, and saponin methods, respectively. The identification rates using the Sepsityper and saponin methods were significantly higher than that using the centrifugation method (Sepsityper vs. centrifugation, pdirectly from blood culture bottles, and could be a less expensive alternative to the Sepsityper method. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  20. Comparative analysis of storage conditions and homogenization methods for tick and flea species for identification by MALDI-TOF MS.

    Science.gov (United States)

    Nebbak, A; El Hamzaoui, B; Berenger, J-M; Bitam, I; Raoult, D; Almeras, L; Parola, P

    2017-12-01

    Ticks and fleas are vectors for numerous human and animal pathogens. Controlling them, which is important in combating such diseases, requires accurate identification, to distinguish between vector and non-vector species. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was applied to the rapid identification of arthropods. The growth of this promising tool, however, requires guidelines to be established. To this end, standardization protocols were applied to species of Rhipicephalus sanguineus (Ixodida: Ixodidae) Latreille and Ctenocephalides felis felis (Siphonaptera: Pulicidae) Bouché, including the automation of sample homogenization using two homogenizer devices, and varied sample preservation modes for a period of 1-6 months. The MS spectra were then compared with those obtained from manual pestle grinding, the standard homogenization method. Both automated methods generated intense, reproducible MS spectra from fresh specimens. Frozen storage methods appeared to represent the best preservation mode, for up to 6 months, while storage in ethanol is also possible, with some caveats for tick specimens. Carnoy's buffer, however, was shown to be less compatible with MS analysis for the purpose of identifying ticks or fleas. These standard protocols for MALDI-TOF MS arthropod identification should be complemented by additional MS spectrum quality controls, to generalize their use in monitoring arthropods of medical interest. © 2017 The Royal Entomological Society.

  1. Evaluation of MALDI-TOF MS (Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry) for routine identification of anaerobic bacteria.

    Science.gov (United States)

    Rodríguez-Sánchez, Belén; Alcalá, Luis; Marín, Mercedes; Ruiz, Adrián; Alonso, Elena; Bouza, Emilio

    2016-12-01

    Information regarding the use of MALDI-TOF MS as an alternative to conventional laboratory methods for the rapid and reliable identification of bacterial isolates is still limited. In this study, MALDI-TOF MS was evaluated on 295 anaerobic isolates previously identified by 16S rRNA gene sequencing and with biochemical tests (Rapid ID 32A system, BioMérieux). In total, 85.8% of the isolates were identified by MALDI-TOF MS at the species level vs 49.8% using the Rapid ID 32A system (p anaerobic isolates in the microbiology laboratory. Its implementation will reduce the turnaround time for a final identification and the number of isolates that require 16S rRNA sequencing. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS

    Science.gov (United States)

    Ling, Ling; Li, Ying; Wang, Sheng; Guo, Liming; Xiao, Chunsheng; Chen, Xuesi; Guo, Xinhua

    2018-01-01

    Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. [Figure not available: see fulltext.

  3. MALDI-TOF MS typing enables the classification of brewing yeasts of the genus Saccharomyces to major beer styles.

    Science.gov (United States)

    Lauterbach, Alexander; Usbeck, Julia C; Behr, Jürgen; Vogel, Rudi F

    2017-01-01

    Brewing yeasts of the genus Saccharomyces are either available from yeast distributor centers or from breweries employing their own "in-house strains". During the last years, the classification and characterization of yeasts of the genus Saccharomyces was achieved by using biochemical and DNA-based methods. The current lack of fast, cost-effective and simple methods to classify brewing yeasts to a beer type, may be closed by Matrix Assisted Laser Desorption/Ionization-Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) upon establishment of a database based on sub-proteome spectra from reference strains of brewing yeasts. In this study an extendable "brewing yeast" spectra database was established including 52 brewing yeast strains of the most important types of bottom- and top-fermenting strains as well as beer-spoiling S. cerevisiae var. diastaticus strains. 1560 single spectra, prepared with a standardized sample preparation method, were finally compared against the established database and investigated by bioinformatic analyses for similarities and distinctions. A 100% separation between bottom-, top-fermenting and S. cerevisiae var. diastaticus strains was achieved. Differentiation between Alt and Kölsch strains was not achieved because of the high similarity of their protein patterns. Whereas the Ale strains show a high degree of dissimilarity with regard to their sub-proteome. These results were supported by MDS and DAPC analysis of all recorded spectra. Within five clusters of beer types that were distinguished, and the wheat beer (WB) cluster has a clear separation from other groups. With the establishment of this MALDI-TOF MS spectra database proof of concept is provided of the discriminatory power of this technique to classify brewing yeasts into different major beer types in a rapid, easy way, and focus brewing trails accordingly. It can be extended to yeasts for specialty beer types and other applications including wine making or baking.

  4. The construction and evaluation of reference spectra for the identification of human pathogenic microorganisms by MALDI-TOF MS.

    Directory of Open Access Journals (Sweden)

    Di Xiao

    Full Text Available Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS is an emerging technique for the rapid and high-throughput identification of microorganisms. There remains a dearth of studies in which a large number of pathogenic microorganisms from a particular country or region are utilized for systematic analyses. In this study, peptide mass reference spectra (PMRS were constructed and evaluated from numerous human pathogens (a total of 1019 strains from 94 species, including enteric (46 species, respiratory (21 species, zoonotic (17 species, and nosocomial pathogens (10 species, using a MALDI-TOF MS Biotyper system (MBS. The PMRS for 380 strains of 52 species were new contributions to the original reference database (ORD. Compared with the ORD, the new reference database (NRD allowed for 28.2% (from 71.5% to 99.7% and 42.3% (from 51.3% to 93.6% improvements in identification at the genus and species levels, respectively. Misidentification rates were 91.7% and 57.1% lower with the NRD than with the ORD for genus and species identification, respectively. Eight genera and 25 species were misidentified. For genera and species that are challenging to accurately identify, identification results must be manually determined and adjusted in accordance with the database parameters. Through augmentation, the MBS demonstrated a high identification accuracy and specificity for human pathogenic microorganisms. This study sought to provide theoretical guidance for using PMRS databases in various fields, such as clinical diagnosis and treatment, disease control, quality assurance, and food safety inspection.

  5. MALDI-TOF MS typing enables the classification of brewing yeasts of the genus Saccharomyces to major beer styles

    Science.gov (United States)

    Lauterbach, Alexander; Usbeck, Julia C.; Behr, Jürgen

    2017-01-01

    Brewing yeasts of the genus Saccharomyces are either available from yeast distributor centers or from breweries employing their own “in-house strains”. During the last years, the classification and characterization of yeasts of the genus Saccharomyces was achieved by using biochemical and DNA-based methods. The current lack of fast, cost-effective and simple methods to classify brewing yeasts to a beer type, may be closed by Matrix Assisted Laser Desorption/Ionization–Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) upon establishment of a database based on sub-proteome spectra from reference strains of brewing yeasts. In this study an extendable “brewing yeast” spectra database was established including 52 brewing yeast strains of the most important types of bottom- and top-fermenting strains as well as beer-spoiling S. cerevisiae var. diastaticus strains. 1560 single spectra, prepared with a standardized sample preparation method, were finally compared against the established database and investigated by bioinformatic analyses for similarities and distinctions. A 100% separation between bottom-, top-fermenting and S. cerevisiae var. diastaticus strains was achieved. Differentiation between Alt and Kölsch strains was not achieved because of the high similarity of their protein patterns. Whereas the Ale strains show a high degree of dissimilarity with regard to their sub-proteome. These results were supported by MDS and DAPC analysis of all recorded spectra. Within five clusters of beer types that were distinguished, and the wheat beer (WB) cluster has a clear separation from other groups. With the establishment of this MALDI-TOF MS spectra database proof of concept is provided of the discriminatory power of this technique to classify brewing yeasts into different major beer types in a rapid, easy way, and focus brewing trails accordingly. It can be extended to yeasts for specialty beer types and other applications including wine making or baking. PMID

  6. MALDI-TOF MS typing enables the classification of brewing yeasts of the genus Saccharomyces to major beer styles.

    Directory of Open Access Journals (Sweden)

    Alexander Lauterbach

    Full Text Available Brewing yeasts of the genus Saccharomyces are either available from yeast distributor centers or from breweries employing their own "in-house strains". During the last years, the classification and characterization of yeasts of the genus Saccharomyces was achieved by using biochemical and DNA-based methods. The current lack of fast, cost-effective and simple methods to classify brewing yeasts to a beer type, may be closed by Matrix Assisted Laser Desorption/Ionization-Time-Of-Flight Mass Spectrometry (MALDI-TOF MS upon establishment of a database based on sub-proteome spectra from reference strains of brewing yeasts. In this study an extendable "brewing yeast" spectra database was established including 52 brewing yeast strains of the most important types of bottom- and top-fermenting strains as well as beer-spoiling S. cerevisiae var. diastaticus strains. 1560 single spectra, prepared with a standardized sample preparation method, were finally compared against the established database and investigated by bioinformatic analyses for similarities and distinctions. A 100% separation between bottom-, top-fermenting and S. cerevisiae var. diastaticus strains was achieved. Differentiation between Alt and Kölsch strains was not achieved because of the high similarity of their protein patterns. Whereas the Ale strains show a high degree of dissimilarity with regard to their sub-proteome. These results were supported by MDS and DAPC analysis of all recorded spectra. Within five clusters of beer types that were distinguished, and the wheat beer (WB cluster has a clear separation from other groups. With the establishment of this MALDI-TOF MS spectra database proof of concept is provided of the discriminatory power of this technique to classify brewing yeasts into different major beer types in a rapid, easy way, and focus brewing trails accordingly. It can be extended to yeasts for specialty beer types and other applications including wine making or baking.

  7. Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification.

    Science.gov (United States)

    Nakamura, Sayaka; Sato, Hiroaki; Tanaka, Reiko; Yaguchi, Takashi

    2016-01-01

    We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus .

  8. Analysis of Phospholipid Mixtures from Biological Tissues by Matrix-Assisted Laser Desorption and Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS): A Laboratory Experiment

    Science.gov (United States)

    Eibisch, Mandy; Fuchs, Beate; Schiller, Jurgen; Sub, Rosmarie; Teuber, Kristin

    2011-01-01

    Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used to investigate the phospholipid (PL) compositions of tissues and body fluids, often without previous separation of the total mixture into the individual PL classes. Therefore, the questions of whether all PL classes are detectable…

  9. Epidemiology of candidemia in Qatar, the Middle East : Performance of MALDI-TOF MS for the identification of Candida species, species distribution, outcome, and susceptibility pattern

    NARCIS (Netherlands)

    Taj-Aldeen, S. J.; Kolecka, A.; Boesten, R.; Alolaqi, A.; Almaslamani, M.; Chandra, P.; Meis, J. F.; Boekhout, T.

    Introduction Bloodstream infections (BSIs) due to Candida spp. constitute the predominant group of hospital-based fungal infections worldwide. A retrospective study evaluated the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the

  10. MALDI-TOF MS and CE-LIF Fingerprinting of Plant Cell Wall Polysaccharide Digests as a Screening Tool for Arabidopsis Cell Wall Mutants

    NARCIS (Netherlands)

    Westphal, Y.; Schols, H.A.; Voragen, A.G.J.; Gruppen, H.

    2010-01-01

    Cell wall materials derived from leaves and hypocotyls of Arabidopsis mutant and wild type plants have been incubated with a mixture of pure and well-defined pectinases, hemicellulases, and cellulases. The resulting oligosaccharides have been subjected to MALDI-TOF MS and CE-LIF analysis. MALDI-TOF

  11. Unusual analyte-matrix adduct ions and mechanism of their formation in MALDI TOF MS of benzene-1,3,5-tricarboxamide and urea compounds

    NARCIS (Netherlands)

    Lou, X.; Fransen, M.; Stals, P.J.M.; Mes, T.; Bovee, R.; Dongen, van J.L.J.; Meijer, E.W.

    2013-01-01

    Analyte-matrix adducts are normally absent under typical matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) conditions. Interestingly, though, in the analysis of several types of organic compounds synthesized in our laboratory, analyte-matrix adduct ion peaks

  12. The optimization and validation of the Biotyper MALDI-TOF MS database for the identification of Gram-positive anaerobic cocci

    NARCIS (Netherlands)

    Veloo, A. C. M.; de Vries, E D; Jean-Pierre, H.; Justesen, U. S.; Morris, T.; Urban, E.; Wybo, I.; van Winkelhoff, A. J.

    OBJECTIVES: Gram-positive anaerobic cocci (GPAC) account for 24-31% of the anaerobic bacteria isolated from human clinical specimens. At present GPAC are underrepresented in the Biotyper MALDI-TOF MS database. Profiles of new species have yet to be added. We present the optimization of the MALDI-TOF

  13. Differentiation of Clinically Relevant mucorales Rhizopus microsporus and R. arrhizus by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS)

    NARCIS (Netherlands)

    Dolatabadi, S.; Kolecka, A.; Versteeg, Matthijs; de Hoog, Sybren G; Boekhout, Teun

    This study addresses the usefulness of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) for reliable identification of the two most frequently occuring clinical species of Rhizopus, namely R. arrhizus with its two varieties arrhizus and delemar and R.

  14. Polyphasic Approach Including MALDI-TOF MS/MS Analysis for Identification and Characterisation of Fusarium verticillioides in Brazilian Corn Kernels

    Directory of Open Access Journals (Sweden)

    Susane Chang

    2016-02-01

    Full Text Available Fusarium verticillioides is considered one of the most important global sources of fumonisins contamination in food and feed. Corn is one of the main commodities produced in the Northeastern Region of Brazil. The present study investigated potential mycotoxigenic fungal strains belonging to the F. verticillioides species isolated from corn kernels in 3 different Regions of the Brazilian State of Pernambuco. A polyphasic approach including classical taxonomy, molecular biology, MALDI-TOF MS and MALDI-TOF MS/MS for the identification and characterisation of the F. verticillioides strains was used. Sixty F. verticillioides strains were isolated and successfully identified by classical morphology, proteomic profiles of MALDI-TOF MS, and by molecular biology using the species-specific primers VERT-1 and VERT-2. FUM1 gene was further detected for all the 60 F. verticillioides by using the primers VERTF-1 and VERTF-2 and through the amplification profiles of the ISSR regions using the primers (GTG5 and (GACA4. Results obtained from molecular analysis shown a low genetic variability among these isolates from the different geographical regions. All of the 60 F. verticillioides isolates assessed by MALDI-TOF MS/MS presented ion peaks with the molecular mass of the fumonisin B1 (721.83 g/mol and B2 (705.83 g/mol.

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

    Science.gov (United States)

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

    2014-10-01

    Fungaemia diagnosis could be improved by reducing the time to identification of yeast from blood cultures. This study aimed to evaluate three rapid methods for the identification of yeast direct from blood cultures; Gram's stain analysis, the AdvanDX Peptide Nucleic Acid in Situ Hybridisation Yeast Traffic Light system (PNA-FISH YTL) and Bruker Sepsityper alongside matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-TOF MS). Fifty blood cultures spiked with a known single yeast strain were analysed by blinded operators experienced in each method. Identifications were compared with MALDI-TOF MS CHROMagar Candida culture and ITS rRNA sequence-based identifications. On first attempt, success rates of 96% (48/50) and 76% (36/50) were achieved using PNA-FISH YTL and Gram's stain respectively. MALDI-TOF MS demonstrated a success rate of 56% (28/50) when applying manufacturer's species log score thresholds and 76% (38/50) using in-house parameters, including lowering the species log score threshold to >1.5. In conclusion, PNA-FISH YTL demonstrated a high success rate successfully identifying yeast commonly encountered in fungaemia. Sepsityper(™) with MALDI-TOF MS was accurate but increased sensitivity is required. Due to the misidentification of commonly encountered yeast Gram's stain analysis demonstrated limited utility in this setting. © 2014 Blackwell Verlag GmbH.

  16. The influence of incubation time, sample preparation and exposure to oxygen on the quality of the MALDI-TOF MS spectrum of anaerobic bacteria

    NARCIS (Netherlands)

    Veloo, A. C. M.; Elgersma, P. E.; Friedrich, A. W.; Nagy, E.; van Winkelhoff, A. J.

    2014-01-01

    With matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), bacteria can be identified quickly and reliably. This accounts especially for anaerobic bacteria. Because growth rate and oxygen sensitivity differ among anaerobic bacteria, we aimed to study the

  17. Shortcomings of of the commercial MALDI-TOF MS database and use of MLSA as an arbiter in the identification of Nocardia species

    Directory of Open Access Journals (Sweden)

    Gema eCarrasco

    2016-04-01

    Full Text Available Nocardia species are difficult to identify, a consequence of the ever increasing number of species known and their homogeneous genetic characteristics. 16S rRNA analysis has been the gold standard for identifying these organisms, but proteomic techniques such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF MS and housekeeping gene analysis, have also been explored. One hundred high (n=25, intermediate (n=20 and low (n=55 prevalence (for Spain Nocardia strains belonging to 30 species were identified via 16S rRNA and MALDI-TOF MS analysis. The manufacturer-provided database MALDI Biotyper library v4.0 (5.627 entries, Bruker Daltonik was employed. In the high prevalence group (N. farcinica, N. abscessus, N. cyriacigeorgica and N. nova, the 16S rRNA and MALDI-TOF MS methods provided the same identification for 76% of the strains examined. For the intermediate prevalence group (N. brasiliensis, N. carnea, N. otitidiscaviarum and N. transvalensis complex, this figure fell to 45%. In the low-prevalence group (22 species, these two methods were concordant only in six strains at the species level. Tetra-gene multi-locus sequencing analysis (MLSA involving the concatemer gyrB-16S rRNA-hsp65-secA1 was used to arbitrate between discrepant identifications (n=67. Overall, the MLSA confirmed the results provided at species level by 16S rRNA analysis in 34.3% of discrepancies, and those provided by MALDI-TOF MS in 13.4%. MALDI-TOF MS could be a strong candidate for the identification of Nocardia species, but only if its reference spectrum database improves, especially with respect to unusual, recently described species and species included in the described Nocardia complexes.

  18. Shortcomings of the Commercial MALDI-TOF MS Database and Use of MLSA as an Arbiter in the Identification of Nocardia Species

    Science.gov (United States)

    Carrasco, Gema; de Dios Caballero, Juan; Garrido, Noelia; Valdezate, Sylvia; Cantón, Rafael; Sáez-Nieto, Juan A.

    2016-01-01

    Nocardia species are difficult to identify, a consequence of the ever increasing number of species known and their homogeneous genetic characteristics. 16S rRNA analysis has been the gold standard for identifying these organisms, but proteomic techniques such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF MS) and housekeeping gene analysis, have also been explored. One hundred high (n = 25), intermediate (n = 20), and low (n = 55) prevalence (for Spain) Nocardia strains belonging to 30 species were identified via 16S rRNA and MALDI-TOF MS analysis. The manufacturer-provided database MALDI Biotyper library v4.0 (5.627 entries, Bruker Daltonik) was employed. In the high prevalence group (Nocardia farcinica, N. abscessus, N. cyriacigeorgica and N. nova), the 16S rRNA and MALDI-TOF MS methods provided the same identification for 76% of the strains examined. For the intermediate prevalence group (N. brasiliensis, N. carnea, N. otitidiscaviarum and N. transvalensis complex), this figure fell to 45%. In the low-prevalence group (22 species), these two methods were concordant only in six strains at the species level. Tetra-gene multi-locus sequencing analysis (MLSA) involving the concatemer gyrB-16S rRNA-hsp65-secA1 was used to arbitrate between discrepant identifications (n = 67). Overall, the MLSA confirmed the results provided at species level by 16S rRNA analysis in 34.3% of discrepancies, and those provided by MALDI-TOF MS in 13.4%. MALDI-TOF MS could be a strong candidate for the identification of Nocardia species, but only if its reference spectrum database improves, especially with respect to unusual, recently described species and species included in the described Nocardia complexes. PMID:27148228

  19. Multicenter evaluation of the Sepsityper™ extraction kit and MALDI-TOF MS for direct identification of positive blood culture isolates using the BD BACTEC™ FX and VersaTREK(®) diagnostic blood culture systems.

    Science.gov (United States)

    Schieffer, K M; Tan, K E; Stamper, P D; Somogyi, A; Andrea, S B; Wakefield, T; Romagnoli, M; Chapin, K C; Wolk, D M; Carroll, K C

    2014-04-01

    (i) Evaluation of delayed time to blood culture extraction by the Sepsityper kit and impact of shipping pellets off-site for MALDI-TOF MS analysis. (ii) Comparison of Sepsityper and laboratory-developed extraction methods from a literature review. Using two blood culture systems (BD BACTEC and VersaTREK), we extracted 411 positive blood cultures using the Sepsityper kit to mimic a potential protocol for institutions without a MALDI-TOF MS. Extracted pellets were shipped and analysed on the Bruker UltraflexIII. Successful extraction of 358 (87·1%) samples was determined by the presence of detectable proteins. MALDI-TOF MS correctly identified 332 (80·8%) samples. Delayed time to extraction did not affect Sepsityper extraction or MALDI-TOF MS accuracy. The extracted pellets remain stable and provide accurate results by MALDI-TOF MS when shipped at room temperature to off-site reference laboratories. This is the first study to show that institutions without a MALDI-TOF MS can take advantage of this innovative technology by shipping a volume of blood to an off-site laboratory for extraction and MALDI-TOF MS analysis. We also performed a literature review to compare various extraction methods. © 2014 The Society for Applied Microbiology.

  20. Identification of protein markers for the occurrence of defrosted material in milk through a MALDI-TOF-MS profiling approach.

    Science.gov (United States)

    Arena, Simona; Salzano, Anna Maria; Scaloni, Andrea

    2016-09-16

    Mozzarella di Bufala Campana is a soft, stretched curd Italian cheese made from fresh buffalo milk that obtained the Protected Designation of Origin (PDO) registration in EU legislation. Seasonality of buffalo milk production, rapid cheese decay and transport of its preserving liquid have relevant practical/economic consequences for mozzarella production; consequently, a progressive diffusion of cheese products realized with frozen curd or frozen milk has recently been observed. In order to meet the demand of the dairy producers and consumers for a reduction of starting material adulterations and for the certification of the raw milk used for cheese manufacturing, we have developed a rapid/robust MALDI-TOF-MS polypeptide profiling procedure that assays material quality through the identification of specific markers of its freshness. Massive analysis of fresh and frozen buffalo milks (stored for different times) was realized to this purpose; a tough statistical evaluation of the resulting data ultimately permitted the typing of milk samples. We identified 28 polypeptide markers of the milk freezing storage, among which 13 and 15 showed down- and over-representation, respectively. Quantitative data were confirmed by an independent analytical approach on selected markers. GLYCAM1-derived phosphopeptides (1-53), β-casein-derived phosphopeptides (1-68), β-casein-derived γ2-, γ3- and γ4-fragments, α-lactalbumin and β-lactoglobulin were components showing the highest significance. The occurrence of the first compounds in buffalo milk is here described for the first time; their formation in the frozen material was ascribed to the activity of plasmin or of unknown bacterial proteases/peptidases stable at low temperatures. In conclusion, data reported here suggest the application of this MALDI-TOF-MS polypeptide profiling platform to other high-quality dairy productions, in which milk freshness has important consequences on final product organoleptic properties. In

  1. Identification of clinical isolates of Aspergillus, including cryptic species, by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Vidal-Acuña, M Reyes; Ruiz-Pérez de Pipaón, Maite; Torres-Sánchez, María José; Aznar, Javier

    2017-12-08

    An expanded library of matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been constructed using the spectra generated from 42 clinical isolates and 11 reference strains, including 23 different species from 8 sections (16 cryptic plus 7 noncryptic species). Out of a total of 379 strains of Aspergillus isolated from clinical samples, 179 strains were selected to be identified by sequencing of beta-tubulin or calmodulin genes. Protein spectra of 53 strains, cultured in liquid medium, were used to construct an in-house reference database in the MALDI-TOF MS. One hundred ninety strains (179 clinical isolates previously identified by sequencing and the 11 reference strains), cultured on solid medium, were blindy analyzed by the MALDI-TOF MS technology to validate the generated in-house reference database. A 100% correlation was obtained with both identification methods, gene sequencing and MALDI-TOF MS, and no discordant identification was obtained. The HUVR database provided species level (score of ≥2.0) identification in 165 isolates (86.84%) and for the remaining 25 (13.16%) a genus level identification (score between 1.7 and 2.0) was obtained. The routine MALDI-TOF MS analysis with the new database, was then challenged with 200 Aspergillus clinical isolates grown on solid medium in a prospective evaluation. A species identification was obtained in 191 strains (95.5%), and only nine strains (4.5%) could not be identified at the species level. Among the 200 strains, A. tubingensis was the only cryptic species identified. We demonstrated the feasibility and usefulness of the new HUVR database in MALDI-TOF MS by the use of a standardized procedure for the identification of Aspergillus clinical isolates, including cryptic species, grown either on solid or liquid media. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For

  2. Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates

    Directory of Open Access Journals (Sweden)

    Michal Strejcek

    2018-06-01

    Full Text Available Many ecological experiments are based on the extraction and downstream analyses of microorganisms from different environmental samples. Due to its high throughput, cost-effectiveness and rapid performance, Matrix Assisted Laser Desorption/Ionization Mass Spectrometry with Time-of-Flight detector (MALDI-TOF MS, which has been proposed as a promising tool for bacterial identification and classification, could be advantageously used for dereplication of recurrent bacterial isolates. In this study, we compared whole-cell MALDI-TOF MS-based analyses of 49 bacterial cultures to two well-established bacterial identification and classification methods based on nearly complete 16S rRNA gene sequence analyses: a phylotype-based approach, using a closest type strain assignment, and a sequence similarity-based approach involving a 98.65% sequence similarity threshold, which has been found to best delineate bacterial species. Culture classification using reference-based MALDI-TOF MS was comparable to that yielded by phylotype assignment up to the genus level. At the species level, agreement between 16S rRNA gene analysis and MALDI-TOF MS was found to be limited, potentially indicating that spectral reference databases need to be improved. We also evaluated the mass spectral similarity technique for species-level delineation which can be used independently of reference databases. We established optimal mass spectral similarity thresholds which group MALDI-TOF mass spectra of common environmental isolates analogically to phylotype- and sequence similarity-based approaches. When using a mass spectrum similarity approach, we recommend a mass range of 4–10 kDa for analysis, which is populated with stable mass signals and contains the majority of phylotype-determining peaks. We show that a cosine similarity (CS threshold of 0.79 differentiate mass spectra analogously to 98.65% species-level delineation sequence similarity threshold, with corresponding precision

  3. Improvement of MALDI-TOF MS profiling for the differentiation of species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex.

    Science.gov (United States)

    Šedo, Ondrej; Nemec, Alexandr; Křížová, Lenka; Kačalová, Magdaléna; Zdráhal, Zbyněk

    2013-12-01

    MALDI-TOF MS is currently becoming the method of choice for rapid identification of bacterial species in routine diagnostics. Yet, this method suffers from the inability to differentiate reliably between some closely related bacterial species including those of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, namely A. baumannii and Acinetobacter nosocomialis. In the present study, we evaluated a protocol which was different from that used in the Bruker Daltonics identification system (MALDI BioTyper) to improve species identification using a taxonomically precisely defined set of 105 strains representing the four validly named species of the ACB complex. The novel protocol is based on the change in matrix composition from alpha-cyano-4-hydroxycinnamic acid (saturated solution in water:acetonitrile:trifluoroacetic acid, 47.5:50:2.5, v/v) to ferulic acid (12.5mgml(-1) solution in water:acetonitrile:formic acid 50:33:17, v/v), while the other steps of sample processing remain unchanged. Compared to the standard protocol, the novel one extended the range of detected compounds towards higher molecular weight, produced signals with better mass resolution, and allowed the detection of species-specific signals. As a result, differentiation of A. nosocomialis and A. baumannii strains by cluster analysis was improved and 13 A. nosocomialis strains, assigned erroneously or ambiguously by using the standard protocol, were correctly identified. Copyright © 2013 Elsevier GmbH. All rights reserved.

  4. Coupling Sodium Dodecyl Sulfate–Capillary Polyacrylamide Gel Electrophoresis with MALDI-TOF-MS via a PTFE Membrane

    Science.gov (United States)

    Lu, Joann J.; Zhu, Zaifang; Wang, Wei; Liu, Shaorong

    2011-01-01

    Sodium dodecyl sulfate (SDS)–polyacrylamide gel electrophoresis (PAGE) is a fundamental analytical technique for proteomic research, and SDS–capillary gel electrophoresis (CGE) is its miniaturized version. Compared to conventional slab-gel electrophoresis, SDS-CGE has many advantages such as increased separation efficiency, reduced separation time and automated operation. SDS-CGE is not widely accepted in proteomic research primarily due to the difficulties in identifying the well-resolved proteins. MALDI–TOF–MS is an outstanding platform for protein identifications. Coupling the two would solve the problem but is extremely challenging because the MS detector has no access to the SDS-CGE resolved proteins and the SDS interferes with MS detection. In this work we introduce an approach to address these issues. We discover that poly(tetrafluoroethylene) (PTFE) membranes are excellent materials for collecting SDS-CGE separated proteins. We demonstrate that we can wash off the SDS bound to the collected proteins and identify these proteins on-membrane with MALDI-TOF-MS. We also show that we can immunoblot and Coomassie-stain the proteins collected on these membranes. PMID:21309548

  5. Development and validation of an extended database for yeast identification by MALDI-TOF MS in Argentina.

    Science.gov (United States)

    Taverna, Constanza Giselle; Mazza, Mariana; Bueno, Nadia Soledad; Alvarez, Christian; Amigot, Susana; Andreani, Mariana; Azula, Natalia; Barrios, Rubén; Fernández, Norma; Fox, Barbara; Guelfand, Liliana; Maldonado, Ivana; Murisengo, Omar Alejandro; Relloso, Silvia; Vivot, Matias; Davel, Graciela

    2018-05-11

    Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microorganisms in clinical laboratories because it is rapid, relatively simple to use, accurate, and can be used for a wide number of microorganisms. Several studies have demonstrated the utility of this technique in the identification of yeasts; however, its performance is usually improved by the extension of the database. Here we developed an in-house database of 143 strains belonging to 42 yeast species in the MALDI Biotyper platform, and we validated the extended database with 388 regional strains and 15 reference strains belonging to 55 yeast species. We also performed an intra- and interlaboratory study to assess reproducibility and analyzed the use of the cutoff values of 1.700 and 2.000 to correctly identify at species level. The creation of an in-house database that extended the manufacturer's database was successful in view of no incorrect identification was introduced. The best performance was observed by using the extended database and a cutoff value of 1.700 with a sensitivity of .94 and specificity of .96. A reproducibility study showed utility to detect deviations and could be used for external quality control. The extended database was able to differentiate closely related species and it has potential in distinguishing the molecular genotypes of Cryptococcus neoformans and Cryptococcus gattii.

  6. NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors

    KAUST Repository

    Gonzalez-Gil, Graciela

    2015-09-22

    Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical fingerprint of the polysaccharide fraction of EPS in anaerobic granules obtained from full-scale reactors treating different types of wastewater. Nuclear magnetic resonance (NMR) signals of the polysaccharide region from the granules were very complex, likely as a result of the diverse microbial population in the granules. Using nonmetric multidimensional scaling (NMDS), the 1H NMR signals of reference polysaccharides (gellan, xanthan, alginate) and those of the anaerobic granules revealed that there were similarities between the polysaccharides extracted from granules and the reference polysaccharide alginate. Further analysis of the exopolysaccharides from anaerobic granules, and reference polysaccharides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that exopolysaccharides from two of the anaerobic granular sludges studied exhibited spectra similar to that of alginate. The presence of sequences related to the synthesis of alginate was confirmed in the metagenomes of the granules. Collectively these results suggest that alginate-like exopolysaccharides are constituents of the EPS matrix in anaerobic granular sludge treating different industrial wastewater. This finding expands the engineered environments where alginate has been found as EPS constituent of microbial aggregates.

  7. MALDI-TOF MS Versus VITEK®2: Comparison of Systems for the Identification of Microorganisms Responsible for Bacteremia.

    Science.gov (United States)

    Febbraro, Filomena; Rodio, Donatella Maria; Puggioni, Gianluca; Antonelli, Guido; Pietropaolo, Valeria; Trancassini, Maria

    2016-12-01

    We evaluated the reliability and accuracy of the combined use of MALDI-TOF MS and classical ID VITEK 2 to identify monomicrobial infection in blood culture bottles. In total, 70 consecutive positive blood cultures were included in this study. Positive blood culture bottles were subjected to Gram staining and subcultured on solid media. Isolates grown from such culture media were used for classical ID using VITEK 2 system. In parallel, an aliquot was subjected to a lysing-centrifugation method and used for the identification with the MALDI-TOF system. Results evidenced the correct genus and species identification of 91.4 % of microorganisms responsible for bacteremia with an agreement to the species and the genus level. If compared with the standard method VITEK 2 , our simple and cost-effective sample preparation method would be very useful for rapid identification of microorganisms using blood culture bottles. In fact, the direct method showed rapid and reliable results, especially for the gram-negative group.

  8. NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors

    KAUST Repository

    Gonzalez-Gil, Graciela; Thomas, Ludivine; Emwas, Abdul-Hamid M.; Lens, Piet N. L.; Saikaly, Pascal

    2015-01-01

    Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical fingerprint of the polysaccharide fraction of EPS in anaerobic granules obtained from full-scale reactors treating different types of wastewater. Nuclear magnetic resonance (NMR) signals of the polysaccharide region from the granules were very complex, likely as a result of the diverse microbial population in the granules. Using nonmetric multidimensional scaling (NMDS), the 1H NMR signals of reference polysaccharides (gellan, xanthan, alginate) and those of the anaerobic granules revealed that there were similarities between the polysaccharides extracted from granules and the reference polysaccharide alginate. Further analysis of the exopolysaccharides from anaerobic granules, and reference polysaccharides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that exopolysaccharides from two of the anaerobic granular sludges studied exhibited spectra similar to that of alginate. The presence of sequences related to the synthesis of alginate was confirmed in the metagenomes of the granules. Collectively these results suggest that alginate-like exopolysaccharides are constituents of the EPS matrix in anaerobic granular sludge treating different industrial wastewater. This finding expands the engineered environments where alginate has been found as EPS constituent of microbial aggregates.

  9. HPLC, NMR and MALDI-TOF MS analysis of condensed tannins from Lithocarpus glaber leaves with potent free radical scavenging activity.

    Science.gov (United States)

    Zhang, Liang Liang; Lin, Yi Ming

    2008-12-04

    Using acid-catalyzed degradation in the presence of cysteamine, the condensed tannins from Lithocarpus glaber leaves were characterized, following thiolysis, by means of reversed-phase HPLC, 13C-NMR and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analyses. The thiolysis reaction products showed the presence of the procyanidin (PC) and prodelphinidin (PD) structures. The 13C-NMR spectrum revealed that the condensed tannins were comprised of PD (72.4%) and PC (27.6%), and with a greater content of cis configuration rather than the trans configuration of C2-C3. The MALDI-TOF MS analysis proved the presence of PD units, and the maximum degree of polymerization (DP) was an undecamer. The antioxidant activity of condensed tannins from L. glaber leaves was evaluated by using a free radical scavenging activity assay.

  10. HPLC, NMR and MALDI-TOF MS Analysis of Condensed Tannins from Lithocarpus glaber Leaves with Potent Free Radical Scavenging Activity

    OpenAIRE

    Zhang, Liang Liang; Lin, Yi Ming

    2008-01-01

    Using acid-catalyzed degradation in the presence of cysteamine, the condensed tannins from Lithocarpus glaber leaves were characterized, following thiolysis, by means of reversed-phase HPLC, 13C-NMR and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analyses. The thiolysis reaction products showed the presence of the procyanidin (PC) and prodelphinidin (PD) structures. The 13C-NMR spectrum revealed that the condensed tannins were comprised of PD (7...

  11. MALDI-TOF MS Analysis of Condensed Tannins with Potent Antioxidant Activity from the Leaf, Stem Bark and Root Bark of Acacia confusa

    OpenAIRE

    Wei; Zhou; Lin; Liao; Chai

    2010-01-01

    The structures of the condensed tannins from leaf, stem bark and root bark of Acacia confusa were characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, and their antioxidant activities were measured using 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging and ferric reducing/antioxidant power (FRAP) assays. The results showed that the condensed tannins from stem bark and root bark include propelargonidin and procyanidi...

  12. Application of MALDI-TOF MS fingerprinting as a quick tool for identification and clustering of foodborne pathogens isolated from food products.

    Science.gov (United States)

    Elbehiry, Ayman; Marzouk, Eman; Hamada, Mohamed; Al-Dubaib, Musaad; Alyamani, Essam; Moussa, Ihab M; AlRowaidhan, Anhar; Hemeg, Hassan A

    2017-10-01

    Foodborne pathogens can be associated with a wide variety of food products and it is very important to identify them to supply safe food and prevent foodborne infections. Since traditional techniques are timeconsuming and laborious, this study was designed for rapid identification and clustering of foodborne pathogens isolated from various restaurants in Al-Qassim region, Kingdom of Saudi Arabia (KSA) using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Sixty-nine bacterial and thirty-two fungal isolates isolated from 80 food samples were used in this study. Preliminary identification was carried out through culture and BD Phoenix™ methods. A confirmatory identification technique was then performed using MALDI-TOF MS. The BD Phoenix results revealed that 97% (67/69 isolates) of bacteria were correctly identified as 75% Enterobacter cloacae, 95.45% Campylobacter jejuni and 100% for Escherichia coli, Salmonella enterica, Staphylococcus aureus, Acinetobacter baumannii, and Klebsiella pneumoniae. While 94.44% (29/32 isolates) of fungi were correctly identified as 77.77% Alternaria alternate, 88.88% Aspergillus niger and 100% for Aspergillus flavus, Penicillium digitatum, Candida albicans and Debaryomyces hansenii. However, all bacterial and fungal isolates were 100% properly identified by MALDI-TOF MS fingerprinting with a score value ≥2.00. A gel view illustrated that the spectral peaks for the identified isolates fluctuate between 3,000 and 10,000 Da. The results of main spectra library (MSP) dendrogram showed that the bacterial and fungal isolates matched with 19 and 9 reference strains stored in the Bruker taxonomy, respectively. Our results indicated that MALDI-TOF MS is a promising technique for fast and accurate identification of foodborne pathogens.

  13. MALDI-TOF MS performance compared to direct examination, culture, and 16S rDNA PCR for the rapid diagnosis of bone and joint infections.

    Science.gov (United States)

    Lallemand, E; Coiffier, G; Arvieux, C; Brillet, E; Guggenbuhl, P; Jolivet-Gougeon, A

    2016-05-01

    The rapid identification of bacterial species involved in bone and joint infections (BJI) is an important element to optimize the diagnosis and care of patients. The aim of this study was to evaluate the usefulness of matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) for the rapid diagnosis of bone infections, directly on synovial fluid (SF) or on crushed osteoarticular samples (CS). From January to October 2013, we prospectively analyzed 111 osteoarticular samples (bone and joint samples, BJS) from 78 patients in care at the University Hospital of Rennes, France. The diagnosis procedure leading to the sample collection was linked to a suspicion of infection, inflammatory disease, arthritis, or for any bone or joint abnormalities. Standard bacteriological diagnosis and molecular biology analysis [16S rRNA polymerase chain reaction (PCR) and sequencing] were conducted. In addition, analysis by MALDI-TOF MS was performed directly on the osteoarticular samples, as soon as the amount allowed. Culture, which remains the gold standard for the diagnosis of BJI, has the highest sensitivity (85.9 %) and remains necessary to test antimicrobial susceptibility. The 16S rDNA PCR results were positive in the group with positive BJI (28.6 %) and negative in the group without infection. Direct examination remains insensitive (31.7 %) but more effective than MALDI-TOF MS directly on the sample (6.3 %). The specificity was 100 % in all cases, except for culture (74.5 %). Bacterial culture remains the gold standard, especially enrichment in blood bottles. Direct analysis of bone samples with MALDI-TOF MS is not useful, possibly due to the low inoculum of BJS.

  14. Preparative isoelectric focusing of microorganisms in cellulose-based separation medium and subsequent analysis by CIEF and MALDI-TOF MS

    Czech Academy of Sciences Publication Activity Database

    Horká, Marie; Šlais, Karel; Šalplachta, Jiří; Růžička, F.

    2017-01-01

    Roč. 990, OCT (2017), s. 185-193 ISSN 0003-2670 R&D Projects: GA ČR(CZ) GA16-03749S; GA MV(CZ) VI20172020069; GA MZd(CZ) NV16-29916A Institutional support: RVO:68081715 Keywords : preparative isoelectric focusing * colored microorganisms * isoelectric points * CIEF and MALDI-TOF MS Subject RIV: CB - Analytical Chemistry, Separation OBOR OECD: Analytical chemistry Impact factor: 4.950, year: 2016

  15. Feasibility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) networking in university hospitals in Brussels.

    Science.gov (United States)

    Martiny, D; Cremagnani, P; Gaillard, A; Miendje Deyi, V Y; Mascart, G; Ebraert, A; Attalibi, S; Dediste, A; Vandenberg, O

    2014-05-01

    The mutualisation of analytical platforms might be used to address rising healthcare costs. Our study aimed to evaluate the feasibility of networking a unique matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) system for common use in several university hospitals in Brussels, Belgium. During a one-month period, 1,055 successive bacterial isolates from the Brugmann University Hospital were identified on-site using conventional techniques; these same isolates were also identified using a MALDI-TOF MS system at the Porte de Hal Laboratory by sending target plates and identification projects via transportation and the INFECTIO_MALDI software (Infopartner, Nancy, France), respectively. The occurrence of transmission problems (MS networking always provided a faster identification result than conventional techniques, except when chromogenic culture media and oxidase tests were used (p MS networking could lead to substantial annual cost savings. MALDI-TOF MS networking presents many advantages, and few conventional techniques (optochin and oxidase tests) are required to ensure the same quality in patient care from the distant laboratory. Nevertheless, such networking should not be considered unless there is a reorganisation of workflow, efficient communication between teams, qualified technologists and a reliable IT department and helpdesk to manage potential connectivity problems.

  16. Species-Level Discrimination of Psychrotrophic Pathogenic and Spoilage Gram-Negative Raw Milk Isolates Using a Combined MALDI-TOF MS Proteomics-Bioinformatics-based Approach.

    Science.gov (United States)

    Vithanage, Nuwan R; Bhongir, Jeevana; Jadhav, Snehal R; Ranadheera, Chaminda S; Palombo, Enzo A; Yeager, Thomas R; Datta, Nivedita

    2017-06-02

    Identification of psychrotrophic pathogenic and spoilage Gram-negative bacteria using rapid and reliable techniques is important in commercial milk processing, as these bacteria can produce heat-resistant proteases and act as postprocessing contaminants in pasteurized milk. Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is a proven technology for identification of bacteria in food, however, may require optimization for identification of pathogenic and spoilage bacteria in milk and dairy products. The current study evaluated the effects of various culture conditions and sample preparation methods on assigning of raw milk isolates to the species level by MALDI-TOF MS. The results indicated that culture media, incubation conditions (temperature and time), and sample preparation significantly affected the identification rates of bacteria to the species level. Nevertheless, the development of spectral libraries of isolates grown on different media using a web tool for hierarchical clustering of peptide mass spectra (SPECLUST) followed by a ribosomal protein based bioinformatics approach significantly enhanced the assigning of bacteria, with at least one unique candidate biomarker peak identified for each species. Phyloproteomic relationships based on spectral profiles were compared to phylogenetic analysis using 16S rRNA gene sequences and demonstrated similar clustering patterns with significant discriminatory power. Thus, with appropriate optimization, MALDI-TOF MS is a valuable tool for species-level discrimination of pathogenic and milk spoilage bacteria.

  17. Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi.

    Science.gov (United States)

    Normand, Anne-Cécile; Cassagne, Carole; Ranque, Stéphane; L'ollivier, Coralie; Fourquet, Patrick; Roesems, Sam; Hendrickx, Marijke; Piarroux, Renaud

    2013-04-08

    The poor reproducibility of matrix-assisted desorption/ionization time-of-flight (MALDI-TOF) spectra limits the effectiveness of the MALDI-TOF MS-based identification of filamentous fungi with highly heterogeneous phenotypes in routine clinical laboratories. This study aimed to enhance the MALDI-TOF MS-based identification of filamentous fungi by assessing several architectures of reference spectrum libraries. We established reference spectrum libraries that included 30 filamentous fungus species with various architectures characterized by distinct combinations of the following: i) technical replicates, i.e., the number of analyzed deposits for each culture used to build a reference meta-spectrum (RMS); ii) biological replicates, i.e., the number of RMS derived from the distinct subculture of each strain; and iii) the number of distinct strains of a given species. We then compared the effectiveness of each library in the identification of 200 prospectively collected clinical isolates, including 38 species in 28 genera.Identification effectiveness was improved by increasing the number of both RMS per strain (plibrary markedly improved the effectiveness of the MALDI-TOF MS-based identification of clinical filamentous fungi.

  18. Matrix-assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Can Precisely Discriminate the Lineages of Listeria monocytogenes and Species of Listeria.

    Science.gov (United States)

    Ojima-Kato, Teruyo; Yamamoto, Naomi; Takahashi, Hajime; Tamura, Hiroto

    2016-01-01

    The genetic lineages of Listeria monocytogenes and other species of the genus Listeria are correlated with pathogenesis in humans. Although matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a prevailing tool for rapid and reliable microbial identification, the precise discrimination of Listeria species and lineages remains a crucial issue in clinical settings and for food safety. In this study, we constructed an accurate and reliable MS database to discriminate the lineages of L. monocytogenes and the species of Listeria (L. monocytogenes, L. innocua, L. welshimeri, L. seeligeri, L. ivanovii, L. grayi, and L. rocourtiae) based on the S10-spc-alpha operon gene encoded ribosomal protein mass spectrum (S10-GERMS) proteotyping method, which relies on both genetic information (genomics) and observed MS peaks in MALDI-TOF MS (proteomics). The specific set of eight biomarkers (ribosomal proteins L24, L6, L18, L15, S11, S9, L31 type B, and S16) yielded characteristic MS patterns for the lineages of L. monocytogenes and the different species of Listeria, and led to the construction of a MS database that was successful in discriminating between these organisms in MALDI-TOF MS fingerprinting analysis followed by advanced proteotyping software Strain Solution analysis. We also confirmed the constructed database on the proteotyping software Strain Solution by using 23 Listeria strains collected from natural sources.

  19. Differentiation of clinically relevant Mucorales Rhizopus microsporus and R. arrhizus by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Dolatabadi, Somayeh; Kolecka, Anna; Versteeg, Matthijs; de Hoog, Sybren G; Boekhout, Teun

    2015-07-01

    This study addresses the usefulness of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS for reliable identification of the two most frequently occurring clinical species of Rhizopus, namely Rhizopus arrhizus with its two varieties, arrhizus and delemar, and Rhizopus microsporus. The test-set comprised 38 isolates of clinical and environmental origin previously identified by internal transcribed spacer (ITS) sequencing of rDNA. Multi-locus sequence data targeting three gene markers (ITS, ACT, TEF ) showed two monophylic clades for Rhizopus arrhizus and Rhizopus microsporus (bootstrap values of 99 %). Cluster analysis confirmed the presence of two distinct clades within Rhizopus arrhizus representing its varieties arrhizus and delemar. The MALDI Biotyper 3.0 Microflex LT platform (Bruker Daltonics) was used to confirm the distinction between Rhizopus arrhizus and Rhizopus microsporus and the presence of two varieties within the species Rhizopus arrhizus. An in-house database of 30 reference main spectra (MSPs) was initially tested for correctness using commercially available databases of Bruker Daltonics. By challenging the database with the same strains of which an in-house database was created, automatic identification runs confirmed that MALDI-TOF MS is able to recognize the strains at the variety level. Based on principal component analysis, two MSP dendrograms were created and showed concordance with the multi-locus tree; thus, MALDI-TOF MS is a useful tool for diagnostics of mucoralean species.

  20. A novel cluster of Mycobacterium abscessus complex revealed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Suzuki, Hiromichi; Yoshida, Shiomi; Yoshida, Atsushi; Okuzumi, Katsuko; Fukusima, Atsuhito; Hishinuma, Akira

    2015-12-01

    Mycobacterium abscessus complex is a rapidly growing mycobacterium consisting of 3 subspecies, M. abscessus, Mycobacterium massiliense, and Mycobacterium bolletii. However, rapid and accurate species identification is difficult. We first evaluated a suitable protocol of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for distinguishing these subspecies. Then, we studied spectral signals by MALDI-TOF MS in 59 M. abscessus, 42 M. massiliense, and 2 M. bolletii. Among several specific spectral signals, 4 signals clearly differentiate M. massiliense from the other 2 subspecies, M. abscessus and M. bolletii. Moreover, 6 of the 42 M. massiliense isolates showed a spectral pattern similar to M. abscessus. These isolates correspond to the distinctive class of M. massiliense (cluster D) which is closer to M. abscessus by the previous variable number tandem repeat analysis. These results indicate that MALDI-TOF MS is not only useful for the identification of 3 subspecies of M. abscessus complex but also capable of distinguishing clusters of M. massiliense. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Rapid Identification of Microorganisms from Positive Blood Culture by MALDI-TOF MS After Short-Term Incubation on Solid Medium.

    Science.gov (United States)

    Curtoni, Antonio; Cipriani, Raffaella; Marra, Elisa Simona; Barbui, Anna Maria; Cavallo, Rossana; Costa, Cristina

    2017-01-01

    Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a useful tool for rapid identification of microorganisms. Unfortunately, its direct application to positive blood culture is still lacking standardized procedures. In this study, we evaluated an easy- and rapid-to-perform protocol for MALDI-TOF MS direct identification of microorganisms from positive blood culture after a short-term incubation on solid medium. This protocol was used to evaluate direct identification of microorganisms from 162 positive monomicrobial blood cultures; at different incubation times (3, 5, 24 h), MALDI-TOF MS assay was performed from the growing microorganism patina. Overall, MALDI-TOF MS concordance with conventional methods at species level was 60.5, 80.2, and 93.8% at 3, 5, and 24 h, respectively. Considering only bacteria, the identification performances at species level were 64.1, 85.0, and 94.1% at 3, 5, and 24 h, respectively. This protocol applied to a commercially available MS typing system may represent, a fast and powerful diagnostic tool for pathogen direct identification and for a promptly and pathogen-driven antimicrobial therapy in selected cases.

  2. Site-specific glycoprofiling of N-linked glycopeptides using MALDI-TOF MS: strong correlation between signal strength and glycoform quantities

    DEFF Research Database (Denmark)

    Thaysen-Andersen, Morten; Mysling, Simon; Højrup, Peter

    2009-01-01

    Site-specific glycoprofiling of N-linked glycopeptides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an emerging technique, but its quantitative accuracy lacks documentation. Thus, a systematic study of widely different glycopeptides was perf......Site-specific glycoprofiling of N-linked glycopeptides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an emerging technique, but its quantitative accuracy lacks documentation. Thus, a systematic study of widely different glycopeptides...... was performed to determine the relationship between the relative abundances of the individual glycoforms and the MALDI-TOF MS signal strength. Glycopeptides derived from glycoproteins containing neutral glycans (ribonuclease B, IgG, and ovalbumin) were initially profiled and yielded excellent and reproducible...... quantitation (correlation coefficient r = 0.9958, n = 5) when evaluated against a normal phase HPLC 2-AB glycan profile. Similarly, precise quantitation was observed for various forms of N-glycans (free, permethylated, and fluorescence-labeled) using MS. In addition, three different sialoglycopeptides from...

  3. Proteomic analysis of plasma proteins in diabetic retinopathy patients by two dimensional electrophoresis and MALDI-Tof-MS.

    Science.gov (United States)

    Gopalakrishnan, Vidhya; Purushothaman, Parthiban; Bhaskar, Anusha

    2015-01-01

    Diabetic retinopathy is a highly specific vascular complication of diabetes mellitus and progresses from mild non-proliferative abnormalities characterized by increased vascular permeability to moderate and severe proliferative diabetic retinopathy characterized by the growth of blood vessels on the retina. The aim of the study was to identify the differentially expressed proteins in diabetic retinopathy using two-dimensional electrophoresis. Blood sample was drawn from subjects with diabetes mellitus (without retinopathy) who served as controls and patients with diabetic retinopathy in tubes containing EDTA as anticoagulant. Albumin and immunoglobulin IgG collectively removed to enrich proteins of lower abundance. 2de was carried out to see if there are any differentially expressed proteins. Approximately 48 and 61 spots were identified in control and diabetic retinopathy respectively, of which three protein spots RBP1 (retinol-binding protein 1), NUD10 (Diphosphoinositol polyphosphohydrolase 3 alpha), NGB (neuroglobin) were down regulated and HBG2 (hemoglobin) and BY55 (CD 160 antigen) were upregulated in diabetic retinopathy. These five protein spots were excised and were subjected to in-gel tryptic digestion, and their identities were determined by ultraflex MALDI-TOF-MS. We report a comprehensive patient-based plasma proteomic approach to the identification of potential biomarkers for diabetic retinopathy screening and detection. We identified 5 different proteins that were differentially expressed in the plasma of control diabetic patients (without retinopathy). Among these five proteins the expression of neuroglobin (NGB) protein varied significantly and may be a potential biomarker in diabetic retinopathy. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Microbial identification and automated antibiotic susceptibility testing directly from positive blood cultures using MALDI-TOF MS and VITEK 2.

    Science.gov (United States)

    Wattal, C; Oberoi, J K

    2016-01-01

    The study addresses the utility of Matrix Assisted Laser Desorption/Ionisation Time-Of-Flight mass spectrometry (MALDI-TOF MS) using VITEK MS and the VITEK 2 antimicrobial susceptibility testing (AST) system for direct identification (ID) and timely AST from positive blood culture bottles using a lysis-filtration method (LFM). Between July and December 2014, a total of 140 non-duplicate mono-microbial blood cultures were processed. An aliquot of positive blood culture broth was incubated with lysis buffer before the bacteria were filtered and washed. Micro-organisms recovered from the filter were first identified using VITEK MS and its suspension was used for direct AST by VITEK 2 once the ID was known. Direct ID and AST results were compared with classical methods using solid growth. Out of the 140 bottles tested, VITEK MS resulted in 70.7 % correct identification to the genus and/ or species level. For the 103 bottles where identification was possible, there was agreement in 97 samples (94.17 %) with classical culture. Compared to the routine method, the direct AST resulted in category agreement in 860 (96.5 %) of 891 bacteria-antimicrobial agent combinations tested. The results of direct ID and AST were available 16.1 hours before those of the standard approach on average. The combined use of VITEK MS and VITEK 2 directly on samples from positive blood culture bottles using a LFM technique can result in rapid and reliable ID and AST results in blood stream infections to result in early institution of targeted treatment. The combination of LFM and AST using VITEK 2 was found to expedite AST more reliably.

  5. Comparison of biomarker based Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) and conventional methods in the identification of clinically relevant bacteria and yeast.

    Science.gov (United States)

    Kassim, Ali; Pflüger, Valentin; Premji, Zul; Daubenberger, Claudia; Revathi, Gunturu

    2017-05-25

    MALDI-TOF MS is an analytical method that has recently become integral in the identification of microorganisms in clinical laboratories. It relies on databases that majorly employ pattern recognition or fingerprinting. Biomarker based databases have also been developed and there is optimism that these may be superior to pattern recognition based databases. This study compared the performance of ribosomal biomarker based MALDI-TOF MS and conventional methods in the identification of selected bacteria and yeast. The study was a cross sectional study identifying clinically relevant bacteria and yeast isolated from varied clinical specimens submitted to a clinical laboratory. The identification of bacteria using conventional Vitek 2™ automated system, serotyping and MALDI-TOF MS was performed as per standard operating procedures. Comparison of sensitivities were then carried out using Pearson Chi-Square test and p-value of bacteria and Gram positive bacteria to the species level. For the Gram positive bacteria, significant difference was observed in the identification of Coagulase negative Staphylococci (p = 0.000) and Enterococcus (p = 0.008). Significant difference was also observed between serotyping and MALDI-TOF MS (p = 0.005) and this was attributed to the lack of identification of Shigella species by MALDI-TOF MS. There was no significant difference observed in the identification of yeast however some species of Candida were unidentified by MALDI-TOF MS. Biomarker based MALDI-TOF MS had good performance in a clinical laboratory setting with high sensitivities in the identification of clinically relevant microorganisms.

  6. Identification of phlebotomine sand flies using one MALDI-TOF MS reference database and two mass spectrometer systems.

    Science.gov (United States)

    Mathis, Alexander; Depaquit, Jérôme; Dvořák, Vit; Tuten, Holly; Bañuls, Anne-Laure; Halada, Petr; Zapata, Sonia; Lehrter, Véronique; Hlavačková, Kristýna; Prudhomme, Jorian; Volf, Petr; Sereno, Denis; Kaufmann, Christian; Pflüger, Valentin; Schaffner, Francis

    2015-05-10

    Rapid, accurate and high-throughput identification of vector arthropods is of paramount importance in surveillance programmes that are becoming more common due to the changing geographic occurrence and extent of many arthropod-borne diseases. Protein profiling by MALDI-TOF mass spectrometry fulfils these requirements for identification, and reference databases have recently been established for several vector taxa, mostly with specimens from laboratory colonies. We established and validated a reference database containing 20 phlebotomine sand fly (Diptera: Psychodidae, Phlebotominae) species by using specimens from colonies or field-collections that had been stored for various periods of time. Identical biomarker mass patterns ('superspectra') were obtained with colony- or field-derived specimens of the same species. In the validation study, high quality spectra (i.e. more than 30 evaluable masses) were obtained with all fresh insects from colonies, and with 55/59 insects deep-frozen (liquid nitrogen/-80 °C) for up to 25 years. In contrast, only 36/52 specimens stored in ethanol could be identified. This resulted in an overall sensitivity of 87 % (140/161); specificity was 100 %. Duration of storage impaired data counts in the high mass range, and thus cluster analyses of closely related specimens might reflect their storage conditions rather than phenotypic distinctness. A major drawback of MALDI-TOF MS is the restricted availability of in-house databases and the fact that mass spectrometers from 2 companies (Bruker, Shimadzu) are widely being used. We have analysed fingerprints of phlebotomine sand flies obtained by automatic routine procedure on a Bruker instrument by using our database and the software established on a Shimadzu system. The sensitivity with 312 specimens from 8 sand fly species from laboratory colonies when evaluating only high quality spectra was 98.3 %; the specificity was 100 %. The corresponding diagnostic values with 55 field

  7. Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory

    Science.gov (United States)

    Li, Xiuyuan; Tang, Yanyan; Lu, Xinxin

    2018-04-01

    Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ 2 = 41.336, P clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. [Figure not available: see fulltext.

  8. Gram-stain plus MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for a rapid diagnosis of urinary tract infection.

    Directory of Open Access Journals (Sweden)

    Almudena Burillo

    Full Text Available Microbiological confirmation of a urinary tract infection (UTI takes 24-48 h. In the meantime, patients are usually given empirical antibiotics, sometimes inappropriately. We assessed the feasibility of sequentially performing a Gram stain and MALDI-TOF MS mass spectrometry (MS on urine samples to anticipate clinically useful information. In May-June 2012, we randomly selected 1000 urine samples from patients with suspected UTI. All were Gram stained and those yielding bacteria of a single morphotype were processed for MALDI-TOF MS. Our sequential algorithm was correlated with the standard semiquantitative urine culture result as follows: Match, the information provided was anticipative of culture result; Minor error, the information provided was partially anticipative of culture result; Major error, the information provided was incorrect, potentially leading to inappropriate changes in antimicrobial therapy. A positive culture was obtained in 242/1000 samples. The Gram stain revealed a single morphotype in 207 samples, which were subjected to MALDI-TOF MS. The diagnostic performance of the Gram stain was: sensitivity (Se 81.3%, specificity (Sp 93.2%, positive predictive value (PPV 81.3%, negative predictive value (NPV 93.2%, positive likelihood ratio (+LR 11.91, negative likelihood ratio (-LR 0.20 and accuracy 90.0% while that of MALDI-TOF MS was: Se 79.2%, Sp 73.5, +LR 2.99, -LR 0.28 and accuracy 78.3%. The use of both techniques provided information anticipative of the culture result in 82.7% of cases, information with minor errors in 13.4% and information with major errors in 3.9%. Results were available within 1 h. Our serial algorithm provided information that was consistent or showed minor errors for 96.1% of urine samples from patients with suspected UTI. The clinical impacts of this rapid UTI diagnosis strategy need to be assessed through indicators of adequacy of treatment such as a reduced time to appropriate empirical treatment or

  9. Selective extraction of phospholipids from dairy products by micro-solid phase extraction based on titanium dioxide microcolumns followed by MALDI-TOF-MS analysis

    DEFF Research Database (Denmark)

    Calvano, Cosima; Jensen, Ole; Zambonin, Carlo

    2009-01-01

    A new micro-solid phase extraction (micro-SPE) procedure based on titanium dioxide microcolumns was developed for the selective extraction of phospholipids (PLs) from dairy products before matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis. All...... the extraction steps (loading, washing, and elution) have been optimized using a synthetic mixture of PLs standard and the procedure was subsequently applied to food samples such as milk, chocolate milk and butter. The whole method demonstrated to be simpler than traditional approaches and it appears very...

  10. Lactococcus garvieae endocarditis in a native valve identified by MALDI-TOF MS and PCR-based 16s rRNA in Spain: A case report

    Directory of Open Access Journals (Sweden)

    V. Heras Cañas

    2015-05-01

    Full Text Available Lactococcus garvieae is a Gram-positive, catalase negative coccus arranged in pairs or short chains, well-known as a fish pathogen. We report a case of Infective Endocarditis (IE by L. garvieae in a native valve from a 68-year-old male with unknown history of contact with raw fish and an extensive history of heart disease. This case highlights the reliability of MALDI-TOF MS compared to conventional methods in the identification of rare microorganisms like this.

  11. An Improved In-house MALDI-TOF MS Protocol for Direct Cost-Effective Identification of Pathogens from Blood Cultures

    Directory of Open Access Journals (Sweden)

    Menglan Zhou

    2017-09-01

    Full Text Available Background: Bloodstream infection is a major cause of morbidity and mortality in hospitalized patients worldwide. Delays in the identification of microorganisms often leads to a poor prognosis. The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS directly to blood culture (BC broth can potentially identify bloodstream infections earlier, and facilitate timely management.Methods: We developed an “in-house” (IH protocol for direct MALDI-TOF MS based identification of organisms in positive BCs. The IH protocol was initially evaluated and improved with spiked BC samples, and its performance was compared with the commercial Sepsityper™ kit using both traditional and modified cut-off values. We then studied in parallel the performance of the IH protocol and the colony MS identifications in positive clinical BC samples using only modified cut-off values. All discrepancies were investigated by “gold standard” of gene sequencing.Results: In 54 spiked BC samples, the IH method showed comparable results with Sepsityper™ after applying modified cut-off values. Specifically, accurate species and genus level identification was achieved in 88.7 and 3.9% of all the clinical monomicrobial BCs (284/301, 94.4%, respectively. The IH protocol exhibited superior performance for Gram negative bacteria than for Gram positive bacteria (92.8 vs. 82.4%. For anaerobes and yeasts, accurate species identification was achieved in 80.0 and 90.0% of the cases, respectively. For polymicrobial cultures (17/301, 5.6%, MALDI-TOF MS correctly identified a single species present in all the polymicrobial BCs under the Standard mode, while using the MIXED method, two species were correctly identified in 52.9% of the samples. Comparisons based on BC bottle type, showed that the BACTEC™ Lytic/10 Anaerobic/F culture vials performed the best.Conclusion: Our study provides a novel and effective sample preparation method

  12. An Improved In-house MALDI-TOF MS Protocol for Direct Cost-Effective Identification of Pathogens from Blood Cultures.

    Science.gov (United States)

    Zhou, Menglan; Yang, Qiwen; Kudinha, Timothy; Sun, Liying; Zhang, Rui; Liu, Chang; Yu, Shuying; Xiao, Meng; Kong, Fanrong; Zhao, Yupei; Xu, Ying-Chun

    2017-01-01

    Background: Bloodstream infection is a major cause of morbidity and mortality in hospitalized patients worldwide. Delays in the identification of microorganisms often leads to a poor prognosis. The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) directly to blood culture (BC) broth can potentially identify bloodstream infections earlier, and facilitate timely management. Methods: We developed an "in-house" (IH) protocol for direct MALDI-TOF MS based identification of organisms in positive BCs. The IH protocol was initially evaluated and improved with spiked BC samples, and its performance was compared with the commercial Sepsityper™ kit using both traditional and modified cut-off values. We then studied in parallel the performance of the IH protocol and the colony MS identifications in positive clinical BC samples using only modified cut-off values. All discrepancies were investigated by "gold standard" of gene sequencing. Results: In 54 spiked BC samples, the IH method showed comparable results with Sepsityper™ after applying modified cut-off values. Specifically, accurate species and genus level identification was achieved in 88.7 and 3.9% of all the clinical monomicrobial BCs (284/301, 94.4%), respectively. The IH protocol exhibited superior performance for Gram negative bacteria than for Gram positive bacteria (92.8 vs. 82.4%). For anaerobes and yeasts, accurate species identification was achieved in 80.0 and 90.0% of the cases, respectively. For polymicrobial cultures (17/301, 5.6%), MALDI-TOF MS correctly identified a single species present in all the polymicrobial BCs under the Standard mode, while using the MIXED method, two species were correctly identified in 52.9% of the samples. Comparisons based on BC bottle type, showed that the BACTEC™ Lytic/10 Anaerobic/F culture vials performed the best. Conclusion: Our study provides a novel and effective sample preparation method for MALDI-TOF MS

  13. NMR, ESI/MS, and MALDI-TOF/MS analysis of pear juice polymeric proanthocyanidins with potent free radical scavenging activity.

    Science.gov (United States)

    Es-Safi, Nour-Eddine; Guyot, Sylvain; Ducrot, Paul-Henri

    2006-09-20

    The structure of a polymeric proanthocyanidin fraction isolated from pear juice was characterized by NMR, ESI/MS, and MALDI-TOF/MS analyses, and its antioxidant activity was investigated using the DPPH free radical scavenging method. The results obtained from 13C NMR analysis showed the predominance of signals representative of procyanidins. Typical signals in the chemical shift region between 70 and 90 ppm demonstrated the exclusive presence of epicatechin units. The results obtained through negative ESI/MS analysis showed singly and doubly charged ions corresponding to the molecular mass of procyanidins with a degree of polymerization up to 22. The spectra obtained through MALDI-TOF/MS analysis revealed the presence of two series of tannin oligomers. Supporting the observations from NMR spectroscopy, the first series consists of well-resolved tannin identified as procyanidin polymers units with chain lengths of up to 25. A second series of monogalloyl flavan-3-ols polymers with polymerization degree up to 25 were also detected. This is the first mass spectrometric evidence confirming the existence of galloylated procyanidin oligomers in pear fruits. Within each of these oligomers, various signals exist suggesting the presence of several oligomeric tannins. The antioxidant properties of the polymeric fraction were investigated through reduction of the DPPH free radical, and the results obtained showed that the polymeric fraction exhibited a higher antioxidant power compared to those of (+)-catechin and B3 procyanidin dimer.

  14. Biomarker- and similarity coefficient-based approaches to bacterial mixture characterization using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Zhang, Lin; Smart, Sonja; Sandrin, Todd R

    2015-11-05

    MALDI-TOF MS profiling has been shown to be a rapid and reliable method to characterize pure cultures of bacteria. Currently, there is keen interest in using this technique to identify bacteria in mixtures. Promising results have been reported with two- or three-isolate model systems using biomarker-based approaches. In this work, we applied MALDI-TOF MS-based methods to a more complex model mixture containing six bacteria. We employed: 1) a biomarker-based approach that has previously been shown to be useful in identification of individual bacteria in pure cultures and simple mixtures and 2) a similarity coefficient-based approach that is routinely and nearly exclusively applied to identification of individual bacteria in pure cultures. Both strategies were developed and evaluated using blind-coded mixtures. With regard to the biomarker-based approach, results showed that most peaks in mixture spectra could be assigned to those found in spectra of each component bacterium; however, peaks shared by two isolates as well as peaks that could not be assigned to any individual component isolate were observed. For two-isolate blind-coded samples, bacteria were correctly identified using both similarity coefficient- and biomarker-based strategies, while for blind-coded samples containing more than two isolates, bacteria were more effectively identified using a biomarker-based strategy.

  15. Confirmation of Fructans biosynthesized in vitro from [1-13C]glucose in asparagus tissues using MALDI-TOF MS and ESI-MS.

    Science.gov (United States)

    Suzuki, Takashi; Maeda, Tomoo; Grant, Suzanne; Grant, Gordon; Sporns, Peter

    2013-05-15

    Accumulation of Fructans was confirmed in asparagus tissues that had been cultured for 2 days on media supplemented with glucose. It is very common that Fructans are biosynthesized from sucrose. We hypothesized however that Fructans could also be biosynthesized from glucose. Stem tissues of in vitro-cultured asparagus were subcultured for 72 h on a medium containing 0.5M of [1-(13)C]glucose. A medium containing 0.5M of normal ((12)C) glucose was used as control. Carbohydrates were extracted from the tissues and analyzed using HPLC, MALDI-TOF MS and ESI-MS. HPLC results indicated that the accumulation of short-chain Fructans was similar in both (13)C-labelled and control samples. Short-chain Fructans of DP=3-7 were detected using MALDI-TOF MS. The molecular mass of each oligomer in the (13)C-labelled sample was higher than the mass of the natural sample by 1 m/z unit per sugar moiety. The results of ESI-MS on the HPLC fractions of neokestose and 1-kestose showed that these oligomers (DP=3) were biosynthesized from exogenous glucose added to the medium. We conclude that not only exogenous sucrose but glucose can induce Fructan biosynthesis; fructans of both inulin type and inulin neoseries are also biosynthesized from glucose accumulated in asparagus tissues; the glucose molecules (or its metabolic products) were incorporated into Fructans as structural monomers. Copyright © 2013 Elsevier GmbH. All rights reserved.

  16. Collagen-based proteinaceous binder-pigment interaction study under UV ageing conditions by MALDI-TOF-MS and principal component analysis.

    Science.gov (United States)

    Romero-Pastor, Julia; Navas, Natalia; Kuckova, Stepanka; Rodríguez-Navarro, Alejandro; Cardell, Carolina

    2012-03-01

    This study focuses on acquiring information on the degradation process of proteinaceous binders due to ultra violet (UV) radiation and possible interactions owing to the presence of historical mineral pigments. With this aim, three different paint model samples were prepared according to medieval recipes, using rabbit glue as proteinaceus binders. One of these model samples contained only the binder, and the other two were prepared by mixing each of the pigments (cinnabar or azurite) with the binder (glue tempera model samples). The model samples were studied by applying Principal Component Analysis (PCA) to their mass spectra obtained with Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). The complementary use of Fourier Transform Infrared Spectroscopy to study conformational changes of secondary structure of the proteinaceous binder is also proposed. Ageing effects on the model samples after up to 3000 h of UV irradiation were periodically analyzed by the proposed approach. PCA on MS data proved capable of identifying significant changes in the model samples, and the results suggested different aging behavior based on the pigment present. This research represents the first attempt to use this approach (PCA on MALDI-TOF-MS data) in the field of Cultural Heritage and demonstrates the potential benefits in the study of proteinaceous artistic materials for purposes of conservation and restoration. Copyright © 2012 John Wiley & Sons, Ltd.

  17. Magnetic graphene composites as both an adsorbent for sample enrichment and a MALDI-TOF MS matrix for the detection of nitropolycyclic aromatic hydrocarbons in PM2.5.

    Science.gov (United States)

    Zhang, Jiangang; Zhang, Li; Li, Ruijin; Hu, Di; Ma, Nengxuan; Shuang, Shaomin; Cai, Zongwei; Dong, Chuan

    2015-03-07

    A simple and rapid method that uses synthesized magnetic graphene composites as both an adsorbent for enrichment and as a matrix in MALDI-TOF MS analysis was developed for the detection of nitropolycyclic hydrocarbons (nitro-PAHs) in PM2.5 samples. Three nitro-PAHs were detected down to sub pg μL(-1) levels based on calculations from an instrumental signal-to-noise better than 3, which shows the feasibility of using the new materials in MALDI-TOF MS as a potential powerful analytical approach for the analysis of nitro-PAHs in PM2.5 samples.

  18. MALDI-TOF MS analysis of condensed tannins with potent antioxidant activity from the leaf, stem bark and root bark of Acacia confusa.

    Science.gov (United States)

    Wei, Shu-Dong; Zhou, Hai-Chao; Lin, Yi-Ming; Liao, Meng-Meng; Chai, Wei-Ming

    2010-06-15

    The structures of the condensed tannins from leaf, stem bark and root bark of Acacia confusa were characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, and their antioxidant activities were measured using 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging and ferric reducing/antioxidant power (FRAP) assays. The results showed that the condensed tannins from stem bark and root bark include propelargonidin and procyanidin, and the leaf condensed tannins include propelargonidin, procyanidin and prodelphinidin, all with the procyanidin dominating. The condensed tannins had different polymer chain lengths, varying from trimers to undecamers for leaf and root bark and to dodecamers for stem bark. The condensed tannins extracted from the leaf, stem bark and root bark all showed a very good DPPH radical scavenging activity and ferric reducing power.

  19. 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.

    Science.gov (United States)

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

    2014-01-01

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

  20. 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.

    Directory of Open Access Journals (Sweden)

    Qiao-Ting Chao

    Full Text Available 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

  1. An improved in-house lysis-filtration protocol for bacterial identification from positive blood culture bottles with high identification rates by MALDI-TOF MS.

    Science.gov (United States)

    Tsuchida, Sachio; Murata, Syota; Miyabe, Akiko; Satoh, Mamoru; Takiwaki, Masaki; Matsushita, Kazuyuki; Nomura, Fumio

    2018-05-01

    Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is now a well-established method for identification of microorganisms from positive blood cultures. Pretreatments to effectively remove non-bacterial proteins are a prerequisite for successful identification, and a variety of protocols have been reported. Although commercially available kits, mainly the Sepsityper Kit, are increasingly used, the identification rates reported often are not satisfactory, particularly for Gram-positive isolates. We developed a new, in-house lysis-filtration protocol and prospectively evaluated its performance compared to the Sepsityper kit. The in-house protocol consists of three simple steps: lysis by ammonium chloride, aspiration with a syringe fitted with a 0.45-μm membrane, and centrifugation to collect microbes. The novel protocol requires only 20 min. Performance of the in-house protocol was evaluated using a total of 117 monomicrobial cases of positive blood culture. Medium from blood culture bottles was pretreated by the in-house protocol or the commercial kit, and isolated cells were subjected to direct identification by mass spectrometry fingerprinting in parallel with conventional subculturing for reference identification. The overall MALDI-TOF MS-based identification rates with score > 1.7 and > 2.0 obtained using the in-house protocol were 99.2% and 85.5%, respectively, whereas those obtained using the Sepsityper Kit were 85.4% and 61.5%, respectively. For Gram-positive cases, the in-house protocol yielded scores >1.7 and > 2.0 at 98.5% and 76.1%, respectively, whereas the commercial kit yielded these scores at 76.1% and 43.3%, respectively. Although these are preliminary results, these values suggest that this easy lysis-filtration protocol deserves assessment in a larger-scale test. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. MALDI-TOF MS enables the rapid identification of the major molecular types within the Cryptococcus neoformans/C. gattii species complex.

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    Carolina Firacative

    Full Text Available BACKGROUND: The Cryptococcus neoformans/C. gattii species complex comprises two sibling species that are divided into eight major molecular types, C. neoformans VNI to VNIV and C. gattii VGI to VGIV. These genotypes differ in host range, epidemiology, virulence, antifungal susceptibility and geographic distribution. The currently used phenotypic and molecular identification methods for the species/molecular types are time consuming and expensive. As Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS offers an effective alternative for the rapid identification of microorganisms, the objective of this study was to examine its potential for the identification of C. neoformans and C. gattii strains at the intra- and inter-species level. METHODOLOGY: Protein extracts obtained via the formic acid extraction method of 164 C. neoformans/C. gattii isolates, including four inter-species hybrids, were studied. RESULTS: The obtained mass spectra correctly identified 100% of all studied isolates, grouped each isolate according to the currently recognized species, C. neoformans and C. gattii, and detected potential hybrids. In addition, all isolates were clearly separated according to their major molecular type, generating greater spectral differences among the C. neoformans molecular types than the C. gattii molecular types, most likely reflecting a closer phylogenetic relationship between the latter. The number of colonies used and the incubation length did not affect the results. No spectra were obtained from intact yeast cells. An extended validated spectral library containing spectra of all eight major molecular types was established. CONCLUSIONS: MALDI-TOF MS is a rapid identification tool for the correct recognition of the two currently recognized human pathogenic Cryptococcus species and offers a simple method for the separation of the eight major molecular types and the detection of hybrid strains within this

  3. The influence of incubation time, sample preparation and exposure to oxygen on the quality of the MALDI-TOF MS spectrum of anaerobic bacteria.

    Science.gov (United States)

    Veloo, A C M; Elgersma, P E; Friedrich, A W; Nagy, E; van Winkelhoff, A J

    2014-12-01

    With matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), bacteria can be identified quickly and reliably. This accounts especially for anaerobic bacteria. Because growth rate and oxygen sensitivity differ among anaerobic bacteria, we aimed to study the influence of incubation time, exposure to oxygen and sample preparation on the quality of the spectrum using the Bruker system. Also, reproducibility and inter-examiner variability were determined. Twenty-six anaerobic species, representing 17 genera, were selected based on gram-stain characteristics, growth rate and colony morphology. Inter-examiner variation showed that experience in the preparation of the targets can be a significant variable. The influence of incubation time was determined between 24 and 96 h of incubation. Reliable species identification was obtained after 48 h of incubation for gram-negative anaerobes and after 72 h for gram-positive anaerobes. Exposure of the cultures to oxygen did not influence the results of the MALDI-TOF MS identifications of all tested gram-positive species. Fusobacterium necrophorum and Prevotella intermedia could not be identified after >24 h and 48 h of exposure to oxygen, respectively. Other tested gram-negative bacteria could be identified after 48 h of exposure to oxygen. Most of the tested species could be identified using the direct spotting method. Bifidobacterium longum and Finegoldia magna needed on-target extraction with 70% formic acid in order to obtain reliable species identification and Peptoniphilus ivorii a full extraction. Spectrum quality was influenced by the amount of bacteria spotted on the target, the homogeneity of the smear and the experience of the examiner. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

  4. Evaluation of repetitive-PCR and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS for rapid strain typing of Bacillus coagulans.

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    Jun Sato

    Full Text Available In order to establish rapid and accurate typing method for Bacillus coagulans strains which is important for controlling in some canned foods and tea-based beverages manufacturing because of the high-heat resistance of the spores and high tolerance of the vegetative cells to catechins and chemicals, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS and repetitive-PCR (rep-PCR were evaluated. For this purpose, 28 strains of B. coagulans obtained from various culture collections were tested. DNA sequence analyses of the genes encoding 16S rRNA and DNA gyrase classified the test strains into two and three groups, respectively, regardless of their phenotypes. Both MALDI-TOF MS and rep-PCR methods classified the test strains in great detail. Strains classified in each group showed similar phenotypes, such as carbohydrate utilization determined using API 50CH. In particular, the respective two pairs of strains which showed the same metabolic characteristic were classified into the same group by both MALDI-TOF MS and rep-PCR methods separating from the other strains. On the other hand, the other strains which have the different profiles of carbohydrate utilization were separated into different groups by these methods. These results suggested that the combination of MALDI-TOF MS and rep-PCR analyses was advantageous for the rapid and detailed typing of bacterial strains in respect to both phenotype and genotype.

  5. Evaluation of repetitive-PCR and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid strain typing of Bacillus coagulans.

    Science.gov (United States)

    Sato, Jun; Nakayama, Motokazu; Tomita, Ayumi; Sonoda, Takumi; Hasumi, Motomitsu; Miyamoto, Takahisa

    2017-01-01

    In order to establish rapid and accurate typing method for Bacillus coagulans strains which is important for controlling in some canned foods and tea-based beverages manufacturing because of the high-heat resistance of the spores and high tolerance of the vegetative cells to catechins and chemicals, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and repetitive-PCR (rep-PCR) were evaluated. For this purpose, 28 strains of B. coagulans obtained from various culture collections were tested. DNA sequence analyses of the genes encoding 16S rRNA and DNA gyrase classified the test strains into two and three groups, respectively, regardless of their phenotypes. Both MALDI-TOF MS and rep-PCR methods classified the test strains in great detail. Strains classified in each group showed similar phenotypes, such as carbohydrate utilization determined using API 50CH. In particular, the respective two pairs of strains which showed the same metabolic characteristic were classified into the same group by both MALDI-TOF MS and rep-PCR methods separating from the other strains. On the other hand, the other strains which have the different profiles of carbohydrate utilization were separated into different groups by these methods. These results suggested that the combination of MALDI-TOF MS and rep-PCR analyses was advantageous for the rapid and detailed typing of bacterial strains in respect to both phenotype and genotype.

  6. An evaluation of three processing methods and the effect of reduced culture times for faster direct identification of pathogens from BacT/ALERT blood cultures by MALDI-TOF MS

    NARCIS (Netherlands)

    M.Sc. A. Jansz; Dr. A.J.C. van den Brule, van den; Dr. P.F.G. Wolffs; Ing J. Stalpers; Drs A.J.M. Loonen

    2011-01-01

    Matrix-assisted laser desorption/ionisation time of-flight mass spectrometry (MALDI-TOF MS) is a fast and reliable method for the identification of bacteria from agar media. Direct identification from positive blood cultures should decrease the time to obtaining the result. In this study, three

  7. Matrix-assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a Reliable Tool to Identify Species of Catalase-negative Gram-positive Cocci not Belonging to the Streptococcus Genus.

    Science.gov (United States)

    Almuzara, Marisa; Barberis, Claudia; Velázquez, Viviana Rojas; Ramirez, Maria Soledad; Famiglietti, Angela; Vay, Carlos

    2016-01-01

    To evaluate the performance of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) by using 190 Catalase-negative Gram-Positive Cocci (GPC) clinical isolates. All isolates were identified by conventional phenotypic tests following the proposed scheme by Ruoff and Christensen and MALDI-TOF MS (Bruker Daltonics, BD, Bremen, Germany). Two different extraction methods (direct transfer formic acid method on spot and ethanol formic acid extraction method) and different cut-offs for genus/specie level identification were used. The score cut-offs recommended by the manufacturer (≥ 2.000 for species-level, 1.700 to 1.999 for genus level and genus level, ≥ 1.700 for species-level and score genus or species. MALDI-TOF MS identification was considered correct when the result obtained from MS database agreed with the phenotypic identification result. When both methods gave discordant results, the 16S rDNA or sodA genes sequencing was considered as the gold standard identification method. The results obtained by MS concordant with genes sequencing, although discordant with conventional phenotyping, were considered correct. MS results discordant with 16S or sod A identification were considered incorrect. Using the score cut-offs recommended by the manufacturer, 97.37% and 81.05% were correctly identified to genus and species level, respectively. On the other hand, using lower cut-off scores for identification, 97.89% and 94.21% isolates were correctly identified to genus and species level respectively by MALDI-TOF MS and no significant differences between the results obtained with two extraction methods were obtained. The results obtained suggest that MALDI-TOF MS has the potential of being an accurate tool for Catalase-negative GPC identification even for those species with difficult diagnosis as Helcococcus , Abiotrophia , Granulicatella , among others. Nevertheless, expansion of the library, especially including more strains with

  8. HPLC-UV, MALDI-TOF-MS and ESI-MS/MS analysis of the mechlorethamine DNA crosslink at a cytosine-cytosine mismatch pair.

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    Pornchai Rojsitthisak

    Full Text Available Mechlorethamine [ClCH(2CH(2N(CH(3CH(2CH(2Cl], a nitrogen mustard alkylating agent, has been proven to form a DNA interstrand crosslink at a cytosine-cytosine (C-C mismatch pair using gel electrophoresis. However, the atomic connectivity of this unusual crosslink is unknown.HPLC-UV, MALDI-TOF-MS, and ESI-MS/MS were used to determine the atomic connectivity of the DNA C-C crosslink formed by mechlorethamine, MALDI-TOF-MS of the HPLC-purified reaction product of mechlorethamine with the DNA duplex d[CTCACACCGTGGTTC]•d[GAACCACCGTGTGAG] (underlined bases are a C-C mismatch pair indicated formation of an interstrand crosslink at m/z 9222.088 [M-2H+Na](+. Following enzymatic digestion of the crosslinked duplex by snake venom phosphodiesterase and calf intestinal phosphatase, ESI-MS/MS indicated the presence of dC-mech-dC [mech = CH(2CH(2N(CH(3CH(2CH(2] at m/z 269.2 [M](2+ (expected m/z 269.6, exact mass 539.27 and its hydrolytic product dC-mech-OH at m/z 329.6 [M](+ (expected m/z 329.2. Fragmentation of dC-mech-dC gave product ions at m/z 294.3 and 236.9 [M](+, which are both due to loss of the 4-amino group of cytosine (as ammonia, in addition to dC and dC+HN(CH(3CH = CH(2, respectively. The presence of m/z 269.2 [M](2+ and loss of ammonia exclude crosslink formation at cytosine N(4 or O(2 and indicate crosslinking through cytosine N(3 with formation of two quaternary ammonium ions.Our results provide an important addition to the literature, as the first example of the use of HPLC and MS for analysis of a DNA adduct at the N(3 position of cytosine.

  9. MALDI-TOF MS for the Identification of Cultivable Organic-Degrading Bacteria in Contaminated Groundwater near Unconventional Natural Gas Extraction Sites

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    Inês C. Santos

    2017-08-01

    Full Text Available Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have been performed to understand if these activities are causing groundwater contamination, particularly with respect to exogenous hydrocarbons and volatile organic compounds. The impact of contaminants on microbial ecology is an area to be explored as alternatives for water treatment are necessary. In this work, we identified cultivable organic-degrading bacteria in groundwater in close proximity to unconventional natural gas extraction. Pseudomonas stutzeri and Acinetobacter haemolyticus were identified using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF MS, which proved to be a simple, fast, and reliable method. Additionally, the potential use of the identified bacteria in water and/or wastewater bioremediation was studied by determining the ability of these microorganisms to degrade toluene and chloroform. In fact, these bacteria can be potentially applied for in situ bioremediation of contaminated water and wastewater treatment, as they were able to degrade both compounds.

  10. MALDI-TOF MS for the Identification of Cultivable Organic-Degrading Bacteria in Contaminated Groundwater near Unconventional Natural Gas Extraction Sites.

    Science.gov (United States)

    Santos, Inês C; Martin, Misty S; Carlton, Doug D; Amorim, Catarina L; Castro, Paula M L; Hildenbrand, Zacariah L; Schug, Kevin A

    2017-08-10

    Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have been performed to understand if these activities are causing groundwater contamination, particularly with respect to exogenous hydrocarbons and volatile organic compounds. The impact of contaminants on microbial ecology is an area to be explored as alternatives for water treatment are necessary. In this work, we identified cultivable organic-degrading bacteria in groundwater in close proximity to unconventional natural gas extraction. Pseudomonas stutzeri and Acinetobacter haemolyticus were identified using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF MS), which proved to be a simple, fast, and reliable method. Additionally, the potential use of the identified bacteria in water and/or wastewater bioremediation was studied by determining the ability of these microorganisms to degrade toluene and chloroform. In fact, these bacteria can be potentially applied for in situ bioremediation of contaminated water and wastewater treatment, as they were able to degrade both compounds.

  11. Atypical yeasts identified as Saccharomyces cerevisiae by MALDI-TOF MS and gene sequencing are the main responsible of fermentation of chicha, a traditional beverage from Peru.

    Science.gov (United States)

    Vallejo, Juan Andrés; Miranda, Patricia; Flores-Félix, José David; Sánchez-Juanes, Fernando; Ageitos, José M; González-Buitrago, José Manuel; Velázquez, Encarna; Villa, Tomás G

    2013-12-01

    Chicha is a drink prepared in several Andean countries from Inca's times by maize fermentation. Currently this fermentation is carried out in familiar artesanal "chicherías" that make one of the most known types of chicha, the "chicha de jora". In this study we isolate and identify the yeasts mainly responsible of the fermentation process in this type of chicha in 10 traditional "chicherías" in Cusco region in Peru. We applied by first time MALDI-TOF MS analysis for the identification of yeast of non-clinic origin and the results showed that all of yeast strains isolated belong to the species Saccharomyces cerevisiae. These results agree with those obtained after the analysis of the D1/D2 and 5.8S-ITS regions. However the chicha strains have a phenotypic profile that differed in more than 40% as compared to that of current S. cerevisiae strains. To the best of our knowledge this is the first report concerning the yeasts involved in chicha fermentation. Copyright © 2013 Elsevier GmbH. All rights reserved.

  12. Characterization of Proteins Present in Isolated Senile Plaques from Alzheimer's Diseased Brains by MALDI-TOF MS with MS/MS.

    Science.gov (United States)

    Kelley, Andrea R; Perry, George; Bach, Stephan B H

    2018-04-18

    The increase of insoluble senile plaques in the brain is a primary hallmark of Alzheimer's disease. The usefulness of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with tandem MS for the characterization of senile plaques from AD brains and the relevance of the components identified to furthering AD research using MS is discussed. Thirty-three components were reproducibly observed within tryptic aliquots of senile plaques from two different AD brains after sample preparation optimization. Additionally, this is one of the first accounts of LIFT being utilized for the direct sequencing of peptides from isolated senile plaques. While many of the species observed coisolated within senile plaques have been linked to AD etiology, if only speculatively, this is the first instance that many of them have been demonstrated to be a part of the plaques themselves. This work is the first step in determining the potential roles that the species may have in the aggregation or proliferation of the plaques.

  13. Proteome-based bacterial identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS): A revolutionary shift in clinical diagnostic microbiology.

    Science.gov (United States)

    Nomura, Fumio

    2015-06-01

    Rapid and accurate identification of microorganisms, a prerequisite for appropriate patient care and infection control, is a critical function of any clinical microbiology laboratory. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a quick and reliable method for identification of microorganisms, including bacteria, yeast, molds, and mycobacteria. Indeed, there has been a revolutionary shift in clinical diagnostic microbiology. In the present review, the state of the art and advantages of MALDI-TOF MS-based bacterial identification are described. The potential of this innovative technology for use in strain typing and detection of antibiotic resistance is also discussed. This article is part of a Special Issue entitled: Medical Proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS.

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    Mohammed Almuhayawi

    Full Text Available Detection and identification of anaerobic bacteria in blood cultures (BC is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux, BACTEC-Plus and -Lytic (Becton Dickinson BioSciences BC bottles in detection and time to detection (TTD of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94% than BacT/ALERT FN Plus (80/100, 80% (p<0.01 in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001. The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h, BACTEC Plus (27 h and finally BacT/ALERT FN Plus (38 h bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76% BacT/ALERT FN, 51/67 (76% BacT/ALERT FN Plus, 53/67 (79% BACTEC Plus and 50/67 (75% BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS.

  15. Direct identification of microorganisms from positive blood cultures using the lysis-filtration technique and matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS): a multicentre study.

    Science.gov (United States)

    Farina, Claudio; Arena, Fabio; Casprini, Patrizia; Cichero, Paola; Clementi, Massimo; Cosentino, Marina; Degl'Innocenti, Roberto; Giani, Tommaso; Luzzaro, Francesco; Mattei, Romano; Mauri, Carola; Nardone, Maria; Rossolini, Gian Maria; Serna Ortega, Paula Andrea; Vailati, Francesca

    2015-04-01

    Microbial identification from blood cultures is essential to institute optimal antibiotic therapy and improve survival possibilities. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied to identify bacteria and yeasts from positive blood cultures broths. The aim of this multicentre study was to evaluate the reliability of the lysis-filtration technique associated with MALDI-TOF MS to directly identify microorganisms from 765 positive blood cultures collected in six Italian hospitals. Overall, 675/765 (78.1%) blood isolates were correctly identified at the species level, with significant differences between Gram-negative and Gram-positive bacteria (92.6%, and 69.8%, respectively). Some difficulties arise in identifying Streptococcus pneumoniae, Staphylococcus aureus, yeasts and anaerobes. The lysis-filtration protocol is a suitable procedure in terms of performance in identifying microorganisms, but it is quite expensive and technically time-consuming since the time of filtration is not regular for all the samples. The application of the MALDI-TOF MS technique to the direct microbial identification from positive blood cultures is a very promising approach, even if more experience must be gained to minimize errors and costs.

  16. Direct identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS from positive blood culture bottles: An opportunity to customize growth conditions for fastidious organisms causing bloodstream infections

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    Megha Sharma

    2017-01-01

    Full Text Available Culture-negative bacteraemia has been an enigmatic entity with respect to its aetiological agents. In an attempt to actively identify those positive blood cultures that escape isolation and detection on routine workflow, an additional step of MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry based detection was carried out directly from the flagged blood culture bottles. Blood samples from 200 blood culture bottles that beeped positive with automated (BACTEC system and showed no growth of organism on routine culture media, were subjected to analysis by MALDI-TOF MS. Forty seven of the 200 (23.5% bacterial aetiology could be established by bottle-based method. Based on these results, growth on culture medium could be achieved for the isolates by providing special growth conditions to the fastidious organisms. Direct identification by MALDI-TOF MS from BACTEC-positive bottles provided an opportunity to isolate those fastidious organisms that failed to grow on routine culture medium by providing them with necessary alterations in growth environment.

  17. Direct identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from positive blood culture bottles: An opportunity to customize growth conditions for fastidious organisms causing bloodstream infections.

    Science.gov (United States)

    Sharma, Megha; Gautam, Vikas; Mahajan, Monika; Rana, Sudesh; Majumdar, Manasi; Ray, Pallab

    2017-10-01

    Culture-negative bacteraemia has been an enigmatic entity with respect to its aetiological agents. In an attempt to actively identify those positive blood cultures that escape isolation and detection on routine workflow, an additional step of MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) based detection was carried out directly from the flagged blood culture bottles. Blood samples from 200 blood culture bottles that beeped positive with automated (BACTEC) system and showed no growth of organism on routine culture media, were subjected to analysis by MALDI-TOF MS. Forty seven of the 200 (23.5%) bacterial aetiology could be established by bottle-based method. Based on these results, growth on culture medium could be achieved for the isolates by providing special growth conditions to the fastidious organisms. Direct identification by MALDI-TOF MS from BACTEC-positive bottles provided an opportunity to isolate those fastidious organisms that failed to grow on routine culture medium by providing them with necessary alterations in growth environment.

  18. The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS.

    Science.gov (United States)

    Almuhayawi, Mohammed; Altun, Osman; Abdulmajeed, Adam Dilshad; Ullberg, Måns; Özenci, Volkan

    2015-01-01

    Detection and identification of anaerobic bacteria in blood cultures (BC) is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux), BACTEC-Plus and -Lytic (Becton Dickinson BioSciences) BC bottles in detection and time to detection (TTD) of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94%) than BacT/ALERT FN Plus (80/100, 80%) (panaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD) and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (panaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS.

  19. Probing the 3-D Structure, Dynamics, and Stability of Bacterial Collagenase Collagen Binding Domain (apo- versus holo-) by Limited Proteolysis MALDI-TOF MS

    Science.gov (United States)

    Sides, Cynthia R.; Liyanage, Rohana; Lay, Jackson O.; Philominathan, Sagaya Theresa Leena; Matsushita, Osamu; Sakon, Joshua

    2012-03-01

    Pairing limited proteolysis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to probe clostridial collagenase collagen binding domain (CBD) reveals the solution dynamics and stability of the protein, as these factors are crucial to CBD effectiveness as a drug-delivery vehicle. MS analysis of proteolytic digests indicates initial cleavage sites, thereby specifying the less stable and highly accessible regions of CBD. Modulation of protein structure and stability upon metal binding is shown through MS analysis of calcium-bound and cobalt-bound CBD proteolytic digests. Previously determined X-ray crystal structures illustrate that calcium binding induces secondary structure transformation in the highly mobile N-terminal arm and increases protein stability. MS-based detection of exposed residues confirms protein flexibility, accentuates N-terminal dynamics, and demonstrates increased global protein stability exported by calcium binding. Additionally, apo- and calcium-bound CBD proteolysis sites correlate well with crystallographic B-factors, accessibility, and enzyme specificity. MS-observed cleavage sites with no clear correlations are explained either by crystal contacts of the X-ray crystal structures or by observed differences between Molecules A and B in the X-ray crystal structures. The study newly reveals the absence of the βA strand and thus the very dynamic N-terminal linker, as corroborated by the solution X-ray scattering results. Cobalt binding has a regional effect on the solution phase stability of CBD, as limited proteolysis data implies the capture of an intermediate-CBD solution structure when cobalt is bound.

  20. Characterization of Multidrug Resistant E. faecalis Strains from Pigs of Local Origin by ADSRRS-Fingerprinting and MALDI -TOF MS; Evaluation of the Compatibility of Methods Employed for Multidrug Resistance Analysis.

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    Aneta Nowakiewicz

    Full Text Available The aim of this study was to characterize multidrug resistant E. faecalis strains from pigs of local origin and to analyse the relationship between resistance and genotypic and proteomic profiles by amplification of DNA fragments surrounding rare restriction sites (ADSRRS-fingerprinting and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI -TOF MS. From the total pool of Enterococcus spp. isolated from 90 pigs, we selected 36 multidrug resistant E. faecalis strains, which represented three different phenotypic resistance profiles. Phenotypic resistance to tetracycline, macrolides, phenicols, and lincomycin and high-level resistance to aminoglycosides were confirmed by the occurrence of at least one corresponding resistance gene in each strain. Based on the analysis of the genotypic and phenotypic resistance of the strains tested, five distinct resistance profiles were generated. As a complement of this analysis, profiles of virulence genes were determined and these profiles corresponded to the phenotypic resistance profiles. The demonstration of resistance to a wide panel of antimicrobials by the strains tested in this study indicates the need of typing to determine the spread of resistance also at the local level. It seems that in the case of E. faecalis, type and scope of resistance strongly determines the genotypic pattern obtained with the ADSRRS-fingerprinting method. The ADSRRS-fingerprinting analysis showed consistency of the genetic profiles with the resistance profiles, while analysis of data with the use of the MALDI- TOF MS method did not demonstrate direct reproduction of the clustering pattern obtained with this method. Our observations were confirmed by statistical analysis (Simpson's index of diversity, Rand and Wallace coefficients. Even though the MALDI -TOF MS method showed slightly higher discrimination power than ADSRRS-fingerprinting, only the latter method allowed reproduction of the

  1. Evaluación de la espectrometría de masas: MALDI-TOF MS para la identificación rápida y confiable de levaduras

    Directory of Open Access Journals (Sweden)

    María S Relloso

    2015-06-01

    Full Text Available La espectrometría de masas, conocida como matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS, es una técnica utilizada en la identificación de microorganismos mediante la creación de un espectro basado en el perfil de proteínas, que es único para una especie dada. El objetivo del presente trabajo fue evaluar la identificación de aislamientos clínicos de levaduras por MALDI-TOF MS en un hospital universitario de Argentina y analizar 2 procedimientos para la extracción de proteínas: el recomendado por el fabricante del equipo y una técnica abreviada rápida. Utilizando el primero de estos procedimientos se analizaron 201 aislamientos identificados previamente por métodos convencionales y se obtuvo coincidencia en la identificación a nivel de especie en el 95,38 % de los aislamientos analizados. Con 100 de estos aislamientos se utilizó, además, el procedimiento abreviado para la extracción de proteínas; se obtuvo una identificación correcta a nivel de género y especie en el 98,0 % de ellos. La espectrometría de masas MALDI-TOF MS demostró ser una técnica rápida, sencilla y precisa para la identificación de levaduras.

  2. MALDI-TOF MS as a Tool To Detect a Nosocomial Outbreak of Extended-Spectrum-β-Lactamase- and ArmA Methyltransferase-Producing Enterobacter cloacae Clinical Isolates in Algeria.

    Science.gov (United States)

    Khennouchi, Nour Chems el Houda; Loucif, Lotfi; Boutefnouchet, Nafissa; Allag, Hamoudi; Rolain, Jean-Marc

    2015-10-01

    Enterobacter cloacae is among the most important pathogens responsible for nosocomial infections and outbreaks. In this study, 77 Enterobacter isolates were collected: 27 isolates from Algerian hospitals (in Constantine, Annaba, and Skikda) and 50 isolates from Marseille, France. All strains were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility testing was performed by the disk diffusion method. PCR was used to detect extended-spectrum-beta-lactamase (ESBL)-encoding, fluoroquinolone resistance-encoding, and aminoglycoside-modifying enzyme (AME) genes. Epidemiological typing was performed using MALDI-TOF MS with data mining approaches, along with multilocus sequence typing (MLST). Sixty-eight isolates (27 from Algeria, 41 from Marseille) were identified by MALDI-TOF MS as E. cloacae. Resistance to antibiotics in the Algerian isolates was significantly higher than that in the strains from Marseille, especially for beta-lactams and aminoglycosides. Eighteen of the 27 Algerian isolates and 11 of the 41 Marseille isolates possessed at least one ESBL-encoding gene: blaCTX-M and/or blaTEM. AME genes were detected in 20 of the 27 Algerian isolates and 8 of the 41 Marseille isolates [ant(2″)-Ia, aac(6')-Ib-cr, aadA1, aadA2, and armA]. Conjugation experiments showed that armA was carried on a transferable plasmid. MALDI-TOF typing showed three separate clusters according to the geographical distribution and species level. An MLST-based phylogenetic tree showed a clade of 14 E. cloacae isolates from a urology unit clustering together in the MALDI-TOF dendrogram, suggesting the occurrence of an outbreak in this unit. In conclusion, the ability of MALDI-TOF to biotype strains was confirmed, and surveillance measures should be implemented, especially for Algerian patients hospitalized in France. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  3. Ribosomal subunit protein typing using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification and discrimination of Aspergillus species.

    Science.gov (United States)

    Nakamura, Sayaka; Sato, Hiroaki; Tanaka, Reiko; Kusuya, Yoko; Takahashi, Hiroki; Yaguchi, Takashi

    2017-04-26

    Accurate identification of Aspergillus species is a very important subject. Mass spectral fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is generally employed for the rapid identification of fungal isolates. However, the results are based on simple mass spectral pattern-matching, with no peak assignment and no taxonomic input. We propose here a ribosomal subunit protein (RSP) typing technique using MALDI-TOF MS for the identification and discrimination of Aspergillus species. The results are concluded to be phylogenetic in that they reflect the molecular evolution of housekeeping RSPs. The amino acid sequences of RSPs of genome-sequenced strains of Aspergillus species were first verified and compared to compile a reliable biomarker list for the identification of Aspergillus species. In this process, we revealed that many amino acid sequences of RSPs (about 10-60%, depending on strain) registered in the public protein databases needed to be corrected or newly added. The verified RSPs were allocated to RSP types based on their mass. Peak assignments of RSPs of each sample strain as observed by MALDI-TOF MS were then performed to set RSP type profiles, which were then further processed by means of cluster analysis. The resulting dendrogram based on RSP types showed a relatively good concordance with the tree based on β-tubulin gene sequences. RSP typing was able to further discriminate the strains belonging to Aspergillus section Fumigati. The RSP typing method could be applied to identify Aspergillus species, even for species within section Fumigati. The discrimination power of RSP typing appears to be comparable to conventional β-tubulin gene analysis. This method would therefore be suitable for species identification and discrimination at the strain to species level. Because RSP typing can characterize the strains within section Fumigati, this method has potential as a powerful and reliable tool in

  4. An evaluation of three processing methods and the effect of reduced culture times for faster direct identification of pathogens from BacT/ALERT blood cultures by MALDI-TOF MS.

    Science.gov (United States)

    Loonen, A J M; Jansz, A R; Stalpers, J; Wolffs, P F G; van den Brule, A J C

    2012-07-01

    Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is a fast and reliable method for the identification of bacteria from agar media. Direct identification from positive blood cultures should decrease the time to obtaining the result. In this study, three different processing methods for the rapid direct identification of bacteria from positive blood culture bottles were compared. In total, 101 positive aerobe BacT/ALERT bottles were included in this study. Aliquots from all bottles were used for three bacterial processing methods, i.e. the commercially available Bruker's MALDI Sepsityper kit, the commercially available Molzym's MolYsis Basic5 kit and a centrifugation/washing method. In addition, the best method was used to evaluate the possibility of MALDI application after a reduced incubation time of 7 h of Staphylococcus aureus- and Escherichia coli-spiked (1,000, 100 and 10 colony-forming units [CFU]) aerobe BacT/ALERT blood cultures. Sixty-six (65%), 51 (50.5%) and 79 (78%) bottles were identified correctly at the species level when the centrifugation/washing method, MolYsis Basic 5 and Sepsityper were used, respectively. Incorrect identification was obtained in 35 (35%), 50 (49.5%) and 22 (22%) bottles, respectively. Gram-positive cocci were correctly identified in 33/52 (64%) of the cases. However, Gram-negative rods showed a correct identification in 45/47 (96%) of all bottles when the Sepsityper kit was used. Seven hours of pre-incubation of S. aureus- and E. coli-spiked aerobe BacT/ALERT blood cultures never resulted in reliable identification with MALDI-TOF MS. Sepsityper is superior for the direct identification of microorganisms from aerobe BacT/ALERT bottles. Gram-negative pathogens show better results compared to Gram-positive bacteria. Reduced incubation followed by MALDI-TOF MS did not result in faster reliable identification.

  5. A statistical design of experiments for optimizing the MALDI-TOF-MS sample preparation of polymers. An application in the assessment of the thermo-mechanical degradation mechanisms of poly (ethylene terephthalate)

    International Nuclear Information System (INIS)

    Badia, J.D.; Stroemberg, E.; Ribes-Greus, A.; Karlsson, S.

    2011-01-01

    The sample preparation procedure for MALDI-TOF MS of polymers is addressed in this study by the application of a statistical Design of Experiments (DoE). Industrial poly (ethylene terephthalate) (PET) was chosen as model polymer. Different experimental settings (levels) for matrixes, analyte/matrix proportions and concentrations of cationization agent were considered. The quality parameters used for the analysis were signal-to-noise ratio and resolution. A closer inspection of the statistical results provided the study not only with the best combination of factors for the MALDI sample preparation, but also with a better understanding of the influence of the different factors, individually or in combination, to the signal. The application of DoE for the improvement of the MALDI measure of PET stated that the best combination of factors and levels was the following: matrix (dithranol), proportion analyte/matrix/cationization agent (1/15/1, V/V/V), and concentration of cationization agent (2 g L -1 ). In a second part, multiple processing by means of successive injection cycles was used to simulate the thermo-mechanical degradation effects on the oligomeric distribution of PET under mechanical recycling. The application of MALDI-TOF-MS showed that thermo-mechanical degradation primarily affected initially predominant cyclic species. Several degradation mechanisms were proposed, remarking intramolecular transesterification and hydrolysis. The ether links of the glycol unit in PET were shown to act as potential reaction sites, driving the main reactions of degradation.

  6. Source-identifying biomarker ions between environmental and clinical Burkholderia pseudomallei using whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Niyompanich, Suthamat; Jaresitthikunchai, Janthima; Srisanga, Kitima; Roytrakul, Sittiruk; Tungpradabkul, Sumalee

    2014-01-01

    Burkholderia pseudomallei is the causative agent of melioidosis, which is an endemic disease in Northeast Thailand and Northern Australia. Environmental reservoirs, including wet soils and muddy water, serve as the major sources for contributing bacterial infection to both humans and animals. The whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (whole-cell MALDI-TOF MS) has recently been applied as a rapid, accurate, and high-throughput tool for clinical diagnosis and microbiological research. In this present study, we employed a whole-cell MALDI-TOF MS approach for assessing its potency in clustering a total of 11 different B. pseudomallei isolates (consisting of 5 environmental and 6 clinical isolates) with respect to their origins and to further investigate the source-identifying biomarker ions belonging to each bacterial group. The cluster analysis demonstrated that six out of eleven isolates were grouped correctly to their sources. Our results revealed a total of ten source-identifying biomarker ions, which exhibited statistically significant differences in peak intensity between average environmental and clinical mass spectra using ClinProTools software. Six out of ten mass ions were assigned as environmental-identifying biomarker ions (EIBIs), including, m/z 4,056, 4,214, 5,814, 7,545, 7,895, and 8,112, whereas the remaining four mass ions were defined as clinical-identifying biomarker ions (CIBIs) consisting of m/z 3,658, 6,322, 7,035, and 7,984. Hence, our findings represented, for the first time, the source-specific biomarkers of environmental and clinical B. pseudomallei.

  7. Conventional Morphology Versus PCR Sequencing, rep-PCR, and MALDI-TOF-MS for Identification of Clinical Aspergillus Isolates Collected Over a 2-Year Period in a University Hospital at Kayseri, Turkey.

    Science.gov (United States)

    Atalay, Altay; Koc, Ayse Nedret; Suel, Ahmet; Sav, Hafize; Demir, Gonca; Elmali, Ferhan; Cakir, Nuri; Seyedmousavi, Seyedmojtaba

    2016-09-01

    Aspergillus species cause a wide range of diseases in humans, including allergies, localized infections, or fatal disseminated diseases. Rapid detection and identification of Aspergillus spp. facilitate effective patient management. In the current study we compared conventional morphological methods with PCR sequencing, rep-PCR, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for the identification of Aspergillus strains. A total of 24 consecutive clinical isolates of Aspergillus were collected during 2012-2014. Conventional morphology and rep-PCR were performed in our Mycology Laboratory. The identification, evaluation, and reporting of strains using MALDI-TOF-MS were performed by BioMérieux Diagnostic, Inc. in Istanbul. DNA sequence analysis of the clinical isolates was performed by the BMLabosis laboratory in Ankara. Samples consisted of 18 (75%) lower respiratory tract specimens, 3 otomycosis (12.5%) ear tissues, 1 sample from keratitis, and 1 sample from a cutaneous wound. According to DNA sequence analysis, 12 (50%) specimens were identified as A. fumigatus, 8 (33.3%) as A. flavus, 3 (12.5%) as A. niger, and 1 (4.2%) as A. terreus. Statistically, there was good agreement between the conventional morphology and rep-PCR and MALDI-TOF methods; kappa values were κ = 0.869, 0.871, and 0.916, respectively (P < 0.001). The good level of agreement between the methods included in the present study and sequence method could be due to the identification of Aspergillus strains that were commonly encountered. Therefore, it was concluded that studies conducted with a higher number of isolates, which include other Aspergillus strains, are required. © 2016 Wiley Periodicals, Inc.

  8. The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Based Typing: Employment of Bioinformatics in a Multicenter Study.

    Science.gov (United States)

    Oberle, Michael; Wohlwend, Nadia; Jonas, Daniel; Maurer, Florian P; Jost, Geraldine; Tschudin-Sutter, Sarah; Vranckx, Katleen; Egli, Adrian

    2016-01-01

    The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains. Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP) including a full-protein extraction protocol. All laboratories provided visually read spectra via flexAnalysis (Bruker, Germany). Raw data from each laboratory allowed calculating the technical and biological reproducibility between centers using BioNumerics (Applied Maths NV, Belgium). Technical and biological reproducibility ranged between 96.8-99.4% and 47.6-94.4%, respectively. The inter-center reproducibility showed a comparable clustering among identical isolates. Principal component analysis indicated a higher tendency to cluster within the same center. Therefore, we used a discriminant analysis, which completely separated the clusters. Next, we defined a reference center and performed a statistical analysis to identify specific peaks to identify the outbreak clusters. Finally, we used a classifier algorithm and a linear support vector machine on the determined peaks as classifier. A validation showed that within the set of the reference center, the identification of the cluster was 100% correct with a large contrast between the score with the correct cluster and the next best scoring cluster. Based on the sufficient technical and biological reproducibility of MALDI-TOF MS based spectra, detection of specific clusters is possible from spectra obtained from different centers. However, we believe that a shared SOP and a bioinformatics approach are required to make the analysis robust and reliable.

  9. The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS Based Typing: Employment of Bioinformatics in a Multicenter Study.

    Directory of Open Access Journals (Sweden)

    Michael Oberle

    Full Text Available The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains.Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP including a full-protein extraction protocol. All laboratories provided visually read spectra via flexAnalysis (Bruker, Germany. Raw data from each laboratory allowed calculating the technical and biological reproducibility between centers using BioNumerics (Applied Maths NV, Belgium.Technical and biological reproducibility ranged between 96.8-99.4% and 47.6-94.4%, respectively. The inter-center reproducibility showed a comparable clustering among identical isolates. Principal component analysis indicated a higher tendency to cluster within the same center. Therefore, we used a discriminant analysis, which completely separated the clusters. Next, we defined a reference center and performed a statistical analysis to identify specific peaks to identify the outbreak clusters. Finally, we used a classifier algorithm and a linear support vector machine on the determined peaks as classifier. A validation showed that within the set of the reference center, the identification of the cluster was 100% correct with a large contrast between the score with the correct cluster and the next best scoring cluster.Based on the sufficient technical and biological reproducibility of MALDI-TOF MS based spectra, detection of specific clusters is possible from spectra obtained from different centers. However, we believe that a shared SOP and a bioinformatics approach are required to make the analysis robust and reliable.

  10. Analysis of Wheat Prolamins, the Causative Agents of Celiac Sprue, Using Reversed Phase High Performance Liquid Chromatography (RP-HPLC and Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS

    Directory of Open Access Journals (Sweden)

    Jaime H. Mejías

    2014-04-01

    Full Text Available Wheat prolamins, commonly known as “gluten”, are a complex mixture of 71–78 proteins, which constitute ~80% of the proteins in the wheat grains and supply 50% of the global dietary protein demand. Prolamins are also responsible for numerous gluten-induced disorders and determine the unique visco-elastic properties of the wheat dough. These properties necessitate the reliable determination of the prolamin composition in wheat grains and their derived products. Therefore, this study examined the impact of HPLC conditions, including column type, column temperature, flow rate, and the gradient of polar and non-polar solvents in the mobile phase, to improve the analytical resolution of prolamins. The following conditions were found optimal for analyses: column temperature 60 °C, flow rate 1.0 mL/min and an elution gradient of 20%–60% of 0.1% trifluoroacetic acid + acetonitrile in 60 min. For further improvement of resolution, gliadin and glutenin extracts were analyzed using MALDI-TOF-MS in combination with HPLC fractionation. Two semi-quantitative methods, densitometry of stained polyacrylamide gels and HPLC, were used to determine relative prolamin quantities and the correspondence between the methods was established. The combinatorial gluten analyses approach developed during the present study was used to analyze prolamin profiles of wheat transformants expressing DEMETER silencing artificial microRNA, and the results are discussed.

  11. Methylobacterium Species Promoting Rice and Barley Growth and Interaction Specificity Revealed with Whole-Cell Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF/MS Analysis.

    Directory of Open Access Journals (Sweden)

    Akio Tani

    Full Text Available Methylobacterium species frequently inhabit plant surfaces and are able to utilize the methanol emitted from plants as carbon and energy sources. As some of the Methylobacterium species are known to promote plant growth, significant attention has been paid to the mechanism of growth promotion and the specificity of plant-microbe interactions. By screening our Methylobacterium isolate collection for the high growth promotion effect in vitro, we selected some candidates for field and pot growth tests for rice and barley, respectively. We found that inoculation resulted in better ripening of rice seeds, and increased the size of barley grains but not the total yield. In addition, using whole-cell matrix-assister laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS analysis, we identified and classified Methylobacterium isolates from Methylobacterium-inoculated rice plants. The inoculated species could not be recovered from the rice plants, and in some cases, the Methylobacterium community structure was affected by the inoculation, but not with predomination of the inoculated species. The isolates from non-inoculated barley of various cultivars grown in the same field fell into just two species. These results suggest that there is a strong selection pressure at the species level of Methylobacterium residing on a given plant species, and that selection of appropriate species that can persist on the plant is important to achieve growth promotion.

  12. Lipidomic fingerprint of almonds (Prunus dulcis L. cv Nonpareil) using TiO₂ nanoparticle based matrix solid-phase dispersion and MALDI-TOF/MS and its potential in geographical origin verification.

    Science.gov (United States)

    Shen, Qing; Dong, Wei; Yang, Mei; Li, Linqiu; Cheung, Hon-Yeung; Zhang, Zhifeng

    2013-08-14

    A matrix solid-phase dispersion (MSPD) procedure with titanium dioxide (TiO2) nanoparticles (NP) as sorbent was developed for the selective extraction of phospholipids from almond samples, and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) was employed for analysis. A remarkable increase in the signals of phospholipid accompanied by a decrease in those of triacylglycerols and diacylglycerols was observed in the relevant mass spectra. The proposed method was applied to five batches of almonds originating from four geographical areas, whereas principal component analysis (PCA) was utilized to normalize the relative amounts of the identified phospholipid species. The results indicated that the lipidomic fingerprint of almonds was successfully established by the negative ion mode spectrum, and the ratio of m/z 833.6 to 835.6 as well as m/z 821.6 could be introduced as potential markers for the differentiation of the tested almonds with different geographical origins. The whole method is of great promise for selective separation of phospholipids from nonphospholipids, especially the glycerides, and superior in fast screening and characterization of phospholipids in almond samples.

  13. A silicon nanomembrane detector for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of large proteins.

    Science.gov (United States)

    Park, Jonghoo; Blick, Robert H

    2013-10-11

    We describe a MALDI-TOF ion detector based on freestanding silicon nanomembrane technology. The detector is tested in a commercial MALDI-TOF mass spectrometer with equimolar mixtures of proteins. The operating principle of the nanomembrane detector is based on phonon-assisted field emission from these silicon nanomembranes, in which impinging ion packets excite electrons in the nanomembrane to higher energy states. Thereby the electrons can overcome the vacuum barrier and escape from the surface of the nanomembrane via field emission. Ion detection is demonstrated of apomyoglobin (16,952 Da), aldolase (39,212 Da), bovine serum albumin (66,430 Da), and their equimolar mixtures. In addition to the three intact ions, a large number of fragment ions are also revealed by the silicon nanomembrane detector, which are not observable with conventional detectors.

  14. A Silicon Nanomembrane Detector for Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS of Large Proteins

    Directory of Open Access Journals (Sweden)

    Jonghoo Park

    2013-10-01

    Full Text Available We describe a MALDI-TOF ion detector based on freestanding silicon nanomembrane technology. The detector is tested in a commercial MALDI-TOF mass spectrometer with equimolar mixtures of proteins. The operating principle of the nanomembrane detector is based on phonon-assisted field emission from these silicon nanomembranes, in which impinging ion packets excite electrons in the nanomembrane to higher energy states. Thereby the electrons can overcome the vacuum barrier and escape from the surface of the nanomembrane via field emission. Ion detection is demonstrated of apomyoglobin (16,952 Da, aldolase (39,212 Da, bovine serum albumin (66,430 Da, and their equimolar mixtures. In addition to the three intact ions, a large number of fragment ions are also revealed by the silicon nanomembrane detector, which are not observable with conventional detectors.

  15. Microorganism Identification Based On MALDI-TOF-MS Fingerprints

    Science.gov (United States)

    Elssner, Thomas; Kostrzewa, Markus; Maier, Thomas; Kruppa, Gary

    Advances in MALDI-TOF mass spectrometry have enabled the ­development of a rapid, accurate and specific method for the identification of bacteria directly from colonies picked from culture plates, which we have named the MALDI Biotyper. The picked colonies are placed on a target plate, a drop of matrix solution is added, and a pattern of protein molecular weights and intensities, "the protein fingerprint" of the bacteria, is produced by the MALDI-TOF mass spectrometer. The obtained protein mass fingerprint representing a molecular signature of the microorganism is then matched against a database containing a library of previously measured protein mass fingerprints, and scores for the match to every library entry are produced. An ID is obtained if a score is returned over a pre-set threshold. The sensitivity of the techniques is such that only approximately 104 bacterial cells are needed, meaning that an overnight culture is sufficient, and the results are obtained in minutes after culture. The improvement in time to result over biochemical methods, and the capability to perform a non-targeted identification of bacteria and spores, potentially makes this method suitable for use in the detect-to-treat timeframe in a bioterrorism event. In the case of white-powder samples, the infectious spore is present in sufficient quantity in the powder so that the MALDI Biotyper result can be obtained directly from the white powder, without the need for culture. While spores produce very different patterns from the vegetative colonies of the corresponding bacteria, this problem is overcome by simply including protein fingerprints of the spores in the library. Results on spores can be returned within minutes, making the method suitable for use in the "detect-to-protect" timeframe.

  16. Serum peptide expression and treatment responses in patients with advanced non-small-cell lung cancer

    Science.gov (United States)

    An, Juan; Tang, Chuan-Hao; Wang, Na; Liu, Yi; Lv, Jin; Xu, Bin; Li, Xiao-Yan; Guo, Wan-Feng; Gao, Hong-Jun; He, Kun; Liu, Xiao-Qing

    2018-01-01

    Epidermal growth factor receptor (EGFR) mutation is an important predictor for response to personalized treatments of patients with advanced non-small-cell lung cancer (NSCLC). However its usage is limited due to the difficult of obtaining tissue specimens. A novel prediction system using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been reported to be a perspective tool in European countries to identify patients who are likely to benefit from EGFR tyrosine kinase inhibitor (TKI) treatment. In the present study, MALDI-TOF MS was used on pretreatment serum samples of patients with advanced non-small-cell lung cancer to discriminate the spectra between disease control and disease progression groups in one cohort of Chinese patients. The candidate features for classification were subsequently validated in a blinded fashion in another set of patients. The correlation between plasma EGFR mutation status and the intensities of representative spectra for classification was evaluated. A total of 103 patients that were treated with EGFR-TKIs were included. It was determined that 8 polypeptides peaks were significant different between the disease control and disease progression group. A total of 6 polypeptides were established in the classification algorithm. The sensitivity of the algorithm to predict treatment responses was 76.2% (16/21) and the specificity was 81.8% (18/22). The accuracy rate of the algorithm was 79.1% (34/43). A total of 3 polypeptides were significantly correlated with EGFR mutations (P=0.04, P=0.03 and P=0.04, respectively). The present study confirmed that MALDI-TOF MS analysis can be used to predict responses to EGFR-TKI treatment of the Asian population where the EGFR mutation status differs from the European population. Furthermore, the expression intensities of the three polypeptides in the classification model were associated with EGFR mutation. PMID:29844828

  17. Serum amyloid A as a prognostic marker in melanoma identified by proteomic profiling.

    Science.gov (United States)

    Findeisen, Peter; Zapatka, Marc; Peccerella, Teresa; Matzk, Heike; Neumaier, Michael; Schadendorf, Dirk; Ugurel, Selma

    2009-05-01

    Currently known prognostic serum biomarkers of melanoma are powerful in metastatic disease, but weak in early-stage patients. This study was aimed to identify new prognostic biomarkers of melanoma by serum mass spectrometry (MS) proteomic profiling, and to validate candidates compared with established markers. Two independent sets of serum samples from 596 melanoma patients were investigated. The first set (stage I = 102; stage IV = 95) was analyzed by matrix assisted laser desorption and ionization time of flight (MALDI TOF) MS for biomarkers differentiating between stage I and IV. In the second set (stage I = 98; stage II = 91; stage III = 87; stage IV = 103), the serum concentrations of the candidate marker serum amyloid A (SAA) and the known biomarkers S100B, lactate dehydrogenase, and C reactive protein (CRP) were measured using immunoassays. MALDI TOF MS revealed a peak at m/z 11.680 differentiating between stage I and IV, which could be identified as SAA. High peak intensities at m/z 11.680 correlated with poor survival. In univariate analysis, SAA was a strong prognostic marker in stage I to III (P = .043) and stage IV (P = .000083) patients. Combination of SAA and CRP increased the prognostic impact to P = .011 in early-stage (I to III) patients. Multivariate analysis revealed sex, stage, tumor load, S100B, SAA, and CRP as independent prognostic factors, with an interaction between SAA and CRP. In stage I to III patients, SAA combined with CRP was superior to S100B in predicting patients' progression-free and overall survival. SAA combined with CRP might be used as prognostic serological biomarkers in early-stage melanoma patients, helping to discriminate low-risk patients from high-risk patients needing adjuvant treatment.

  18. Bacillus anthracis secretome time course under host-simulated conditions and identification of immunogenic proteins

    Directory of Open Access Journals (Sweden)

    Whittington Jessica

    2007-07-01

    Full Text Available Abstract Background The secretion time course of Bacillus anthracis strain RA3R (pXO1+/pXO2- during early, mid, and late log phase were investigated under conditions that simulate those encountered in the host. All of the identified proteins were analyzed by different software algorithms to characterize their predicted mode of secretion and cellular localization. In addition, immunogenic proteins were identified using sera from humans with cutaneous anthrax. Results A total of 275 extracellular proteins were identified by a combination of LC MS/MS and MALDI-TOF MS. All of the identified proteins were analyzed by SignalP, SecretomeP, PSORT, LipoP, TMHMM, and PROSITE to characterize their predicted mode of secretion, cellular localization, and protein domains. Fifty-three proteins were predicted by SignalP to harbor the cleavable N-terminal signal peptides and were therefore secreted via the classical Sec pathway. Twenty-three proteins were predicted by SecretomeP for secretion by the alternative Sec pathway characterized by the lack of typical export signal. In contrast to SignalP and SecretomeP predictions, PSORT predicted 171 extracellular proteins, 7 cell wall-associated proteins, and 6 cytoplasmic proteins. Moreover, 51 proteins were predicted by LipoP to contain putative Sec signal peptides (38 have SpI sites, lipoprotein signal peptides (13 have SpII sites, and N-terminal membrane helices (9 have transmembrane helices. The TMHMM algorithm predicted 25 membrane-associated proteins with one to ten transmembrane helices. Immunogenic proteins were also identified using sera from patients who have recovered from anthrax. The charge variants (83 and 63 kDa of protective antigen (PA were the most immunodominant secreted antigens, followed by charge variants of enolase and transketolase. Conclusion This is the first description of the time course of protein secretion for the pathogen Bacillus anthracis. Time course studies of protein secretion and

  19. Monitoring of barley starch amylolysis by gravitational field flow fractionation and MALDI-TOF MS

    Czech Academy of Sciences Publication Activity Database

    Mazanec, Karel; Dyčka, Filip; Bobálová, Janette

    2011-01-01

    Roč. 91, č. 15 (2011), s. 2756-2761 ISSN 0022-5142 R&D Projects: GA MŠk 1M0570; GA MŠk 1M06030; GA MŠk 2B06037 Institutional research plan: CEZ:AV0Z40310501 Keywords : barley * starch * malting process Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 1.436, year: 2011

  20. MALDI-TOF MS for quality control of high protein content sport supplements.

    Science.gov (United States)

    De Ceglie, Cristina; Calvano, Cosima D; Zambonin, Carlo G

    2015-06-01

    High protein content sport nutritional supplements are found as powder products containing, as ingredients, amino acids and proteins with important nutritional values as milk, soy and egg proteins. An EU Food Supplements Directive (2002) requires that supplements should be safe, both in dosages and in purity. It is important, then, to develop rapid and sensitive methods to be employed for the quality control of these substances. In this work, we apply, for the first time, matrix-assisted laser desorption ionization-mass spectrometry as a fast, reproducible and sensitive method for the quality control of sport nutritional supplements based on proteins. To this aim, several commercial egg- and/or milk-based powder products have been processed by in gel or in solution digestion and analyzed in comparison to pure standard products. This strategy allowed to assess the reliability of the indications on proteins (as caseins, whey proteins and ovalbumin) declared in the label of several sport nutritional supplements. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Cytosolic proteome profiling of aminoglycosides resistant Mycobacterium tuberculosis clinical isolates using MALDI-TOF/MS

    Directory of Open Access Journals (Sweden)

    Divakar Sharma

    2016-11-01

    Full Text Available Emergence of extremely drug resistant tuberculosis (XDR-TB is the consequence of the failure of second line TB treatment. Aminoglycosides are the important second line anti-TB drugs used to treat the multi drug resistant tuberculosis (MDR-TB. Main known mechanism of action of aminoglycosides is to inhibit the protein synthesis by inhibiting the normal functioning of ribosome. Primary target of aminoglycosides are the ribosomal RNA and its associated proteins. Various mechanisms have been proposed for aminoglycosides resistance but still some are unsolved. As proteins are involved in most of the biological processes, these act as a potential diagnostic markers and drug targets. In the present study we analyzed the purely cytosolic proteome of amikacin (AK and kanamycin (KM resistant Mycobacterium tuberculosis isolates by proteomic and bioinformatic approaches. Twenty protein spots were found to have over expressed in resistant isolates and were identified. Among these Rv3208A, Rv2623, Rv1360, Rv2140c, Rv1636 and Rv2185c are six proteins with unknown functions or undefined role. Docking results showed that AK and KM binds to the conserved domain (DUF, USP-A, Luciferase, PEBP and Polyketidecyclase/dehydrase domain of these hypothetical proteins and over expression of these proteins might neutralize/modulate the effect of drug molecules. TBPred and GPS-PUP predicted cytoplasmic nature and potential pupylation sites within these identified proteins respectively. String analysis also suggested that over expressed proteins along with their interactive partners might be involved in aminoglycosides resistance. Cumulative effect of these over expressed proteins could be involved in AK and KM resistance by mitigating the toxicity, repression of drug target and neutralizing affect. These findings need further exploitation for the expansion of newer therapeutics or diagnostic markers against AK and KM resistance so that an extreme condition like XDR-TB can be prevented.

  2. Cytosolic Proteome Profiling of Aminoglycosides Resistant Mycobacterium tuberculosis Clinical Isolates Using MALDI-TOF/MS.

    Science.gov (United States)

    Sharma, Divakar; Lata, Manju; Singh, Rananjay; Deo, Nirmala; Venkatesan, Krishnamurthy; Bisht, Deepa

    2016-01-01

    Emergence of extensively drug resistant tuberculosis (XDR-TB) is the consequence of the failure of second line TB treatment. Aminoglycosides are the important second line anti-TB drugs used to treat the multi drug resistant tuberculosis (MDR-TB). Main known mechanism of action of aminoglycosides is to inhibit the protein synthesis by inhibiting the normal functioning of ribosome. Primary target of aminoglycosides are the ribosomal RNA and its associated proteins. Various mechanisms have been proposed for aminoglycosides resistance but still some are unsolved. As proteins are involved in most of the biological processes, these act as a potential diagnostic markers and drug targets. In the present study we analyzed the purely cytosolic proteome of amikacin (AK) and kanamycin (KM) resistant Mycobacterium tuberculosis isolates by proteomic and bioinformatic approaches. Twenty protein spots were found to have over expressed in resistant isolates and were identified. Among these Rv3208A, Rv2623, Rv1360, Rv2140c, Rv1636, and Rv2185c are six proteins with unknown functions or undefined role. Docking results showed that AK and KM binds to the conserved domain (DUF, USP-A, Luciferase, PEBP and Polyketidecyclase/dehydrase domain) of these hypothetical proteins and over expression of these proteins might neutralize/modulate the effect of drug molecules. TBPred and GPS-PUP predicted cytoplasmic nature and potential pupylation sites within these identified proteins, respectively. String analysis also suggested that over expressed proteins along with their interactive partners might be involved in aminoglycosides resistance. Cumulative effect of these over expressed proteins could be involved in AK and KM resistance by mitigating the toxicity, repression of drug target and neutralizing affect. These findings need further exploitation for the expansion of newer therapeutics or diagnostic markers against AK and KM resistance so that an extreme condition like XDR-TB can be prevented.

  3. Characterization and differentiation of aflatoxigenic species of Aspergillus section Flavi by MALDI-TOF MS

    OpenAIRE

    Rodrigues, P.; Kallow, W.; Erhard, M.; Welker, M.; Kozakiewicz, Z.; Lima, Nelson; Venâncio, Armando

    2007-01-01

    Aspergillus is a large genus, with a complex taxonomy. The genus is easily identifiedd by its characteristic conidiophore, but species identification and differentiation is complex, mainly because it is traditionally based on a range of morphological features. Aspergillus subgenus Circumdati section Flavi, also refered to as the A.dflavus group, has attracted worldwide attention for its industrial use and toxigenic potential. Sectiond Flavi is divided in two groups of species. One includes th...

  4. A polyphasic approach for black Aspergillus identification using MALDI-TOF MS.

    OpenAIRE

    Rodrigues, Paula; Soares, Célia; Santos, Cledir; Fraga, Marcelo; Venâncio, Armando; Lima, Nelson

    2009-01-01

    The Aspergillus section Nigri is among the best studied fungi, having different commercial applications, but also causing biodeterioration of commodities and food spoilage. Although being well studied, their identification is not straightforward, and, recently, new species have been described in this section1,2,3. These new species were not only separated from their relatives in the section by morphological distinction but also from molecular point of view. The concept of species is clearly a...

  5. Characterization of Dickeya and Pectobacterium species by capillary electrophoretic techniques and MALDI-TOF MS

    Czech Academy of Sciences Publication Activity Database

    Šalplachta, Jiří; Kubesová, Anna; Horký, J.; Matoušková, H.; Tesařová, Marie; Horká, Marie

    2015-01-01

    Roč. 407, č. 25 (2015), s. 7625-7635 ISSN 1618-2642 R&D Projects: GA MV VG20112015021 Institutional support: RVO:68081715 Keywords : bacteria * electrophoretic techniques * MALDI Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.125, year: 2015 http://hdl.handle.net/11104/0250090

  6. Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling.

    Directory of Open Access Journals (Sweden)

    Thi-Nguyen-Ny Tran

    Full Text Available BACKGROUND: The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets. METHODOLOGY/PRINCIPAL FINDINGS: We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279-modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%. Third, we classified 10 of 18 teeth (56% collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I in human ancient and modern dental pulp, respectively. CONCLUSIONS/SIGNIFICANCE: Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.

  7. An innovative strategy for sulfopeptides analysis using MALDI-TOF MS reflectron positive ion mode.

    Science.gov (United States)

    Cantel, Sonia; Brunel, Luc; Ohara, Keiichiro; Enjalbal, Christine; Martinez, Jean; Vasseur, Jean-Jacques; Smietana, Michael

    2012-08-01

    Sulfation of tyrosine residues is a key posttranslational modification in the regulation of various cellular processes. As such, the detection and localization of tyrosine sulfation is an essential step toward the elucidation of the physiological and pathological roles of this process. Despite substantial advances, intact sulfated peptides are still difficult to detect by MALDI-MS due to the extreme lability of the sulfo-moiety. The present report demonstrates for the first time how intact sulfated peptides can be directly and specifically detected by MALDI-MS in positive reflectron mode by using pyrenemethylguanidine (pmg) as a noncovalent derivatizing agent and an ionization enhancer. This new method allows the determination of the degree of sulfation of sulfopeptides pure or in mixtures. Moreover, the observation of specific peaks in the mass spectra enables a rapid and unambiguous discrimination between phospho- and sulfopeptides. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS

    NARCIS (Netherlands)

    Lista, F.; Reubsaet, F.A.G.; Santis, R. de; Parchen, R.R.; Jong, A.L. de; Kieboom, J.; Laaken, A.L. van der; Voskamp-Visser, I.A.I.; Fillo, S.; Jansen, H.J. de; Plas, J. van der; Paauw, A.

    2011-01-01

    Background: The genus Brucella contains highly infectious species that are classified as biological threat agents. The timely detection and identification of the microorganism involved is essential for an effective response not only to biological warfare attacks but also to natural outbreaks.

  9. Classification of Ancient Mammal Individuals Using Dental Pulp MALDI-TOF MS Peptide Profiling

    Science.gov (United States)

    Tran, Thi-Nguyen-Ny; Aboudharam, Gérard; Gardeisen, Armelle; Davoust, Bernard; Bocquet-Appel, Jean-Pierre; Flaudrops, Christophe; Belghazi, Maya; Raoult, Didier; Drancourt, Michel

    2011-01-01

    Background The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets. Methodology/Principal Findings We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279–modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%). Third, we classified 10 of 18 teeth (56%) collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I) in human ancient and modern dental pulp, respectively. Conclusions/Significance Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals. PMID:21364886

  10. Rapid detection of AAC(6')-Ib-cr production using a MALDI-TOF MS strategy.

    Science.gov (United States)

    Pardo, C-A; Tan, R N; Hennequin, C; Beyrouthy, R; Bonnet, R; Robin, F

    2016-12-01

    Plasmid-mediated quinolone resistance mechanisms have become increasingly prevalent among Enterobacteriaceae strains since the 1990s. Among these mechanisms, AAC(6')-Ib-cr is the most difficult to detect. Different detection methods have been developed, but they require expensive procedures such as Sanger sequencing, pyrosequencing, polymerase chain reaction (PCR) restriction, or the time-consuming phenotypic method of Wachino. In this study, we describe a simple matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method which can be easily implemented in clinical laboratories that use the MALDI-TOF technique for bacterial identification. We tested 113 strains of Enterobacteriaceae, of which 64 harbored the aac(6')-Ib-cr gene. We compared two MALDI-TOF strategies, which differed by their norfloxacin concentration (0.03 vs. 0.5 g/L), and the method of Wachino with the PCR and sequencing strategy used as the reference. The MALDI-TOF strategy, performed with 0.03 g/L norfloxacin, and the method of Wachino yielded the same high performances (Se = 98 %, Sp = 100 %), but the turnaround time of the MALDI-TOF strategy was faster (<5 h), simpler, and inexpensive (<1 Euro). Our study shows that the MALDI-TOF strategy has the potential to become a major method for the detection of many different enzymatic resistance mechanisms.

  11. LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise

    Directory of Open Access Journals (Sweden)

    Di Nicola Marta

    2007-03-01

    Full Text Available Abstract Background Mass spectrometry protein profiling is a promising tool for biomarker discovery in clinical proteomics. However, the development of a reliable approach for the separation of protein signals from noise is required. In this paper, LIMPIC, a computational method for the detection of protein peaks from linear-mode MALDI-TOF data is proposed. LIMPIC is based on novel techniques for background noise reduction and baseline removal. Peak detection is performed considering the presence of a non-homogeneous noise level in the mass spectrum. A comparison of the peaks collected from multiple spectra is used to classify them on the basis of a detection rate parameter, and hence to separate the protein signals from other disturbances. Results LIMPIC preprocessing proves to be superior than other classical preprocessing techniques, allowing for a reliable decomposition of the background noise and the baseline drift from the MALDI-TOF mass spectra. It provides lower coefficient of variation associated with the peak intensity, improving the reliability of the information that can be extracted from single spectra. Our results show that LIMPIC peak-picking is effective even in low protein concentration regimes. The analytical comparison with commercial and freeware peak-picking algorithms demonstrates its superior performances in terms of sensitivity and specificity, both on in-vitro purified protein samples and human plasma samples. Conclusion The quantitative information on the peak intensity extracted with LIMPIC could be used for the recognition of significant protein profiles by means of advanced statistic tools: LIMPIC might be valuable in the perspective of biomarker discovery.

  12. Effects of low dose radiation on differential expression of serum protein in mice

    International Nuclear Information System (INIS)

    Chen Wei; He Ying; Shen Xianrong

    2014-01-01

    The aim is to find out the key proteins related with low dose radiation (Ld) by parametric technology, which provided the theory foundation for LDR protection Two-dimensional electrophoresis (2-DE) was performed on serum protein Differential expression proteins were identified by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and database analysis Compared with the control group, 7 altered proteins was definite in terms of apolipoprotein C-Ⅲ, beta-globin parotid secretory protein alpha-2-macroglobulin precursor, mouse transthyretin, C1qc protein and clusterin. Some proteins related with LDR are found. It may provide some new explanations for the mechanism of LDR. (authors)

  13. Clinical study on the time courses of serum myosin light chain I levels in patients with acute myocardial infarction

    International Nuclear Information System (INIS)

    Nakanishi, Masako; Saiki, Yasuhiko; Ui, Kazuyo

    1992-01-01

    Changes of serum myosin light chain I (Myosin LCI) concentrations and creatine kinase (CK) activities were serially measured in 23 patients with acute myocardial infarction. Intracoronary thrombolysis was performed in 14 patients (ICT group) while the remaining 9 patients were treated in the conventional manner (non ICT group). The relationships between the maximum levels of serum Myosin LCI or CK and a myocardial infarct size index or left ventricular function were evaluated in 18 patients. The myocardial infarct size index was determined by 201 Tl myocardial scintigrams performed in the chronic phase. Multiple peaks of Myosin LCI were observed in 64% (9/14) of the ICT group and the first peak in 6 of these patients appeared much earlier in the same time as CK peak than in the non-ICT group, while multiple peaks were seen only in one case in the non-ICT group. The infarct size index by 201 Tl myocardial SPECT correlated with maximum Myosin LCI levels (r=0.88, p<0.001, n=10) and CK activities (r=0.67, p<0.05, n=10). These results indicate that the measurement of serum Myosin LCI is very useful for estimating the extent of myocardial damage and suggest that myocardial degeneration occurs at a very early phase of myocardial infarction. (author)

  14. Nanotexture Optimization by Oxygen Plasma of Mesoporous Silica Thin Film for Enrichment of Low Molecular Weight Peptides Captured from Human Serum

    Science.gov (United States)

    Hu, Ye; Peng, Yang; Brousseau, Louis; Bouamrani, Ali; Liu, Xuewu; Ferrari, Mauro

    2010-01-01

    This study investigated the optimization of mesoporous silica thin films by nanotexturing using oxygen plasma versus thermal oxidation. Calcination in oxygen plasma provides superior control over pore formation with regard to the pore surface and higher fidelity to the structure of the polymer template. The resulting porous film offers an ideal substrate for the selective partitioning of peptides from complex mixtures. The improved chemico-physical characteristics of porous thin films (pore size distribution, nanostructure, surface properties and pore connectivity) were systematically characterized with XRD, Ellipsometry, FTIR, TEM and N2 adsorption/desorption. The enrichment of low molecular weight proteins captured from human serum on mesoporous silica thin films fabricated by both methodologies were investigated by comparison of their MALDI-TOF MS profiles. This novel on-chip fractionation technology offers advantages in recovering the low molecular weight peptides from human serum, which has been recognized as an informative resource for early diagnosis of cancer and other diseases. PMID:21179395

  15. Serum peptide/protein profiling by mass spectrometry provides diagnostic information independently of CA125 in women with an ovarian tumor

    DEFF Research Database (Denmark)

    Callesen, Anne; Madsen, Jonna S; Iachina, Maria

    2010-01-01

    In the present study, the use of a robust and sensitive mass spectrometry based protein profiling analysis was tested as diagnostic tools for women with an ovarian tumor. The potential additional diagnostic value of serum protein profiles independent of the information provided by CA125 were also...... investigated. Protein profiles of 113 serum samples from women with an ovarian tumor (54 malign and 59 benign) were generated using MALDI-TOF MS. A total of 98 peaks with a significant difference (pwomen with benign tumors/cysts and malignant ovarian tumors were identified. After...... average linkage clustering, a profile of 46 statistical significant mass peaks was identified to distinguish malignant tumors and benign tumors/cysts. In the subgroup of women with normal CA125 values (

  16. Serum proteomic analysis reveals potential serum biomarkers for occupational medicamentosa-like dermatitis caused by trichloroethylene.

    Science.gov (United States)

    Huang, Peiwu; Ren, Xiaohu; Huang, Zhijun; Yang, Xifei; Hong, Wenxu; Zhang, Yanfang; Zhang, Hang; Liu, Wei; Huang, Haiyan; Huang, Xinfeng; Wu, Desheng; Yang, Linqing; Tang, Haiyan; Zhou, Li; Li, Xuan; Liu, Jianjun

    2014-08-17

    Trichloroethylene (TCE) is an industrial solvent with widespread occupational exposure and also a major environmental contaminant. Occupational medicamentosa-like dermatitis induced by trichloroethylene (OMLDT) is an autoimmune disease and it has become one major hazard in China. In this study, sera from 3 healthy controls and 3 OMLDT patients at different disease stages were used for a screening study by 2D-DIGE and MALDI-TOF-MS/MS. Eight proteins including transthyretin (TTR), retinol binding protein 4 (RBP4), haptoglobin, clusterin, serum amyloid A protein (SAA), apolipoprotein A-I, apolipoprotein C-III and apolipoprotein C-II were found to be significantly altered among the healthy, acute-stage, healing-stage and healed-stage groups. Specifically, the altered expression of TTR, RBP4 and haptoglobin were further validated by Western blot analysis and ELISA. Our data not only suggested that TTR, RBP4 and haptoglobin could serve as potential serum biomarkers of OMLDT, but also indicated that measurement of TTR, RBP4 and haptoglobin or their combination could help aid in the diagnosis, monitoring the progression and therapy of the disease. Copyright © 2014. Published by Elsevier Ireland Ltd.

  17. Identification of phlebotomine sand flies using one MALDI-TOF MS reference database and two mass spectrometer systems

    Czech Academy of Sciences Publication Activity Database

    Mathis, A.; Depaquit, J.; Dvořák, V.; Tuten, H.; Banuls, A.-L.; Halada, Petr; Zapata, S.; Lehrter, V.; Hlaváčková, K.; Prudhomme, J.; Volf, P.; Sereno, D.; Kaufmann, Ch.; Pflueger, V.; Schaffner, F.

    2015-01-01

    Roč. 8, MAY 2015 (2015) ISSN 1756-3305 R&D Projects: GA ČR(CZ) GA15-04329S Institutional support: RVO:61388971 Keywords : Arthropod identification * Bruker * Centralized reference database Subject RIV: CE - Biochemistry Impact factor: 3.234, year: 2015

  18. Positionsspezifischer Nachweis und relative Quantifizierung von Modifikationen des alpha-s1-Caseins in Milch mittels MALDI-TOF-MS

    OpenAIRE

    Vollmer, Gregor

    2013-01-01

    Milch und Milchprodukte spielen eine bedeutende Rolle in der menschlichen Ernährung. Vor der Abgabe an den Verbraucher wird Milch in den allermeisten Fällen hitzebehandelt, um mikrobielle Stabilität sicherzustellen und die Haltbarkeit zu verlängern. Allerdings kann diese Hitzebehandlung die in Milch enthaltenen Nährstoffe, unter anderem Kohlenhydrate, Lipide, Proteine und Vitamine, erheblich schädigen. Vitamine werden durch starke Erhitzung zerstört, bei den Lipiden kann es zu Abbaureaktionen...

  19. Differentiation of Cronobacter spp. by tryptic digestion of the cell suspension followed by MALDI-TOF MS analysis

    Czech Academy of Sciences Publication Activity Database

    Krásný, Lukáš; Rohlová, E.; Růžičková, E.; Šantrůček, J.; Hynek, R.; Hochel, I.

    2014-01-01

    Roč. 98, MAR 2014 (2014), s. 105-113 ISSN 0167-7012 R&D Projects: GA ČR GAP503/10/0664 Institutional support: RVO:61388971 Keywords : Biotyper * Cronobacter * MALDI - TOF Subject RIV: CE - Biochemistry Impact factor: 2.026, year: 2014

  20. Identification of Candida species isolated from vulvovaginitis in Mashhad, Iran by Use of MALDI-TOF MS

    Directory of Open Access Journals (Sweden)

    Majid Alizadeh

    2017-12-01

     Of the 65 isolates analyzed, 61 (93.8% were recognised by MALDI-TOF mass spectrometry and for four isolates (6.1% only not relabile identifications were achieved. In this study, the most frequently isolated species were Candida albicans (58.5%, followed by Candida tropicalis (16.9%, Candida glabrata (7.7%, Candida parapsilosis (7.7% and Candida guillermondii (3.1%.  Conclusion presented results demonstrate that the MALDI TOF mass spectrometry is a fast and reliable technique, and has the potential to replace conventional phenotypic identification of Candida species and other yeast strains routinely isolated in clinical microbiology laboratories.

  1. MALDI-TOF MS contribution to diagnosis of melioidosis in a nonendemic country in three French travellers

    Directory of Open Access Journals (Sweden)

    V. Walewski

    2016-07-01

    Full Text Available Melioidosis is an endemic disease in Southeast Asia and northern Australia. An increasing number of cases are being reported in nonendemic countries, making the diagnosis less obvious. We discuss the identification of Burkholderia pseudomallei using matrix-assisted desorption ionization–time of flight mass spectrometry on the occasion of recent cases of imported melioidosis in French travellers.

  2. Weak cation exchange magnetic beads coupled with matrix-assisted laser desorption ionization-time of flight-mass spectrometry in screening serum protein markers in osteopenia.

    Science.gov (United States)

    He, Wei-Tao; Liang, Bo-Cheng; Shi, Zhen-Yu; Li, Xu-Yun; Li, Chun-Wen; Shi, Xiao-Lin

    2016-01-01

    The present study aimed at investigating the weak cation magnetic separation technology and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) in screening serum protein markers of osteopenia from ten postmenopausal women and ten postmenopausal women without osteopenia as control group, to find a new method for screening biomarkers and establishing a diagnostic model for primary type I osteoporosis. Serum samples were collected from postmenopausal women with osteopenia and postmenopausal women with normal bone mass. Proteins were extracted from serum samples by weak cation exchange magnetic beads technology, and mass spectra acquisition was done by MALDI-TOF-MS. The visualization and comparison of data sets, statistical peak evaluation, model recognition, and discovery of biomarker candidates were handled by the proteinchip data analysis system software(ZJU-PDAS). The diagnostic models were established using genetic arithmetic based support vector machine (SVM). The SVM result with the highest Youden Index was selected as the model. Combinatorial Peaks having the highest accuracy in distinguishing different samples were selected as potential biomarker. From the two group serum samples, a total of 133 differential features were selected. Ten features with significant intensity differences were screened. In the pair-wise comparisons, processing of MALDI-TOF spectra resulted in the identification of ten differential features between postmenopausal women with osteopenia and postmenopausal women with normal bone mass. The difference of features by Youden index showed that the highest features had a mass to charge ratio of 1699 and 3038 Da. A diagnosis model was established with these two peaks as the candidate marker, and the specificity of the model is 100 %, the sensitivity was 90 % by leave-one-out cross validation test. The two groups of specimens in SVM results on the scatter plot could be clearly distinguished. The peak

  3. Serum protein identification and quantification of the corona of 5, 15 and 80 nm gold nanoparticles

    International Nuclear Information System (INIS)

    Schäffler, Martin; Semmler-Behnke, Manuela; Takenaka, Shinji; Wenk, Alexander; Schleh, Carsten; Johnston, Blair D; Kreyling, Wolfgang G; Sarioglu, Hakan; Hauck, Stefanie M

    2013-01-01

    When nanoparticles (NP) enter the body they come into contact with body fluids containing proteins which can adsorb to their surface. These proteins may influence the NP interactions with the biological vicinity, eventually determining their biological fate inside the body. Adsorption of the most abundantly binding proteins was studied after an in vitro 24 hr incubation of monodisperse, negatively charged 5, 15 and 80 nm gold spheres (AuNP) in mouse serum by a two-step analysis: proteomic protein identification and quantitative protein biochemistry. The adsorbed proteins were separated from non-adsorbed proteins by centrifugation and gel electrophoresis and identified using a MALDI-TOF-MS-Proteomics-Analyzer. Quantitative analysis of proteins in gel bands by protein densitometry, required the focus on predominantly binding serum proteins. Numerous proteins adsorbed to the AuNP depending on their size, e.g. apolipoproteins or complement C3. The qualitative and quantitative amount of adsorbed proteins differed between 5, 15 and 80 nm AuNP. Band intensities of adsorbed proteins decreased with increasing AuNP sizes based not only on their mass but also on their surface area. Summarizing, the AuNP surface is covered with serum proteins containing transport and immune related proteins among others. Hence, protein binding depends on the size, surface area and curvature of the AuNP. (paper)

  4. Proteomic analysis of swine serum following highly virulent classical swine fever virus infection

    Directory of Open Access Journals (Sweden)

    Guo Huan-cheng

    2011-03-01

    Full Text Available Abstract Background Classical swine fever virus (CSFV belongs to the genus Pestivirus within the family Flaviviridae. Virulent strains of classical swine fever virus (CSFV cause severe disease in pigs characterized by immunosuppression, thrombocytopenia and disseminated intravascular coagulation, which causes significant economic losses to the pig industry worldwide. Methods To reveal proteomic changes in swine serum during the acute stage of lethal CSFV infection, 5 of 10 pigs were inoculated with the virulent CSFV Shimen strain, the remainder serving as uninfected controls. A serum sample was taken at 3 days post-infection from each swine, at a stage when there were no clinical symptoms other than increased rectal temperatures (≥40°C. The samples were treated to remove serum albumin and immunoglobulin (IgG, and then subjected to two-dimension differential gel electrophoresis. Results Quantitative intensity analysis revealed 17 protein spots showing at least 1.5-fold quantitative alteration in expression. Ten spots were successfully identified by MALDI-TOF MS or LTQ MS. Expression of 4 proteins was increased and 6 decreased in CSFV-infected pigs. Functions of these proteins included blood coagulation, anti-inflammatory activity and angiogenesis. Conclusion These proteins with altered expression may have important implications in the pathogenesis of classical swine fever and provide a clue for identification of biomarkers for classical swine fever early diagnosis.

  5. Magnetic Bead-Based Serum Peptidome Profiling in Patients with Gestational Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Tingting Ai

    2015-01-01

    Full Text Available Gestational diabetes mellitus (GDM is a frequent medical condition during pregnancy. Early diagnosis and treatment of GDM are crucial for both the mother and the baby. In the present study, we aimed to identify specific biomarkers to assist in the early detection of GDM and give some clues to the possible causes of GDM by comparing serum peptide profile differences between GDM patients and healthy controls. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS was used in combination with weak cation exchange magnetic bead (WCX-MB. Levels of four peptides (4418.9, 2219.7, 2211.5, and 1533.4 Da were significantly different. Interestingly, three of them (4418.9, 2211.5, and 1533.4 Da were identified when GDM patients with two degrees of glucose intolerance were compared. Additionally, peptides 2211.5 and 1533.4 Da showed a decreasing trend as glucose intolerance increased, while peptide 4418.9 Da exhibited the reverse tendency. In conclusion, our study provides novel insights into the altered serum peptide profile of GDM patients. The specific candidate biomarkers may contribute to the development of GDM.

  6. A computational platform for MALDI-TOF mass spectrometry data: application to serum and plasma samples.

    Science.gov (United States)

    Mantini, Dante; Petrucci, Francesca; Pieragostino, Damiana; Del Boccio, Piero; Sacchetta, Paolo; Candiano, Giovanni; Ghiggeri, Gian Marco; Lugaresi, Alessandra; Federici, Giorgio; Di Ilio, Carmine; Urbani, Andrea

    2010-01-03

    Mass spectrometry (MS) is becoming the gold standard for biomarker discovery. Several MS-based bioinformatics methods have been proposed for this application, but the divergence of the findings by different research groups on the same MS data suggests that the definition of a reliable method has not been achieved yet. In this work, we propose an integrated software platform, MASCAP, intended for comparative biomarker detection from MALDI-TOF MS data. MASCAP integrates denoising and feature extraction algorithms, which have already shown to provide consistent peaks across mass spectra; furthermore, it relies on statistical analysis and graphical tools to compare the results between groups. The effectiveness in mass spectrum processing is demonstrated using MALDI-TOF data, as well as SELDI-TOF data. The usefulness in detecting potential protein biomarkers is shown comparing MALDI-TOF mass spectra collected from serum and plasma samples belonging to the same clinical population. The analysis approach implemented in MASCAP may simplify biomarker detection, by assisting the recognition of proteomic expression signatures of the disease. A MATLAB implementation of the software and the data used for its validation are available at http://www.unich.it/proteomica/bioinf. (c) 2009 Elsevier B.V. All rights reserved.

  7. Evaluation of Beauveria bassiana infection in the hemolymph serum proteins of the housefly, Musca domestica L. (Diptera: Muscidae).

    Science.gov (United States)

    Mishra, Sapna; Kumar, Peeyush; Malik, Anushree

    2017-11-01

    Beauveria bassiana plays a prominent role in biocontrol of houseflies, Musca domestica (L.). Thus, a deeper insight into immune response of M. domestica during B. bassiana infection was warranted to assist the production of more efficient mycoinsecticides. The present study investigates changes in protein profile of M. domestica hemolymph serum post B. bassiana infection using two-dimensional difference gel electrophoresis (2D-DIGE) followed by identification of selected proteins by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The non-infected or control group of flies showed an expression of 54 proteins, while M. domestica infected with B. bassiana expressed a total of 68 hemolymph serum proteins. Thirty three proteins were expressed in both groups of houseflies, whereas 35 proteins were exclusively expressed in infected flies and 21 proteins were exclusively expressed in control flies. Among the 33 proteins which were expressed in both groups of houseflies, 17 proteins showed downregulation, while16 proteins were upregulated in the infected flies compared to the non-infected ones. The results from this study are expected to facilitate better understanding of insect's immune response mechanism.

  8. Identification of Kininogen 1 as a Serum Protein Marker of Colorectal Adenoma in Patients with a Family History of Colorectal Cancer

    Science.gov (United States)

    Yu, Jiekai; Huang, Yanqin; Lin, Chen; Li, Xiaofen; Fang, Xuefeng; Zhong, Chenhan; Yuan, Ying; Zheng, Shu

    2018-01-01

    The serum protein markers of colorectal adenoma in patients with a family history of colorectal cancer have been rarely reported. Serum samples from colorectal adenoma patients with or without a family history of colorectal cancer and healthy controls were profiled using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS). The model to distinguish colorectal adenoma patients with a family history of colorectal cancer from atypical hereditary colorectal families (CRA-H) and sporadic colorectal adenoma patients without a family history of colorectal cancer (CRA-S) was established with 85.0% accuracy. The model distinguishing CRA-H from healthy individuals was established with 90.0% specificity and 86.7% sensitivity. Additionally, five peaks (2202, 5821, 3260, 2480, and 2218) showing differential expression in advanced colorectal adenoma patients with a family history of colorectal cancer were selected. The protein Kininogen 1 (KNG1) was identified in colorectal adenoma patients and validated using Western Blotting. KNG1 may be a biomarker for colorectal adenoma patients with a family history of colorectal cancer. PMID:29535795

  9. Detection of Serum Protein Biomarkers for the Diagnosis and Staging of Hepatoblastoma

    Directory of Open Access Journals (Sweden)

    Wei Zhao

    2015-06-01

    Full Text Available The present study aimed to identify serum biomarkers for the detection of hepatoblastoma (HB. Serum samples were collected from 71 HB patients (stage I, n = 19; stage II, n = 19, stage III, n = 19; and stage IV, n = 14 and 23 age- and sex-matched healthy children. Differential expression of serum protein markers were screened using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS, and the target proteins were isolated and purified using HPLC and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS, SEQUEST, and bioinformatics analysis. Differential protein expression was confirmed by enzyme-linked immunosorbent analysis (ELISA. SELDI-TOF-MS screening identified a differentially expressed protein with an m/z of 9348 Da, which was subsequently identified as Apo A–I; its expression was significantly lower in the HB group as compared to the normal control group (1546.67 ± 757.81 vs. 3359.21 ± 999.36, respectively; p < 0.01. Although the expression level decreased with increasing disease stage, pair-wise comparison revealed significant differences in Apo A–I expression between the normal group and the HB subgroups (p < 0.01. ELISA verified the reduced expression of Apo A–I in the HB group. Taken together, these results suggest that Apo A–I may represent a serum protein biomarker of HB. Further studies will assess the value of using Apo A–I expression for HB diagnosis and staging.

  10. Exploration of Serum Proteomic Profiling and Diagnostic Model That Differentiate Crohn's Disease and Intestinal Tuberculosis.

    Directory of Open Access Journals (Sweden)

    Fenming Zhang

    Full Text Available To explore the diagnostic models of Crohn's disease (CD, Intestinal tuberculosis (ITB and the differential diagnostic model between CD and ITB by analyzing serum proteome profiles.Serum proteome profiles from 30 CD patients, 21 ITB patients and 30 healthy controls (HCs were analyzed by using weak cationic magnetic beads combined with MALDI-TOF-MS technique to detect the differentially expressed proteins of serum samples. Three groups were made and compared accordingly: group of CD patients and HCs, group of ITB patients and HCs, group of CD patients and ITB patients. Wilcoxon rank sum test was used to screen the ten most differentiated protein peaks (P < 0.05. Genetic algorithm combining with support vector machine (SVM was utilized to establish the optimal diagnostic models for CD, ITB and the optimal differential diagnostic model between CD and ITB. The predictive effects of these models were evaluated by Leave one out (LOO cross validation method.There were 236 protein peaks differently expressed between group of CD patients and HCs, 305 protein peaks differently expressed between group of ITB patients and HCs, 332 protein peaks differently expressed between group of CD patients and ITB patients. Ten most differentially expressed peaks were screened out between three groups respectively (P < 0.05 to establish diagnostic models and differential diagnostic model. A diagnostic model comprising of four protein peaks (M/Z 4964, 3029, 2833, 2900 can well distinguish CD patients and HCs, with a specificity and sensitivity of 96.7% and 96.7% respectively. A diagnostic model comprising four protein peaks (M/Z 3030, 2105, 2545, 4210 can well distinguish ITB patients and HCs, with a specificity and sensitivity of 93.3% and 95.2% respectively. A differential diagnostic model comprising three potential biomarkers protein peaks (M/Z 4267, 4223, 1541 can well distinguish CD patients and ITB patients, with a specificity and sensitivity of 76.2% and 80

  11. Proteomic profiling reveals α1-antitrypsin, α1-microglobulin, and clusterin as preeclampsia-related serum proteins in pregnant women.

    Science.gov (United States)

    Hsu, Te-Yao; Hsieh, T'sang-T'ang; Yang, Kuender D; Tsai, Ching-Chang; Ou, Chia-Yu; Cheng, Bi-Hua; Wong, Yi-Hsun; Hung, Hsuan-Ning; Chou, An-Kuo; Hsiao, Chang-Chun; Lin, Hao

    2015-10-01

    Preeclampsia is a major cause of mortality in pregnant women but the underlying mechanism remains unclear to date. In this study, we attempted to identify candidate proteins that might be associated with preeclampsia in pregnant women by means of proteomics tools. Differentially expressed proteins in serum samples obtained from pregnant women with severe preeclampsia (n = 8) and control participants (n = 8) were identified using two-dimensional gel electrophoresis (2-DE) followed by peptide mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Additional serum samples from 50 normal and 41 pregnant women with severe preeclampsia were analyzed by immunoassay for validation. Ten protein spots were found to be upregulated significantly in women with severe preeclampsia. These protein spots had the peptide mass fingerprints matched to α1-antitrypsin, α1-microglobulin, clusterin, and haptoglobin. Immunoassays in an independent series of serum samples showed that serum α1-antitrypsin, α1-microglobulin, and clusterin levels of severe preeclampsia patients (n = 41) were significantly higher than those in the normal participants (n = 50; α1-antitrypsin 295.95 ± 50.94 mg/dL vs. 259.31 ± 33.90 mg/dL, p = 0.02; α1-microglobulin 0.029 ± 0.004 mg/mL vs. 0.020 ± 0.004 mg/mL, p proteins by proteomics analysis enables further understanding of the pathophysiology of preeclampsia. Further studies are warranted to investigate the role of these biomarkers in prediction of this disease. Copyright © 2015. Published by Elsevier B.V.

  12. Rapid identification and antimicrobial susceptibility testing of positive blood cultures using MALDI-TOF MS and a modification of the standardised disc diffusion test: a pilot study.

    LENUS (Irish Health Repository)

    Fitzgerald, C

    2016-04-27

    In an era when clinical microbiology laboratories are under increasing financial pressure, there is a need for inexpensive, yet effective, rapid microbiology tests. The aim of this study was to evaluate a novel modification of standard methodology for the identification and antimicrobial susceptibility testing (AST) of pathogens in positive blood cultures, reducing the turnaround time of laboratory results by 24 h.

  13. Identification of immature stages of phlebotomine sand flies using MALDI-TOF MS and mapping of mass spectra during sand fly life cycle

    Czech Academy of Sciences Publication Activity Database

    Halada, Petr; Hlaváčková, K.; Dvořák, V.; Volf, P.

    2018-01-01

    Roč. 93, FEB 2018 (2018), s. 47-56 ISSN 0965-1748 R&D Projects: GA ČR(CZ) GA15-04329S Institutional support: RVO:61388971 Keywords : Phlebotomine sand flies * Larvae * Pupae Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.756, year: 2016

  14. Superiority of SDS lysis over saponin lysis for direct bacterial identification from positive blood culture bottle by MALDI-TOF MS.

    Science.gov (United States)

    Caspar, Yvan; Garnaud, Cécile; Raykova, Mariya; Bailly, Sébastien; Bidart, Marie; Maubon, Danièle

    2017-05-01

    Fast species diagnosis has an important health care impact, as rapid and specific antibacterial therapy is of clear benefit for patient's outcome. Here, a new protocol for species identification directly from positive blood cultures is proposed. Four in-house protocols for bacterial identification by MS directly from clinical positive blood cultures evaluating two lytic agents, SDS and saponin, and two protein extraction schemes, fast (FP) and long (LP) are compared. One hundred and sixty-eight identification tests are carried out on 42 strains. Overall, there are correct identifications to the species level in 90% samples for the SDS-LP, 60% for the SDS-FP, 48% for the saponin LP, and 43% for the saponin FP. Adapted scores allowed 92, 86, 72, and 53% identification for SDS-LP, SDS-FP, saponin LP, and saponin FP, respectively. Saponin lysis is associated with a significantly lower score compared to SDS (0.87 [0.83-0.92], p-value saponin lysis and the application of this rapid and cost-effective protocol in daily routine for microbiological agents implicated in septicemia. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species.

    Science.gov (United States)

    Kim, Young Jin; Kim, Si Hyun; Park, Hyun-Jung; Park, Hae-Geun; Park, Dongchul; Song, Sae Am; Lee, Hee Joo; Yong, Dongeun; Choi, Jun Yong; Kook, Joong-Ki; Kim, Hye Ran; Shin, Jeong Hwan

    2016-08-01

    All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 0, 2, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively. MALDI-TOF could be used as the primary tool for identification of Clostridium species. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Finding diabetic nephropathy biomarkers in the plasma peptidome by high-throughput magnetic bead processing and MALDI-TOF-MS analysis

    DEFF Research Database (Denmark)

    Hansen, Henning G; Overgaard, Julie; Lajer, Maria

    2010-01-01

    Diabetic nephropathy (DN) is the most common cause of end-stage renal disease and improved biomarkers would help identify high-risk individuals. The aim of this study was to discover candidate biomarkers for DN in the plasma peptidome in an in-house cross-sectional cohort (n=122) of type 1 diabet...

  17. MALDI-TOF MS applied to apoC-III glycoforms of patients with congenital disorders affecting O-glycosylation. Comparison with two-dimensional electrophoresis

    NARCIS (Netherlands)

    Yen-Nicolay, S.; Boursier, C.; Rio, M. del; Lefeber, D.J.; Pilon, A.; Seta, N.; Bruneel, A.

    2015-01-01

    PURPOSE: The O-glycan abnormalities accompanying some congenital disorders of glycosylation, namely conserved oligomeric Golgi-congenital disorders of glycosylation (COG-CDGs) and ATP6V0A2-CDGs, are mainly detected using electrophoresis methods applied to circulating apolipoprotein C-III. The

  18. Combination of capillary isoelectric focusing in a tapered capillary with MALDI-TOF MS for rapid and reliable identification of Dickeya species from plant samples

    Czech Academy of Sciences Publication Activity Database

    Horká, Marie; Šalplachta, Jiří; Karásek, Pavel; Kubesová, Anna; Horký, J.; Matoušková, H.; Šlais, Karel; Roth, Michal

    2013-01-01

    Roč. 85, č. 14 (2013), s. 6806-6812 ISSN 0003-2700 R&D Projects: GA MV VG20112015021; GA ČR(CZ) GAP106/12/0522 Institutional support: RVO:68081715 Keywords : capillary isoelectric focusing * matrix-assisted laser desorption/ionization time-of-flight mass spectrometry * Dickeya spp. bacteria Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 5.825, year: 2013

  19. MALDI-TOF MS analysis of the self-termination products in the anionic methyl methacrylate/tert-butyl acrylate block copolymerization

    Czech Academy of Sciences Publication Activity Database

    Vlček, Petr; Čadová, Eva; Horský, Jiří; Janata, Miroslav

    2015-01-01

    Roč. 72, č. 9 (2015), s. 2227-2239 ISSN 0170-0839 Institutional support: RVO:61389013 Keywords : anionic polymerization * acrylates * block copolymer Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.371, year: 2015

  20. Prediction of Streptococcus uberis clinical mastitis risk using Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) in dairy herds.

    Science.gov (United States)

    Archer, Simon C; Bradley, Andrew J; Cooper, Selin; Davies, Peers L; Green, Martin J

    2017-09-01

    The purpose of this study was to evaluate whether the risk of Streptococcus uberis clinical mastitis at cow level could be predicted from the historical presence of specific strains of S. uberis on dairy farms. Matrix-assisted laser desorption ionization time of flight mass spectrometry was used to identify S. uberis isolates potentially capable of contagious transmission. Data were available from 10,652 cows from 52 English and Welsh dairy farms over a 14 month period, and 521 isolates of S. uberis from clinical mastitis cases were available for analysis. As well as the temporal herd history of clinical mastitis associated with particular S. uberis strains, other exposure variables included cow parity, stage of lactation, milk yield, and somatic cell count. Observations were structured longitudinally as repeated weekly measures through the study period for each cow. Data were analyzed in a Bayesian framework using multilevel logistic regression models. Similarity of mass spectral profiles between isolates of S. uberis from consecutive clinical cases of mastitis in herds was used to indicate potential for contagious phenotypic characteristics. Cross validation showed that new isolates with these characteristics could be identified with an accuracy of 90% based on bacterial protein mass spectral characteristics alone. The cow-level risk in any week of these S. uberis clinical mastitis cases increased with the presence of the same specific strains of S. uberis in other cows in the herd during the previous 2 weeks. The final statistical model indicated there would be a 2-3 fold increase in the risk of S. uberis clinical mastitis associated with particular strains if these occurred in the herd 1 and 2 weeks previously. The results suggest that specific strains of S. uberis may be involved with contagious transmission, and predictions based on their occurrence could be used as an early warning surveillance system to enhance the control of S. uberis mastitis. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  1. Identification of strains with phenotypes similar to those of Staphylococcus aureus isolated from table chicken eggs using MALDI-TOF MS and genotyping methods

    Directory of Open Access Journals (Sweden)

    Marek Agnieszka

    2015-06-01

    Full Text Available The aim of the study was to identify the affinity of 10 Staphylococcus strains isolated from table chicken eggs to specific species. Preliminary analysis performed by API ID32 Staph test identified these strains as S. aureus, but they exhibited a negative reaction in the tube coagulase test. Thus, the analysed strains were initially characterised as Staphylococcus aureus-like (SAL. Further characterisation was performed by genotypic methods, using restriction fragment length polymorphism (RFLP of the coagulase gene (coa and sequencing of the gene rpoB. An attempt was also made to identify the isolated Staphylococcus strains by MALDI-TOF mass spectrometry. The results indicated that none of the strains tested belonged to the species S. aureus. The rpoB sequences of five isolates showed the highest sequence similarity to S. haemolyticus, three isolates to S. chromogenes, and one isolate to S. epidermidis. One strain (SAL4 remained unidentified in this analysis. The results obtained using mass spectrometry were comparable to those based on gene sequence analysis. Strain SAL4, which could not be identified by sequencing, was identified by MALDI-TOF as Staphylococcus chromogenes.

  2. S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data.

    Science.gov (United States)

    López-Fernández, Hugo; Araújo, José E; Jorge, Susana; Glez-Peña, Daniel; Reboiro-Jato, Miguel; Santos, Hugo M; Fdez-Riverola, Florentino; Capelo, José L

    2018-03-01

    2D-gel electrophoresis is widely used in combination with MALDI-TOF mass spectrometry in order to analyze the proteome of biological samples. For instance, it can be used to discover proteins that are differentially expressed between two groups (e.g. two disease conditions, case vs. control, etc.) thus obtaining a set of potential biomarkers. This procedure requires a great deal of data processing in order to prepare data for analysis or to merge and integrate data from different sources. This kind of work is usually done manually (e.g. copying and pasting data into spreadsheet files), which is highly time consuming and distracts the researcher from other important, core tasks. Moreover, engaging in a repetitive process in a non-automated, handling-based manner is prone to error, thus threatening reliability and reproducibility. The objective of this paper is to present S2P, an open source software to overcome these drawbacks. S2P is implemented in Java on top of the AIBench framework, and relies on well-established open source libraries to accomplish different tasks. S2P is an AIBench based desktop multiplatform application, specifically aimed to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner. Different case studies are presented in order to show the usefulness of S2P. S2P is open source and free to all users at http://www.sing-group.org/s2p. Through its user-friendly GUI interface, S2P dramatically reduces the time that researchers need to invest in order to prepare data for analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A Silicon Nanomembrane Detector for Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of Large Proteins

    OpenAIRE

    Park, Jonghoo; Blick, Robert

    2013-01-01

    We describe a MALDI-TOF ion detector based on freestanding silicon nanomembrane technology. The detector is tested in a commercial MALDI-TOF mass spectrometer with equimolar mixtures of proteins. The operating principle of the nanomembrane detector is based on phonon-assisted field emission from these silicon nanomembranes, in which impinging ion packets excite electrons in the nanomembrane to higher energy states. Thereby the electrons can overcome the vacuum barrier and escape from the surf...

  4. Efficient identification of Malassezia yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)

    NARCIS (Netherlands)

    Kolecka, A; Khayhan, K; Arabatzis, M; Velegraki, A; Kostrzewa, M; Andersson, A; Scheynius, A; Cafarchia, C; Iatta, R; Montagna, M T; Youngchim, S; Cabañes, F J; Hoopman, P; Kraak, B; Groenewald, M; Boekhout, T

    BACKGROUND: Infections caused by Malassezia yeasts are most likely underdiagnosed, because fatty acid supplementation is needed for growth. Rapid identification of Malassezia species is essential for appropriate treatment of Malassezia-related skin infections, fungaemia and nosocomial outbreaks in

  5. Characterization of Enterococcus species isolated from marine recreational waters by MALDI-TOF MS and Rapid ID API® 20 Strep system.

    Science.gov (United States)

    Christ, Ana Paula Guarnieri; Ramos, Solange Rodrigues; Cayô, Rodrigo; Gales, Ana Cristina; Hachich, Elayse Maria; Sato, Maria Inês Zanoli

    2017-05-15

    MALDI-TOF Mass Spectrometry Biotyping has proven to be a reliable method for identifying bacteria at the species level based on the analysis of the ribosomal proteins mass fingerprint. We evaluate the usefulness of this method to identify Enterococcus species isolated from marine recreational water at Brazilian beaches. A total of 127 Enterococcus spp. isolates were identified to species level by bioMérieux's API® 20 Strep and MALDI-TOF systems. The biochemical test identified 117/127 isolates (92%), whereas MALDI identified 100% of the isolates, with an agreement of 63% between the methods. The 16S rRNA gene sequencing of isolates with discrepant results showed that MALDI-TOF and API® correctly identified 74% and 11% of these isolates, respectively. This discrepancy probably relies on the bias of the API® has to identify clinical isolates. MALDI-TOF proved to be a feasible approach for identifying Enterococcus from environmental matrices increasing the rapidness and accuracy of results. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Direct identification from positive blood broth culture by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Barberino, Maria Goreth; Silva, Marcio de Oliveira; Arraes, Ana Carolina Palmeiras; Correia, Luís Cláudio; Mendes, Ana Verena

    Bloodstream infections (BSIs) are among the most concerning bacterial infections. They are one of the leading causes of morbidity and mortality, and occur in 30-70% of critical care patients. The prompt identification of the causative microorganism can help choosing the appropriate antimicrobial therapy that will lead to better clinical outcomes. Blood culture is one of the most relevant tests for microbiological diagnosis of bacterial infections. The introduction of the MALDI-TOF microbiological diagnosis significantly decreased the time of identifying microorganisms. However, it depends on the growth on solid culture medium. In this study, 538 bottles of positive blood cultures were evaluated to test the accuracy of an in house modified protocol. The study sample consisted of 198 Gram-negative and 350 Gram-positive bacteria. In all, 460 (83.94%) species were identified based on the direct plate findings. The protocol allowed the identification of 185/198 (93.43%) of the Gram-negative bacteria, including aerobes, anaerobes, and non-fermenters, and 275/350 (78.85%) of the Gram-positive bacteria. The proposed method has the potential to provide accurate results in comparison to the traditional method with the potential to reduce the turnaround time for the results and optimize antimicrobial therapy in BSI. Copyright © 2017 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

  7. Direct identification from positive blood broth culture by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS

    Directory of Open Access Journals (Sweden)

    Maria Goreth Barberino

    2017-05-01

    Full Text Available Bloodstream infections (BSIs are among the most concerning bacterial infections. They are one of the leading causes of morbidity and mortality, and occur in 30–70% of critical care patients. The prompt identification of the causative microorganism can help choosing the appropriate antimicrobial therapy that will lead to better clinical outcomes. Blood culture is one of the most relevant tests for microbiological diagnosis of bacterial infections. The introduction of the MALDI-TOF microbiological diagnosis significantly decreased the time of identifying microorganisms. However, it depends on the growth on solid culture medium. In this study, 538 bottles of positive blood cultures were evaluated to test the accuracy of an in house modified protocol. The study sample consisted of 198 Gram-negative and 350 Gram-positive bacteria. In all, 460 (83.94% species were identified based on the direct plate findings. The protocol allowed the identification of 185/198 (93.43% of the Gram-negative bacteria, including aerobes, anaerobes, and non-fermenters, and 275/350 (78.85% of the Gram-positive bacteria. The proposed method has the potential to provide accurate results in comparison to the traditional method with the potential to reduce the turnaround time for the results and optimize antimicrobial therapy in BSI.

  8. Rapid identification of bacteria from bioMérieux BacT/ALERT blood culture bottles by MALDI-TOF MS.

    Science.gov (United States)

    Haigh, J D; Green, I M; Ball, D; Eydmann, M; Millar, M; Wilks, M

    2013-01-01

    Several studies have reported poor results when trying to identify microorganisms directly from the bioMérieux BacT/ALERT blood culture system using matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) mass spectrometry. The aim of this study is to evaluate two new methods, Sepsityper and an enrichment method for direct identification of microorganisms from this system. For both methods the samples were processed using the Bruker Microflex LT mass spectrometer (Biotyper) using the Microflex Control software to obtain spectra. The results from direct analysis were compared with those obtained by subculture and subsequent identification. A total of 350 positive blood cultures were processed simultaneously by the two methods. Fifty-three cultures were polymocrobial or failed to grow any organism on subculture, and these results were not included as there was either no subculture result, or for polymicrobial cultures it was known that the Biotyper would not be able to distinguish the constituent organisms correctly. Overall, the results showed that, contrary to previous reports, it is possible to identify bacteria directly from bioMérieux blood culture bottles, as 219/297 (74%) correct identifications were obtained using the Bruker Sepsityper method and 228/297 (77%) were obtained for the enrichment method when there is only one organism was present. Although the enrichment method was simpler, the reagent costs for the Sepsityper method were approximately pound 4.00 per sample compared to pound 0.50. An even simpler and cheaper method, which was less labour-intensive and did not require further reagents, was investigated. Seventy-seven specimens from positive signalled blood cultures were analysed by inoculating prewarmed blood agar plates and analysing any growth after 1-, 2- and 4-h periods of incubation at 37 degrees C, by either direct transfer or alcohol extraction. This method gave the highest number of correct identifications, 66/77 (86%), and was cheaper and less labour-intensive than either of the two above methods.

  9. Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus.

    Science.gov (United States)

    Teng, Jade L L; Huang, Yi; Tse, Herman; Chen, Jonathan H K; Tang, Ying; Lau, Susanna K P; Woo, Patrick C Y

    2014-10-20

    Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the "sanguinis group." As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the "mitis group." On the basis of the findings, we propose a novel group, named "sinensis group," to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Identification of serum biomarkers for occupational medicamentosa-like dermatitis induced by trichloroethylene using mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Wen-Xu; Liu, Wei [Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055 (China); Zhang, Yanfang [Shenzhen Prevention and Treatment Center for Occupational Disease, Shenzhen 518001 (China); Huang, Peiwu; Yang, Xifei; Ren, Xiaohu; Ye, Jinbo; Huang, Haiyan [Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055 (China); Tang, Haiyan [Shenzhen Prevention and Treatment Center for Occupational Disease, Shenzhen 518001 (China); Zhou, Guifeng [Medical School of Hunan Normal University, Changsha 410006 (China); Huang, Xinfeng; Zhuang, Zhixiong [Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055 (China); Liu, Jianjun, E-mail: bio-research@hotmail.com [Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055 (China)

    2013-11-15

    Occupational medicamentosa-like dermatitis induced by trichloroethylene (OMLDT) is an autoimmune disease and it has become a serious occupational health hazard. In the present study, we collected fasting blood samples from patients with OMLDT (n = 18) and healthy volunteers (n = 33) to explore serum peptidome patterns. Peptides in sera were purified using weak cation exchange magnetic beads (MB-WCX), and analyzed by matrix-assisted laser desorption ionization time-of-flight-mass spectrometry (MALDI-TOF-MS) and ClinProTools bioinformatics software. The intensities of thirty protein/peptide peaks were significantly different between the healthy control and OMLDT patients. A pattern of three peaks (m/z 2106.3, 2134.5, and 3263.67) was selected for supervised neural network (SNN) model building to separate the OMLDT patients from the healthy controls with a sensitivity of 95.5% and a specificity of 73.8%. Furthermore, two peptide peaks of m/z 4091.61 and 4281.69 were identified as fragments of ATP-binding cassette transporter family A member 12 (ABCA12), and cationic trypsinogen (PRRS1), respectively. Our findings not only show that specific proteomic fingerprints in the sera of OMLDT patients can be served as a differentiated tool of OMLDT patients with high sensitivity and high specificity, but also reveal the novel correlation between OMLDT with ABC transports and PRRS1, which will be of potential value for clinical and mechanistic studies of OMLDT. - Highlights: • Identify 30 differential protein/peptide peaks between OMLDT and healthy control • The test sensitivity and test specificity were 95.5% and 73.8%, respectively. • ABCA12 and PRSS1 were identified as potential biomarkers in OMLDT patients.

  11. Identification of serum biomarkers for occupational medicamentosa-like dermatitis induced by trichloroethylene using mass spectrometry

    International Nuclear Information System (INIS)

    Hong, Wen-Xu; Liu, Wei; Zhang, Yanfang; Huang, Peiwu; Yang, Xifei; Ren, Xiaohu; Ye, Jinbo; Huang, Haiyan; Tang, Haiyan; Zhou, Guifeng; Huang, Xinfeng; Zhuang, Zhixiong; Liu, Jianjun

    2013-01-01

    Occupational medicamentosa-like dermatitis induced by trichloroethylene (OMLDT) is an autoimmune disease and it has become a serious occupational health hazard. In the present study, we collected fasting blood samples from patients with OMLDT (n = 18) and healthy volunteers (n = 33) to explore serum peptidome patterns. Peptides in sera were purified using weak cation exchange magnetic beads (MB-WCX), and analyzed by matrix-assisted laser desorption ionization time-of-flight-mass spectrometry (MALDI-TOF-MS) and ClinProTools bioinformatics software. The intensities of thirty protein/peptide peaks were significantly different between the healthy control and OMLDT patients. A pattern of three peaks (m/z 2106.3, 2134.5, and 3263.67) was selected for supervised neural network (SNN) model building to separate the OMLDT patients from the healthy controls with a sensitivity of 95.5% and a specificity of 73.8%. Furthermore, two peptide peaks of m/z 4091.61 and 4281.69 were identified as fragments of ATP-binding cassette transporter family A member 12 (ABCA12), and cationic trypsinogen (PRRS1), respectively. Our findings not only show that specific proteomic fingerprints in the sera of OMLDT patients can be served as a differentiated tool of OMLDT patients with high sensitivity and high specificity, but also reveal the novel correlation between OMLDT with ABC transports and PRRS1, which will be of potential value for clinical and mechanistic studies of OMLDT. - Highlights: • Identify 30 differential protein/peptide peaks between OMLDT and healthy control • The test sensitivity and test specificity were 95.5% and 73.8%, respectively. • ABCA12 and PRSS1 were identified as potential biomarkers in OMLDT patients

  12. Interaction of singlet oxygen with bovine serum albumin and the role of the protein nano-compartmentalization.

    Science.gov (United States)

    Giménez, Rodrigo E; Vargová, Veronika; Rey, Valentina; Turbay, M Beatriz Espeche; Abatedaga, Inés; Morán Vieyra, Faustino E; Paz Zanini, Verónica I; Mecchia Ortiz, Juan H; Katz, Néstor E; Ostatná, Veronika; Borsarelli, Claudio D

    2016-05-01

    Singlet molecular oxygen ((1)O2) contributes to protein damage triggering biophysical and biochemical changes that can be related with aging and oxidative stress. Serum albumins, such as bovine serum albumin (BSA), are abundant proteins in blood plasma with different biological functions. This paper presents a kinetic and spectroscopic study of the (1)O2-mediated oxidation of BSA using the tris(2,2'-bipyridine)ruthenium(II) cation [Ru(bpy)3](2+) as sensitizer. BSA quenches efficiently (1)O2 with a total (chemical+physical interaction) rate constant kt(BSA)=7.3(±0.4)×10(8)M(-1)s(-1), where the chemical pathway represented 37% of the interaction. This efficient quenching by BSA indicates the participation of several reactive residues. MALDI-TOF MS analysis of intact BSA confirmed that after oxidation by (1)O2, the mass protein increased the equivalent of 13 oxygen atoms. Time-resolved emission spectra analysis of BSA established that Trp residues were oxidized to N'-formylkynurenine, being the solvent-accessible W134 preferentially oxidized by (1)O2 as compared with the buried W213. MS confirmed oxidation of at least two Tyr residues to form dihydroxyphenylalanine, with a global reactivity towards (1)O2 six-times lower than for Trp residues. Despite the lack of MS evidences, kinetic and chemical analysis also suggested that residues other than Trp and Tyr, e.g. Met, must react with (1)O2. Modeling of the 3D-structure of BSA indicated that the oxidation pattern involves a random distribution of (1)O2 into BSA; allowing also the interaction of (1)O2 with buried residues by its diffusion from the bulk solvent through interconnected internal hydrophilic and hydrophobic grooves. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Microheterogeneity of transthyretin in serum and ascitic fluid of ovarian cancer patients

    International Nuclear Information System (INIS)

    Gericke, Beate; Raila, Jens; Sehouli, Jalid; Haebel, Sophie; Könsgen, Dominique; Mustea, Alexander; Schweigert, Florian J

    2005-01-01

    Transthyretin (TTR), a traditional biomarker for nutritional and inflammatory status exists in different molecular variants of yet unknown importance. A truncated form of TTR has recently been described to be part of a set of biomarkers for the diagnosis of ovarian cancer. The main aim of the study was therefore to characterize differences in microheterogeneity between ascitic fluid and plasma of women affected with ovarian cancer and to evaluate the tumor site as the possible source of TTR. Subjects were 48 women with primary invasive epithelial ovarian cancer or recurrent ovarian carcinoma. The control group consisted of 20 postmenopausal women. TTR and retinol-binding protein (RBP) levels were measured by enzyme-linked immunoassay (ELISA) and C-reactive protein (CRP) levels by a high-sensitivity latex particle turbidimetric assay. The molecular heterogeneity of TTR was analysed using immunoprecipitation and matrix-associated laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Presence of TTR in tumor tissue was determined with indirect peroxidase immunostaining. TTR and RBP (μg/ml) levels in serum were 148.5 ± 96.7 and 22.5 ± 14.8 in affected women compared to 363.3 ± 105.5 and 55.8 ± 9.3 in healthy postmenopausal women (p < 0.01). In ascitic fluid, levels were 1.02 ± 0.24 and 4.63 ± 1.57 μg/ml, respectively. The mean levels of TTR and RBP in serum showed a tendency to decrease with the severity of the disease and were lower in affected women whose CRP levels were > 40 mg/ml (p = 0.08 for TTR; p < 0.05 for RBP). No differences in TTR microheterogeneity were observed between TTR isolated from serum of affected and healthy women or from ascitic fluid. TTR occurred rather consistently in four variants. Mass signals were at 13758 ± 7, 13876 ± 13 (greatest intensity), 13924 ± 21 and 14062 ± 24 Da, representing native, S-cysteinylated, S-cysteinglycinylated and glutathionylated TTR, respectively. Serum of healthy and affected women

  14. Reconstructing biochemical pathways from time course data.

    Science.gov (United States)

    Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago

    2007-03-01

    Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.

  15. Time course of clinical change following neurofeedback.

    Science.gov (United States)

    Rance, Mariela; Walsh, Christopher; Sukhodolsky, Denis G; Pittman, Brian; Qiu, Maolin; Kichuk, Stephen A; Wasylink, Suzanne; Koller, William N; Bloch, Michael; Gruner, Patricia; Scheinost, Dustin; Pittenger, Christopher; Hampson, Michelle

    2018-05-02

    Neurofeedback - learning to modulate brain function through real-time monitoring of current brain state - is both a powerful method to perturb and probe brain function and an exciting potential clinical tool. For neurofeedback effects to be useful clinically, they must persist. Here we examine the time course of symptom change following neurofeedback in two clinical populations, combining data from two ongoing neurofeedback studies. This analysis reveals a shared pattern of symptom change, in which symptoms continue to improve for weeks after neurofeedback. This time course has several implications for future neurofeedback studies. Most neurofeedback studies are not designed to test an intervention with this temporal pattern of response. We recommend that new studies incorporate regular follow-up of subjects for weeks or months after the intervention to ensure that the time point of greatest effect is sampled. Furthermore, this time course of continuing clinical change has implications for crossover designs, which may attribute long-term, ongoing effects of real neurofeedback to the control intervention that follows. Finally, interleaving neurofeedback sessions with assessments and examining when clinical improvement peaks may not be an appropriate approach to determine the optimal number of sessions for an application. Copyright © 2018 Elsevier Inc. All rights reserved.

  16. An earthworm protease cleaving serum fibronectin and decreasing HBeAg in HepG2.2.15 cells

    Directory of Open Access Journals (Sweden)

    Zhao Jing

    2008-11-01

    Full Text Available Abstract Background Virus-binding activity is one of the important functions of fibronectin (FN. It has been reported that a high concentration of FN in blood improves the transmission frequency of hepatitis viruses. Therefore, to investigate a protease that hydrolyzes FN rapidly is useful to decrease the FN concentration in blood and HBV infection. So far, however, no specific protease digesting FN in serum has been reported. Methods We employed a purified earthworm protease to digest serum proteins. The rapidly cleaved protein (FN was identified by MALDI-TOF MS and western blotting. The cleavage sites were determined by N-terminus amino acid residues sequencing. The protease was orally administrated to rats to investigate whether serum FN in vivo became decreased. The serum FN was determined by western blotting and ELISA. In cytological studies, the protease was added to the medium in the culture of HepG2.2.15 cells and then HBsAg and HBeAg were determined by ELISA. Results The protease purified from earthworm Eisenia fetida was found to function as a fibronectinase (FNase. The cleavage sites on FN by the FNase were at R and K, exhibiting a trypsin alkaline serine-like function. The earthworm fibronectinase (EFNase cleaved FN at four sites, R259, R1005, K1557 and R2039, among which the digested fragments at R259, K1557 and R2039 were related to the virus-binding activity as reported. The serum FN was significantly decreased when the earthworm fibronectinase was orally administrated to rats. The ELISA results showed that the secretion of HBeAg from HepG2.2.15 cells was significantly inhibited in the presence of the FNase. Conclusion The earthworm fibronectinase (EFNase cleaves FN much faster than the other proteins in serum, showing a potential to inhibit HBV infection through its suppressing the level of HBeAg. This suggests that EFNase is probably used as one of the candidates for the therapeutic agents to treat hepatitis virus infection.

  17. The solubilisation of boar sperm membranes by different detergents - a microscopic, MALDI-TOF MS, 31P NMR and PAGE study on membrane lysis, extraction efficiency, lipid and protein composition

    Directory of Open Access Journals (Sweden)

    Müller Karin

    2009-11-01

    Full Text Available Abstract Background Detergents are often used to isolate proteins, lipids as well as "detergent-resistant membrane domains" (DRMs from cells. Different detergents affect different membrane structures according to their physico-chemical properties. However, the effects of different detergents on membrane lysis of boar spermatozoa and the lipid composition of DRMs prepared from the affected sperm membranes have not been investigated so far. Results Spermatozoa were treated with the selected detergents Pluronic F-127, sodium cholate, CHAPS, Tween 20, Triton X-100 and Brij 96V. Different patterns of membrane disintegration were observed by light and electron microscopy. In accordance with microscopic data, different amounts of lipids and proteins were released from the cells by the different detergents. The biochemical methods to assay the phosphorus and cholesterol contents as well as 31P NMR to determine the phospholipids were not influenced by the presence of detergents since comparable amounts of lipids were detected in the organic extracts from whole cell suspensions after exposure to each detergent. However, matrix-assisted laser desorption and ionization time-of-flight mass spectrometry applied to identify phospholipids was essentially disturbed by the presence of detergents which exerted particular suppression effects on signal intensities. After separation of the membrane fractions released by detergents on a sucrose gradient only Triton X-100 and sodium cholate produced sharp turbid DRM bands. Only membrane solubilisation by Triton X-100 leads to an enrichment of cholesterol, sphingomyelin, phosphatidylinositol and phosphatidylethanolamine in a visible DRM band accompanied by a selective accumulation of proteins. Conclusion The boar sperm membranes are solubilised to a different extent by the used detergents. Particularly, the very unique DRMs isolated after Triton X-100 exposure are interesting candidates for further studies regarding the architecture of sperm.

  18. Antagonistic effects of Bacillus subtilis subsp. subtilis and B. amyloliquefaciens against Macrophomina phaseolina: SEM study of fungal changes and UV-MALDI-TOF MS analysis of their bioactive compounds.

    Science.gov (United States)

    Torres, M J; Brandan, C Pérez; Petroselli, G; Erra-Balsells, R; Audisio, M C

    2016-01-01

    The antifungal effect of Bacillus subtilis subsp. subtilis PGPMori7 and Bacillus amyloliquefaciens PGPBacCA1 was evaluated against Macrophomina phaseolina (Tassi) Goid. Cell suspension (CS), cell-free supernatant (CFS) and the lipopeptide fraction (LF) of PGPMori7 and PGPBacCA1 were screened against three different M. phaseolina strains. CS exhibited the highest inhibitory effect (around 50%) when compared to those of CFS and LF, regardless of the fungal strain studied. The synthesis of lipopeptides was studied by UV-MALDI TOF. Chemical analysis of Bacillus metabolite synthesis revealed that surfactin and iturin were mainly produced in liquid medium. Potential fengycin was also co-produced when both Bacillus were cultivated in solid medium. In co-culture assays, the bacterial colony-fungal mycelium interface at the inhibition zone was evaluated by both scanning electron microscopy (SEM) and UV-MALDI TOF, the former to determine the structural changes on M. phaseolina cells and the latter to identify the main bioactive molecules involved in the inhibitory effect. PGPBacCA1 produced surfactin, iturin and fengycin in the inhibition zone while PGPMori7 only produced these metabolites within its colony and not in the narrow inhibition zone. Interestingly, SEM revealed that PGPBacCA1 induced damage in M. phaseolina sclerotia, generating a fungicidal effect as no growth was observed when normal growth conditions were reestablished. In turn, PGPMori7 inhibited the growth of the Macrophomina mycelium without fungal injury, resulting only in a fungistatic activity. From these results, it was determined that the two bacilli significantly inhibited the growth of an important phytopathogenic fungus by at least two different mechanisms: lipopeptide synthesis and competition among microorganisms. Copyright © 2015 Elsevier GmbH. All rights reserved.

  19. Identification of Low Molecular Weight Glutenin Alleles by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) in Common Wheat (Triticum aestivum L.)

    Science.gov (United States)

    Islam, Shahidul; Applebee, Marie; Appels, Rudi; Yan, Yueming; Ma, Wujun

    2015-01-01

    Low molecular weight glutenin subunits (LMW-GS) play an important role in determining dough properties and breadmaking quality. However, resolution of the currently used methodologies for analyzing LMW-GS is rather low which prevents an efficient use of genetic variations associated with these alleles in wheat breeding. The aim of the current study is to evaluate and develop a rapid, simple, and accurate method to differentiate LMW-GS alleles using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. A set of standard single LMW-GS allele lines as well as a suite of well documented wheat cultivars were collected from France, CIMMYT, and Canada. Method development and optimization were focused on protein extraction procedures and MALDI-TOF instrument settings to generate reproducible diagnostic spectrum peak profiles for each of the known wheat LMW-GS allele. Results revealed a total of 48 unique allele combinations among the studied genotypes. Characteristic MALDI-TOF peak patterns were obtained for 17 common LMW-GS alleles, including 5 (b, a or c, d, e, f), 7 (a, b, c, d or i, f, g, h) and 5 (a, b, c, d, f) patterns or alleles for the Glu-A3, Glu-B3, and Glu-D3 loci, respectively. In addition, some reproducible MALDI-TOF peak patterns were also obtained that did not match with any known alleles. The results demonstrated a high resolution and throughput nature of MALDI-TOF technology in analyzing LMW-GS alleles, which is suitable for application in wheat breeding programs in processing a large number of wheat lines with high accuracy in limited time. It also suggested that the variation of LMW-GS alleles is more abundant than what has been defined by the current nomenclature system that is mainly based on SDS-PAGE system. The MALDI-TOF technology is useful to differentiate these variations. An international joint effort may be needed to assign allele symbols to these newly identified alleles and determine their effects on end-product quality attributes. PMID:26407296

  20. OmpU as a biomarker for rapid discrimination between toxigenic and epidemic Vibrio cholerae O1/O139 and non-epidemic Vibrio cholerae in a modified MALDI-TOF MS assay

    NARCIS (Netherlands)

    Paauw, A.; Trip, H.; Niemcewicz, M.; Sellek, R.; Heng, J.M.E.; Mars-Groenendijk, R.H.; Jong, A.L. de; Majchrzykiewicz-Koehorst, J.A.; Olsen, J.S.; Tsivtsivadze, E.

    2014-01-01

    Background Cholera is an acute diarrheal disease caused by Vibrio cholerae. Outbreaks are caused by a genetically homogenous group of strains from serogroup O1 or O139 that are able to produce the cholera toxin. Rapid detection and identification of these epidemic strains is essential for an

  1. Rapid Detection and Identification of Candidemia by Direct Blood Culturing on Solid Medium by Use of Lysis-Centrifugation Method Combined with Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS)

    Science.gov (United States)

    Idelevich, Evgeny A.; Grünastel, Barbara

    2016-01-01

    ABSTRACT Candida sepsis is a life-threatening condition with increasing prevalence. In this study, direct blood culturing on solid medium using a lysis-centrifugation procedure enabled successful Candida species identification by matrix-assisted laser desorption–ionization time of flight mass spectrometry on average 3.8 h (Sabouraud agar) or 7.4 h (chocolate agar) before the positivity signal for control samples in Bactec mycosis-IC/F or Bactec Plus aerobic/F bottles, respectively. Direct culturing on solid medium accelerated candidemia diagnostics compared to that with automated broth-based systems. PMID:27795344

  2. Investigations on aberrant glycosylation of glycosphingolipids in colorectal cancer tissues using liquid chromatography and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS).

    Science.gov (United States)

    Holst, Stephanie; Stavenhagen, Kathrin; Balog, Crina I A; Koeleman, Carolien A M; McDonnell, Liam M; Mayboroda, Oleg A; Verhoeven, Aswin; Mesker, Wilma E; Tollenaar, Rob A E M; Deelder, André M; Wuhrer, Manfred

    2013-11-01

    Cancer is a leading cause of death and alterations of glycosylation are characteristic features of malignant cells. Colorectal cancer is one of the most common cancers and its exact causes and biology are not yet well understood. Here, we compared glycosylation profiles of colorectal tumor tissues and corresponding control tissues of 13 colorectal cancer patients to contribute to the understanding of this cancer. Using MALDI-TOF(/TOF)-MS and 2-dimensional LC-MS/MS we characterized enzymatically released and 2-aminobenzoic acid labeled glycans from glycosphingolipids. Multivariate data analysis revealed significant differences between tumor and corresponding control tissues. Main discriminators were obtained, which represent the overall alteration in glycosylation of glycosphingolipids during colorectal cancer progression, and these were found to be characterized by (1) increased fucosylation, (2) decreased acetylation, (3) decreased sulfation, (4) reduced expression of globo-type glycans, as well as (5) disialyl gangliosides. The findings of our current research confirm former reports, and in addition expand the knowledge of glycosphingolipid glycosylation in colorectal cancer by revealing new glycans with discriminative power and characteristic, cancer-associated glycosylation alterations. The obtained discriminating glycans can contribute to progress the discovery of biomarkers to improve diagnostics and patient treatment.

  3. Investigations on Aberrant Glycosylation of Glycosphingolipids in Colorectal Cancer Tissues Using Liquid Chromatography and Matrix-Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF-MS)*

    Science.gov (United States)

    Holst, Stephanie; Stavenhagen, Kathrin; Balog, Crina I. A.; Koeleman, Carolien A. M.; McDonnell, Liam M.; Mayboroda, Oleg A.; Verhoeven, Aswin; Mesker, Wilma E.; Tollenaar, Rob A. E. M.; Deelder, André M.; Wuhrer, Manfred

    2013-01-01

    Cancer is a leading cause of death and alterations of glycosylation are characteristic features of malignant cells. Colorectal cancer is one of the most common cancers and its exact causes and biology are not yet well understood. Here, we compared glycosylation profiles of colorectal tumor tissues and corresponding control tissues of 13 colorectal cancer patients to contribute to the understanding of this cancer. Using MALDI-TOF(/TOF)-MS and 2-dimensional LC-MS/MS we characterized enzymatically released and 2-aminobenzoic acid labeled glycans from glycosphingolipids. Multivariate data analysis revealed significant differences between tumor and corresponding control tissues. Main discriminators were obtained, which represent the overall alteration in glycosylation of glycosphingolipids during colorectal cancer progression, and these were found to be characterized by (1) increased fucosylation, (2) decreased acetylation, (3) decreased sulfation, (4) reduced expression of globo-type glycans, as well as (5) disialyl gangliosides. The findings of our current research confirm former reports, and in addition expand the knowledge of glycosphingolipid glycosylation in colorectal cancer by revealing new glycans with discriminative power and characteristic, cancer-associated glycosylation alterations. The obtained discriminating glycans can contribute to progress the discovery of biomarkers to improve diagnostics and patient treatment. PMID:23878401

  4. Využití metod HPLC a MALDI-TOF MS pro stanovení glutenu v bezlepkových surovinách a potravinách

    Czech Academy of Sciences Publication Activity Database

    Gabrovská, D.; Rysová, J.; Šalplachta, Jiří; Řehulka, Pavel; Chmelík, Josef

    2002-01-01

    Roč. 96, č. 6 (2002), s. 486-487 ISSN 0009-2770. [Sjezd chemických společností /54./. Brno, 30.06.2002-04.07.2002] R&D Projects: GA MZe QD1023 Institutional research plan: CEZ:AV0Z4031919 Keywords : gluten * gluten -free * MALDI-TOF Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 0.336, year: 2002

  5. Direct identification of bacteria from BacT/ALERT anaerobic positive blood cultures by MALDI-TOF MS: MALDI Sepsityper kit versus an in-house saponin method for bacterial extraction.

    Science.gov (United States)

    Meex, Cécile; Neuville, Florence; Descy, Julie; Huynen, Pascale; Hayette, Marie-Pierre; De Mol, Patrick; Melin, Pierrette

    2012-11-01

    In cases of bacteraemia, a rapid species identification of the causal agent directly from positive blood culture broths could assist clinicians in the timely targeting of empirical antimicrobial therapy. For this purpose, we evaluated the direct identification of micro-organisms from BacT/ALERT (bioMérieux) anaerobic positive blood cultures without charcoal using the Microflex matrix-assisted laser desorption/ionization (MALDI) time of flight MS (Bruker), after bacterial extraction by using two different methods: the MALDI Sepsityper kit (Bruker) and an in-house saponin lysis method. Bruker's recommended criteria for identification were expanded in this study, with acceptance of the species identification when the first three results with the best matches with the MALDI Biotyper database were identical, whatever the scores were. In total, 107 monobacterial cultures and six polymicrobial cultures from 77 different patients were included in this study. Among monomicrobial cultures, we identified up to the species level 67 and 66 % of bacteria with the MALDI Sepsityper kit and the saponin method, respectively. There was no significant difference between the two extraction methods. The direct species identification was particularly inconclusive for Gram-positive bacteria, as only 58 and 52 % of them were identified to the species level with the MALDI Sepsityper kit and the saponin method, respectively. Results for Gram-negative bacilli were better, with 82.5 and 90 % of correct identification to the species level with the MALDI Sepsityper kit and the saponin method, respectively. No misidentifications were given by the direct procedures when compared with identifications provided by the conventional method. Concerning the six polymicrobial blood cultures, whatever the extraction method used, a correct direct identification was only provided for one of the isolated bacteria on solid medium in all cases. The analysis of the time-to-result demonstrated a reduction in the turnaround time for identification ranging from 1 h 06 min to 24 h 44 min, when performing the blood culture direct identification in comparison with the conventional method, whatever the extraction method.

  6. Rapid Detection and Identification of Candidemia by Direct Blood Culturing on Solid Medium by Use of Lysis-Centrifugation Method Combined with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Idelevich, Evgeny A; Grünastel, Barbara; Becker, Karsten

    2017-01-01

    Candida sepsis is a life-threatening condition with increasing prevalence. In this study, direct blood culturing on solid medium using a lysis-centrifugation procedure enabled successful Candida species identification by matrix-assisted laser desorption-ionization time of flight mass spectrometry on average 3.8 h (Sabouraud agar) or 7.4 h (chocolate agar) before the positivity signal for control samples in Bactec mycosis-IC/F or Bactec Plus aerobic/F bottles, respectively. Direct culturing on solid medium accelerated candidemia diagnostics compared to that with automated broth-based systems. Copyright © 2016 American Society for Microbiology.

  7. Analysis of post-operative changes in serum protein expression profiles from colorectal cancer patients by MALDI-TOF mass spectrometry: a pilot methodological study

    Directory of Open Access Journals (Sweden)

    Marsh Simon

    2010-04-01

    Full Text Available Abstract Background Mass spectrometry-based protein expression profiling of blood sera can be used to discriminate colorectal cancer (CRC patients from unaffected individuals. In a pilot methodological study, we have evaluated the changes in protein expression profiles of sera from CRC patients that occur following surgery to establish the potential of this approach for monitoring post-surgical response and possible early prediction of disease recurrence. Methods In this initial pilot study, serum specimens from 11 cancer patients taken immediately prior to surgery and at approximately 6 weeks following surgery were analysed alongside 10 normal control sera by matrix-assisted laser desorption ionisation time of-flight-mass spectrometry (MALDI-TOF MS. Using a two-sided t-test the top 20 ranked protein peaks that discriminate normal from pre-operative sera were identified. These were used to classify post-operative sera by hierarchical clustering analysis (Spearman's Rank correlation and, as an independent 'test' dataset, by k-nearest neighbour and weighted voting supervised learning algorithms. Results Hierarchical cluster analysis classified post-operative sera from all six early Dukes' stage (A and B patients as normal. The remaining five post-operative sera from more advanced Dukes' stages (C1 and C2 were classified as cancer. Analysis by supervised learning algorithms similarly grouped all advanced Dukes' stages as cancer, with four of the six post-operative sera from early Dukes' stages being classified as normal (P = 0.045; Fisher's exact test. Conclusions The results of this pilot methodological study illustrate the proof-of-concept of using protein expression profiling of post-surgical blood sera from individual patients to monitor disease course. Further validation on a larger patient cohort and using an independent post-operative sera dataset would be required to evaluate the potential clinical relevance of this approach. Prospective

  8. Comparative Time Course Profiles of Phthalate Stereoisomers in Mice

    Science.gov (United States)

    ABSTRACT More efficient models are needed to assess potential carcinogenicity hazard of environmental chemicals. Here we evaluated time course profiles for two reference phthalates, di(2-ethylhexyl) phthalate (DEHP) and its stereoisomer di-n-octyl phthalate (DNOP), to identify...

  9. Distribution and time course of corticosterone excretion in faeces and urine of female mice with varying systemic concentrations

    DEFF Research Database (Denmark)

    Kalliokoski, Otto; Hau, Jann; Jacobsen, Kirsten R

    2010-01-01

    distribution and time course of corticosterone excretion, after intravenous injection of varying corticosterone concentrations, was investigated in female mice. Female BALB/c mice excreted 60% of all corticosterone in the urine with an approximate delay of 5h from tail vein administration. The remaining 40......% were excreted in faeces, with an approximate delay of 9h from administration. The faecal/urinary excretion ratio, as well as time course of excretion, remained unaltered by administration of various doses of corticosterone covering the entire physiological range of serum corticosterone. Although...

  10. Clinical implications of ST segment time-course recovery patterns ...

    African Journals Online (AJOL)

    Arun Kumar Agnihotri

    Journal home page: http://www.akspublication.com/ijmu. Original Work. 3. Copyrighted © by Dr. ... KEY WORDS: Exercise stress test; ST segment time course patterns. INTRODUCTIONᴪ .... using simple descriptive statistics (mean ± SD) and contingency .... two patients who had the recovery time of less than. 3 minutes, had ...

  11. Modeling Fan Effects on the Time Course of Associative Recognition

    Science.gov (United States)

    Schneider, Darryl W.; Anderson, John R.

    2012-01-01

    We investigated the time course of associative recognition using the response signal procedure, whereby a stimulus is presented and followed after a variable lag by a signal indicating that an immediate response is required. More specifically, we examined the effects of associative fan (the number of associations that an item has with other items…

  12. Correlation of PTPN11 polymorphism at intron 3 with gastric cancer

    Directory of Open Access Journals (Sweden)

    Li ZHANG

    2011-05-01

    Full Text Available Objective To explore the correlation of protein-tyrosine-phosphatase nonreceptor-type 11(PTPN11 polymorphism at intron 3 with gastric cancer in Chinese population,and the feasibility and accuracy of employing mastrix-assisted laser desorption ionization time-of-flight mass spectrogram(MALDI-TOF-MS in genotyping of this SNP.Methods Two hundred and forty-seven patients with gastric cancer,212 cancer-free patients and 160 cord blood samples were enrolled in present study.Genotypes of PTPN11 G/A polymorphism at intron 3 were determined by MALDI-TOF-MS analysis,and direct sequencing of PCR products with 20 samples of the gene locus was done for checking the accuracy of MALDI-TOF-MS.Histological examination,Helicobacter pylori culture,rapid urease test,serum anti-H.pylori antibodies(ELISA and urease colloidal gold test were performed to evaluate H.pylori infection.Results Direct sequencing of 20 random selected samples were well consistent with the MALDI-TOF-MS results.The rates of H.pylori infection were 73.68% in gastric cancer patients and 75.47% in cancer-free patients,implying no significant difference between the two groups.The distributions of genotypes were in Hardy Weinberg equilibrium in both gastric cancer patients and controls.There were no significant differences in the genotype frequencies between the 2 groups(P>0.05.Compared with the GG genotype,GA+AA genotype could not influence the risk of gastric cancer.When stratified for status,PTPN11 polymorphism was not associated with age,gender and H.pylori infection states in both cancer patients and controls.Conclusion It seems that PTPN11 G/A polymorphism at intron 3 has no affection on the risk of gastric cancer in Chinese population.

  13. Time course of dynamic range adaptation in the auditory nerve

    Science.gov (United States)

    Wang, Grace I.; Dean, Isabel; Delgutte, Bertrand

    2012-01-01

    Auditory adaptation to sound-level statistics occurs as early as in the auditory nerve (AN), the first stage of neural auditory processing. In addition to firing rate adaptation characterized by a rate decrement dependent on previous spike activity, AN fibers show dynamic range adaptation, which is characterized by a shift of the rate-level function or dynamic range toward the most frequently occurring levels in a dynamic stimulus, thereby improving the precision of coding of the most common sound levels (Wen B, Wang GI, Dean I, Delgutte B. J Neurosci 29: 13797–13808, 2009). We investigated the time course of dynamic range adaptation by recording from AN fibers with a stimulus in which the sound levels periodically switch from one nonuniform level distribution to another (Dean I, Robinson BL, Harper NS, McAlpine D. J Neurosci 28: 6430–6438, 2008). Dynamic range adaptation occurred rapidly, but its exact time course was difficult to determine directly from the data because of the concomitant firing rate adaptation. To characterize the time course of dynamic range adaptation without the confound of firing rate adaptation, we developed a phenomenological “dual adaptation” model that accounts for both forms of AN adaptation. When fitted to the data, the model predicts that dynamic range adaptation occurs as rapidly as firing rate adaptation, over 100–400 ms, and the time constants of the two forms of adaptation are correlated. These findings suggest that adaptive processing in the auditory periphery in response to changes in mean sound level occurs rapidly enough to have significant impact on the coding of natural sounds. PMID:22457465

  14. The time course of attention modulation elicited by spatial uncertainty.

    Science.gov (United States)

    Huang, Dan; Liang, Huilou; Xue, Linyan; Wang, Meijian; Hu, Qiyi; Chen, Yao

    2017-09-01

    Uncertainty regarding the target location is an influential factor for spatial attention. Modulation in spatial uncertainty can lead to adjustments in attention scope and variations in attention effects. Hence, investigating spatial uncertainty modulation is important for understanding the underlying mechanism of spatial attention. However, the temporal dynamics of this modulation remains unclear. To evaluate the time course of spatial uncertainty modulation, we adopted a Posner-like attention orienting paradigm with central or peripheral cues. Different numbers of cues were used to indicate the potential locations of the target and thereby manipulate the spatial uncertainty level. The time interval between the onsets of the cue and the target (stimulus onset asynchrony, SOA) varied from 50 to 2000ms. We found that under central cueing, the effect of spatial uncertainty modulation could be detected from 200 to 2000ms after the presence of the cues. Under peripheral cueing, the effect of spatial uncertainty modulation was observed from 50 to 2000ms after cueing. Our results demonstrate that spatial uncertainty modulation produces robust and sustained effects on target detection speed. The time course of this modulation is influenced by the cueing method, which suggests that discrepant processing procedures are involved under different cueing conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Time course of brain activation elicited by basic emotions.

    Science.gov (United States)

    Hot, Pascal; Sequeira, Henrique

    2013-11-13

    Whereas facial emotion recognition protocols have shown that each discrete emotion has a specific time course of brain activation, there is no electrophysiological evidence to support these findings for emotional induction by complex pictures. Our objective was to specify the differences between the time courses of brain activation elicited by feelings of happiness and, with unpleasant pictures, by feelings of disgust and sadness. We compared event-related potentials (ERPs) elicited by the watching of high-arousing pictures from the International Affective Picture System, selected to induce specific emotions. In addition to a classical arousal effect on late positive components, we found specific ERP patterns for each emotion in early temporal windows (emotion to be associated with different brain processing after 140 ms, whereas happiness and sadness differed in ERPs elicited at the frontal and central sites after 160 ms. Our findings highlight the limits of the classical averaging of ERPs elicited by different emotions inside the same valence and suggest that each emotion could elicit a specific temporal pattern of brain activation, similar to those observed with emotional face recognition.

  16. Binding Isotherms and Time Courses Readily from Magnetic Resonance.

    Science.gov (United States)

    Xu, Jia; Van Doren, Steven R

    2016-08-16

    Evidence is presented that binding isotherms, simple or biphasic, can be extracted directly from noninterpreted, complex 2D NMR spectra using principal component analysis (PCA) to reveal the largest trend(s) across the series. This approach renders peak picking unnecessary for tracking population changes. In 1:1 binding, the first principal component captures the binding isotherm from NMR-detected titrations in fast, slow, and even intermediate and mixed exchange regimes, as illustrated for phospholigand associations with proteins. Although the sigmoidal shifts and line broadening of intermediate exchange distorts binding isotherms constructed conventionally, applying PCA directly to these spectra along with Pareto scaling overcomes the distortion. Applying PCA to time-domain NMR data also yields binding isotherms from titrations in fast or slow exchange. The algorithm readily extracts from magnetic resonance imaging movie time courses such as breathing and heart rate in chest imaging. Similarly, two-step binding processes detected by NMR are easily captured by principal components 1 and 2. PCA obviates the customary focus on specific peaks or regions of images. Applying it directly to a series of complex data will easily delineate binding isotherms, equilibrium shifts, and time courses of reactions or fluctuations.

  17. The time course of ethanol tolerance: associative learning

    Directory of Open Access Journals (Sweden)

    J.L.O. Bueno

    2007-11-01

    Full Text Available The effect of different contextual stimuli on different ethanol-induced internal states was investigated during the time course of both the hypothermic effect of the drug and of drug tolerance. Minimitters were surgically implanted in 16 Wistar rats to assess changes in their body temperature under the effect of ethanol. Rat groups were submitted to ethanol or saline trials every other day. The animals were divided into two groups, one receiving a constant dose (CD of ethanol injected intraperitoneally, and the other receiving increasing doses (ID during the 10 training sessions. During the ethanol training sessions, conditioned stimuli A (tone and B (buzzer were presented at "state +" (35 min after drug injection and "state -" (170 min after drug injection, respectively. Conditioned stimuli C (bip and D (white noise were presented at moments equivalent to stimuli A and B, respectively, but during the saline training sessions. All stimuli lasted 15 min. The CD group, but not the ID group, developed tolerance to the hypothermic effect of ethanol. Stimulus A (associated with drug "state +" induced hyperthermia with saline injection in the ID group. Stimulus B (associated with drug "state -" reduced ethanol tolerance in the CD group and modulated the hypothermic effect of the drug in the ID group. These results indicate that contextual stimuli acquire modulatory conditioned properties that are associated with the time course of both the action of the drug and the development of drug tolerance.

  18. Illusory conjunctions reflect the time course of the attentional blink.

    Science.gov (United States)

    Botella, Juan; Privado, Jesús; de Liaño, Beatriz Gil-Gómez; Suero, Manuel

    2011-07-01

    Illusory conjunctions in the time domain are binding errors for features from stimuli presented sequentially but in the same spatial position. A similar experimental paradigm is employed for the attentional blink (AB), an impairment of performance for the second of two targets when it is presented 200-500 msec after the first target. The analysis of errors along the time course of the AB allows the testing of models of illusory conjunctions. In an experiment, observers identified one (control condition) or two (experimental condition) letters in a specified color, so that illusory conjunctions in each response could be linked to specific positions in the series. Two items in the target colors (red and white, embedded in distractors of different colors) were employed in four conditions defined according to whether both targets were in the same or different colors. Besides the U-shaped function for hits, the errors were analyzed by calculating several response parameters reflecting characteristics such as the average position of the responses or the attentional suppression during the blink. The several error parameters cluster in two time courses, as would be expected from prevailing models of the AB. Furthermore, the results match the predictions from Botella, Barriopedro, and Suero's (Journal of Experimental Psychology: Human Perception and Performance, 27, 1452-1467, 2001) model for illusory conjunctions.

  19. The time course of attentional modulation on emotional conflict processing.

    Science.gov (United States)

    Zhou, Pingyan; Yang, Guochun; Nan, Weizhi; Liu, Xun

    2016-01-01

    Cognitive conflict resolution is critical to human survival in a rapidly changing environment. However, emotional conflict processing seems to be particularly important for human interactions. This study examined whether the time course of attentional modulation on emotional conflict processing was different from cognitive conflict processing during a flanker task. Results showed that emotional N200 and P300 effects, similar to colour conflict processing, appeared only during the relevant task. However, the emotional N200 effect preceded the colour N200 effect, indicating that emotional conflict can be identified earlier than cognitive conflict. Additionally, a significant emotional N100 effect revealed that emotional valence differences could be perceived during early processing based on rough aspects of input. The present data suggest that emotional conflict processing is modulated by top-down attention, similar to cognitive conflict processing (reflected by N200 and P300 effects). However, emotional conflict processing seems to have more time advantages during two different processing stages.

  20. The time course of explicit and implicit categorization.

    Science.gov (United States)

    Smith, J David; Zakrzewski, Alexandria C; Herberger, Eric R; Boomer, Joseph; Roeder, Jessica L; Ashby, F Gregory; Church, Barbara A

    2015-10-01

    Contemporary theory in cognitive neuroscience distinguishes, among the processes and utilities that serve categorization, explicit and implicit systems of category learning that learn, respectively, category rules by active hypothesis testing or adaptive behaviors by association and reinforcement. Little is known about the time course of categorization within these systems. Accordingly, the present experiments contrasted tasks that fostered explicit categorization (because they had a one-dimensional, rule-based solution) or implicit categorization (because they had a two-dimensional, information-integration solution). In Experiment 1, participants learned categories under unspeeded or speeded conditions. In Experiment 2, they applied previously trained category knowledge under unspeeded or speeded conditions. Speeded conditions selectively impaired implicit category learning and implicit mature categorization. These results illuminate the processing dynamics of explicit/implicit categorization.

  1. On the Time Course of Vocal Emotion Recognition

    Science.gov (United States)

    Pell, Marc D.; Kotz, Sonja A.

    2011-01-01

    How quickly do listeners recognize emotions from a speaker's voice, and does the time course for recognition vary by emotion type? To address these questions, we adapted the auditory gating paradigm to estimate how much vocal information is needed for listeners to categorize five basic emotions (anger, disgust, fear, sadness, happiness) and neutral utterances produced by male and female speakers of English. Semantically-anomalous pseudo-utterances (e.g., The rivix jolled the silling) conveying each emotion were divided into seven gate intervals according to the number of syllables that listeners heard from sentence onset. Participants (n = 48) judged the emotional meaning of stimuli presented at each gate duration interval, in a successive, blocked presentation format. Analyses looked at how recognition of each emotion evolves as an utterance unfolds and estimated the “identification point” for each emotion. Results showed that anger, sadness, fear, and neutral expressions are recognized more accurately at short gate intervals than happiness, and particularly disgust; however, as speech unfolds, recognition of happiness improves significantly towards the end of the utterance (and fear is recognized more accurately than other emotions). When the gate associated with the emotion identification point of each stimulus was calculated, data indicated that fear (M = 517 ms), sadness (M = 576 ms), and neutral (M = 510 ms) expressions were identified from shorter acoustic events than the other emotions. These data reveal differences in the underlying time course for conscious recognition of basic emotions from vocal expressions, which should be accounted for in studies of emotional speech processing. PMID:22087275

  2. Time course of recovery of idiopathic vocal fold paralysis.

    Science.gov (United States)

    Husain, Solomon; Sadoughi, Babak; Mor, Niv; Levin, Ariana M; Sulica, Lucian

    2018-01-01

    To clarify the time course of recovery in patients with idiopathic vocal fold paralysis. Retrospective chart review. Medical records for all patients with idiopathic vocal fold paralysis over a 10-year period were reviewed to obtain demographic and clinical information, including onset of disease and recovery of vocal function. Stroboscopic exams of patients who recovered voice were reviewed blindly to assess return of vocal fold motion. Thirty-eight of 55 patients (69%) recovered vocal function. Time course of recovery could be assessed in 34 patients who did not undergo injection augmentation. The mean time to recovery was 152.8 ± 109.3 days (left, 179.8 ± 111.3 days; right, 105.3 ± 93.7 days; P = .088). Two-thirds of patients recovered within 6 months. Probability of recovery declined over time. Five of 22 patients who recovered voice had return of vocal fold motion; 17 did not. The mean time to recovery did not differ between these groups (return of motion, 127.4 ± 132.3 days; no return of motion, 160.1 ± 105.1 days; P = .290). Sixty-nine percent of patients with idiopathic vocal fold paralysis recovered vocal function, two-thirds doing so within 6 months of onset. Age, gender, laterality, use of injection augmentation did not influence recovery rate. Declining probability of recovery over time leads us to consider framework surgery after 6 months in patients with idiopathic paralysis. 4. Laryngoscope, 128:148-152, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  3. Time Course of Resolution of Hyperprolactinemia After Transsphenoidal Surgery Among Patients Presenting with Pituitary Stalk Compression.

    Science.gov (United States)

    Zaidi, Hasan A; Cote, David J; Castlen, Joseph P; Burke, William T; Liu, Yong-Hui; Smith, Timothy R; Laws, Edward R

    2017-01-01

    Primary lactotroph disinhibition, or stalk effect, occurs when mechanical compression of the pituitary stalk disrupts the tonic inhibition by dopamine released by the hypothalamus. The resolution of pituitary stalk effect-related hyperprolactinemia postoperatively has not been studied in a large cohort of patients. We performed a retrospective review to investigate the time course of recovery of lactotroph disinhibition after transsphenoidal surgery. Medical records were retrospectively reviewed for all patients undergoing transsphenoidal surgery with the senior author from April 2008 to November 2014. Of 556 pituitary adenomas, 289 (52.0%) were eliminated: 77 (13.9%) had an immunohistochemically confirmed prolactinoma, 119 (21.4%) patients had previous surgery, 93 (16.7%) had incomplete medical records, leaving 267 patients (48.0%) for final analysis. Of these patients, 72 (27.0%) had increased serum prolactin levels (≥23.3 ng/mL), suggestive of pituitary stalk effect (maximum prolactin level = 148.0 ng/mL). Patients with stalk effect were more likely than those with normal serum prolactin levels to present with menstrual dysfunction (29.7% vs. 19.4%; P Transsphenoidal surgery can provide durable normalization of serum prolactin levels and related symptoms caused by pituitary stalk compression-related lactotroph disinhibition. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Time-course of attention biases in social phobia.

    Science.gov (United States)

    Schofield, Casey A; Inhoff, Albrecht W; Coles, Meredith E

    2013-10-01

    Theoretical models of social phobia implicate preferential attention to social threat in the maintenance of anxiety symptoms, though there has been limited work characterizing the nature of these biases over time. The current study utilized eye-movement data to examine the time-course of visual attention over 1500ms trials of a probe detection task. Nineteen participants with a primary diagnosis of social phobia based on DSM-IV criteria and 20 non-clinical controls completed this task with angry, fearful, and happy face trials. Overt visual attention to the emotional and neutral faces was measured in 50ms segments across the trial. Over time, participants with social phobia attend less to emotional faces and specifically less to happy faces compared to controls. Further, attention to emotional relative to neutral expressions did not vary notably by emotion for participants with social phobia, but control participants showed a pattern after 1000ms in which over time they preferentially attended to happy expressions and avoided negative expressions. Findings highlight the importance of considering attention biases to positive stimuli as well as the pattern of attention between groups. These results suggest that attention "bias" in social phobia may be driven by a relative lack of the biases seen in non-anxious participants. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. The time course of attentional deployment in contextual cueing.

    Science.gov (United States)

    Jiang, Yuhong V; Sigstad, Heather M; Swallow, Khena M

    2013-04-01

    The time course of attention is a major characteristic on which different types of attention diverge. In addition to explicit goals and salient stimuli, spatial attention is influenced by past experience. In contextual cueing, behaviorally relevant stimuli are more quickly found when they appear in a spatial context that has previously been encountered than when they appear in a new context. In this study, we investigated the time that it takes for contextual cueing to develop following the onset of search layout cues. In three experiments, participants searched for a T target in an array of Ls. Each array was consistently associated with a single target location. In a testing phase, we manipulated the stimulus onset asynchrony (SOA) between the repeated spatial layout and the search display. Contextual cueing was equivalent for a wide range of SOAs between 0 and 1,000 ms. The lack of an increase in contextual cueing with increasing cue durations suggests that as an implicit learning mechanism, contextual cueing cannot be effectively used until search begins.

  6. Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data.

    Science.gov (United States)

    Tan, Qihua; Thomassen, Mads; Burton, Mark; Mose, Kristian Fredløv; Andersen, Klaus Ejner; Hjelmborg, Jacob; Kruse, Torben

    2017-06-06

    Modeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.

  7. Tracing the time course of picture--word processing.

    Science.gov (United States)

    Smith, M C; Magee, L E

    1980-12-01

    A number of independent lines of research have suggested that semantic and articulatory information become available differentially from pictures and words. The first of the experiments reported here sought to clarify the time course by which information about pictures and words becomes available by considering the pattern of interference generated when incongruent pictures and words are presented simultaneously in a Stroop-like situation. Previous investigators report that picture naming is easily disrupted by the presence of a distracting word but that word naming is relatively immune to interference from an incongruent picture. Under the assumption that information available from a completed process may disrupt an ongoing process, these results suggest that words access articulatory information more rapidly than do pictures. Experiment 1 extended this paradigm by requiring subjects to verify the category of the target stimulus. In accordance with the hypothesis that picture access the semantic code more rapidly than words, there was a reversal in the interference pattern: Word categorization suffered considerable disruption, whereas picture categorization was minimally affected by the presence of an incongruent word. Experiment 2 sought to further test the hypothesis that access to semantic and articulatory codes is different for pictures and words by examining memory for those items following naming or categorization. Categorized words were better recognized than named words, whereas the reverse was true for pictures, a result which suggests that picture naming involves more extensive processing than picture categorization. Experiment 3 replicated this result under conditions in which viewing time was held constant. The last experiment extended the investigation of memory differences to a situation in which subjects were required to generate the superordinate category name. Here, memory for categorized pictures was as good as memory for named pictures. Category

  8. Alterations of retinol-binding protein 4 species in patients with different stages of chronic kidney disease and their relation to lipid parameters

    DEFF Research Database (Denmark)

    Henze, Andrea; Frey, Simone K; Raila, Jens

    2010-01-01

    ) was assessed in serum of 45 healthy controls and 52 patients with stage 2-5 of CKD using ELISA and RBP4 immunoprecipitation with subsequent MALDI-TOF-MS analysis. A reduction of glomerular filtration rate was accompanied by a gradual elevation of RBP4 serum levels and relative amounts of RBP4-LL. Correlation...... analysis revealed a strong association of the RBP4-TTR ratio with parameters of lipid metabolism and with diabetes-related factors. In conclusion, RBP4 serum concentration and the appearance of RBP4-LL seem to be influenced by kidney function. Furthermore, the RBP4-TTR ratio may provide diagnostic...

  9. Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data

    DEFF Research Database (Denmark)

    Tan, Qihua; Thomassen, Mads; Burton, Mark

    2017-01-01

    the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray...... time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health....

  10. Time course of arterial vascular adaptations to inactivity and paralyses in humans.

    NARCIS (Netherlands)

    Groot, P.C.E. de; Kuppevelt, D. van; Pons, C.; Snoek, G.V.E.; Woude, L.H.V. van der; Hopman, M.T.E.

    2003-01-01

    PURPOSE: The aim of the present study was to assess the time course of vascular adaptations to inactivity and paralyses in humans. The spinal cord-injured (SCI) population offers a unique "human model of nature" to assess peripheral vascular adaptations and its time course to extreme inactivity and

  11. MoS_2/Ag nanohybrid: A novel matrix with synergistic effect for small molecule drugs analysis by negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

    International Nuclear Information System (INIS)

    Zhao, Yaju; Deng, Guoqing; Liu, Xiaohui; Sun, Liang; Li, Hui; Cheng, Quan; Xi, Kai; Xu, Danke

    2016-01-01

    This paper reports a facile synthesis of molybdenum disulfide nanosheets/silver nanoparticles (MoS_2/Ag) hybrid and its use as an effective matrix in negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The nanohybrid exerts a strong synergistic effect, leading to high performance detection of small molecule analytes including amino acids, peptides, fatty acids and drugs. The enhancement of laser desorption/ionization (LDI) efficiency is largely attributed to the high surface roughness and large surface area for analyte adsorption, better dispersibility, increased thermal conductivity and enhanced UV energy absorption as compared to pure MoS_2. Moreover, both Ag nanoparticles and the edge of the MoS_2 layers function as deprotonation sites for proton capture, facilitating the charging process in negative ion mode and promoting formation of negative ions. As a result, the MoS_2/Ag nanohybrid proves to be a highly attractive matrix in MALDI-TOF MS, with desired features such as high desorption/ionization efficiency, low fragmentation interference, high salt tolerance, and no sweet-spots for mass signal. These characteristic properties allowed for simultaneous analysis of eight different drugs and quantification of acetylsalicylic acid in the spiked human serum. This work demonstrates for the first time the fabrication and application of a novel MoS_2/Ag hybrid, and provides a new platform for use in the rapid and high throughput analysis of small molecules by mass spectrometry. - Highlights: • MoS_2/Ag nanohybrid was applied as a novel matrix in negative-ion MALDI-TOF MS. • The MoS_2/Ag nanohybrid exerted synergistic effect on the detection of small molecules. • The MoS_2/Ag nanohybrid showed good signal reproducibility and low background interferences comparing to organic matrices. • MoS_2/Ag allows simultaneous analysis of multiple drugs and quantification of acetylsalicylic acid in spiked serum samples.

  12. Bile salt-induced cholesterol crystal formation from model bile vesicles: a time course study

    NARCIS (Netherlands)

    van de Heijning, B. J.; Stolk, M. F.; van Erpecum, K. J.; Renooij, W.; Groen, A. K.; vanBerge-Henegouwen, G. P.

    1994-01-01

    Precipitation of cholesterol crystals from vesicles is an important step in the pathogenesis of cholesterol gallstones. Little is known, however, about the kinetics and the mechanisms involved in cholesterol crystallization. Therefore, the time course of cholesterol crystal precipitation and lipid

  13. The time-course of cortico-limbic neural responses to air hunger

    OpenAIRE

    Binks, Andrew P.; Evans, Karleyton C.; Reed, Jeffrey D.; Moosavi, Shakeeb H.; Banzett, Robert B.

    2014-01-01

    Several studies have mapped brain regions associated with acute dyspnea perception. However, the time-course of brain activity during sustained dyspnea is unknown. Our objective was to determine the time-course of neural activity when dyspnea is sustained. Eight healthy subjects underwent brain blood oxygen level dependent functional magnetic imaging (BOLD-fMRI) during mechanical ventilation with constant mild hypercapnia (~45 mmHg). Subjects rated dyspnea (air hunger) via visual analog scale...

  14. Anxiety and its time courses during radiotherapy for non-metastatic breast cancer: A longitudinal study

    OpenAIRE

    Lewis, Florence; Merckaert, Isabelle; Liénard, Aurore; Libert, Yves; Etienne, Anne-Marie; Reynaert, Christine; Slachmuylder, Jean-Louis; Scalliet, Pierre; Van Houtte, Paul; COUCKE, Philippe; Salamon, Emile; Razavi, Darius

    2014-01-01

    Purpose: To our knowledge, no study has specifically assessed the time course of anxiety during radiotherapy (RT). The objective of this study was to assess anxiety time courses in patients with nonmetastatic breast cancer. Material and methods: This multicenter, descriptive longitudinal study included 213 consecutive patients with breast cancer who completed visual analog scales (VASs) assessing state anxiety before and after the RT simulation and the first and last five RT se...

  15. Smoothing dynamic positron emission tomography time courses using functional principal components

    OpenAIRE

    Jiang, Ci-Ren; Aston, John A. D.; Wang, Jane-Ling

    2009-01-01

    A functional smoothing approach to the analysis of PET time course data is presented. By borrowing information across space and accounting for this pooling through the use of a non-parametric covariate adjustment, it is possible to smooth the PET time course data thus reducing the noise. A new model for functional data analysis, the Multiplicative Nonparametric Random Effects Model, is introduced to more accurately account for the variation in the data. A locally adaptive bandwidth choice hel...

  16. Stable isotopic labeling-based quantitative targeted glycomics (i-QTaG).

    Science.gov (United States)

    Kim, Kyoung-Jin; Kim, Yoon-Woo; Kim, Yun-Gon; Park, Hae-Min; Jin, Jang Mi; Hwan Kim, Young; Yang, Yung-Hun; Kyu Lee, Jun; Chung, Junho; Lee, Sun-Gu; Saghatelian, Alan

    2015-01-01

    Mass spectrometry (MS) analysis combined with stable isotopic labeling is a promising method for the relative quantification of aberrant glycosylation in diseases and disorders. We developed a stable isotopic labeling-based quantitative targeted glycomics (i-QTaG) technique for the comparative and quantitative analysis of total N-glycans using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We established the analytical procedure with the chemical derivatizations (i.e., sialic acid neutralization and stable isotopic labeling) of N-glycans using a model glycoprotein (bovine fetuin). Moreover, the i-QTaG using MALDI-TOF MS was evaluated with various molar ratios (1:1, 1:2, 1:5) of (13) C6 /(12) C6 -2-aminobenzoic acid-labeled glycans from normal human serum. Finally, this method was applied to direct comparison of the total N-glycan profiles between normal human sera (n = 8) and prostate cancer patient sera (n = 17). The intensities of the N-glycan peaks from i-QTaG method showed a good linearity (R(2) > 0.99) with the amount of the bovine fetuin glycoproteins. The ratios of relative intensity between the isotopically 2-AA labeled N-glycans were close to the theoretical molar ratios (1:1, 1:2, 1:5). We also demonstrated that the up-regulation of the Lewis antigen (~82%) in sera from prostate cancer patients. In this proof-of-concept study, we demonstrated that the i-QTaG method, which enables to achieve a reliable comparative quantitation of total N-glycans via MALDI-TOF MS analysis, has the potential to diagnose and monitor alterations in glycosylation associated with disease states or biotherapeutics. © 2015 American Institute of Chemical Engineers.

  17. Altered time course of amygdala activation during speech anticipation in social anxiety disorder.

    Science.gov (United States)

    Davies, Carolyn D; Young, Katherine; Torre, Jared B; Burklund, Lisa J; Goldin, Philippe R; Brown, Lily A; Niles, Andrea N; Lieberman, Matthew D; Craske, Michelle G

    2017-02-01

    Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Participants (SAD n=58; HC n=16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task. Repeated measures multi-level modeling analyses were used to examine group differences in time course activity during speech vs. control anticipation for regions of interest, including bilateral amygdala, insula, ventral striatum, and dorsal anterior cingulate cortex. The time course of amygdala activity was more prolonged and less variable throughout speech anticipation in SAD participants compared to HCs, whereas the overall magnitude of amygdala response did not differ between groups. Magnitude and time course of activity was largely similar between groups across other regions of interest. Analyses were restricted to regions of interest and task order was the same across participants due to the nature of deception instructions. Sustained amygdala time course during anticipation may uniquely reflect heightened detection of threat or deficits in emotion regulation in socially anxious individuals. Findings highlight the importance of examining temporal dynamics of amygdala responding. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Performance of two resin-containing blood culture media in detection of bloodstream infections and in direct matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) broth assays for isolate identification: clinical comparison of the BacT/Alert Plus and Bactec Plus systems.

    Science.gov (United States)

    Fiori, Barbara; D'Inzeo, Tiziana; Di Florio, Viviana; De Maio, Flavio; De Angelis, Giulia; Giaquinto, Alessia; Campana, Lara; Tanzarella, Eloisa; Tumbarello, Mario; Antonelli, Massimo; Sanguinetti, Maurizio; Spanu, Teresa

    2014-10-01

    We compared the clinical performances of the BacT/Alert Plus (bioMérieux) and Bactec Plus (Becton Dickinson) aerobic and anaerobic blood culture (BC) media with adsorbent polymeric beads. Patients ≥ 16 years old with suspected bloodstream infections (BSIs) were enrolled in intensive care units and infectious disease wards. A single 40-ml blood sample was collected from each and used to inoculate (10 ml/bottle) one set of BacT/Alert Plus cultures and one set of Bactec Plus cultures, each set consisting of one aerobic and one anaerobic bottle. Cultures were incubated ≤ 5 days in the BacT/Alert 3D and Bactec FX instruments, respectively. A total of 128 unique BSI episodes were identified based on the recovery of clinically significant growth in 212 aerobic cultures (106 BacT/Alert and 106 Bactec) and 151 anaerobic cultures (82 BacT/Alert and 69 Bactec). The BacT/Alert aerobic medium had higher recovery rates for Gram-positive cocci (P = 0.024), whereas the Bactec aerobic medium was superior for recovery of Gram-negative bacilli (P = 0.006). BacT/Alert anaerobic medium recovery rates exceeded those of the Bactec anaerobic medium for total organisms (P = 0.003), Gram-positive cocci (P = 0.013), and Escherichia coli (P = 0.030). In terms of capacity for diagnosing the 128 septic episodes, the BacT/Alert and Bactec sets were comparable, although the former sets diagnosed more BSIs caused by Gram-positive cocci (P = 0.008). They also allowed earlier identification of coagulase-negative staphylococcal growth (mean, 2.8 h; P = 0.003) and growth in samples from patients not on antimicrobial therapy that yielded positive results (mean, 1.3 h; P direct matrix-assisted laser desorption ionization-time of flight mass spectrometry assay of BC broths. The BacT/Alert Plus media line appears to be a reliable, timesaving tool for routine detection of BSIs in the population we studied, although further studies are needed to evaluate their performance in other settings. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  19. Time course analyses of orthographic and phonological priming effects during word recognition in a transparent orthography.

    Science.gov (United States)

    Zeguers, M H T; Snellings, P; Huizenga, H M; van der Molen, M W

    2014-10-01

    In opaque orthographies, the activation of orthographic and phonological codes follows distinct time courses during visual word recognition. However, it is unclear how orthography and phonology are accessed in more transparent orthographies. Therefore, we conducted time course analyses of masked priming effects in the transparent Dutch orthography. The first study used targets with small phonological differences between phonological and orthographic primes, which are typical in transparent orthographies. Results showed consistent orthographic priming effects, yet phonological priming effects were absent. The second study explicitly manipulated the strength of the phonological difference and revealed that both orthographic and phonological priming effects became identifiable when phonological differences were strong enough. This suggests that, similar to opaque orthographies, strong phonological differences are a prerequisite to separate orthographic and phonological priming effects in transparent orthographies. Orthographic and phonological priming appeared to follow distinct time courses, with orthographic codes being quickly translated into phonological codes and phonology dominating the remainder of the lexical access phase.

  20. The Time-Course of Lexical Activation during Sentence Comprehension in People with Aphasia

    Science.gov (United States)

    Ferrill, Michelle; Love, Tracy; Walenski, Matthew; Shapiro, Lewis P.

    2012-01-01

    Purpose: To investigate the time-course of processing of lexical items in auditorily presented canonical (subject-verb-object) constructions in young, neurologically unimpaired control participants and participants with left-hemisphere damage and agrammatic aphasia. Method: A cross modal picture priming (CMPP) paradigm was used to test 114 control…

  1. The time course of working memory effects on visual attention differs depending on memory type

    NARCIS (Netherlands)

    Dombrowe, I.; Olivers, C.N.L.; Donk, M.

    2010-01-01

    Previous work has generated inconsistent results with regard to what extent working memory (WM) content guides visual attention. Some studies found effects of easy to verbalize stimuli, whereas others only found an influence of visual memory content. To resolve this, we compared the time courses of

  2. An Analysis of the Time Course of Lexical Processing during Reading

    Science.gov (United States)

    Sheridan, Heather; Reichle, Erik D.

    2016-01-01

    Reingold, Reichle, Glaholt, and Sheridan (2012) reported a gaze-contingent eye-movement experiment in which survival-curve analyses were used to examine the effects of word frequency, the availability of parafoveal preview, and initial fixation location on the time course of lexical processing. The key results of these analyses suggest that…

  3. Time course of the antiproteinuric and antihypertensive effects of direct renin inhibition in type 2 diabetes

    DEFF Research Database (Denmark)

    Persson, F; Rossing, P; Schjoedt, K J

    2008-01-01

    Inhibition of renin with an active site inhibitor, aliskiren, lowers blood pressure (BP) in diabetic patients. Here, we studied the time course of the antihypertensive and antiproteinuric effect of renin inhibition in 15 patients with type 2 diabetes and elevated urinary albumin/creatinine ratios...

  4. The time course of myonuclear accretion during hypertrophy in young adult and older rat plantaris muscle

    NARCIS (Netherlands)

    van der Meer, S.F.T.; Jaspers, R.T.; Jones, D.A.; Degens, H.

    2011-01-01

    To investigate whether accretion of myonuclei precedes or follows the increase in fibre cross-sectional area and whether this time course is affected by age, left plantaris muscle of 5- and 25-month-old male Wistar rats was overloaded by denervation of its synergists for 1, 2 or 4 weeks.

  5. The time-course of alpha neurofeedback training effects in healthy participants

    NARCIS (Netherlands)

    Dekker, M.K.J.; Sitskoorn, M.M.; Denissen, A.; van Boxtel, G.J.M.

    2014-01-01

    The time-course of alpha neurofeedback training (NFT) was investigated in 18 healthy participants who received 15 sessions of training (eyes open), each consisting of three training periods (data are from Van Boxtel et al., 2012). Here we report on the within- and between-session training effects

  6. The time course of temporal preparation in an applied setting: a study of gaming behavior

    NARCIS (Netherlands)

    Los, S.A.; Hoorn, J.F.; Grin, M.; van den Burg, E.

    2013-01-01

    We examined the time course of temporal preparation in the practice of computer gaming. Participants held an infrared rifle to shoot animated figures ("terrorists") that appeared from an elevator that opened briefly after the sound of a bell. The sound was either loud or soft and the interval

  7. Adverse radiation effect after stereotactic radiosurgery for brain metastases : incidence, time course, and risk factors

    NARCIS (Netherlands)

    Sneed, Penny K.; Mendez, Joe; Vemer-van den Hoek, Johanna; Seymour, Zachary A.; Ma, Lijun; Molinaro, Annette M.; Fogh, Shannon E.; Nakamura, Jean L.; McDermott, Michael W.

    OBJECT The authors sought to determine the incidence, time course, and risk factors for overall adverse radiation effect (ARE) and symptomatic ARE after stereotactic radiosurgery (SRS) for brain metastases. METHODS All cases of brain metastases treated from 1998 through 2009 with Gamma Knife SRS at

  8. The visual-auditory color-word Stroop asymmetry and its time course

    NARCIS (Netherlands)

    Roelofs, A.P.A.

    2005-01-01

    Four experiments examined crossmodal versions of the Stroop task in order (1) to look for Stroop asymmetries in color naming, spoken-word naming, and written-word naming and to evaluate the time course of these asymmetries, and (2) to compare these findings to current models of the Stroop effect.

  9. More powerful significant testing for time course gene expression data using functional principal component analysis approaches.

    Science.gov (United States)

    Wu, Shuang; Wu, Hulin

    2013-01-16

    One of the fundamental problems in time course gene expression data analysis is to identify genes associated with a biological process or a particular stimulus of interest, like a treatment or virus infection. Most of the existing methods for this problem are designed for data with longitudinal replicates. But in reality, many time course gene experiments have no replicates or only have a small number of independent replicates. We focus on the case without replicates and propose a new method for identifying differentially expressed genes by incorporating the functional principal component analysis (FPCA) into a hypothesis testing framework. The data-driven eigenfunctions allow a flexible and parsimonious representation of time course gene expression trajectories, leaving more degrees of freedom for the inference compared to that using a prespecified basis. Moreover, the information of all genes is borrowed for individual gene inferences. The proposed approach turns out to be more powerful in identifying time course differentially expressed genes compared to the existing methods. The improved performance is demonstrated through simulation studies and a real data application to the Saccharomyces cerevisiae cell cycle data.

  10. Elucidation of time-dependent systems biology cell response patterns with time course network enrichment

    DEFF Research Database (Denmark)

    Wiwie, Christian; Rauch, Alexander; Haakonsson, Anders

    2018-01-01

    , no methods exist to integrate time series data with networks, thus preventing the identification of time-dependent systems biology responses. We close this gap with Time Course Network Enrichment (TiCoNE). It combines a new kind of human-augmented clustering with a novel approach to network enrichment...

  11. The Slow Developmental Time Course of Real-Time Spoken Word Recognition

    Science.gov (United States)

    Rigler, Hannah; Farris-Trimble, Ashley; Greiner, Lea; Walker, Jessica; Tomblin, J. Bruce; McMurray, Bob

    2015-01-01

    This study investigated the developmental time course of spoken word recognition in older children using eye tracking to assess how the real-time processing dynamics of word recognition change over development. We found that 9-year-olds were slower to activate the target words and showed more early competition from competitor words than…

  12. The initial time-course of headache in patients with spontaneous subarachnoid hemorrhage

    NARCIS (Netherlands)

    Čomić, Hata; Rinkel, Gabriel J.E.; Vergouwen, Mervyn D.I.

    2017-01-01

    Background If acute severe headache disappears early after its onset, the question arises whether subarachnoid hemorrhage (SAH) should still be ruled out. We studied the initial time-course and minimal duration of headache in a consecutive series of neurologically intact patients with spontaneous

  13. The Magnitude and Time Course of Muscle Cross-section Decrease in Intensive Care Unit Patients

    NARCIS (Netherlands)

    Haaf, D. Ten; Hemmen, B.; Meent, H. van de; Bovend'Eerdt, T.J.H.

    2017-01-01

    OBJECTIVE: Bedriddenness and immobilization of patients at an intensive care unit may result in muscle atrophy and devaluation in quality of life. The exact effect of immobilization on intensive care unit patients is not known. The aim of this study was to investigate the magnitude and time course

  14. Efficacy and Time Course of Theta Burst Stimulation in Healthy Humans

    NARCIS (Netherlands)

    Wischnewski, M.; Schutter, D.J.L.G.

    2015-01-01

    BACKGROUND: In the past decade research has shown that continuous (cTBS) and intermittent theta burst stimulation (iTBS) alter neuronal excitability levels in the primary motor cortex. OBJECTIVE: Quantitatively review the magnitude and time course on cortical excitability of cTBS and iTBS. METHODS:

  15. TIME-COURSE OF ACTION AND INTUBATING CONDITIONS FOLLOWING VECURONIUM, ROCURONIUM AND MIVACURIUM

    NARCIS (Netherlands)

    WIERDA, JMKH; HOMMES, FDM; NAP, HJA; VANDENBROEK, L

    The purpose of this study was to compare the time course of action and tracheal intubating conditions of vecuronium, rocuronium, and mivacurium in anaesthetised patients. Anaesthesia consisted of thiopentone, fentanyl, N2O/O-2 and isoflurane. After a 2 x ED(50) dose the first attempt at tracheal

  16. Time-course analysis of the accumulation of phenols in tomato ...

    African Journals Online (AJOL)

    i.e. cv. Fukuju No. 2) were mock inoculated with buffer only or singly and doubly with potato Virus X (PVX) and/or an attenuated strain (L11A) of tobacco mosaic virus (TMV-L11A) in greenhouse experiments. Time-course analysis of the ...

  17. Novel, Improved Sample Preparation for Rapid, Direct Identification from Positive Blood Cultures Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry

    OpenAIRE

    Schubert, Sören; Weinert, Kirsten; Wagner, Chris; Gunzl, Beatrix; Wieser, Andreas; Maier, Thomas; Kostrzewa, Markus

    2011-01-01

    Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used for rapid and reliable identification of bacteria and yeast grown on agar plates. Moreover, MALDI-TOF MS also holds promise for bacterial identification from blood culture (BC) broths in hospital laboratories. The most important technical step for the identification of bacteria from positive BCs by MALDI-TOF MS is sample preparation to remove blood cells and host proteins. We present a m...

  18. Microbial uptake of radiolabeled substrates: estimates of growth rates from time course measurements

    International Nuclear Information System (INIS)

    Li, W.K.W.

    1984-01-01

    The uptake of [ 3 H]glucose and a mixture of 3 H-labeled amino acids was measured, in time course fashion, in planktonic microbial assemblages of the eastern tropical Pacific Ocean. The average generation times of those portions of the assemblages able to utilize these substrates were estimated from a simple exponential growth model. Other workers have independently used this model in its integrated or differential form. A mathematical verification and an experimental demonstration of the equivalence of the two approaches are presented. A study was made of the size distribution of heterotrophic activity, using time course measurements. It was found that the size distribution and the effect of sample filtration before radiolabeling were dependent on time of incubation. In principle, it was possible to ascribe these time dependences to differences in th specific growth rate and initial standing stock of the microbial assemblages. 33 references

  19. The time course of location-avoidance learning in fear of spiders.

    Science.gov (United States)

    Rinck, Mike; Koene, Marieke; Telli, Sibel; Moerman-van den Brink, Wiltine; Verhoeven, Barbara; Becker, Eni S

    2016-01-01

    Two experiments were designed to study the time course of avoidance learning in spider fearfuls (SFs) under controlled experimental conditions. To achieve this, we employed an immersive virtual environment (IVE): While walking freely through a virtual art museum to search for specific paintings, the participants were exposed to virtual spiders. Unbeknown to the participants, only two of four museum rooms contained spiders, allowing for avoidance learning. Indeed, the more SF the participants were, the faster they learned to avoid the rooms that contained spiders (Experiment. 1), and within the first six trials, high fearfuls already developed a preference for starting their search task in rooms without spiders (Experiment 2). These results illustrate the time course of avoidance learning in SFs, and they speak to the usefulness of IVEs in fundamental anxiety research.

  20. The time-course of cortico-limbic neural responses to air hunger.

    Science.gov (United States)

    Binks, Andrew P; Evans, Karleyton C; Reed, Jeffrey D; Moosavi, Shakeeb H; Banzett, Robert B

    2014-12-01

    Several studies have mapped brain regions associated with acute dyspnea perception. However, the time-course of brain activity during sustained dyspnea is unknown. Our objective was to determine the time-course of neural activity when dyspnea is sustained. Eight healthy subjects underwent brain blood oxygen level dependent functional magnetic imaging (BOLD-fMRI) during mechanical ventilation with constant mild hypercapnia (∼ 45 mm Hg). Subjects rated dyspnea (air hunger) via visual analog scale (VAS). Tidal volume (V(T)) was alternated every 90 s between high VT (0.96 ± 0.23 L) that provided respiratory comfort (12 ± 6% full scale) and low V(T) (0.48 ± 0.08 L) which evoked air hunger (56 ± 11% full scale). BOLD signal was extracted from a priori brain regions and combined with VAS data to determine air hunger related neural time-course. Air hunger onset was associated with BOLD signal increases that followed two distinct temporal profiles within sub-regions of the anterior insula, anterior cingulate and prefrontal cortices (cortico-limbic circuitry): (1) fast, BOLD signal peak 40s. BOLD signal during air hunger offset followed fast and slow temporal profiles symmetrical, but inverse (signal decreases) to the time-courses of air hunger onset. We conclude that differential cortico-limbic circuit elements have unique contributions to dyspnea sensation over time. We suggest that previously unidentified sub-regions are responsible for either the acute awareness or maintenance of dyspnea. These data enhance interpretation of previous studies and inform hypotheses for future dyspnea research. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. A permutation-based multiple testing method for time-course microarray experiments

    Directory of Open Access Journals (Sweden)

    George Stephen L

    2009-10-01

    Full Text Available Abstract Background Time-course microarray experiments are widely used to study the temporal profiles of gene expression. Storey et al. (2005 developed a method for analyzing time-course microarray studies that can be applied to discovering genes whose expression trajectories change over time within a single biological group, or those that follow different time trajectories among multiple groups. They estimated the expression trajectories of each gene using natural cubic splines under the null (no time-course and alternative (time-course hypotheses, and used a goodness of fit test statistic to quantify the discrepancy. The null distribution of the statistic was approximated through a bootstrap method. Gene expression levels in microarray data are often complicatedly correlated. An accurate type I error control adjusting for multiple testing requires the joint null distribution of test statistics for a large number of genes. For this purpose, permutation methods have been widely used because of computational ease and their intuitive interpretation. Results In this paper, we propose a permutation-based multiple testing procedure based on the test statistic used by Storey et al. (2005. We also propose an efficient computation algorithm. Extensive simulations are conducted to investigate the performance of the permutation-based multiple testing procedure. The application of the proposed method is illustrated using the Caenorhabditis elegans dauer developmental data. Conclusion Our method is computationally efficient and applicable for identifying genes whose expression levels are time-dependent in a single biological group and for identifying the genes for which the time-profile depends on the group in a multi-group setting.

  2. The time course of the influence of colour terms on visual processing

    OpenAIRE

    Forder, Lewis

    2016-01-01

    This thesis explores whether colour terms (e.g., “red”, “blue”, “purple”, etc.) influence visual processing of colour, and if so, the time course of any effect. Broadly, this issue relates to debate concerning whether language affects the way we perceive the world (i.e., the theory of linguistic relativity). Three of the experiments conducted used the event-related potential method (ERP), taking electrophysiological measurements of visual processing and visual cognition in human participants....

  3. Time course of Chinese monosyllabic spoken word recognition: evidence from ERP analyses.

    Science.gov (United States)

    Zhao, Jingjing; Guo, Jingjing; Zhou, Fengying; Shu, Hua

    2011-06-01

    Evidence from event-related potential (ERP) analyses of English spoken words suggests that the time course of English word recognition in monosyllables is cumulative. Different types of phonological competitors (i.e., rhymes and cohorts) modulate the temporal grain of ERP components differentially (Desroches, Newman, & Joanisse, 2009). The time course of Chinese monosyllabic spoken word recognition could be different from that of English due to the differences in syllable structure between the two languages (e.g., lexical tones). The present study investigated the time course of Chinese monosyllabic spoken word recognition using ERPs to record brain responses online while subjects listened to spoken words. During the experiment, participants were asked to compare a target picture with a subsequent picture by judging whether or not these two pictures belonged to the same semantic category. The spoken word was presented between the two pictures, and participants were not required to respond during its presentation. We manipulated phonological competition by presenting spoken words that either matched or mismatched the target picture in one of the following four ways: onset mismatch, rime mismatch, tone mismatch, or syllable mismatch. In contrast to the English findings, our findings showed that the three partial mismatches (onset, rime, and tone mismatches) equally modulated the amplitudes and time courses of the N400 (a negative component that peaks about 400ms after the spoken word), whereas, the syllable mismatched words elicited an earlier and stronger N400 than the three partial mismatched words. The results shed light on the important role of syllable-level awareness in Chinese spoken word recognition and also imply that the recognition of Chinese monosyllabic words might rely more on global similarity of the whole syllable structure or syllable-based holistic processing rather than phonemic segment-based processing. We interpret the differences in spoken word

  4. Peroxiredoxin I protein, a potential biomarker of hydronephrosis in fetal mice exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin.

    Science.gov (United States)

    Liu, Mingxue; Liu, Jing; Liu, Xing; Wei, Guanghui

    2014-06-01

    In previous studies, we established an animal model of human congenital hydronephrosis with exposure of developing mice to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), but the etiopathogenesis is not entirely clear. The present study was to identify the changes that may be involved in the etiology at the protein level. C57BL/6J mice fetuses were treated with TCDD. Comparative proteomic analysis was adopted to identify the proteins associated with hydronephrosis induced by TCDD. Two-dimensional electrophoresis display revealed that 19 protein spots were differentially expressed in the upper urinary tract tissues in fetal mice after exposure to TCDD. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) identified 12 up-regulated proteins: peroxiredoxin I (Prx I), cadherin 6, gamma-actin, radixin, desmin, type II transforming growth factor-beta receptor, chromogranin B, serum albumin precursor, transferrin, hypothetical protein LOC70984, lipk protein, and zinc finger protein 336. Histochemical staining indicated that Prx I protein was positively expressed in the ureteric epithelium in the treated group, and not in the control group, which is consistent with MALDI-TOF-MS. Prx I protein may be a potential biomarker or responsive protein of hydronephrosis in fetal mice induced by TCDD. Copyright © 2013 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

  5. Diabetes patients show different time-course of myocardial perfusion improvement after coronary artery bypass grafting

    International Nuclear Information System (INIS)

    Lee, J. J.; Seok, J. W.; Eo, J. S.

    2005-01-01

    Diabetes mellitus is an independent risk factor of cardiovascular disease. Diabetes is known to cause microangiopathy. The microangiopathy is hardly detectable on the coronary angiography. Myocardial perfusion imaging shows the resultant perfusion status which reflects the microangiopathy. For patients who underwent revascularization, the microangiopathy could affect the myocardial perfusion improvement. Diabetes patients probably experience the different myocardial perfusion improvement as compared to the non-diabetes patients although they have similar angiographic findings. The aim of this study is to find out whether there is a time-course difference of perfusion improvement between the diabetes and non diabetes patients who showed patent angiographic findings after coronary artery grafting surgery (CABG). A total of 129 patients who underwent coronary artery bypass grafting surgery were enrolled in this study. Myocardial SPECTs performed at previous, short-term (3 month), and mid-term (1 year) to CABG. One-year follow up angiography was done 411±121 days after surgery. Graft patency was determined according to the FitzGibbon et al. Segments were assigned to vascular territories using a 20 segment model. The segments of excellent patency were included in this study. Time course differences of concerned segments were analyzed using RMANOVA. The number of segments enrolled was 764 of diabetes and 1083 of non-diabetes. At short-term follow up, reversibility score was 2.8±8.1% in diabetes and 0.3±7.5% in non-diabetes. At long-term follow up, reversibility score was 1.8±8.0% in diabetes and 0.1±7.3% in non-diabetes. The time-course of reversibility score was significantly different between the diabetes and non diabetes (p<0.001) Diabetic segments showed high residual reversibility score than non-diabetic segments after CABG although the angiographic finding was patent in both groups. This result is maybe attributable to microangiopathy induced by diabetes

  6. Time course of cognitive recovery after propofol anaesthesia: a level of processing approach.

    Science.gov (United States)

    N'Kaoua, Bernard; Véron, Anne-Lise H; Lespinet, Véronique C; Claverie, Bernard; Sztark, François

    2002-09-01

    The aim of this study was to investigate the time course of recovery of verbal memory after general anaesthesia, as a function of the level (shallow or deep) of processing induced at the time of encoding. Thirty-one patients anaesthetized with propofol and alfentanil were compared with 28 control patients receiving only alfentanil. Memory functions were assessed the day before and 1, 6 and 24 hr after operation. Results show that for the anaesthetized group, shallow processing was impaired for 6 hr after surgery whereas the deeper processing was not recovered even at 24 hr. In addition, no specific effect of age was found.

  7. Comparative analysis of clustering methods for gene expression time course data

    Directory of Open Access Journals (Sweden)

    Ivan G. Costa

    2004-01-01

    Full Text Available This work performs a data driven comparative study of clustering methods used in the analysis of gene expression time courses (or time series. Five clustering methods found in the literature of gene expression analysis are compared: agglomerative hierarchical clustering, CLICK, dynamical clustering, k-means and self-organizing maps. In order to evaluate the methods, a k-fold cross-validation procedure adapted to unsupervised methods is applied. The accuracy of the results is assessed by the comparison of the partitions obtained in these experiments with gene annotation, such as protein function and series classification.

  8. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

    DEFF Research Database (Denmark)

    Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe

    2017-01-01

    The increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course ab......The increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time...

  9. The Natural Time Course of Membrane Alterations During Peritoneal Dialysis Is Partly Altered by Peritonitis.

    Science.gov (United States)

    van Esch, Sadie; Struijk, Dirk G; Krediet, Raymond T

    2016-01-01

    ♦ The quality of the peritoneal membrane can deteriorate over time. Exposure to glucose-based dialysis solutions is the most likely culprit. Because peritonitis is a common complication of peritoneal dialysis (PD), distinguishing between the effect of glucose exposure and a possible additive effect of peritonitis is difficult. The aim of the present study was to compare the time-course of peritoneal transport characteristics in patients without a single episode of peritonitis-representing the natural course-and in patients who experienced 1 or more episodes of peritonitis during long-term follow-up. ♦ This prospective, single-center cohort study enrolled incident adult PD patients who started PD during 1990-2010. A standard peritoneal permeability analysis was performed in the first year of PD treatment and was repeated every year. The results in patients without a single episode of peritonitis ("no-peritonitis group") were compared with the results obtained in patients who experienced 1 or more peritonitis episodes ("peritonitis group") during a follow-up of 4 years. ♦ The 124 patients analyzed included 54 in the no-peritonitis group and 70 in the peritonitis group. The time-course of small-solute transport was different in the groups, with the peritonitis group showing an earlier and more pronounced increase in the mass transfer area coefficient for creatinine (p = 0.07) and in glucose absorption (p = 0.048). In the no-peritonitis group, the net ultrafiltration rate (NUFR) and the transcapillary ultrafiltration rate (TCUFR) both showed a steep increase from the 1st to the 2nd year of PD that was absent in the peritonitis group. Both groups showed a decrease in the NUFR after year 3. A decrease in the TCUFR occurred only in the peritonitis group. That decrease was already present after the year 1 in patients with severe peritonitis. The time-course of free water transport showed a continuous increase in the patients without peritonitis, but a decrease in the

  10. Analysis of anabolic steroids in hair: time courses in guinea pigs.

    Science.gov (United States)

    Shen, Min; Xiang, Ping; Yan, Hui; Shen, Baohua; Wang, Mengye

    2009-09-01

    Sensitive, specific, and reproducible methods for the quantitative determination of eight anabolic steroids in guinea pig hair have been developed using LC/MS/MS and GC/MS/MS. Methyltestosterone, stanozolol, methandienone, nandrolone, trenbolone, boldenone, methenolone and DHEA were administered intraperitoneally in guinea pigs. After the first injection, black hair segments were collected on shaved areas of skin. The analysis of these segments revealed the distribution of anabolic steroids in the guinea pig hair. The major components in hair are the parent anabolic steroids. The time courses of the concentrations of the steroids in hair (except methenolone, which does not deposit in hair) demonstrated that the peak concentrations were reached on days 2-4, except stanozolol, which peaked on day 10 after administration. The concentrations in hair appeared to be related to the physicochemical properties of the drug compound and to the dosage. These studies on the distribution of drugs in the hair shaft and on the time course of their concentration changes provide information relevant to the optimal time and method of collecting hair samples. Such studies also provide basic data that will be useful in the application of hair analysis in the control of doping and in the interpretation of results.

  11. Time course of cortisol loss in hair segments under immersion in hot water.

    Science.gov (United States)

    Li, Jifeng; Xie, Qiaozhen; Gao, Wei; Xu, Youyun; Wang, Shuang; Deng, Huihua; Lu, Zuhong

    2012-02-18

    Hair cortisol is supposed to be a good biomarker of chronic stress. Major loss of hair cortisol in long-term exposure to environmental factors affected strongly its proper assessment of chronic stress in human. However, there was no research on time course of hair cortisol loss during the long-term exposure. Hair samples with longer than 1cm in the posterior vertex region were cut as close as possible to the scalp. The 1-cm hair samples were treated by ultraviolet irradiation or immersion in shampoo solution or water immersion at 40, 65 and 80°C. Hair cortisol content was determined with high performance liquid chromatography tandem mass spectrometry. Ultraviolet irradiation and immersion in shampoo solution and hot water gave rise to the significant cortisol loss in hair. Hair cortisol content was sharply decreased with water immersion duration during initial stage and slowly decreased in the following stage. The 2-stage loss process with water immersion duration modeled to some extent time course of hair cortisol loss in long-term exposure to external environments. Cortisol from hair samples closest to the scalp in the posterior vertex could represent more accurately central hypothalamo-pituitary-adrenal activity. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Difference-based clustering of short time-course microarray data with replicates

    Directory of Open Access Journals (Sweden)

    Kim Jihoon

    2007-07-01

    Full Text Available Abstract Background There are some limitations associated with conventional clustering methods for short time-course gene expression data. The current algorithms require prior domain knowledge and do not incorporate information from replicates. Moreover, the results are not always easy to interpret biologically. Results We propose a novel algorithm for identifying a subset of genes sharing a significant temporal expression pattern when replicates are used. Our algorithm requires no prior knowledge, instead relying on an observed statistic which is based on the first and second order differences between adjacent time-points. Here, a pattern is predefined as the sequence of symbols indicating direction and the rate of change between time-points, and each gene is assigned to a cluster whose members share a similar pattern. We evaluated the performance of our algorithm to those of K-means, Self-Organizing Map and the Short Time-series Expression Miner methods. Conclusions Assessments using simulated and real data show that our method outperformed aforementioned algorithms. Our approach is an appropriate solution for clustering short time-course microarray data with replicates.

  13. Time course influences transfer of visual perceptual learning across spatial location.

    Science.gov (United States)

    Larcombe, S J; Kennard, C; Bridge, H

    2017-06-01

    Visual perceptual learning describes the improvement of visual perception with repeated practice. Previous research has established that the learning effects of perceptual training may be transferable to untrained stimulus attributes such as spatial location under certain circumstances. However, the mechanisms involved in transfer have not yet been fully elucidated. Here, we investigated the effect of altering training time course on the transferability of learning effects. Participants were trained on a motion direction discrimination task or a sinusoidal grating orientation discrimination task in a single visual hemifield. The 4000 training trials were either condensed into one day, or spread evenly across five training days. When participants were trained over a five-day period, there was transfer of learning to both the untrained visual hemifield and the untrained task. In contrast, when the same amount of training was condensed into a single day, participants did not show any transfer of learning. Thus, learning time course may influence the transferability of perceptual learning effects. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Electrophysiological assessment of the time course of bilingual visual word recognition: Early access to language membership.

    Science.gov (United States)

    Yiu, Loretta K; Pitts, Michael A; Canseco-Gonzalez, Enriqueta

    2015-08-01

    Previous research examining the time course of lexical access during word recognition suggests that phonological processing precedes access to semantic information, which in turn precedes access to syntactic information. Bilingual word recognition likely requires an additional level: knowledge of which language a specific word belongs to. Using the recording of event-related potentials, we investigated the time course of access to language membership information relative to semantic (Experiment 1) and syntactic (Experiment 2) encoding during visual word recognition. In Experiment 1, Spanish-English bilinguals viewed a series of printed words while making dual-choice go/nogo and left/right hand decisions based on semantic (whether the word referred to an animal or an object) and language membership information (whether the word was in English or in Spanish). Experiment 2 used a similar paradigm but with syntactic information (whether the word was a noun or a verb) as one of the response contingencies. The onset and peak latency of the N200, a component related to response inhibition, indicated that language information is accessed earlier than semantic information. Similarly, language information was also accessed earlier than syntactic information (but only based on peak latency). We discuss these findings with respect to models of bilingual word recognition and language comprehension in general. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. The time course of perceptual grouping: the role of segregation and shape formation.

    Science.gov (United States)

    Razpurker-Apfeld, Irene; Kimchi, Ruth

    2007-07-01

    The time course of perceptual grouping was examined in two experiments, using a primed matching task. In different conditions, elements were grouped into columns/rows by common lightness, into a shape (triangle/ arrow or square/cross) by common lightness, and into a shape without segregation of elements. The results showed an early and rapid grouping into columns/rows by common lightness and into a shape when no segregation from other elements was involved. Goodness of shape (i.e., triangle/arrow vs. square/cross) had no influence on how early grouping was evident, but the relatively poorer shapes appeared to consolidate with time. In contrast, grouping into a shape that involved segregation and required resolving figure-ground relations between segregated units, as grouping into a shape by common lightness, consumed time, regardless of shape goodness. These results suggest that the time course of grouping varies as a function of the processes involved in it (e.g., segregation and shape formation) and the conditions prevailing for each process.

  16. Anxiety and its time courses during radiotherapy for non-metastatic breast cancer: A longitudinal study

    International Nuclear Information System (INIS)

    Lewis, Florence; Merckaert, Isabelle; Liénard, Aurore; Libert, Yves; Etienne, Anne-Marie; Reynaert, Christine; Slachmuylder, Jean-Louis; Scalliet, Pierre; Paul, Van Houtte; Coucke, Philippe

    2014-01-01

    Purpose: To our knowledge, no study has specifically assessed the time course of anxiety during radiotherapy (RT). The objective of this study was to assess anxiety time courses in patients with non-metastatic breast cancer. Material and methods: This multicenter, descriptive longitudinal study included 213 consecutive patients with breast cancer who completed visual analog scales (VASs) assessing state anxiety before and after the RT simulation and the first and last five RT sessions. Results: Pre- and post-session anxiety mean levels were highest at the RT simulation (respectively, 2.9 ± 2.9 and 1.6 ± 2.5) and first RT session (respectively, 3.4 ± 2.9 and 2.0 ± 2.4), then declined rapidly. Clinically relevant mean differences (⩾1 cm on the VAS) between pre- and post-simulation/session VAS scores were found only for the RT simulation (−1.3 ± 2.7; p < 0.001) and first RT session (−1.4 ± 2.4; p < 0.001). Five percent to 16% of patients presented clinically relevant anxiety (pre- and post-simulation/session VAS scores ⩾ 4 cm) throughout treatment. Conclusions: To optimize care, RT team members should offer all patients appropriate information about treatment at the simulation, check patients’ understanding, and identify patients with clinically relevant anxiety requiring appropriate support throughout RT

  17. Time course for arm and chest muscle thickness changes following bench press training

    Science.gov (United States)

    Ogasawara, Riki; Thiebaud, Robert S.; Loenneke, Jeremy P.; Loftin, Mark

    2012-01-01

    The purpose of this study was to investigate the time course of hypertrophic adaptations in both the upper arm and trunk muscles following high-intensity bench press training. Seven previously untrained young men (aged 25 ± 3 years) performed free-weight bench press training 3 days (Monday, Wednesday and Friday) per week for 24 weeks. Training intensity and volume were set at 75% of one repetition maximum (1-RM) and 30 repetitions (3 sets of 10 repetitions, with 2−3 min of rest between sets), respectively. Muscle thickness (MTH) was measured using B-mode ultrasound at three sites: the biceps and triceps brachii and the pectoralis major. Measurements were taken a week prior to the start of training, before the training session on every Monday and 3 days after the final training session. Pairwise comparisons from baseline revealed that pectoralis major MTH significantly increased after week-1 (p = 0.002), triceps MTH increased after week-5 (p = 0.001) and 1-RM strength increased after week-3 (p = 0.001) while no changes were observed in the biceps MTH from baseline. Significant muscle hypertrophy was observed earlier in the chest compared to that of the triceps. Our results indicate that the time course of the muscle hypertrophic response differs between the upper arm and chest. PMID:24265879

  18. The Impact of Feedback on the Different Time Courses of Multisensory Temporal Recalibration

    Directory of Open Access Journals (Sweden)

    Matthew A. De Niear

    2017-01-01

    Full Text Available The capacity to rapidly adjust perceptual representations confers a fundamental advantage when confronted with a constantly changing world. Unexplored is how feedback regarding sensory judgments (top-down factors interacts with sensory statistics (bottom-up factors to drive long- and short-term recalibration of multisensory perceptual representations. Here, we examined the time course of both cumulative and rapid temporal perceptual recalibration for individuals completing an audiovisual simultaneity judgment task in which they were provided with varying degrees of feedback. We find that in the presence of feedback (as opposed to simple sensory exposure temporal recalibration is more robust. Additionally, differential time courses are seen for cumulative and rapid recalibration dependent upon the nature of the feedback provided. Whereas cumulative recalibration effects relied more heavily on feedback that informs (i.e., negative feedback rather than confirms (i.e., positive feedback the judgment, rapid recalibration shows the opposite tendency. Furthermore, differential effects on rapid and cumulative recalibration were seen when the reliability of feedback was altered. Collectively, our findings illustrate that feedback signals promote and sustain audiovisual recalibration over the course of cumulative learning and enhance rapid trial-to-trial learning. Furthermore, given the differential effects seen for cumulative and rapid recalibration, these processes may function via distinct mechanisms.

  19. Time course of effects of emotion on item memory and source memory for Chinese words.

    Science.gov (United States)

    Wang, Bo; Fu, Xiaolan

    2011-05-01

    Although many studies have investigated the effect of emotion on memory, it is unclear whether the effect of emotion extends to all aspects of an event. In addition, it is poorly understood how effects of emotion on item memory and source memory change over time. This study examined the time course of effects of emotion on item memory and source memory. Participants learned intentionally a list of neutral, positive, and negative Chinese words, which were presented twice, and then took test of free recall, followed by recognition and source memory tests, at one of eight delayed points of time. The main findings are (within the time frame of 2 weeks): (1) Negative emotion enhances free recall, whereas there is only a trend that positive emotion enhances free recall. In addition, negative and positive emotions have different points of time at which their effects on free recall reach the greatest magnitude. (2) Negative emotion reduces recognition, whereas positive emotion has no effect on recognition. (3) Neither positive nor negative emotion has any effect on source memory. The above findings indicate that effect of emotion does not necessarily extend to all aspects of an event and that valence is a critical modulating factor in effect of emotion on item memory. Furthermore, emotion does not affect the time course of item memory and source memory, at least with a time frame of 2 weeks. This study has implications for establishing the theoretical model regarding the effect of emotion on memory. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. Illusory conjunctions in the time domain and the resulting time-course of the attentional blink.

    Science.gov (United States)

    Botella, Juan; Arend, Isabel; Suero, Manuel

    2004-05-01

    Illusory conjunctions in the time domain are errors made in binding stimulus features presented In the same spatial position in Rapid Serial Visual Presentation (RSVP) conditions. Botella, Barriopedro, and Suero (2001) devised a model to explain how the distribution of responses originating from stimuli around the target in the series is generated. They proposed two routes consisting of two sequential attempts to make a response. The second attempt (sophisticated guessing) is only employed if the first one (focal attention) fails in producing an integrated perception. This general outline enables specific predictions to be made and tested related to the efficiency of focal attention in generating responses in the first attempt. Participants had to report the single letter in an RSVP stream of letters that was presented in a previously specified color (first target, T1) and then report whether an X (second target, T2) was or was not presented. Performance on T2 showed the typical U-shaped function across the T1-T2 lag that reflects the attentional blink phenomenon. However, as was predicted by Botella, Barriopedro, and Suero's model, the time-course of the interference was shorter for trials with a correct response to T1 than for trials with a T1 error. Furthermore, longer time-courses of interference associated with pre-target and post-target errors to the first target were indistinguishable.

  1. PAVA: Physiological and Anatomical Visual Analytics for Mapping of Tissue-Specific Concentration and Time-Course Data

    Science.gov (United States)

    We describe the development and implementation of a Physiological and Anatomical Visual Analytics tool (PAVA), a web browser-based application, used to visualize experimental/simulated chemical time-course data (dosimetry), epidemiological data and Physiologically-Annotated Data ...

  2. CLINICAL-PHARMACOLOGY OF ROCURONIUM (ORG-9426) - STUDY OF THE TIME-COURSE OF ACTION, DOSE REQUIREMENT, REVERSIBILITY, AND PHARMACOKINETICS

    NARCIS (Netherlands)

    VANDENBROEK, L; WIERDA, JMKH; SMEULERS, NJ; VANSANTEN, GJ; LECLERCQ, MGL; HENNIS, PJ

    1994-01-01

    Study Objective: To evaluate the time course of action, dose requirement, reversibility, and pharmacokinetics of rocuronium (Org 9426) under 3 anesthetic techniques (nitrous oxide-fentanyl supplemented with propofol halothane, or isoflurane). Design: Prospective, randomized study. Setting: Operating

  3. Catecholaminergic activation in acute myocardial infarction: time course and relation to left ventricular performance

    DEFF Research Database (Denmark)

    Petersen, Claus Leth; Nielsen, Jens Rokkedal; Petersen, Bodil Laub

    2003-01-01

    AIM: The study was designed to assess (1) the time course of catecholaminergic activation in acute myocardial infarction (AMI) as estimated by adrenaline (ADR) and noradrenaline (NOR) concentrations, and (2) to relate activation of these hormones to predict the outcome of cardiac performance......-ventricular ejection fraction (LVEF). RESULTS: In the study group as a whole, the concentrations of ADR decreased from (mean +/- SEM) 0.80 +/- 0.12 nmol/l on admission to 0.33 +/- 0.03 nmol/l at discharge (p ... of both ADR and NOR on admission were correlated to LVEF at discharge (r = -0.56, p ADR and NOR after 1 year follow-up was 0...

  4. Time-course of attention for threatening pictures in high and low trait anxiety.

    Science.gov (United States)

    Koster, Ernst H W; Verschuere, Bruno; Crombez, Geert; Van Damme, Stefaan

    2005-08-01

    Cognitive studies about anxiety suggest that the interplay between automatic and strategic biases in attention to threat is related to the persistence of fear. In the present study, the time-course of attention to pictures with varying threat levels was investigated in high trait anxious (HTA, n=21) and low trait anxious (LTA, n=22) students. In a visual probe detection task, high and mild threat pictures were presented at three durations: 100, 500, and 1250 ms. Results indicated that all individuals attended to the high threat pictures for the 100 ms condition. Differential responding between HTA and LTA individuals was found for the 500 ms condition: only HTA individuals showed an attentional bias for mild threatening stimuli. For the 1250 ms condition, the HTA individuals attended away from high and mild threat pictures. The observed pattern of differential attention to threatening pictures may explain the persistence of fear in HTA individuals.

  5. Time-course of the DSM-5 cannabis withdrawal symptoms in poly-substance abusers

    DEFF Research Database (Denmark)

    Hesse, Morten; Thylstrup, Birgitte

    2013-01-01

    Background Evidence is accumulating that a cannabis withdrawal syndrome is common, of clinical significance, and has a clear time course. Up till now, very limited data exist on the cannabis withdrawal symptoms in patients with co-morbid substance use disorders, other than cannabis use and tobacco...... the DSM-5 Withdrawal Symptom Check List with withdrawal symptoms from all classes of substances, with no indication that the described symptoms should be attributed to withdrawal. Self-reported time since last use of cannabis was used as a predictor of cannabis withdrawal severity. Results...... With the exception of loss of appetite, time since last use of cannabis was associated with all types of withdrawal symptoms listed in the DSM-5. Only four of 19 symptoms intended to measure withdrawal from other substances were related to time since last use of cannabis, including vivid, unpleasant dreams...

  6. Time course of radiometric detection of positive blood cultures in childhood

    International Nuclear Information System (INIS)

    Meadow, W.L.; Schwartz, I.K.

    1986-01-01

    We have determined the time course of radiometric detection of microbial growth in 2348 positive blood culture specimens obtained at Wyler Children's Hospital during a 5-year interval. Overall 72 and 88% of isolates were detected within 48 and 72 hours after sampling, respectively. For pathogenic organisms aerobic detection was generally more rapid and more inclusive than anaerobic detection. At 48 hours of incubation the detection of six potential pathogens (Salmonella sp., Haemophilus influenzae, Group D streptococci, Neisseria meningitidis, coagulase-negative staphylococci, Candida sp.) was significantly delayed compared with detection of other pathogenic organisms recovered from blood. At 72 hours of incubation the detection rates remained less than 95% for H. influenzae, Staphylococcus aureus, Klebsiella sp., coagulase-negative staphylococci, Group D streptococci and Candida sp. These data should assist clinical decisions regarding duration of antibiotic therapy for the presumptive diagnosis of bacteremia in children

  7. Time course of primary and secondary hyperalgesia after heat injury to the skin

    DEFF Research Database (Denmark)

    Møiniche, S; Dahl, J B; Kehlet, H

    1993-01-01

    the injury in any volunteer. These findings suggest post-injury development of secondary hyperalgesia to be a dynamic process, closely related in time to a peripheral nociceptive input, with reversal to normal when the peripheral lesion disappears. These observations may be relevant to the concept of "pre......We have examined the time course of, and relationship between, primary and secondary hyperalgesia after thermal injury to the skin in humans. Burn injuries (15 x 25 mm rectangular thermode, 49 degrees C, 5 min) were produced in eight healthy, unmedicated male volunteers, on the medial side...... of the right calf, on two occasions at least 8 days apart. Heat pain detection thresholds (HPDT), heat pain tolerance (HPT), mechanical pain detection threshold (MPDT) and the intensity of burn-injury induced erythema (skin erythema index, SEI) were assessed inside the burn injury. HPT was assessed only in one...

  8. Time course of radiometric detection of positive blood cultures in childhood

    Energy Technology Data Exchange (ETDEWEB)

    Meadow, W.L.; Schwartz, I.K.

    1986-05-01

    We have determined the time course of radiometric detection of microbial growth in 2348 positive blood culture specimens obtained at Wyler Children's Hospital during a 5-year interval. Overall 72 and 88% of isolates were detected within 48 and 72 hours after sampling, respectively. For pathogenic organisms aerobic detection was generally more rapid and more inclusive than anaerobic detection. At 48 hours of incubation the detection of six potential pathogens (Salmonella sp., Haemophilus influenzae, Group D streptococci, Neisseria meningitidis, coagulase-negative staphylococci, Candida sp.) was significantly delayed compared with detection of other pathogenic organisms recovered from blood. At 72 hours of incubation the detection rates remained less than 95% for H. influenzae, Staphylococcus aureus, Klebsiella sp., coagulase-negative staphylococci, Group D streptococci and Candida sp. These data should assist clinical decisions regarding duration of antibiotic therapy for the presumptive diagnosis of bacteremia in children.

  9. Time-course mortality and radiosensitivity indices in Tribolium spp. developing from irradiated pupae

    International Nuclear Information System (INIS)

    Hasan, Md Mahbub

    1999-01-01

    Effects of gamma irradiation (1-5 Krad) on the time-course mortality and radiosensitivity indices in adults of Tribolium anaphe, T. brevicornis, T. castaneum, T. destructor, T. freemani developing from irradiated 1 day old and pre-emergence (4-5 day old) pupae were studied. Adult longevity was significantly (P<0.001) affected by irradiation and was linearly dose dependent. T. destructor was markedly more radioresistant than the other species at all dose levels and had a longer life expectancy. The mean survival times of adults developing from irradiated early and late pupae were shorter in females than in males for all the species. The radiosensitivity indices did not vary widely among the species and these values decreased as the dose increased in all the species which clearly indicate that the resistance of the species was dose-dependent. (author)

  10. Homophonic and semantic priming of Japanese Kanji words: a time course study.

    Science.gov (United States)

    Chen, Hsi-Chin; Yamauchi, Takashi; Tamaoka, Katsuo; Vaid, Jyotsna

    2007-02-01

    In an examination of the time course of activation of phonological and semantic information in processing kanji script, two lexical decision experiments were conducted with native readers of Japanese. Kanji targets were preceded at short (85-msec) and long (150-msec) intervals by homophonic, semantically related, or unrelated primes presented in kanji (Experiment 1) or by hiragana transcriptions of the kanji primes (Experiment 2). When primes were in kanji, semantic relatedness facilitated kanji target recognition at both intervals but homophonic relatedness did not. When primes were in hiragana, kanji target recognition was facilitated by homophonic relatedness at both intervals and by semantic relatedness only at the longer interval. The absence of homophonic priming of kanji targets by kanji primes challenges the universal phonology principle's claim that phonology is central to accessing meaning from print. The stimuli used in the present study may be downloaded from www.psychonomic.org/archive.

  11. Time course based artifact identification for independent components of resting state fMRI

    Directory of Open Access Journals (Sweden)

    Christian eRummel

    2013-05-01

    Full Text Available In functional magnetic resonance imaging (fMRI coherent oscillations of the blood oxygen level dependent (BOLD signal can be detected. These arise when brain regions respond to external stimuli or are activated by tasks. The same networks have been characterized during wakeful rest when functional connectivity of the human brain is organized in generic resting state networks (RSN. Alterations of RSN emerge as neurobiological markers of pathological conditions such as altered mental state. In single-subject fMRI data the coherent components can be identified by blind source separation of the pre-processed BOLD data using spatial independent component analysis (ICA and related approaches. The resulting maps may represent physiological RSNs or may be due to various artifacts. In this methodological study, we propose a conceptually simple and fully automatic time course based filtering procedure to detect obvious artifacts in the ICA output for resting state fMRI. The filter is trained on six and tested on 29 healthy subjects, yielding mean filter accuracy, sensitivity and specificity of 0.80, 0.82 and 0.75 in out-of-sample tests. To estimate the impact of clearly artifactual single-subject components on group resting state studies we analyze unfiltered and filtered output with a second level ICA procedure. Although the automated filter does not reach performance values of visual analysis by human raters, we propose that resting state compatible analysis of ICA time courses could be very useful to complement the existing map or task/event oriented artifact classification algorithms.

  12. Safety and Time Course of Drip-and-Ship in Treatment of Acute Ischemic Stroke.

    Science.gov (United States)

    Ishihara, Hideyuki; Oka, Fumiaki; Oku, Takayuki; Shinoyama, Mizuya; Suehiro, Eiichi; Sugimoto, Kazutaka; Suzuki, Michiyasu

    2017-11-01

    The drip-and-ship approach allows intravenous tissue plasminogen activator therapy and adjuvant endovascular treatment in acute ischemic stroke, even in rural areas. Here, we examined the safety and time course of the drip-and-ship approach. Fifty consecutive cases treated with the drip-and-ship approach (drip-and-ship group) in June 2009 to March 2016 were retrospectively examined. Changes in mean blood pressure, systemic complications, and neurological complications were compared according to method of transportation. Time courses were compared between drip-and-ship and direct admission groups during the same period. In the drip-and-ship group, 33 and 17 patients were transferred to hospital by ambulance and helicopter, respectively. One patient suffered hemorrhagic infarction during transportation by ambulance. Mean blood pressure change was lower in patients transferred by helicopter than ambulance (<5 mmHg versus 12.2 mmHg, respectively). The mean onset-to-door times in the drip-and-ship and direct admission groups were 71 and 64 minutes, respectively, and mean door-to-needle times were 70 and 47 minutes, respectively (P =.002). Although mean transportation time from the primary stroke hospital to our hospital was 32 minutes, the entry-to-exit time from the primary stroke hospital was 113 minutes. Thereafter, there was an average delay of 100 minutes until reperfusion compared with the direct admission group. Drip-and-ship was relatively safe in this small series. Transportation by helicopter was less stressful for acute ischemic stroke patients. It is important to reduce door-to-needle time and needle-to-departure time in the primary stroke hospital to minimize the time until treatment in cases of acute ischemic stroke. Copyright © 2017. Published by Elsevier Inc.

  13. Skin complications in deep brain stimulation for Parkinson's disease: frequency, time course, and risk factors.

    Science.gov (United States)

    Sixel-Döring, Friederike; Trenkwalder, Claudia; Kappus, Christoph; Hellwig, Dieter

    2010-02-01

    Deep brain stimulation (DBS) has been recognized as an efficacious treatment for movement disorders. Its beneficial effects however may be lost due to skin complications such as erosions or infections over the implanted foreign material. We sought to document skin complications in the entire Parkinson's disease patient population who received a DBS system at the Marburg/Kassel implantation centre since the start of our DBS program in January 2002 to analyze frequency, time course, and possible risk factors. We investigated 85 consecutive patients with Parkinson's disease (PD) from a single center/single surgeon DBS series for the occurrence of skin complications and analyzed localization, time course, and possible risk factors. Mean follow-up was 3 years (range 1-7 years). In total, 21/85 patients (24.7%) suffered a total of 30 single skin complications. Sixty percent of all incidents occurred within the first post-operative year. Forty percent of all incidents occurred later than the first year following primary implantation. Complications involved the burr hole cap in 37%, the course of the cables in 33%, and the impulse generator (IPG) site in 30%. Six of 21 patients suffered recurring skin complications. Eight patients permanently lost their DBS system. Factor analysis for age, gender, disease duration, disease severity, the incidence of hypertension or diabetes as well as a 2-day period with externalized electrodes for continuous test stimulation did not have any statistically significant impact on skin complications. We conclude that (1) PD patients have a risk for skin complications after DBS as long as the system remains in situ and (2) there are at present no identifiable risk factors for skin complications after DBS, other than PD itself.

  14. Hearing Shapes: Event-related Potentials Reveal the Time Course of Auditory-Visual Sensory Substitution.

    Science.gov (United States)

    Graulty, Christian; Papaioannou, Orestis; Bauer, Phoebe; Pitts, Michael A; Canseco-Gonzalez, Enriqueta

    2018-04-01

    In auditory-visual sensory substitution, visual information (e.g., shape) can be extracted through strictly auditory input (e.g., soundscapes). Previous studies have shown that image-to-sound conversions that follow simple rules [such as the Meijer algorithm; Meijer, P. B. L. An experimental system for auditory image representation. Transactions on Biomedical Engineering, 39, 111-121, 1992] are highly intuitive and rapidly learned by both blind and sighted individuals. A number of recent fMRI studies have begun to explore the neuroplastic changes that result from sensory substitution training. However, the time course of cross-sensory information transfer in sensory substitution is largely unexplored and may offer insights into the underlying neural mechanisms. In this study, we recorded ERPs to soundscapes before and after sighted participants were trained with the Meijer algorithm. We compared these posttraining versus pretraining ERP differences with those of a control group who received the same set of 80 auditory/visual stimuli but with arbitrary pairings during training. Our behavioral results confirmed the rapid acquisition of cross-sensory mappings, and the group trained with the Meijer algorithm was able to generalize their learning to novel soundscapes at impressive levels of accuracy. The ERP results revealed an early cross-sensory learning effect (150-210 msec) that was significantly enhanced in the algorithm-trained group compared with the control group as well as a later difference (420-480 msec) that was unique to the algorithm-trained group. These ERP modulations are consistent with previous fMRI results and provide additional insight into the time course of cross-sensory information transfer in sensory substitution.

  15. Deep brain stimulation effects in dystonia: time course of electrophysiological changes in early treatment.

    Science.gov (United States)

    Ruge, Diane; Tisch, Stephen; Hariz, Marwan I; Zrinzo, Ludvic; Bhatia, Kailash P; Quinn, Niall P; Jahanshahi, Marjan; Limousin, Patricia; Rothwell, John C

    2011-08-15

    Deep brain stimulation to the internal globus pallidus is an effective treatment for primary dystonia. The optimal clinical effect often occurs only weeks to months after starting stimulation. To better understand the underlying electrophysiological changes in this period, we assessed longitudinally 2 pathophysiological markers of dystonia in patients prior to and in the early treatment period (1, 3, 6 months) after deep brain stimulation surgery. Transcranial magnetic stimulation was used to track changes in short-latency intracortical inhibition, a measure of excitability of GABA(A) -ergic corticocortical connections and long-term potentiation-like synaptic plasticity (as a response to paired associative stimulation). Deep brain stimulation remained on for the duration of the study. Prior to surgery, inhibition was reduced and plasticity increased in patients compared with healthy controls. Following surgery and commencement of deep brain stimulation, short-latency intracortical inhibition increased toward normal levels over the following months with the same monotonic time course as the patients' clinical benefit. In contrast, synaptic plasticity changed rapidly, following a nonmonotonic time course: it was absent early (1 month) after surgery, and then over the following months increased toward levels observed in healthy individuals. We postulate that before surgery preexisting high levels of plasticity form strong memories of dystonic movement patterns. When deep brain stimulation is turned on, it disrupts abnormal basal ganglia signals, resulting in the absent response to paired associative stimulation at 1 month. Clinical benefit is delayed because engrams of abnormal movement persist and take time to normalize. Our observations suggest that plasticity may be a driver of long-term therapeutic effects of deep brain stimulation in dystonia. Copyright © 2011 Movement Disorder Society.

  16. Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

    Directory of Open Access Journals (Sweden)

    Boris P Hejblum

    2015-06-01

    Full Text Available Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial, and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

  17. A method to identify differential expression profiles of time-course gene data with Fourier transformation.

    Science.gov (United States)

    Kim, Jaehee; Ogden, Robert Todd; Kim, Haseong

    2013-10-18

    Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization.The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be

  18. The time course of individual face recognition: A pattern analysis of ERP signals.

    Science.gov (United States)

    Nemrodov, Dan; Niemeier, Matthias; Mok, Jenkin Ngo Yin; Nestor, Adrian

    2016-05-15

    An extensive body of work documents the time course of neural face processing in the human visual cortex. However, the majority of this work has focused on specific temporal landmarks, such as N170 and N250 components, derived through univariate analyses of EEG data. Here, we take on a broader evaluation of ERP signals related to individual face recognition as we attempt to move beyond the leading theoretical and methodological framework through the application of pattern analysis to ERP data. Specifically, we investigate the spatiotemporal profile of identity recognition across variation in emotional expression. To this end, we apply pattern classification to ERP signals both in time, for any single electrode, and in space, across multiple electrodes. Our results confirm the significance of traditional ERP components in face processing. At the same time though, they support the idea that the temporal profile of face recognition is incompletely described by such components. First, we show that signals associated with different facial identities can be discriminated from each other outside the scope of these components, as early as 70ms following stimulus presentation. Next, electrodes associated with traditional ERP components as well as, critically, those not associated with such components are shown to contribute information to stimulus discriminability. And last, the levels of ERP-based pattern discrimination are found to correlate with recognition accuracy across subjects confirming the relevance of these methods for bridging brain and behavior data. Altogether, the current results shed new light on the fine-grained time course of neural face processing and showcase the value of novel methods for pattern analysis to investigating fundamental aspects of visual recognition. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Time course for tail regression during metamorphosis of the ascidian Ciona intestinalis.

    Science.gov (United States)

    Matsunobu, Shohei; Sasakura, Yasunori

    2015-09-01

    In most ascidians, the tadpole-like swimming larvae dramatically change their body-plans during metamorphosis and develop into sessile adults. The mechanisms of ascidian metamorphosis have been researched and debated for many years. Until now information on the detailed time course of the initiation and completion of each metamorphic event has not been described. One dramatic and important event in ascidian metamorphosis is tail regression, in which ascidian larvae lose their tails to adjust themselves to sessile life. In the present study, we measured the time associated with tail regression in the ascidian Ciona intestinalis. Larvae are thought to acquire competency for each metamorphic event in certain developmental periods. We show that the timing with which the competence for tail regression is acquired is determined by the time since hatching, and this timing is not affected by the timing of post-hatching events such as adhesion. Because larvae need to adhere to substrates with their papillae to induce tail regression, we measured the duration for which larvae need to remain adhered in order to initiate tail regression and the time needed for the tail to regress. Larvae acquire the ability to adhere to substrates before they acquire tail regression competence. We found that when larvae adhered before they acquired tail regression competence, they were able to remember the experience of adhesion until they acquired the ability to undergo tail regression. The time course of the events associated with tail regression provides a valuable reference, upon which the cellular and molecular mechanisms of ascidian metamorphosis can be elucidated. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Synthesis and evaluation of artificial antigens for astragaloside IV

    Directory of Open Access Journals (Sweden)

    Sheng-lan Yu

    Full Text Available The objective of this study was to produce artificial antigens for astragaloside IV that could be used to prepare antibodies against astragaloside IV screened in Radix astragali (Astragalus membranaceus (Fisch Bunge, Fabaceae and its preparations, using an indirect ELISA. Astragaloside IV was coupled to carrier proteins, bovine serum albumin and ovalbumin using the sodium periodate method and was then evaluated using SDS-PAGE, MALDI-TOF MS and animal immunizations. The coupling ratio of astragaloside IV to bovine serum albumin ratio was determined to be thirteen, and the indirect ELISA demonstrated that three groups of mice immunized with astragaloside IV-bovine serum albumin produced anti-astragaloside IV- bovine serum albumin-specific antibody, with a minimum serum titer of 1:9600. A method for synthesizing highly immunogenic astragaloside IV artificial antigens was successfully developed thus indicating its feasibility in the establishment of a fast immunoassay for astragaloside IV content determination in Radix astragali and its products.

  1. Rapid typing of Mannheimia haemolytica major genotypes 1 and 2 using MALDI-TOF mass spectrometry

    Science.gov (United States)

    Genotype 2 M. haemolytica predominantly associate over genotype 1 with the lungs of cattle with respiratory disease and ICEs containing antimicrobial resistance genes. Distinct protein masses were detected by MALDI-TOF MS between genotype 1 and 2 strains. MALDI-TOF MS could rapidly differentiate ge...

  2. Mass spectrometry

    DEFF Research Database (Denmark)

    Nyvang Hartmeyer, Gitte; Jensen, Anne Kvistholm; Böcher, Sidsel

    2010-01-01

    Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently being introduced for the rapid and accurate identification of bacteria. We describe 2 MALDI-TOF MS identification cases - 1 directly on spinal fluid and 1 on grown bacteria. Rapidly obtained...

  3. The importance of matrix-assisted laser desorption ionization–time of flight mass spectrometry for correct identification of Clostridium difficile isolated from chromID C. difficile chromogenic agar

    Directory of Open Access Journals (Sweden)

    Jonathan H.K. Chen

    2017-10-01

    Full Text Available The clinical workflow of using chromogenic agar and matrix-assisted laser desorption ionization time-of-fight mass spectrometry (MALDI-TOF MS for Clostridium difficile identification was evaluated. The addition of MALDI-TOF MS identification after the chromID C. difficile chromogenic agar culture could significantly improve the diagnostic accuracy of C. difficile.

  4. Time course of scopolamine effect on memory consolidation and forgetting in rats.

    Science.gov (United States)

    Popović, Miroljub; Giménez de Béjar, Verónica; Popović, Natalija; Caballero-Bleda, María

    2015-02-01

    The effect of scopolamine on the consolidation and forgetting of emotional memory has not been completely elucidated yet. The aim of the present study was to investigate the time course of scopolamine effect on consolidation and forgetting of passive avoidance response. In a first experiment of the present study, we tested the effect of scopolamine (1mg/kg, i.p., immediately after acquisition), on 24h and 48h retention performance of the step-through passive avoidance task, in adult male Wistar rats. On the 24h retested trial, the latency of the passive avoidance response was significantly lower, while on the 48h retested trial it was significantly higher in scopolamine than in the saline-treated group. In a second experiment, we assessed the 24h time course of scopolamine (1mg/kg) effect on memory consolidation in passive avoidance task. We found that scopolamine administration only within the first six and half hours after acquisition improved memory consolidation in 48h retention performance. Finally, a third experiment was performed on the saline- and scopolamine-treated rats (given immediately after acquisition) that on the 48h retention test did not step through into the dark compartment during the cut-off time. These animals were retested weekly for up to first three months, and after that, every three months until the end of experiment (i.e., 15 months after acquisition). The passive avoidance response in the saline treated group lasted up to 6 weeks after acquisition, while in the scopolamine treated group 50% of animals conserved the initial level of passive avoidance response until the experiment end point. In conclusion, the present data suggest that (1) improving or impairment effect of scopolamine given in post-training periods depends on delay of retention trial, (2) memory consolidation process could be modify by scopolamine within first six and half hours after training and (3) scopolamine could delay forgetting of emotional memory. Copyright

  5. A time course analysis of the extracellular proteome of Aspergillus nidulans growing on sorghum stover

    Directory of Open Access Journals (Sweden)

    Saykhedkar Sayali

    2012-07-01

    Full Text Available Abstract Background Fungi are important players in the turnover of plant biomass because they produce a broad range of degradative enzymes. Aspergillus nidulans, a well-studied saprophyte and close homologue to industrially important species such as A. niger and A. oryzae, was selected for this study. Results A. nidulans was grown on sorghum stover under solid-state culture conditions for 1, 2, 3, 5, 7 and 14 days. Based on analysis of chitin content, A. nidulans grew to be 4-5% of the total biomass in the culture after 2 days and then maintained a steady state of 4% of the total biomass for the next 12 days. A hyphal mat developed on the surface of the sorghum by day one and as seen by scanning electron microscopy the hyphae enmeshed the sorghum particles by day 5. After 14 days hyphae had penetrated the entire sorghum slurry. Analysis (1-D PAGE LC-MS/MS of the secretome of A. nidulans, and analysis of the breakdown products from the sorghum stover showed a wide range of enzymes secreted. A total of 294 extracellular proteins were identified with hemicellulases, cellulases, polygalacturonases, chitinases, esterases and lipases predominating the secretome. Time course analysis revealed a total of 196, 166, 172 and 182 proteins on day 1, 3, 7 and 14 respectively. The fungus used 20% of the xylan and cellulose by day 7 and 30% by day 14. Cellobiose dehydrogenase, feruloyl esterases, and CAZy family 61 endoglucanases, all of which are thought to reduce the recalcitrance of biomass to hydrolysis, were found in high abundance. Conclusions Our results show that A. nidulans secretes a wide array of enzymes to degrade the major polysaccharides and lipids (but probably not lignin by 1 day of growth on sorghum. The data suggests simultaneous breakdown of hemicellulose, cellulose and pectin. Despite secretion of most of the enzymes on day 1, changes in the relative abundances of enzymes over the time course indicates that the set of enzymes

  6. Time course of gene expression profiling in the liver of experimental mice infected with Echinococcus multilocularis.

    Directory of Open Access Journals (Sweden)

    Renyong Lin

    Full Text Available BACKGROUND: Alveolar echinococcosis (AE is a severe chronic parasitic disease which behaves like a slow-growing liver cancer. Clinical observations suggest that the parasite, Echinococcus multilocularis (E. multilocularis influences liver homeostasis and hepatic cell metabolism. However, this has never been analyzed during the time course of infection in the common model of secondary echinococcosis in experimental mice. METHODOLOGY/PRINCIPAL FINDINGS: Gene expression profiles were assessed using DNA microarray analysis, 1, 2, 3 and 6 months after injection of E. multilocularis metacestode in the liver of susceptible mice. Data were collected at different time points to monitor the dynamic behavior of gene expression. 557 differentially expressed genes were identified at one or more time points, including 351 up-regulated and 228 down-regulated genes. Time-course analysis indicated, at the initial stage of E. multilocularis infection (month 1-2, that most of up-regulated pathways were related to immune processes and cell trafficking such as chemokine-, mitogen-activated protein kinase (MAPK signaling, and down-regulated pathways were related to xenobiotic metabolism; at the middle stage (month 3, MAPK signaling pathway was maintained and peroxisome proliferator-activated receptor (PPAR signaling pathway emerged; at the late stage (month 6, most of up-regulated pathways were related to PPAR signaling pathway, complement and coagulation cascades, while down-regulated pathways were related to metabolism of xenobiotics by cytochrome P450. Quantitative RT-PCR analysis of a random selection of 19 genes confirmed the reliability of the microarray data. Immunohistochemistry analysis showed that proliferating cell nuclear antigen (PCNA was increased in the liver of E. multilocularis infected mice from 2 months to 6 months. CONCLUSIONS: E. multilocularis metacestode definitely exerts a deep influence on liver homeostasis, by modifying a number of gene

  7. Attentional bias to briefly presented emotional distractors follows a slow time course in visual cortex.

    Science.gov (United States)

    Müller, Matthias M; Andersen, Søren K; Hindi Attar, Catherine

    2011-11-02

    A central controversy in the field of attention is how the brain deals with emotional distractors and to what extent they capture attentional processing resources reflexively due to their inherent significance for guidance of adaptive behavior and survival. Especially, the time course of competitive interactions in early visual areas and whether masking of briefly presented emotional stimuli can inhibit biasing of processing resources in these areas is currently unknown. We recorded frequency-tagged potentials evoked by a flickering target detection task in the foreground of briefly presented emotional or neutral pictures that were followed by a mask in human subjects. We observed greater competition for processing resources in early visual cortical areas with shortly presented emotional relative to neutral pictures ~275 ms after picture offset. This was paralleled by a reduction of target detection rates in trials with emotional pictures ~400 ms after picture offset. Our finding that briefly presented emotional distractors are able to bias attention well after their offset provides evidence for a rather slow feedback or reentrant neural competition mechanism for emotional distractors that continues after the offset of the emotional stimulus.

  8. The time course of implicit processing of erotic pictures: an event-related potential study.

    Science.gov (United States)

    Feng, Chunliang; Wang, Lili; Wang, Naiyi; Gu, Ruolei; Luo, Yue-Jia

    2012-12-13

    The current study investigated the time course of the implicit processing of erotic stimuli using event-related potentials (ERPs). ERPs elicited by erotic pictures were compared with those by three other types of pictures: non-erotic positive, negative, and neutral pictures. We observed that erotic pictures evoked enhanced neural responses compared with other pictures at both early (P2/N2) and late (P3/positive slow wave) temporal stages. These results suggested that erotic pictures selectively captured individuals' attention at early stages and evoked deeper processing at late stages. More importantly, the amplitudes of P2, N2, and P3 only discriminated between erotic and non-erotic (i.e., positive, neutral, and negative) pictures. That is, no difference was revealed among non-erotic pictures, although these pictures differed in both valence and arousal. Thus, our results suggest that the erotic picture processing is beyond the valence and arousal. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Fast logic?: Examining the time course assumption of dual process theory.

    Science.gov (United States)

    Bago, Bence; De Neys, Wim

    2017-01-01

    Influential dual process models of human thinking posit that reasoners typically produce a fast, intuitive heuristic (i.e., Type-1) response which might subsequently be overridden and corrected by slower, deliberative processing (i.e., Type-2). In this study we directly tested this time course assumption. We used a two response paradigm in which participants have to give an immediate answer and afterwards are allowed extra time before giving a final response. In four experiments we used a range of procedures (e.g., challenging response deadline, concurrent load) to knock out Type 2 processing and make sure that the initial response was intuitive in nature. Our key finding is that we frequently observe correct, logical responses as the first, immediate response. Response confidence and latency analyses indicate that these initial correct responses are given fast, with high confidence, and in the face of conflicting heuristic responses. Findings suggest that fast and automatic Type 1 processing also cues a correct logical response from the start. We sketch a revised dual process model in which the relative strength of different types of intuitions determines reasoning performance. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Identification of driving network of cellular differentiation from single sample time course gene expression data

    Science.gov (United States)

    Chen, Ye; Wolanyk, Nathaniel; Ilker, Tunc; Gao, Shouguo; Wang, Xujing

    Methods developed based on bifurcation theory have demonstrated their potential in driving network identification for complex human diseases, including the work by Chen, et al. Recently bifurcation theory has been successfully applied to model cellular differentiation. However, there one often faces a technical challenge in driving network prediction: time course cellular differentiation study often only contains one sample at each time point, while driving network prediction typically require multiple samples at each time point to infer the variation and interaction structures of candidate genes for the driving network. In this study, we investigate several methods to identify both the critical time point and the driving network through examination of how each time point affects the autocorrelation and phase locking. We apply these methods to a high-throughput sequencing (RNA-Seq) dataset of 42 subsets of thymocytes and mature peripheral T cells at multiple time points during their differentiation (GSE48138 from GEO). We compare the predicted driving genes with known transcription regulators of cellular differentiation. We will discuss the advantages and limitations of our proposed methods, as well as potential further improvements of our methods.

  11. Time course and dimensions of postural control changes following neuromuscular training in youth field hockey athletes.

    Science.gov (United States)

    Zech, Astrid; Klahn, Philipp; Hoeft, Jon; zu Eulenburg, Christine; Steib, Simon

    2014-02-01

    Injury prevention effects of neuromuscular training have been partly attributed to postural control adaptations. Uncertainty exists regarding the magnitude of these adaptations and on how they can be adequately monitored. The objective was to determine the time course of neuromuscular training effects on functional, dynamic and static balance measures. Thirty youth (14.9 ± 3 years) field hockey athletes were randomised to an intervention or control group. The intervention included a 20-min neuromuscular warm-up program performed twice weekly for 10 weeks. Balance assessments were performed at baseline, week three, week six and post-intervention. They included the star excursion balance test (SEBT), balance error scoring system (BESS), jump-landing time to stabilization (TTS) and center of pressure (COP) sway velocity during single-leg standing. No baseline differences were found between groups in demographic data and balance measures. Adherence was at 86%. All balance measures except the medial-lateral TTS improved significantly over time (p controls (31.8 ± 22.1%). There were no significant group by time interactions in the SEBT, TTS and COP sway velocity. Neuromuscular training was effective in improving postural control in youth team athletes. However, this effect was not reflected in all balance measures suggesting that the neuromuscular training did not influence all dimensions of postural control. Further studies are needed to confirm the potential of specific warm-up programs to improve postural control.

  12. Time course of emotion-related responding during distraction and reappraisal.

    Science.gov (United States)

    Schönfelder, Sandra; Kanske, Philipp; Heissler, Janine; Wessa, Michèle

    2014-09-01

    Theoretical accounts of emotion regulation (ER) discriminate various cognitive strategies to voluntarily modify emotional states. Amongst these, attentional deployment (i.e. distraction) and cognitive change (i.e. reappraisal), have been shown to successfully down-regulate emotions. Neuroimaging studies found that both strategies differentially engage neural structures associated with selective attention, working memory and cognitive control. The aim of this study was to further delineate similarities and differences between the ER strategies reappraisal and distraction by investigating their temporal brain dynamics using event-related potentials (ERPs) and their patterns of facial expressive behavior. Twenty-one participants completed an ER experiment in which they had to either passively view positive, neutral and negative pictures, reinterpret them to down-regulate affective responses (reappraisal), or solve a concurrently presented mathematical equation (distraction). Results demonstrate the efficacy of both strategies in the subjective control of emotion, accompanied by reductions of facial expressive activity (Corrugator supercilii and Zygomaticus major). ERP results indicated that distraction, compared with reappraisal, yielded a stronger and earlier attenuation of the late positive potential (LPP) magnitude for negative pictures. For positive pictures, only distraction but not reappraisal had significant effect on LPP attenuation. The results support the process model of ER, separating subtypes of cognitive strategies based on their specific time course. © The Author (2013). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  13. Time course and degree of hyperinflation with metronome-paced tachypnea in COPD patients.

    Science.gov (United States)

    Weigt, S Samuel; Abrazado, Marlon; Kleerup, Eric C; Tashkin, Donald P; Cooper, Christopher B

    2008-10-01

    In COPD patients, tachypnea should increase (dynamic) hyperinflation by shortening expiratory time. We developed a method to evaluate the time course and degree of dynamic hyperinflation during metronome-paced tachypnea. Fourteen patients with stable COPD (FEV(1) 43 +/- 13% predicted) were studied. Inspiratory capacity (IC) was measured breathing through a flow transducer. Subjects paced their respiratory rate (f(R)) at 20/min, 30/min and 40/min for 60-second periods in response to audible tones generated by a computer. IC measurements were obtained at baseline and after 30 and 60 seconds at each f(R). End-tidal carbon dioxide was monitored and f(R) was allowed to return to baseline between periods of tachypnea. Tachypnea produced reductions in IC of 200 +/- 240 ml, 380 +/- 330 ml and 540 +/- 300 ml after 30 seconds at 20/min, 30/min and 40/min, respectively. IC reduction at 60 seconds was similar to 30 seconds for each f(R). In patients with moderate-to-severe COPD, the dynamic hyperinflation induced by metronome-paced tachypnea was shown to occur rapidly and be complete by 30 seconds for a given f(R). Controlled increments in f(R) produced stepwise increases in dynamic hyperinflation. This standardized method could be a useful and easier method of assessing dynamic hyperinflation in COPD patients before and after therapeutic interventions.

  14. The time course of short-term hypertrophy in the absence of eccentric muscle damage.

    Science.gov (United States)

    Stock, Matt S; Mota, Jacob A; DeFranco, Ryan N; Grue, Katherine A; Jacobo, A Unique; Chung, Eunhee; Moon, Jordan R; DeFreitas, Jason M; Beck, Travis W

    2017-05-01

    It has been proposed that the increase in skeletal muscle mass observed during the initial weeks of initiating a resistance training program is concomitant with eccentric muscle damage and edema. We examined the time course of muscle hypertrophy during 4 weeks of concentric-only resistance training. Thirteen untrained men performed unilateral concentric-only dumbbell curls and shoulder presses twice per week for 4 weeks. Sets of 8-12 repetitions were performed to failure, and training loads were increased during each session. Subjects consumed 500 ml of whole milk during training. Assessments of soreness, lean mass, echo intensity, muscle thickness, relaxed and flexed arm circumference, and isokinetic strength were performed every 72 or 96 h. Soreness, echo intensity, relaxed circumference, and peak torque data did not significantly change. Significant increases in lean mass, muscle thickness, and flexed circumference were observed within seven training sessions. Lean mass was elevated at tests #7 (+109.3 g, p = .002) and #8 (+116.1 g, p = .035), with eight different subjects showing changes above the minimal difference of 139.1 g. Muscle thickness was elevated at tests #6 (+0.23 cm, p = .004), #7 (+0.31 cm, p hypertrophy may occur in the absence of eccentric muscle damage within seven training sessions.

  15. Time course of development of metastasis in irradiated Lewis lung carcinoma

    International Nuclear Information System (INIS)

    Ohizumi, Yukio; Maezawa, Hiroshi; Mori, Tomoyuki

    1988-01-01

    The influence of local irradiation on the development of metastases and primary tumor volume was studied in Lewis lung carcinoma growing intramuscularly in the hind leg of C57BL/6 mice. The time course of development of metastases was determined from the size of the lung colonies at autopsy by determining the growth rate of the colonies. Irradiation within five days after tumor cell injection inhibited the incidence of metastases in accordance with irradiation dose. For irradiation more than seven days after the injection, promotion of metastases was observed around the time of the experiment as a function of irradiation dose and tumor volume. After the irradiation phase, the development of metastases was inhibited in accordance with radiation dose. When delay in metastasis was defined as additional days needed to develop two or ten colonies compared with controls, the relationship between delay and dose was linear. At the regrowth phase of the primary tumor, the incidence of metastases from the irradiated tumor was reduced in comparison with that from unirradiated tumors of the same size. Inhibition of metastases was observed only at 5 Gy and showed slight dose-dependency. Mechanisms in the development of metastases as they related to these findings are also discussed. (autho)

  16. Flavour generation during commercial barley and malt roasting operations: a time course study.

    Science.gov (United States)

    Yahya, Hafiza; Linforth, Robert S T; Cook, David J

    2014-02-15

    The roasting of barley and malt products generates colour and flavour, controlled principally by the time course of product temperature and moisture content. Samples were taken throughout the industrial manufacture of three classes of roasted product (roasted barley, crystal malt and black malt) and analysed for moisture content, colour and flavour volatiles. Despite having distinct flavour characteristics, the three products contained many compounds in common. The product concentrations through manufacture of 15 flavour compounds are used to consider the mechanisms (Maillard reaction, caramelisation, pyrolysis) by which they were formed. The use of water sprays resulted in transient increases in formation of certain compounds (e.g., 2-cyclopentene-1,4-dione) and a decrease in others (e.g., pyrrole). The study highlights rapid changes in colour and particularly flavour which occur at the end of roasting and onwards to the cooling floor. This highlights the need for commercial maltsters to ensure consistency of procedures from batch to batch. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Audiovisual semantic interactions between linguistic and nonlinguistic stimuli: The time-courses and categorical specificity.

    Science.gov (United States)

    Chen, Yi-Chuan; Spence, Charles

    2018-04-30

    We examined the time-courses and categorical specificity of the crossmodal semantic congruency effects elicited by naturalistic sounds and spoken words on the processing of visual pictures (Experiment 1) and printed words (Experiment 2). Auditory cues were presented at 7 different stimulus onset asynchronies (SOAs) with respect to the visual targets, and participants made speeded categorization judgments (living vs. nonliving). Three common effects were observed across 2 experiments: Both naturalistic sounds and spoken words induced a slowly emerging congruency effect when leading by 250 ms or more in the congruent compared with the incongruent condition, and a rapidly emerging inhibitory effect when leading by 250 ms or less in the incongruent condition as opposed to the noise condition. Only spoken words that did not match the visual targets elicited an additional inhibitory effect when leading by 100 ms or when presented simultaneously. Compared with nonlinguistic stimuli, the crossmodal congruency effects associated with linguistic stimuli occurred over a wider range of SOAs and occurred at a more specific level of the category hierarchy (i.e., the basic level) than was required by the task. A comprehensive framework is proposed to provide a dynamic view regarding how meaning is extracted during the processing of visual or auditory linguistic and nonlinguistic stimuli, therefore contributing to our understanding of multisensory semantic processing in humans. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  18. The Onset and Time Course of Semantic Priming during Rapid Recognition of Visual Words

    Science.gov (United States)

    Hoedemaker, Renske S.; Gordon, Peter C.

    2016-01-01

    In two experiments, we assessed the effects of response latency and task-induced goals on the onset and time course of semantic priming during rapid processing of visual words as revealed by ocular response tasks. In Experiment 1 (Ocular Lexical Decision Task), participants performed a lexical decision task using eye-movement responses on a sequence of four words. In Experiment 2, the same words were encoded for an episodic recognition memory task that did not require a meta-linguistic judgment. For both tasks, survival analyses showed that the earliest-observable effect (Divergence Point or DP) of semantic priming on target-word reading times occurred at approximately 260 ms, and ex-Gaussian distribution fits revealed that the magnitude of the priming effect increased as a function of response time. Together, these distributional effects of semantic priming suggest that the influence of the prime increases when target processing is more effortful. This effect does not require that the task include a metalinguistic judgment; manipulation of the task goals across experiments affected the overall response speed but not the location of the DP or the overall distributional pattern of the priming effect. These results are more readily explained as the result of a retrospective rather than a prospective priming mechanism and are consistent with compound-cue models of semantic priming. PMID:28230394

  19. The time course of spoken word recognition in Mandarin Chinese: a unimodal ERP study.

    Science.gov (United States)

    Huang, Xianjun; Yang, Jin-Chen; Zhang, Qin; Guo, Chunyan

    2014-10-01

    In the present study, two experiments were carried out to investigate the time course of spoken word recognition in Mandarin Chinese using both event-related potentials (ERPs) and behavioral measures. To address the hypothesis that there is an early phonological processing stage independent of semantics during spoken word recognition, a unimodal word-matching paradigm was employed, in which both prime and target words were presented auditorily. Experiment 1 manipulated the phonological relations between disyllabic primes and targets, and found an enhanced P2 (200-270 ms post-target onset) as well as a smaller early N400 to word-initial phonological mismatches over fronto-central scalp sites. Experiment 2 manipulated both phonological and semantic relations between monosyllabic primes and targets, and replicated the phonological mismatch-associated P2, which was not modulated by semantic relations. Overall, these results suggest that P2 is a sensitive electrophysiological index of early phonological processing independent of semantics in Mandarin Chinese spoken word recognition. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Must analysis of meaning follow analysis of form? A time course analysis.

    Science.gov (United States)

    Feldman, Laurie B; Milin, Petar; Cho, Kit W; Moscoso Del Prado Martín, Fermín; O'Connor, Patrick A

    2015-01-01

    Many models of word recognition assume that processing proceeds sequentially from analysis of form to analysis of meaning. In the context of morphological processing, this implies that morphemes are processed as units of form prior to any influence of their meanings. Some interpret the apparent absence of differences in recognition latencies to targets (SNEAK) in form and semantically similar (sneaky-SNEAK) and in form similar and semantically dissimilar (sneaker-SNEAK) prime contexts at a stimulus onset asynchrony (SOA) of 48 ms as consistent with this claim. To determine the time course over which degree of semantic similarity between morphologically structured primes and their targets influences recognition in the forward masked priming variant of the lexical decision paradigm, we compared facilitation for the same targets after semantically similar and dissimilar primes across a range of SOAs (34-100 ms). The effect of shared semantics on recognition latency increased linearly with SOA when long SOAs were intermixed (Experiments 1A and 1B) and latencies were significantly faster after semantically similar than dissimilar primes at homogeneous SOAs of 48 ms (Experiment 2) and 34 ms (Experiment 3). Results limit the scope of form-then-semantics models of recognition and demonstrate that semantics influences even the very early stages of recognition. Finally, once general performance across trials has been accounted for, we fail to provide evidence for individual differences in morphological processing that can be linked to measures of reading proficiency.

  1. Time course of the response of carbohydrate metabolism to unloading of the soleus

    Science.gov (United States)

    Henriksen, Erik J.; Tischler, Marc E.

    1988-01-01

    The time course of the response of carbohydrate metabolism to unloading was studied in the soleus muscle of rats subjected to tail-cast suspension. In the fresh soleus, 12 hours of unloading led to higher concentrations of glycogen and lower activity ratios of both glycogen synthase and glycogen phosphorylase. These changes were still evident on day three. Thereafter, the increased glycogen concentration apparently diminished the activity ratio of glycogen synthase, leading to a subsequent fall in the total glycogen content after day one. After 24 hours of unloading, when no significant atrophy was detectable, there was no differential response to insulin for in vitro glucose metabolism. On day three, the soleus atrophied significantly and displayed a greater sensitivity to insulin for most of these parameters compared to the weight-bearing control muscle. However, insulin sensitivity for glycogen synthesis was unchanged. These results showed that the increased sensitivity to insulin of the unloaded soleus is associated with the degree of muscle atrophy, likely due to an increased insulin binding capacity relative to muscle mass. This study also showed that insulin regulation of glucose uptake and of glycogen synthesis is affected differentially in the unloaded soleus muscle.

  2. The time course from gender categorization to gender-stereotype activation.

    Science.gov (United States)

    Zhang, Xiaobin; Li, Qiong; Sun, Shan; Zuo, Bin

    2018-02-01

    Social categorization is the foundation of stereotype activation, and the process from social categorization to stereotype activation is rapid. However, the time from social categorization to stereotype activation is unknown. This study involves a real-time measurement of the time course of gender-stereotype activation beginning with gender categorization using event-related potential technology with a face as the priming stimulus. We found that 195 ms after a face stimulus was presented, brain waves stimulated by male or female gender categorization showed a clear separation, with male faces stimulating larger N200 waves. In addition, 475 ms after a face stimulus appeared or 280 ms after the gendercategorization process occurred, gender-stereotype-consistent and gender-stereotype-inconsistent stimuli were distinct, with gender-stereotype-inconsistent stimuli inducing larger N400 waves. These results indicate that during gender-stereotype activation by face perception, gender categorization occurs approximately 195 ms after seeing a face stimulus and a gender stereotype is activated at approximately 475 ms.

  3. The time-course of feature interference in agreement comprehension: Multiple mechanisms and asymmetrical attraction.

    Science.gov (United States)

    Tanner, Darren; Nicol, Janet; Brehm, Laurel

    2014-10-01

    Attraction interference in language comprehension and production may be as a result of common or different processes. In the present paper, we investigate attraction interference during language comprehension, focusing on the contexts in which interference arises and the time-course of these effects. Using evidence from event-related brain potentials (ERPs) and sentence judgment times, we show that agreement attraction in comprehension is best explained as morphosyntactic interference during memory retrieval. This stands in contrast to attraction as a message-level process involving the representation of the subject NP's number features, which is a strong contributor to attraction in production. We thus argue that the cognitive antecedents of agreement attraction in comprehension are non-identical with those of attraction in production, and moreover, that attraction in comprehension is primarily a consequence of similarity-based interference in cue-based memory retrieval processes. We suggest that mechanisms responsible for attraction during language comprehension are a subset of those involved in language production.

  4. The time course of morphological processing during spoken word recognition in Chinese.

    Science.gov (United States)

    Shen, Wei; Qu, Qingqing; Ni, Aiping; Zhou, Junyi; Li, Xingshan

    2017-12-01

    We investigated the time course of morphological processing during spoken word recognition using the printed-word paradigm. Chinese participants were asked to listen to a spoken disyllabic compound word while simultaneously viewing a printed-word display. Each visual display consisted of three printed words: a semantic associate of the first constituent of the compound word (morphemic competitor), a semantic associate of the whole compound word (whole-word competitor), and an unrelated word (distractor). Participants were directed to detect whether the spoken target word was on the visual display. Results indicated that both the morphemic and whole-word competitors attracted more fixations than the distractor. More importantly, the morphemic competitor began to diverge from the distractor immediately at the acoustic offset of the first constituent, which was earlier than the whole-word competitor. These results suggest that lexical access to the auditory word is incremental and morphological processing (i.e., semantic access to the first constituent) that occurs at an early processing stage before access to the representation of the whole word in Chinese.

  5. Time-course of myocardial perfusion and fatty acid metabolism after coronary reperfusion

    International Nuclear Information System (INIS)

    Sochor, H.; Pachinger, O.; Ogris, E.; Probst, P.; Kaindl, F.

    1985-01-01

    To investigate the relationship and time-course of myocardial perfusion and behaviour of fatty acid uptake and clearance following reperfusion, the authors studied 19 patients after successful intracoronary thrombolysis with Tl-201 and I-123 hepta-decanoic acid (HDA) and planar imaging. Pts were studied acute (A: 48 hours), early (E:6-8 days) and late (L:6-12 months). %-defect size and relative tracer uptake were determined for both markers as well as t1/2 of the early clearance phase for HDA. Late Tl was done as stress test study after dipyridamole infusion. As in a previous report acute HDA uptake-defects were larger than Tl (38 +- 10% vs 24 +- 9%, p<0.05) suggesting a larger area of metabolic impairment than outlined by perfusion. HDA and Tl uptake at A correlated significantly (p<0.01, r=0.86) but HDA uptake was 19% lower than Tl and not different at E and L. Tl stress studies exhibited in 74% reversible ischemia in the area of ''metabolic recovery''. The authors conclude that early after reperfusion uptake of HDA is frequently impaired despite improved perfusion suggesting metabolic derangement showing a slow recovery over time. A multiple tracer approach including metabolic markers may improve the characterization of reperfused myocardium

  6. Must analysis of meaning follow analysis of form? A time course analysis

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    Laurie eFeldman

    2015-03-01

    Full Text Available Many models of word recognition assume that processing proceeds sequentially from analysis of form to analysis of meaning. In the context of morphological processing, this implies that morphemes are processed as units of form prior to any influence of their meanings. Some interpret the apparent absence of differences in recognition latencies to targets (SNEAK in form and semantically similar (sneaky-SNEAK and in form similar and semantically dissimilar (sneaker-SNEAK prime contexts at an SOA of 48 ms as consistent with this claim. To determine the time course over which degree of semantic similarity between morphologically structured primes and their targets influences recognition in the forward masked priming variant of the lexical decision paradigm, we compared facilitation for the same targets after semantically similar and dissimilar primes across a range of SOAs. The effect of shared semantics on recognition latency increased linearly with SOA when long SOAs were intermixed (Exp. 1 and latencies were significantly faster after semantically similar than dissimilar primes at homogeneous SOAs of 48 ms (Exp. 2 and 34 ms (Exp. 3. Results limit the scope of form-then-semantics models of recognition and demonstrate that semantics influences even the very early stages of recognition. Finally, once general behavior across trials has been accounted for, we fail to provide evidence for individual differences in morphological processing that can be linked to measures of reading proficiency.

  7. A time-course study of long term over-expression of ARR19 in mice

    Science.gov (United States)

    Qamar, Imteyaz; Ahmad, Mohammad Faiz; Narayanasamy, Arul

    2015-01-01

    A leucine-rich protein, ARR19 (androgen receptor corepressor-19 kDa), is highly expressed in male reproductive organs and moderately in others. Previously, we have reported that ARR19 is differentially expressed in adult Leydig cells during the testis development and inhibits steroidogenesis by reducing the expression of steroidogenic enzymes. Whereas in prostate, ARR19 represses the transcriptional activity of AR (androgen receptor), it is important for male sexual differentiation and maturation in prostate and epididymis, through the recruitment of HDAC4. In this study we show that long term adenovirus mediated overexpression of ARR19 in mice testis has the potential of inhibiting the differentiation of testicular and prostatic cells by reducing the size of testis and prostate but has no effect on the growth of seminal vesicles. Further, it reduces the level of progesterone and testosterone by reducing the steroidogenic enzymes such as 3HSD, P450c17 and StAR. This is the first study reporting a time-course analysis of the implications of long term overexpression of ARR19 in mice testis and its effect on other organs such as prostate and seminal vesicles. Taken together, these results suggest that ARR19 may play an important role in the differentiation of male reproductive organs such as testis and prostate. PMID:26260329

  8. Reduced glomerular angiotensin II receptor density in diabetes mellitus in the rat: time course and mechanism

    International Nuclear Information System (INIS)

    Wilkes, B.M.

    1987-01-01

    Glomerular angiotensin II receptors are reduced in number in early diabetes mellitus, which may contribute to hyperfiltration and glomerular injury. The time course and role of the renin-angiotensin-aldosterone system in the pathogenesis of the receptor abnormality were studied in male Sprague-Dawley rats made diabetic with streptozotocin (65 mg, iv). Glomerular angiotensin II receptors were measured by Scatchard analysis; insulin, renin activity, angiotensin II, and aldosterone were measured by RIA. Diabetes mellitus was documented at 24 h by a rise in plasma glucose (vehicle-injected control, 133 +/- 4; diabetic, 482 +/- 22 mg/dl and a fall in plasma insulin (control, 53.1 +/- 5.7; diabetic, 35.6 +/- 4.0 microIU/ml. At 24 h glomerular angiotensin II receptor density was decreased by 26.5% in diabetic rats (control, 75.5 +/- 9.6 X 10(6); diabetic, 55.5 +/- 8.3 X 10(6) receptors/glomerulus. Receptor occupancy could not explain the defect, because there was reduced binding in diabetic glomeruli after pretreatment with 3 M MgCl 2 , a maneuver that caused dissociation of previously bound hormone. There was a progressive return of the receptor density toward normal over the 60 days following induction of diabetes, with diabetic glomeruli measuring 22.7%, 14.8%, and 3.7% fewer receptors than age-matched controls at 11 days, 1 month, and 2 months, respectively

  9. Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

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    Liang-Hui Chu

    Full Text Available Angiogenesis involves stimulation of endothelial cells (EC by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome" could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A. We used the Short Time-series Expression Miner (STEM to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC and human microvascular EC (MEC. The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

  10. The time-course analysis of gene expression during wound healing in mouse skin.

    Science.gov (United States)

    Kagawa, Shinichiro; Matsuo, Aya; Yagi, Yoichi; Ikematsu, Kazuya; Tsuda, Ryouichi; Nakasono, Ichiro

    2009-03-01

    RNA analysis has been applied to forensic work to determine wound age. We investigated mRNA expression using quantitative RT-PCR of ten genes, including c-fos, fosB, mitogen-activated protein kinase phosphatase-1 (MKP-1), CD14, chemokine (C-C motif) ligand 9 (CCL9), placenta growth factor (PlGF), mast cell protease-5 (MCP-5), growth arrest specific 5 (Gas5), beta-2 microglobulin (B2M) and major urinary protein-1 (MUP-1), in terms of repair response in adult mice. The expression level of c-fos, fosB and MKP-1 transcripts increased drastically, peaked within 1h, and that of the CD14 and CCL9 transcripts peaked from 12 to 24h. An increase in PlGF and MCP-5 mRNA appeared on about day 5. Gas5, B2M and MUP-1 transcripts showed no significant change. Each gene had differentially expressional patterns with time-course. Our result implied that the observation of the 7 genes in wounded skin could serve to aid in the accurate diagnosis of wound age.

  11. The time course of activation of object shape and shape+colour representations during memory retrieval.

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    Toby J Lloyd-Jones

    Full Text Available Little is known about the timing of activating memory for objects and their associated perceptual properties, such as colour, and yet this is important for theories of human cognition. We investigated the time course associated with early cognitive processes related to the activation of object shape and object shape+colour representations respectively, during memory retrieval as assessed by repetition priming in an event-related potential (ERP study. The main findings were as follows: (1 we identified a unique early modulation of mean ERP amplitude during the N1 that was associated with the activation of object shape independently of colour; (2 we also found a subsequent early P2 modulation of mean amplitude over the same electrode clusters associated with the activation of object shape+colour representations; (3 these findings were apparent across both familiar (i.e., correctly coloured - yellow banana and novel (i.e., incorrectly coloured - blue strawberry objects; and (4 neither of the modulations of mean ERP amplitude were evident during the P3. Together the findings delineate the timing of object shape and colour memory systems and support the notion that perceptual representations of object shape mediate the retrieval of temporary shape+colour representations for familiar and novel objects.

  12. The time course of activation of object shape and shape+colour representations during memory retrieval.

    Science.gov (United States)

    Lloyd-Jones, Toby J; Roberts, Mark V; Leek, E Charles; Fouquet, Nathalie C; Truchanowicz, Ewa G

    2012-01-01

    Little is known about the timing of activating memory for objects and their associated perceptual properties, such as colour, and yet this is important for theories of human cognition. We investigated the time course associated with early cognitive processes related to the activation of object shape and object shape+colour representations respectively, during memory retrieval as assessed by repetition priming in an event-related potential (ERP) study. The main findings were as follows: (1) we identified a unique early modulation of mean ERP amplitude during the N1 that was associated with the activation of object shape independently of colour; (2) we also found a subsequent early P2 modulation of mean amplitude over the same electrode clusters associated with the activation of object shape+colour representations; (3) these findings were apparent across both familiar (i.e., correctly coloured - yellow banana) and novel (i.e., incorrectly coloured - blue strawberry) objects; and (4) neither of the modulations of mean ERP amplitude were evident during the P3. Together the findings delineate the timing of object shape and colour memory systems and support the notion that perceptual representations of object shape mediate the retrieval of temporary shape+colour representations for familiar and novel objects.

  13. Time-course of cadmium-induced acute hepatotoxicity in the rat liver: the role of apoptosis

    Energy Technology Data Exchange (ETDEWEB)

    Tzirogiannis, Konstantinos N.; Panoutsopoulos, Georgios I.; Hereti, Rosa I.; Alexandropoulou, Katerina N.; Basayannis, Aristidis C.; Mykoniatis, Michael G. [Department of Experimental Pharmacology, Medical School, Athens University, 75 Mikras Asias St., 115 27, Athens (Greece); Demonakou, Maria D. [Histopathology Laboratory, Sismanoglion G.D. Hospital, Sismanogliou 1, Marousi, Attiki 151 27 (Greece)

    2003-12-01

    Exposure to toxic metals and pollutants is a major environmental problem. Cadmium is a metal causing acute hepatic injury but the mechanism of this phenomenon is poorly understood. In the present study, we investigated the mechanism and time-course of cadmium-induced liver injury in rats, with emphasis being placed on apoptosis in parenchymal and nonparenchymal liver cells. Cadmium (3.5 mg/kg body weight) was injected intraperitoneally and the rats were killed 0, 9, 12, 16, 24, 48 and 60 h later. The extent of liver injury was evaluated for necrosis, apoptosis, peliosis, mitoses and inflammatory infiltration in hematoxylin-eosin-stained liver sections, and by assaying serum enzyme activities. The number of cells that died via apoptosis was quantified by TUNEL assay. The identification of nonparenchymal liver cells and activated Kupffer cells was performed histochemically. Liver regeneration was evaluated by assaying the activity of liver thymidine kinase and by the rate of {sup 3}H-thymidine incorporation into DNA. Both cadmium-induced necrotic cell death and parenchymal cell apoptosis showed a biphasic elevation at 12 and 48 h and peaked at 48 and 12 h, respectively. Nonparenchymal cell apoptosis peaked at 48 h. Peliosis hepatis, another characteristic form of liver injury, was first observed at 16 h and, at all time points, closely correlated with the apoptotic index of nonparenchymal liver cells, where the lesion was also maximial at 48 h. Kupffer cell activation and neutrophil infiltration were minimal for all time points examined. Based on thymidine kinase activity, liver regeneration was found to discern a classic biphasic peak pattern at 12 and 48 h. It was very interesting to observe that cadmium-induced liver injury did not involve inflammation at any time point. Apoptosis seems to be a major mechanism for the removal of damaged cells, and constitutes the major type of cell death in nonparenchymal liver cells. Apoptosis of nonparenchymal cells is the basis

  14. Adverse radiation effect after stereotactic radiosurgery for brain metastases: incidence, time course, and risk factors.

    Science.gov (United States)

    Sneed, Penny K; Mendez, Joe; Vemer-van den Hoek, Johanna G M; Seymour, Zachary A; Ma, Lijun; Molinaro, Annette M; Fogh, Shannon E; Nakamura, Jean L; McDermott, Michael W

    2015-08-01

    The authors sought to determine the incidence, time course, and risk factors for overall adverse radiation effect (ARE) and symptomatic ARE after stereotactic radiosurgery (SRS) for brain metastases. All cases of brain metastases treated from 1998 through 2009 with Gamma Knife SRS at UCSF were considered. Cases with less than 3 months of follow-up imaging, a gap of more than 8 months in imaging during the 1st year, or inadequate imaging availability were excluded. Brain scans and pathology reports were reviewed to ensure consistent scoring of dates of ARE, treatment failure, or both; in case of uncertainty, the cause of lesion worsening was scored as indeterminate. Cumulative incidence of ARE and failure were estimated with the Kaplan-Meier method with censoring at last imaging. Univariate and multivariate Cox proportional hazards analyses were performed. Among 435 patients and 2200 brain metastases evaluable, the median patient survival time was 17.4 months and the median lesion imaging follow-up was 9.9 months. Calculated on the basis of 2200 evaluable lesions, the rates of treatment failure, ARE, concurrent failure and ARE, and lesion worsening with indeterminate cause were 9.2%, 5.4%, 1.4%, and 4.1%, respectively. Among 118 cases of ARE, approximately 60% were symptomatic and 85% occurred 3-18 months after SRS (median 7.2 months). For 99 ARE cases managed without surgery or bevacizumab, the probabilities of improvement observed on imaging were 40%, 57%, and 76% at 6, 12, and 18 months after onset of ARE. The most important risk factors for ARE included prior SRS to the same lesion (with 20% 1-year risk of symptomatic ARE vs 3%, 4%, and 8% for no prior treatment, prior whole brain radiotherapy [WBRT], or concurrent WBRT) and any of these volume parameters: target, prescription isodose, 12-Gy, or 10-Gy volume. Excluding lesions treated with repeat SRS, the 1-year probabilities of ARE were 2.1 cm, target volume > 1.2 cm(3), prescription isodose volume > 1.8 cm(3

  15. Time course in calpain activity and autolysis in slow and fast skeletal muscle during clenbuterol treatment.

    Science.gov (United States)

    Douillard, Aymeric; Galbes, Olivier; Rossano, Bernadette; Vernus, Barbara; Bonnieu, Anne; Candau, Robin; Py, Guillaume

    2011-02-01

    Calpains are Ca2+ cysteine proteases that have been proposed to be involved in the cytoskeletal remodeling and wasting of skeletal muscle. Cumulative evidence also suggests that β2-agonists can lead to skeletal muscle hypertrophy through a mechanism probably related to calcium-dependent proteolytic enzyme. The aim of our study was to monitor calpain activity as a function of clenbuterol treatment in both slow and fast phenotype rat muscles. For this purpose, for 21 days we followed the time course of the calpain activity and of the ubiquitous calpain 1 and 2 autolysis, as well as muscle remodeling in the extensor digitorum longus (EDL) and soleus muscles of male Wistar rats treated daily with clenbuterol (4 mg·kg-1). A slow to fast fiber shift was observed in both the EDL and soleus muscles after 9 days of treatment, while hypertrophy was observed only in EDL after 9 days of treatment. Soleus muscle but not EDL muscle underwent an early apoptonecrosis phase characterized by hematoxylin and eosin staining. Total calpain activity was increased in both the EDL and soleus muscles of rats treated with clenbuterol. Moreover, calpain 1 autolysis increased significantly after 14 days in the EDL, but not in the soleus. Calpain 2 autolysis increased significantly in both muscles 6 hours after the first clenbuterol injection, indicating that clenbuterol-induced calpain 2 autolysis occurred earlier than calpain 1 autolysis. Together, these data suggest a preferential involvement of calpain 2 autolysis compared with calpain 1 autolysis in the mechanisms underlying the clenbuterol-induced skeletal muscle remodeling.

  16. Time course Analysis of Gene expression patterns in ZebrafIsh Eye during Optic Nerve Regeneration

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    Amy T. Mccurley

    2010-01-01

    Full Text Available It is well-established that neurons in the adult mammalian central nervous system (CNS are terminally differentiated and, if injured, will be unable to regenerate their connections. In contrast to mammals, zebrafish and other teleosts display a robust neuroregenerative response. Following optic nerve crush (ONX, retinal ganglion cells (RGC regrow their axons to synapse with topographically correct targets in the optic tectum, such that vision is restored in ~21 days. What accounts for these differences between teleostean and mammalian responses to neural injury is not fully understood. A time course analysis of global gene expression patterns in the zebrafish eye after ONX can help to elucidate cellular and molecular mechanisms that contribute to a successful neuroregeneration. To define different phases of regeneration after ONX, alpha tubulin 1 ( tuba1 and growth-associated protein 43 ( gap43 , markers previously shown to correspond to morphophological events, were measured by real time quantitative PCR (qPCR. Microarray analysis was then performed at defined intervals (6 hours, 1, 4, 12, and 21 days post-ONX and compared to SHAM. Results show that optic nerve damage induces multiple, phase-related transcriptional programs, with the maximum number of genes changed and highest fold-change occurring at 4 days. Several functional groups affected by optic nerve regeneration, including cell adhesion, apoptosis, cell cycle, energy metabolism, ion channel activity, and calcium signaling, were identified. Utilizing the whole eye allowed us to identify signaling contributions from the vitreous, immune and glial cells as well as the neural cells of the retina. Comparisons between our dataset and transcriptional profiles from other models of regeneration in zebrafish retina, heart and fin revealed a subset of commonly regulated transcripts, indicating shared mechanisms in different regenerating tissues. Knowledge of gene expression patterns in all

  17. Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response

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    Nasrine Bendjilali

    2017-01-01

    Full Text Available Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen.

  18. Pancreatic cellular injury after cardiac surgery with cardiopulmonary bypass: frequency, time course and risk factors.

    Science.gov (United States)

    Nys, Monique; Venneman, Ingrid; Deby-Dupont, Ginette; Preiser, Jean-Charles; Vanbelle, Sophie; Albert, Adelin; Camus, Gérard; Damas, Pierre; Larbuisson, Robert; Lamy, Maurice

    2007-05-01

    Although often clinically silent, pancreatic cellular injury (PCI) is relatively frequent after cardiac surgery with cardiopulmonary bypass; and its etiology and time course are largely unknown. We defined PCI as the simultaneous presence of abnormal values of pancreatic isoamylase and immunoreactive trypsin (IRT). The frequency and time evolution of PCI were assessed in this condition using assays for specific exocrine pancreatic enzymes. Correlations with inflammatory markers were searched for preoperative risk factors. One hundred ninety-three patients submitted to cardiac surgery were enrolled prospectively. Blood IRT, amylase, pancreatic isoamylase, lipase, and markers of inflammation (alpha1-protease inhibitor, alpha2-macroglobulin, myeloperoxidase) were measured preoperatively and postoperatively until day 8. The postoperative increase in plasma levels of pancreatic enzymes and urinary IRT was biphasic in all patients: early after surgery and later (from day 4 to 8 after surgery). One hundred thirty-three patients (69%) experienced PCI, with mean IRT, isoamylase, and alpha1-protease inhibitor values higher for each sample than that in patients without PCI. By multiple regression analysis, we found preoperative values of plasma IRT >or=40 ng/mL, amylase >or=42 IU/mL, and pancreatic isoamylase >or=20 IU/L associated with a higher incidence of postsurgery PCI (P < 0.005). In the PCI patients, a significant correlation was found between the 4 pancreatic enzymes and urinary IRT, total calcium, myeloperoxidase, alpha1-protease inhibitor, and alpha2-macroglobulin. These data support a high prevalence of postoperative PCI after cardiac surgery with cardiopulmonary bypass, typically biphasic and clinically silent, especially when pancreatic enzymes were elevated preoperatively.

  19. Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

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    Ciira wa Maina

    2014-05-01

    Full Text Available Gene transcription mediated by RNA polymerase II (pol-II is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2. The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ERα and FOXA1 binding in their proximal promoter regions.

  20. Time course of the hemoglobin mass response to natural altitude training in elite endurance cyclists.

    Science.gov (United States)

    Garvican, L; Martin, D; Quod, M; Stephens, B; Sassi, A; Gore, C

    2012-02-01

    To determine the time course of hemoglobin mass (Hb(mass)) to natural altitude training, Hb(mass), erythropoietin [EPO], reticulocytes, ferritin and soluble transferrin receptor (sTfR) were measured in 13 elite cyclists during, and 10 days after, 3 weeks of sea level (n=5) or altitude (n=8, 2760 m) training. Mean Hb(mass), with a typical error of ∼2%, increased during the first 11 days at altitude (mean ± standard deviation 2.9 ± 2.0%) and was 3.5 ± 2.5% higher than baseline after 19 days. [EPO] increased 64.2 ± 18.8% after 2 nights at altitude but was not different from baseline after 12 nights. Hb(mass) and [EPO] did not increase in sea level. Reticulocytes (%) were slightly elevated in altitude at Days 5 and 12 (18.9 ± 17.7% and 20.4 ± 25.3%), sTfR was elevated at Day 12 (18.9 ± 15.0%), but both returned to baseline by Day 20. Hb(mass) and [EPO] decreased on descent to sea level while ferritin increased. The mean increase in Hb(mass) observed after 11 days (∼300 h) of altitude training was beyond the measurement error and consitent with the mean increase after 300 h of simulated live high:train low altitude. Our results suggest that in elite cyclists, Hb(mass) increases progressively with 3 weeks of natural altitude exposure, with greater increases expected as exposure persists. © 2010 John Wiley & Sons A/S.

  1. Time course effects of lithium administration on spatial memory acquisition and cholinergic marker expression in rats

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    M H Karimfar

    2009-08-01

    Full Text Available Background: The effects of chronic lithium exposure on spatial memory in rats remain controversial. In this study a time course of the effects of lithium, administered systemically, on spatial memory acquisition in Morris water maze was investigated. Material and Methods: Lithium (600 mg/L was administered to four groups of rats in their drinking water; the first group of animals received lithium for one week, the second group for two weeks, the third group for three weeks, and the fourth group for four weeks.  As controls, four groups of animals received only normal drinking water for the same period of time.  Toward the end of their lithium or water treatment, all animals were trained for four days; each day included one block and each block contained four trials.  Test trials were conducted 48 hrs after completion of the lithium treatment. Escape latency, traveled distance and swimming speed were evaluated during testing trials. Brain tissues from animals were processed according to the standard protocols for immunohistochemical analysis.  Results: Lithium treatment decreased escape latency and traveled distance, but not swimming speed, compared with controls, suggesting significant spatial memory acquisition enhancement by lithium. Quantitative analysis showed that lithium, particularly after four weeks of exposure, significantly increased the number and density of immunostained ChAT-containing (choline acetyltransferase neurons in the medial septal area in comparison with control groups.  There was also a significant correlation between the number of immunostained ChAT neurons and behavioral measures. Conclusion: These results suggest that chronic oral administration of lithium causes spatial memory acquisition improvement in rats and an increase in ChAT immunostaining levels in medial septal nuclei.

  2. Molecular time-course and the metabolic basis of entry into dauer in Caenorhabditis elegans.

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    Pan-Young Jeong

    Full Text Available When Caenorhabditis elegans senses dauer pheromone (daumone, signaling inadequate growth conditions, it enters the dauer state, which is capable of long-term survival. However, the molecular pathway of dauer entry in C. elegans has remained elusive. To systematically monitor changes in gene expression in dauer paths, we used a DNA microarray containing 22,625 gene probes corresponding to 22,150 unique genes from C. elegans. We employed two different paths: direct exposure to daumone (Path 1 and normal growth media plus liquid culture (Path 2. Our data reveal that entry into dauer is accomplished through the multi-step process, which appears to be compartmentalized in time and according to metabolic flux. That is, a time-course of dauer entry in Path 1 shows that dauer larvae formation begins at post-embryonic stage S4 (48 h and is complete at S6 (72 h. Our results also suggest the presence of a unique adaptive metabolic control mechanism that requires both stage-specific expression of specific genes and tight regulation of different modes of fuel metabolite utilization to sustain the energy balance in the context of prolonged survival under adverse growth conditions. It is apparent that worms entering dauer stage may rely heavily on carbohydrate-based energy reserves, whereas dauer larvae utilize fat or glyoxylate cycle-based energy sources. We created a comprehensive web-based dauer metabolic database for C. elegans (www.DauerDB.org that makes it possible to search any gene and compare its relative expression at a specific stage, or evaluate overall patterns of gene expression in both paths. This database can be accessed by the research community and could be widely applicable to other related nematodes as a molecular atlas.

  3. EEG can track the time course of successful reference resolution in small visual worlds

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    Christian eBrodbeck

    2015-11-01

    Full Text Available Previous research has shown that language comprehenders resolve reference quickly and incrementally, but not much is known about the neural processes and representations that are involved. Studies of visual short-term memory suggest that access to the representation of an item from a previously seen display is associated with a negative evoked potential at posterior electrodes contralateral to the spatial location of that item in the display. In this paper we demonstrate that resolving the reference of a noun phrase in a recently seen visual display is associated with an event-related potential that is analogous to this effect. Our design was adapted from the visual world paradigm: in each trial, participants saw a display containing 3 simple objects, followed by a question about the objects, such as Was the pink fish next to a boat?, presented word by word. Questions differed in whether the color adjective allowed the reader to identify the referent of the noun phrase or not (i.e., whether one or more objects of the named color were present. Consistent with our hypothesis, we observed that reference resolution by the adjective was associated with a negative evoked potential at posterior electrodes contralateral to spatial location of the referent, starting approximately 333 ms after the onset of the adjective. The fact that the laterality of the effect depended upon the location of the referent within the display suggests that reference resolution in visual domains involves, at some level, a modality-specific representation. In addition, the effect gives us an estimate of the time course of processing from perception of the written word to the point at which its meaning is brought into correspondence with the referential domain.

  4. Time course of polyhexamethyleneguanidine phosphate-induced lung inflammation and fibrosis in mice.

    Science.gov (United States)

    Song, Jeongah; Kim, Woojin; Kim, Yong-Bum; Kim, Bumseok; Lee, Kyuhong

    2018-04-15

    Pulmonary fibrosis is a chronic progressive disease with unknown etiology and has poor prognosis. Polyhexamethyleneguanidine phosphate (PHMG-P) causes acute interstitial pneumonia and pulmonary fibrosis in humans when it exposed to the lung. In a previous study, when rats were exposed to PHMG-P through inhalation for 3 weeks, lung inflammation and fibrosis was observed even after 3 weeks of recovery. In this study, we aimed to determine the time course of PHMG-P-induced lung inflammation and fibrosis. We compared pathological action of PHMG-P with that of bleomycin (BLM) and investigated the mechanism underlying PHMG-P-induced lung inflammation and fibrosis. PHMG-P (0.9 mg/kg) or BLM (1.5 mg/kg) was intratracheally administered to mice. At weeks 1, 2, 4 and 10 after instillation, the levels of inflammatory and fibrotic markers and the expression of inflammasome proteins were measured. The inflammatory and fibrotic responses were upregulated until 10 and 4 weeks in the PHMG-P and BLM groups, respectively. Immune cell infiltration and considerable collagen deposition in the peribronchiolar and interstitial areas of the lungs, fibroblast proliferation, and hyperplasia of type II epithelial cells were observed. NALP3 inflammasome activation was detected in the PHMG-P group until 4 weeks, which is suspected to be the main reason for the persistent inflammatory response and exacerbation of fibrotic changes. Most importantly, the pathological changes in the PHMG-P group were similar to those observed in humidifier disinfectant-associated patients. A single exposure of PHMG-P led to persistent pulmonary inflammation and fibrosis for at least 10 weeks. Copyright © 2018. Published by Elsevier Inc.

  5. Identifying significant temporal variation in time course microarray data without replicates

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    Porter Weston

    2009-03-01

    Full Text Available Abstract Background An important component of time course microarray studies is the identification of genes that demonstrate significant time-dependent variation in their expression levels. Until recently, available methods for performing such significance tests required replicates of individual time points. This paper describes a replicate-free method that was developed as part of a study of the estrous cycle in the rat mammary gland in which no replicate data was collected. Results A temporal test statistic is proposed that is based on the degree to which data are smoothed when fit by a spline function. An algorithm is presented that uses this test statistic together with a false discovery rate method to identify genes whose expression profiles exhibit significant temporal variation. The algorithm is tested on simulated data, and is compared with another recently published replicate-free method. The simulated data consists both of genes with known temporal dependencies, and genes from a null distribution. The proposed algorithm identifies a larger percentage of the time-dependent genes for a given false discovery rate. Use of the algorithm in a study of the estrous cycle in the rat mammary gland resulted in the identification of genes exhibiting distinct circadian variation. These results were confirmed in follow-up laboratory experiments. Conclusion The proposed algorithm provides a new approach for identifying expression profiles with significant temporal variation without relying on replicates. When compared with a recently published algorithm on simulated data, the proposed algorithm appears to identify a larger percentage of time-dependent genes for a given false discovery rate. The development of the algorithm was instrumental in revealing the presence of circadian variation in the virgin rat mammary gland during the estrous cycle.

  6. Study on the P-wave feature time course as early predictors of paroxysmal atrial fibrillation

    International Nuclear Information System (INIS)

    Martínez, Arturo; Alcaraz, Raúl; Rieta, José J

    2012-01-01

    Atrial fibrillation (AF) is the most common cardiac arrhythmia in clinical practice, increasing the risk of stroke and all-cause mortality. Its mechanisms are poorly understood, thus leading to different theories and controversial interpretation of its behavior. In this respect, it is unknown why AF is self-terminating in certain individuals, which is called paroxysmal AF (PAF), and not in others. Within the context of biomedical signal analysis, predicting the onset of PAF with a reasonable advance has been a clinical challenge in recent years. By predicting arrhythmia onset, the loss of normal sinus rhythm could be addressed by means of preventive treatments, thus minimizing risks for the patients and improving their quality of life. Traditionally, the study of PAF onset has been undertaken through a variety of features characterizing P-wave spatial diversity from the standard 12-lead electrocardiogram (ECG) or from signal-averaged ECGs. However, the variability of features from the P-wave time course before PAF onset has not been exploited yet. This work introduces a new alternative to assess time diversity of the P-wave features from single-lead ECG recordings. Furthermore, the method is able to assess the risk of arrhythmia 1 h before its onset, which is a relevant advance in order to provide clinically useful PAF risk predictors. Results were in agreement with the electrophysiological changes taking place in the atria. Hence, P-wave features presented an increasing variability as PAF onset approximates, thus suggesting intermittently disturbed conduction in the atrial tissue. In addition, high PAF risk prediction accuracy, greater than 90%, has been reached in the two considered scenarios, i.e. discrimination between healthy individuals and PAF patients and between patients far from PAF and close to PAF onset. Nonetheless, more long-term studies have to be analyzed and validated in future works. (paper)

  7. Time course of pulmonary burden in mice exposed to residual oil fly ash

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    Giovanna Marcella Cavalcante Carvalho

    2014-09-01

    Full Text Available Residual oil fly ash (ROFA is a common pollutant in areas where oil is burned. This particulate matter with a broad distribution of particle diameters can be inhaled by human beings and putatively damage their respiratory system. Although some studies deal with cultured cells, animals, and even epidemiological issues, so far a comprehensive analysis of respiratory outcomes as a function of the time elapsed after exposure to a low dose of ROFA is wanted. Thus, we aimed to investigate the time course of mechanical, histological, and inflammatory lung changes, as well as neutrophils in the blood, in mice exposed to ROFA until 5 days after exposure. BALB/c mice (25±5 g were randomly divided into 7 groups and intranasally instilled with either 10 µL of sterile saline solution (0.9% NaCl, CTRL or ROFA (0.2 µg in 10 L of saline solution. Pulmonary mechanics, histology (normal and collapsed alveoli, mononuclear and polymorphonuclear cells, and ultrastructure, neutrophils (in blood and bronchoalveolar lavage fluid were determined at 6 h in CTRL and at 6, 24, 48, 72, 96 and 120 h after ROFA exposure. ROFA contained metal elements, especially iron, polycyclic aromatic hydrocarbons, and organochlorines. Lung resistive pressure augmented early (6 h in the course of lung injury and other mechanical, histological and inflammatory parameters increased at 24 h, returning to control values at 120 h. Blood neutrophilia was present only at 24 and 48 h after exposure. Swelling of endothelial cells with adherent neutrophils was detected after ROFA instillation. No neutrophils were present in the lavage fluid. In conclusion, the exposure to ROFA, even in low doses, induced early changes in pulmonary mechanics, lung histology and accumulation of neutrophils in blood of mice that lasted for four days and disappeared spontaneously.

  8. Time course of pulmonary burden in mice exposed to residual oil fly ash.

    Science.gov (United States)

    Carvalho, Giovanna Marcella Cavalcante; Nagato, Lilian Katiê da Silva; Fagundes, Sheila da Silva; Dos Santos, Flávia Brandão; Calheiros, Andrea Surrage; Malm, Olaf; Bozza, Patricia Torres; Saldiva, Paulo Hilário N; Faffe, Débora Souza; Rocco, Patricia Rieken Macedo; Zin, Walter Araujo

    2014-01-01

    Residual oil fly ash (ROFA) is a common pollutant in areas where oil is burned. This particulate matter (PM) with a broad distribution of particle diameters can be inhaled by human beings and putatively damage their respiratory system. Although some studies deal with cultured cells, animals, and even epidemiological issues, so far a comprehensive analysis of respiratory outcomes as a function of the time elapsed after exposure to a low dose of ROFA is wanted. Thus, we aimed to investigate the time course of mechanical, histological, and inflammatory lung changes, as well as neutrophils in the blood, in mice exposed to ROFA until 5 days after exposure. BALB/c mice (25 ± 5 g) were randomly divided into 7 groups and intranasally instilled with either 10 μL of sterile saline solution (0.9% NaCl, CTRL) or ROFA (0.2 μg in 10 μL of saline solution). Pulmonary mechanics, histology (normal and collapsed alveoli, mononuclear and polymorphonuclear cells, and ultrastructure), neutrophils (in blood and bronchoalveolar lavage fluid) were determined at 6 h in CTRL and at 6, 24, 48, 72, 96, and 120 h after ROFA exposure. ROFA contained metal elements, especially iron, polycyclic aromatic hydrocarbons (PAHs), and organochlorines. Lung resistive pressure augmented early (6 h) in the course of lung injury and other mechanical, histological and inflammatory parameters increased at 24 h, returning to control values at 120 h. Blood neutrophilia was present only at 24 and 48 h after exposure. Swelling of endothelial cells with adherent neutrophils was detected after ROFA instillation. No neutrophils were present in the lavage fluid. In conclusion, the exposure to ROFA, even in low doses, induced early changes in pulmonary mechanics, lung histology and accumulation of neutrophils in blood of mice that lasted for 4 days and disappeared spontaneously.

  9. Time Course of Heart Rate Variability Response to PM2.5 Exposure from Secondhand Smoke.

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    Jennifer L Garza

    Full Text Available Exposure to secondhand smoke (SHS has been associated with decreased heart rate variability (HRV. However, the time course of this association is unclear. Therefore, the objective of this study was to investigate the association between 15-240 minute SHS-related fine particulate matter (PM2.5 moving averages and indices of HRV.With a panel study design, we used personal monitors to continuously measure PM2.5 and HRV of 35 participants who were exposed to SHS for approximately 6 hours.We observed negative, significant associations between 5-minute HRV indices and 15 minute PM2.5 moving averages and 240 minute PM2.5 moving averages: there was a significant (p<0.01 7.5% decrease in the 5-minute square root of the mean squared differences of successive normal heart beats associated with (RMSSD, and a significant (p<0.01 14.7% decrease in the 5-minute high frequency (HF power associated with the 15 minute PM2.5 moving averages; there was also a significant (p<0.01 46.9% decrease in the 5-minute RMSSD, and a significant (p<0.01 77.7% decrease in the 5-minute high frequency (HF power associated with the 240 minute PM2.5 moving averages.Our findings that exposure to SHS related PM2.5 was associated with HRV support the hypothesis that SHS can affect the cardiovascular system. The negative associations reported between short and longer term PM2.5 and HRV indicate adverse effects of SHS on the cardiovascular system.

  10. Time-course of exercise and its association with 12-month bone changes

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    Vainionpää Aki

    2009-11-01

    Full Text Available Abstract Background Exercise has been shown to have positive effects on bone density and strength. However, knowledge of the time-course of exercise and bone changes is scarce due to lack of methods to quantify and qualify daily physical activity in long-term. The aim was to evaluate the association between exercise intensity at 3, 6 and 12 month intervals and 12-month changes in upper femur areal bone mineral density (aBMD and mid-femur geometry in healthy premenopausal women. Methods Physical activity was continuously assessed with a waist-worn accelerometer in 35 healthy women (35-40 years participating in progressive high-impact training. To describe exercise intensity, individual average daily numbers of impacts were calculated at five acceleration levels (range 0.3-9.2 g during time intervals of 0-3, 0-6, and 0-12 months. Proximal femur aBMD was measured with dual x-ray absorptiometry and mid-femur geometry was evaluated with quantitative computed tomography at the baseline and after 12 months. Physical activity data were correlated with yearly changes in bone density and geometry, and adjusted for confounding factors and impacts at later months of the trial using multivariate analysis. Results Femoral neck aBMD changes were significantly correlated with 6 and 12 months' impact activity at high intensity levels (> 3.9 g, r being up to 0.42. Trochanteric aBMD changes were associated even with first three months of exercise exceeding 1.1 g (r = 0.39-0.59, p r = 0.38-0.52, p Conclusion The number of high acceleration impacts during 6 months of training was positively associated with 12-month bone changes at the femoral neck, trochanter and mid-femur. These results can be utilized when designing feasible training programs to prevent bone loss in premenopausal women. Trial registration Clinical trials.gov NCT00697957

  11. Weekly Time Course of Neuro-Muscular Adaptation to Intensive Strength Training.

    Science.gov (United States)

    Brown, Niklas; Bubeck, Dieter; Haeufle, Daniel F B; Weickenmeier, Johannes; Kuhl, Ellen; Alt, Wilfried; Schmitt, Syn

    2017-01-01

    Detailed description of the time course of muscular adaptation is rarely found in literature. Thus, models of muscular adaptation are difficult to validate since no detailed data of adaptation are available. In this article, as an initial step toward a detailed description and analysis of muscular adaptation, we provide a case report of 8 weeks of intense strength training with two active, male participants. Muscular adaptations were analyzed on a morphological level with MRI scans of the right quadriceps muscle and the calculation of muscle volume, on a voluntary strength level by isometric voluntary contractions with doublet stimulation (interpolated twitch technique) and on a non-voluntary level by resting twitch torques. Further, training volume and isokinetic power were closely monitored during the training phase. Data were analyzed weekly for 1 week prior to training, pre-training, 8 weeks of training and 2 weeks of detraining (no strength training). Results show a very individual adaptation to the intense strength training protocol. While training volume and isokinetic power increased linearly during the training phase, resting twitch parameters decreased for both participants after the first week of training and stayed below baseline until de-training. Voluntary activation level showed an increase in the first 4 weeks of training, while maximum voluntary contraction showed only little increase compared to baseline. Muscle volume increased for both subjects. Especially training status seemed to influence the acute reaction to intense strength training. Fatigue had a major influence on performance and could only be overcome by one participant. The results give a first detailed insight into muscular adaptation to intense strength training on various levels, providing a basis of data for a validation of muscle fatigue and adaptation models.

  12. Time-course comparison of xenobiotic activators of CAR and PPARα in mouse liver

    International Nuclear Information System (INIS)

    Ross, Pamela K.; Woods, Courtney G.; Bradford, Blair U.; Kosyk, Oksana; Gatti, Daniel M.; Cunningham, Michael L.; Rusyn, Ivan

    2009-01-01

    Constitutive androstane receptor (CAR) and peroxisome proliferator activated receptor (PPAR)α are transcription factors known to be primary mediators of liver effects, including carcinogenesis, by phenobarbital-like compounds and peroxisome proliferators, respectively, in rodents. Many similarities exist in the phenotypes elicited by these two classes of agents in rodent liver, and we hypothesized that the initial transcriptional responses to the xenobiotic activators of CAR and PPARα will exhibit distinct patterns, but at later time-points these biological pathways will converge. In order to capture the global transcriptional changes that result from activation of these nuclear receptors over a time-course in the mouse liver, microarray technology was used. First, differences in basal expression of liver genes between C57Bl/6J wild-type and Car-null mice were examined and 14 significantly differentially expressed genes were identified. Next, mice were treated with phenobarbital (100 mg/kg by gavage for 24 h, or 0.085% w/w diet for 7 or 28 days), and liver gene expression changes with regards to both time and treatment were identified. While several pathways related to cellular proliferation and metabolism were affected by phenobarbital in wild-type mice, no significant changes in gene expression were found over time in the Car-nulls. Next, we determined commonalities and differences in the temporal response to phenobarbital and WY-14,643, a prototypical activator of PPAR α. Gene expression signatures from livers of wild-type mice C57Bl6/J mice treated with PB or WY-14,643 were compared. Similar pathways were affected by both compounds; however, considerable time-related differences were present. This study establishes common gene expression fingerprints of exposure to activators of CAR and PPARα in rodent liver and demonstrates that despite similar phenotypic changes, molecular pathways differ between classes of chemical carcinogens

  13. ISPC effect is not observed when the word comes too late: A time course analysis

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    Nart Bedin Atalay

    2014-12-01

    Full Text Available The item-specific proportion congruency (ISPC effect is demonstrated by a smaller Stroop effect observed for mostly incongruent items compared to mostly congruent items. Currently, there is a continuing debate on whether conflict driven item-specific control processes or stimulus-response contingency learning account for the ISPC effect. In the present study, we conducted two experiments to investigate the time course of the ISPC effect with a stimulus onset asynchrony (SOA manipulation. Both negative and positive SOAs were used in order to manipulate the contingency learning between the word and the color dimensions. We also combined this SOA manipulation with a set size manipulation (Bugg & Hutchison, 2013 to moderate the contribution of contingency learning and item-specific processes to the observed ISPC effect. We expected that the change in the magnitude of the ISPC effect as a result of SOA would follow different patterns for the 2-item and 4-item set conditions. Results showed that the SOA manipulation influenced the ISPC effect. Specifically, when the word followed the color with a 200 ms delay, the observed ISPC effect was smaller, if at all present, than the ISPC effects in other negative and positive SOA conditions, regardless of set size. In conclusion, our results showed that the ISPC effect was not observed if the word arrived too late. We also conducted additional awareness and RT distribution analyses (delta plots to further investigate the ISPC effect. These analyses showed that a higher percentage of participants were aware of the ISPC manipulation in the 2-item set condition compared to the 4-item set condition. Delta plots revealed that the ISPC effect was smaller for fastest responses and increased as the responses got slower.

  14. Time course of ongoing activity during neuritis and following axonal transport disruption.

    Science.gov (United States)

    Satkeviciute, Ieva; Goodwin, George; Bove, Geoffrey M; Dilley, Andrew

    2018-05-01

    Local nerve inflammation (neuritis) leads to ongoing activity and axonal mechanical sensitivity (AMS) along intact nociceptor axons and disrupts axonal transport. This phenomenon forms the most feasible cause of radiating pain, such as sciatica. We have previously shown that axonal transport disruption without inflammation or degeneration also leads to AMS but does not cause ongoing activity at the time point when AMS occurs, despite causing cutaneous hypersensitivity. However, there have been no systematic studies of ongoing activity during neuritis or noninflammatory axonal transport disruption. In this study, we present the time course of ongoing activity from primary sensory neurons following neuritis and vinblastine-induced axonal transport disruption. Whereas 24% of C/slow Aδ-fiber neurons had ongoing activity during neuritis, few (disruption of axonal transport without inflammation does not lead to ongoing activity in sensory neurons, including nociceptors, but does cause a rapid and transient development of AMS. Because it is proposed that AMS underlies mechanically induced radiating pain, and a transient disruption of axonal transport (as previously reported) leads to transient AMS, it follows that processes that disrupt axonal transport, such as neuritis, must persist to maintain AMS and the associated symptoms. NEW & NOTEWORTHY Many patients with radiating pain lack signs of nerve injury on clinical examination but may have neuritis, which disrupts axonal transport. We have shown that axonal transport disruption does not induce ongoing activity in primary sensory neurons but does cause transient axonal mechanical sensitivity. The present data complete a profile of key axonal sensitivities following axonal transport disruption. Collectively, this profile supports that an active peripheral process is necessary for maintained axonal sensitivities.

  15. Time Course Changes in Selected Biochemical Stress Indices in Broilers Exposed to Short-term Noise

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    Iveta Bedáňová

    2010-01-01

    Full Text Available Time course changes in selected biochemical stress indices (corticosterone, triglycerides, glucose, cholesterol following short-term noise exposure at 100 dB for 28 min were studied in broilers aged 42 days. Corticosterone concentrations were found to increase during the first 10 min of noise exposure and to differ significantly from the control (background sound – 50 dB at Time 10 min and 14 min, then decreased continually and at 28 min returned to the initial prestress value. Triglyceride concentrations increased in broilers exposed to 100 dB noise during the first 12 min with a significant difference from the control at 12 min and 14 min. Glucose concentrations were higher due to 100 dB noise exposure for almost the entire period monitored, with significant differences between 100 dB and control broilers at 6 min and from 10 min to 14 min. Similarly as for the corticosterone concentration, a drop in triglycerides and glucose concentrations was seen approximately from Time 14 min and a return to the pre-stress value at 28 min. The cholesterol concentrations showed various temporal patterns with no significant difference between 100 dB and control broilers in this experiment. The pattern of response found in the study indicates that 100 dB noise represents a stress factor in broilers, however, there is the ability of broilers to adapt to an increased level of noise at this intensity after the first 14 min of exposure. The findings obtained in the study may contribute to expanding detailed knowledge of physiological stress responses to this specific noise stimulus in poultry, and could thereby be used to improve the welfare of broilers in intensive housing systems.

  16. Postoperative enhancement on breast MRI: Time course and pattern of changes.

    Science.gov (United States)

    Mahoney, Mary C; Sharda, Radhika G

    2018-04-23

    Expected postoperative enhancement on breast MRI can appear similar to enhancement seen in recurrent or residual malignancy. Our aim was to assess the time course and patterns of enhancement at the surgical site, thereby helping to distinguish between benign and malignant postoperative enhancement. In 200 MRI scans performed in 153 patients after breast conservation treatment, 43 after surgical excision of atypia, and 4 patients after benign excisional biopsy were categorized by postoperative time interval. We defined 4 patterns of morphologic enhancement on MRI: cavity wall/seroma (Pattern I); thin linear (Pattern II); mass (Pattern III); and fat necrosis (Pattern IV). Of 200 MRI scans, 66 (33%) demonstrated enhancement at the surgical site. Enhancement typically decreased through the postoperative follow-up period. Enhancement was observed in 41% (28/68) of cases beyond the 18-month interval but was uncommon after 5 years. Pattern III enhancement was the morphologic pattern seen most commonly with malignancy (5/19 cases, 26%). When associated with delayed washout kinetics, it was even more strongly predictive of malignancy (4/5 cases, 80%). In patients with a history of excisional biopsy and no prior radiation treatment, the percentage of MRI scans showing enhancement was significantly lower than (21% vs 49% with P-value .0027) in patients who had undergone radiation. Enhancement at the surgical site occurred in one-third of cases up to 5 years after surgery, particularly in patients who underwent both radiation and surgery. Mass enhancement, particularly in conjunction with delayed washout kinetics, is most predictive of malignancy and should prompt biopsy or re-excision. © 2018 Wiley Periodicals, Inc.

  17. Time course of dichoptic masking in normals and suppression in amblyopes.

    Science.gov (United States)

    Zhou, Jiawei; McNeal, Suzanne; Babu, Raiju J; Baker, Daniel H; Bobier, William R; Hess, Robert F

    2014-04-17

    To better understand the relationship between dichoptic masking in normal vision and suppression in amblyopia we address three questions: First, what is the time course of dichoptic masking in normals and amblyopes? Second, is interocular suppression low-pass or band-pass in its spatial dependence? And third, in the above two regards, is dichoptic masking in normals different from amblyopic suppression? We measured the dependence of dichoptic masking in normal controls and amblyopes on the temporal duration of presentation under three conditions; monocular (the nontested eye-i.e., dominant eye of normals or nonamblyopic eye of amblyopes, being patched), dichoptic-luminance (the nontested eye seeing a mean luminance-i.e., a DC component) and dichoptic-contrast (the nontested eye seeing high-contrast visual noise). The subject had to detect a letter in the other eye, the contrast of which was varied. We found that threshold elevation relative to the patched condition occurred in both normals and amblyopes when the nontested eye saw either 1/f or band-pass filtered noise, but not just mean luminance (i.e., there was no masking from the DC component that corresponds to a channel responsive to a spatial frequency of 0 cyc/deg); longer presentation of the target (corresponding to lower temporal frequencies) produced greater threshold elevation. Dichoptic masking exhibits similar properties in both subject groups, being low-pass temporally and band-pass spatially, so that masking was greatest at the longest presentation durations and was not greatly affected by mean luminance in the nontested eye. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

  18. Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis.

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    Pui Shan Wong

    Full Text Available Fistulifera sp. strain JPCC DA0580 is a newly sequenced pennate diatom that is capable of simultaneously growing and accumulating lipids. This is a unique trait, not found in other related microalgae so far. It is able to accumulate between 40 to 60% of its cell weight in lipids, making it a strong candidate for the production of biofuel. To investigate this characteristic, we used RNA-Seq data gathered at four different times while Fistulifera sp. strain JPCC DA0580 was grown in oil accumulating and non-oil accumulating conditions. We then adapted gene set enrichment analysis (GSEA to investigate the relationship between the difference in gene expression of 7,822 genes and metabolic functions in our data. We utilized information in the KEGG pathway database to create the gene sets and changed GSEA to use re-sampling so that data from the different time points could be included in the analysis. Our GSEA method identified photosynthesis, lipid synthesis and amino acid synthesis related pathways as processes that play a significant role in oil production and growth in Fistulifera sp. strain JPCC DA0580. In addition to GSEA, we visualized the results by creating a network of compounds and reactions, and plotted the expression data on top of the network. This made existing graph algorithms available to us which we then used to calculate a path that metabolizes glucose into triacylglycerol (TAG in the smallest number of steps. By visualizing the data this way, we observed a separate up-regulation of genes at different times instead of a concerted response. We also identified two metabolic paths that used less reactions than the one shown in KEGG and showed that the reactions were up-regulated during the experiment. The combination of analysis and visualization methods successfully analyzed time-course data, identified important metabolic pathways and provided new hypotheses for further research.

  19. The Time Course of the Probability of Transition Into and Out of REM Sleep

    Science.gov (United States)

    Bassi, Alejandro; Vivaldi, Ennio A.; Ocampo-Garcés, Adrián

    2009-01-01

    Study Objectives: A model of rapid eye movement (REM) sleep expression is proposed that assumes underlying regulatory mechanisms operating as inhomogenous Poisson processes, the overt results of which are the transitions into and out of REM sleep. Design: Based on spontaneously occurring REM sleep episodes (“Episode”) and intervals without REM sleep (“Interval”), 3 variables are defined and evaluated over discrete 15-second epochs using a nonlinear logistic regression method: “Propensity” is the instantaneous rate of into-REM transition occurrence throughout an Interval, “Volatility” is the instantaneous rate of out-of-REM transition occurrence throughout an Episode, and “Opportunity” is the probability of being in non-REM (NREM) sleep at a given time throughout an Interval, a requisite for transition. Setting: 12:12 light:dark cycle, isolated boxes. Participants: Sixteen male Sprague-Dawley rats Interventions: None. Spontaneous sleep cycles. Measurements and Results: The highest levels of volatility and propensity occur, respectively, at the very beginning of Episodes and Intervals. The new condition stabilizes rapidly, and variables reach nadirs at minute 1.25 and 2.50, respectively. Afterward, volatility increases markedly, reaching values close to the initial level. Propensity increases moderately, the increment being stronger through NREM sleep bouts occurring at the end of long Intervals. Short-term homeostasis is evidenced by longer REM sleep episodes lowering propensity in the following Interval. Conclusions: The stabilization after transitions into Episodes or Intervals and the destabilization after remaining for some time in either condition may be described as resulting from continuous processes building up during Episodes and Intervals. These processes underlie the overt occurrence of transitions. Citation: Bassi A; Vivaldi EA; Ocampo-Garcées A. The time course of the probability of transition into and out of REM sleep. SLEEP 2009

  20. Time course of NMR images and T1 values associated with hypertensive intracerebral hematoma

    International Nuclear Information System (INIS)

    Inao, Suguru; Furuse, Masahiro; Saso, Katsuyoshi; Yoshida, Kazuo; Motegi, Yoshimasa; Kaneoke, Yoshiki; Kamata, Noriko; Izawa, Akira

    1986-01-01

    The present study describes time courses in tissue T 1 values, as well as in NMR imagings, associated with hypertensive intracerebral hematoma (ICH). Non-operative 21 cases of ICH were examined by FONAR QED 80-α NMR system, which possessed dual modes of image display and focal T 1 measurement (static magnetic field : 433 gauss). As the first step of examination SSFP images are displayed and then, at the regions of interest, absolute values of T 1 are measured by field focusing technique. The extent of ICH was revealed as high density zone in NMR imaging, occasionally represented much wider extent of high density area than the finding on X-ray CT. Prolonged T 1 values were obtained from such high density zone. This widespread high density area was regarded to reflect the spread of perifocal brain edema. T 1 value of the hematoma itself was rather shortened in its initial phase within 2 weeks, thereafter followed by prolongation in the time lapse. This seemed to reflect the alterations in the properties of hematoma such as clot formation in earlier phase and resolution in later phase. On the contrary, T 1 in the brain tissue surrounded to hematoma was apparently prolonged in the early phase within 2 weeks, representing the maximal values of 312 msec arround 2 to 4 weeks after the onset, and then gradually normalized in the period over 1 month. This alteration in tissue T 1 likely represents the processes of edema formation and its regression in perifocal zone. T 1 values measured in perifocal region might be available for the evaluation of edema state in association with cerebrovascular accident. (author)

  1. Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response.

    Science.gov (United States)

    Bendjilali, Nasrine; MacLeon, Samuel; Kalra, Gurmannat; Willis, Stephen D; Hossian, A K M Nawshad; Avery, Erica; Wojtowicz, Olivia; Hickman, Mark J

    2017-01-05

    Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq) analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR) consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen. Copyright © 2017 Bendjilali et al.

  2. Time course of protein synthesis-dependent phase of olfactory memory in the cricket Gryllus bimaculatus.

    Science.gov (United States)

    Matsumoto, Yukihisa; Noji, Sumihare; Mizunami, Makoto

    2003-04-01

    The cricket Gryllus bimaculatus forms a stable olfactory memory that lasts for practically a lifetime. As a first step to elucidate the cellular mechanisms of olfactory learning and memory retention in crickets, we studied the dependency of memory retention on the de novo brain protein synthesis by injecting the protein synthesis inhibitor cycloheximide (CHX) into the head capsule. Injection of CHX inhibited (3)H-leucine incorporation into brain proteins by > 90% for 3 hr. Crickets were trained to associate peppermint odor with water (reward) and vanilla odor with saline solution (non-reward) and were injected with CHX before or at different times after training. Their odor preferences were tested at 2 hr, 1 day and 4 days after training. Memory retention at 2 hr after training was unaffected by CHX injection. However, the level of retention at 1 day and 4 days after training was lowered when CHX was injected 1 hour before training or at 1 hr or 6 hr after training. To study the time course of the development of CHX-sensitive memory phase, crickets that had been injected with CHX at 1 hr after training were tested at different times from 2 to 12 hr after training. The level of retention was unaffected up to 4 hr after training but significantly lowered at 5 hr after training, and the CHX-sensitive memory phase developed gradually during the next several hours. CHX dissociates two phases of olfactory memory in crickets: earlier protein synthesis-independent phase ( 5 hr) protein synthesis-dependent phase.

  3. Time course of reversed cardiac remodeling after pulmonary endarterectomy in patients with chronic pulmonary thromboembolism

    Energy Technology Data Exchange (ETDEWEB)

    Iino, Misako; Dymarkowski, Steven; Chaothawee, Lertlak; Bogaert, Jan [UZ Leuven, Department of Radiology, Leuven (Belgium); Delcroix, Marion [UZ Leuven, Department of Pneumology, Leuven (Belgium)

    2008-04-15

    To evaluate the time course of reversed remodeling after pulmonary endarterectomy (PEA) in patients with chronic thromboembolic pulmonary hypertension(CTPEH), we studied 22 patients (age: 60 {+-} 13 years) with MRI immediately before, 1 month, 3 months, and 6 months after PEA. MRI included assessment of biventricular function, aortic and pulmonary artery(PA) flow, and right ventricular (RV) overload using the ratio of RV-to-biventricular diameter. Except in one patient, who died 2 months post-surgery, clinical improvement occurred early after PEA (NYHA class: 3.3 {+-} 0.6 to 1.5 {+-} 0.8, p < 0.0001) with a decrease of systolic pulmonary artery pressures (79 {+-} 14 to 44 {+-} 14 mmHg, p < 0.0001). At 1 month post PEA, RV end-diastolic volumes decreased (198 {+-} 72 to 137 {+-} 59 ml, p < 0.0001), and the RV ejection fraction (EF) improved (31 {+-} 9 to 47 {+-} 10%, p < 0.0001). No further significant improvement in pulmonary pressures or RV function occurred at 3 months or 6 months. Although no significant change was found in LV volumes or function, aortic flow increased early after surgery. PEA had only a beneficial effect on right PA flow. RV overload decreased early after PEA (ratio RV-to-biventricular diameter: before: 0.67 {+-} 0.04, after: 0.54 {+-} 0.06, p < 0.0001), showing a good correlation with the improvement in RVEF (r = 0.7, P < 0.0001). In conclusion, reversed cardiac remodeling occurs early after PEA, to slow down after 1 month. At 6 months, cardiac remodeling is incomplete as witnessed by low-normal RV function and residually elevated PA pressures. (orig.)

  4. Time course of ozone-induced changes in breathing pattern in healthy exercising humans.

    Science.gov (United States)

    Schelegle, Edward S; Walby, William F; Adams, William C

    2007-02-01

    We examined the time course of O3-induced changes in breathing pattern in 97 healthy human subjects (70 men and 27 women). One- to five-minute averages of breathing frequency (f(B)) and minute ventilation (Ve) were used to generate plots of cumulative breaths and cumulative exposure volume vs. time and cumulative exposure volume vs. cumulative breaths. Analysis revealed a three-phase response; delay, no response detected; onset, f(B) began to increase; response, f(B) stabilized. Regression analysis was used to identify four parameters: time to onset, number of breaths at onset, cumulative inhaled dose of ozone at onset of O3-induced tachypnea, and the percent change in f(B). The effect of altering O3 concentration, Ve, atropine treatment, and indomethacin treatment were examined. We found that the lower the O3 concentration, the greater the number of breaths at onset of tachypnea at a fixed ventilation, whereas number of breaths at onset of tachypnea remains unchanged when Ve is altered and O3 concentration is fixed. The cumulative inhaled dose of O3 at onset of tachypnea remained constant and showed no relationship with the magnitude of percent change in f(B). Atropine did not affect any of the derived parameters, whereas indomethacin did not affect time to onset, number of breaths at onset, or cumulative inhaled dose of O3 at onset of tachypnea but did attenuate percent change in f(B). The results are discussed in the context of dose response and intrinsic mechanisms of action.

  5. The gene expression and immunohistochemical time-course of diphenylcyclopropenone induced contact allergy in healthy humans following repeated epicutaneous challenges

    DEFF Research Database (Denmark)

    Mose, K F; Burton, M; Thomassen, M

    2017-01-01

    challenges with DPCP to find the predominant gene expression pattern, ii) the time-course of cell infiltration following repeated DPCP challenges, and iii) the transcriptome of a repeated CA exposure model. We obtained punch biopsies from control and DPCP exposed skin from ten DPCP sensitized individuals...

  6. Eye-movement evidence of the time-course of attentional bias for threatening pictures in test-anxious students

    NARCIS (Netherlands)

    Dong, Y.; Beuckelaer, A. de; Yu, L.; Zhou, R

    2017-01-01

    Protocols for measuring attentional bias to threat in test-anxiety, a special form of trait-anxiety, are rarely found in the literature. In our eye-tracking study, we introduced a new protocol, and studied the time-course of attention to test-related pictures with varying threat levels in 22 high

  7. Effects of Phonological and Orthographic Shifts on Children's Processing of Written Morphology: A Time-Course Study

    Science.gov (United States)

    Quémart, Pauline; Casalis, Séverine

    2014-01-01

    We report two experiments that investigated whether phonological and/or orthographic shifts in a base word interfere with morphological processing by French 3rd, 4th, and 5th graders and adults (as a control group) along the time course of visual word recognition. In both experiments, prime-target pairs shared four possible relationships:…

  8. Young Chinese Children's Anger and Distress: Emotion Category and Intensity Identified by the Time Course of Behaviors

    Science.gov (United States)

    He, Jie; Qiu, Peihua; Park, Ka Young; Xu, Qinmei; Potegal, Michael

    2013-01-01

    A hierarchical cluster analysis of the time course of the videotaped reactions of 75 Chinese 2-4-year olds to mothers' toy-removal identified Distress, Low Anger, and High Anger behavior clusters. Anger often begins at low intensity; some children then escalate. The face-validity of Low and High Anger-cluster classifications was supported in that…

  9. Time-courses of lung function and respiratory muscle pressure generating capacity after spinal cord injury : a prospective cohort study

    NARCIS (Netherlands)

    Mueller, Gabi; de Groot, Sonja; van der Woude, Lucas; Hopman, Maria T E

    OBJECTIVE: To investigate the time-courses of lung function and respiratory muscle pressure generating capacity after spinal cord injury. DESIGN: Multi-centre, prospective cohort study. SUBJECTS: One hundred and nine subjects with recent, motor complete spinal cord injury. METHODS: Lung function and

  10. Time Course of the Rabbit's Conditioned Nictitating Membrane Movements during Acquisition, Extinction, and Reacquisition

    Science.gov (United States)

    Kehoe, E. James; Ludvig, Elliot A.; Sutton, Richard S.

    2014-01-01

    The present experiment tested whether or not the time course of a conditioned eyeblink response, particularly its duration, would expand and contract, as the magnitude of the conditioned response (CR) changed massively during acquisition, extinction, and reacquisition. The CR duration remained largely constant throughout the experiment, while CR…

  11. MoS{sub 2}/Ag nanohybrid: A novel matrix with synergistic effect for small molecule drugs analysis by negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Yaju, E-mail: daisy19900911@hotmail.com [State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023 (China); Deng, Guoqing, E-mail: denggqq@sina.com [Department of Polymer Science and Engineering, Nanjing University, Nanjing, 210023 (China); Liu, Xiaohui, E-mail: lcswyh@126.com [State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023 (China); Sun, Liang, E-mail: sunliang@nju.edu.cn [State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023 (China); Li, Hui, E-mail: lihui@nju.edu.cn [State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023 (China); Cheng, Quan, E-mail: quan.cheng@ucr.edu [Department of Chemistry, University of California, Riverside, CA, 92521 (United States); Xi, Kai, E-mail: xikai@nju.edu.cn [Department of Polymer Science and Engineering, Nanjing University, Nanjing, 210023 (China); Xu, Danke, E-mail: xudanke@nju.edu.cn [State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023 (China)

    2016-09-21

    This paper reports a facile synthesis of molybdenum disulfide nanosheets/silver nanoparticles (MoS{sub 2}/Ag) hybrid and its use as an effective matrix in negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The nanohybrid exerts a strong synergistic effect, leading to high performance detection of small molecule analytes including amino acids, peptides, fatty acids and drugs. The enhancement of laser desorption/ionization (LDI) efficiency is largely attributed to the high surface roughness and large surface area for analyte adsorption, better dispersibility, increased thermal conductivity and enhanced UV energy absorption as compared to pure MoS{sub 2}. Moreover, both Ag nanoparticles and the edge of the MoS{sub 2} layers function as deprotonation sites for proton capture, facilitating the charging process in negative ion mode and promoting formation of negative ions. As a result, the MoS{sub 2}/Ag nanohybrid proves to be a highly attractive matrix in MALDI-TOF MS, with desired features such as high desorption/ionization efficiency, low fragmentation interference, high salt tolerance, and no sweet-spots for mass signal. These characteristic properties allowed for simultaneous analysis of eight different drugs and quantification of acetylsalicylic acid in the spiked human serum. This work demonstrates for the first time the fabrication and application of a novel MoS{sub 2}/Ag hybrid, and provides a new platform for use in the rapid and high throughput analysis of small molecules by mass spectrometry. - Highlights: • MoS{sub 2}/Ag nanohybrid was applied as a novel matrix in negative-ion MALDI-TOF MS. • The MoS{sub 2}/Ag nanohybrid exerted synergistic effect on the detection of small molecules. • The MoS{sub 2}/Ag nanohybrid showed good signal reproducibility and low background interferences comparing to organic matrices. • MoS{sub 2}/Ag allows simultaneous analysis of multiple drugs and quantification of

  12. Novel risk stratification with time course assessment of in-hospital mortality in patients with acute heart failure.

    Directory of Open Access Journals (Sweden)

    Takeshi Yagyu

    Full Text Available Patients with acute heart failure (AHF show various clinical courses during hospitalization. We aimed to identify time course predictors of in-hospital mortality and to establish a sequentially assessable risk model.We enrolled 1,035 consecutive AHF patients into derivation (n = 597 and validation (n = 438 cohorts. For risk assessments at admission, we utilized Get With the Guidelines-Heart Failure (GWTG-HF risk scores. We examined significant predictors of in-hospital mortality from 11 variables obtained during hospitalization and developed a risk stratification model using multiple logistic regression analysis. Across both cohorts, 86 patients (8.3% died during hospitalization. Using backward stepwise selection, we identified five time-course predictors: catecholamine administration, minimum platelet concentration, maximum blood urea nitrogen, total bilirubin, and C-reactive protein levels; and established a time course risk score that could sequentially assess a patient's risk status. The addition of a time course risk score improved the discriminative ability of the GWTG-HF risk score (c-statistics in derivation and validation cohorts: 0.776 to 0.888 [p = 0.002] and 0.806 to 0.902 [p<0.001], respectively. A calibration plot revealed a good relationship between observed and predicted in-hospital mortalities in both cohorts (Hosmer-Lemeshow chi-square statistics: 6.049 [p = 0.642] and 5.993 [p = 0.648], respectively. In each group of initial low-intermediate risk (GWTG-HF risk score <47 and initial high risk (GWTG-HF risk score ≥47, in-hospital mortality was about 6- to 9-fold higher in the high time course risk score group than in the low-intermediate time course risk score group (initial low-intermediate risk group: 20.3% versus 2.2% [p<0.001], initial high risk group: 57.6% versus 8.5% [p<0.001].A time course assessment related to in-hospital mortality during the hospitalization of AHF patients can clearly categorize a patient's on

  13. The time course of retrograde trans-synaptic degeneration following occipital lobe damage in humans.

    Science.gov (United States)

    Jindahra, Panitha; Petrie, Aviva; Plant, Gordon T

    2012-02-01

    Following damage to the human post-geniculate visual pathway retrograde trans-synaptic degeneration of the optic nerve fibres occurs. It has been known for some time from investigations carried out in primates that a decline in the number of retinal ganglion cells follows occipital lobectomy. However, this is not detectable in all species studied and whether this occurs in humans was controversial until recent studies that have shown that following lesions of the occipital lobe, the retinal nerve fibre layer thickness measured by optical coherence tomography is reduced and corresponding shrinkage of the optic tract can be demonstrated by magnetic resonance imaging. The time course of the degeneration in humans is, however, unknown. In the present study, we have used optical coherence tomography to demonstrate for the first time progressive thinning of the retinal nerve fibre layer following occipital lobe/optic radiation damage due to stroke. First, in a group of 38 patients the measurement was taken on a single occasion at a known time interval since the stroke, ranging from 6 days to 67 years. Here, a negative straight line relationship (linear regression r = 0.54, P < 0.001) was found between nerve fibre layer thickness and elapsed time since injury in log years, giving a rate of decline of 9.08 µm per log year after adjusting for age. This indicates a decelerating rate of loss that differs from the rate of decline found with chronological age in this same group, which shows a steady rate of thinning by 0.4 µm per year (P = 0.006) after adjusting for duration of the disease. In a second study serial measurements were taken following the acute event in a group of seven patients with homonymous hemianopia; here a negative straight line relationship was found between time and nerve fibre layer thickness in micrometres over a period of data collection beginning at a mean of 36.9 days post-stroke (range 5-112) and ending at a mean of 426.6 days post

  14. Time course of recovery following resistance training leading or not to failure.

    Science.gov (United States)

    Morán-Navarro, Ricardo; Pérez, Carlos E; Mora-Rodríguez, Ricardo; de la Cruz-Sánchez, Ernesto; González-Badillo, Juan José; Sánchez-Medina, Luis; Pallarés, Jesús G

    2017-12-01

    To describe the acute and delayed time course of recovery following resistance training (RT) protocols differing in the number of repetitions (R) performed in each set (S) out of the maximum possible number (P). Ten resistance-trained men undertook three RT protocols [S × R(P)]: (1) 3 × 5(10), (2) 6 × 5(10), and (3) 3 × 10(10) in the bench press (BP) and full squat (SQ) exercises. Selected mechanical and biochemical variables were assessed at seven time points (from - 12 h to + 72 h post-exercise). Countermovement jump height (CMJ) and movement velocity against the load that elicited a 1 m s -1 mean propulsive velocity (V1) and 75% 1RM in the BP and SQ were used as mechanical indicators of neuromuscular performance. Training to muscle failure in each set [3 × 10(10)], even when compared to completing the same total exercise volume [6 × 5(10)], resulted in a significantly higher acute decline of CMJ and velocity against the V1 and 75% 1RM loads in both BP and SQ. In contrast, recovery from the 3 × 5(10) and 6 × 5(10) protocols was significantly faster between 24 and 48 h post-exercise compared to 3 × 10(10). Markers of acute (ammonia, growth hormone) and delayed (creatine kinase) fatigue showed a markedly different course of recovery between protocols, suggesting that training to failure slows down recovery up to 24-48 h post-exercise. RT leading to failure considerably increases the time needed for the recovery of neuromuscular function and metabolic and hormonal homeostasis. Avoiding failure would allow athletes to be in a better neuromuscular condition to undertake a new training session or competition in a shorter period of time.

  15. Molecular glues for manipulating enzymes: trypsin inhibition by benzamidine-conjugated molecular glues† †Electronic supplementary information (ESI) available: Synthesis of TEG–BA, Gluen–BA, mGluen–BA and Gluen–Ph; 1H NMR, 13C NMR, MALDI-TOF MS, electronic absorption, and CD spectra; zeta potential distributions; SLS plots; DLS histograms; and related experimental procedures. See DOI: 10.1039/c5sc00524h Click here for additional data file.

    Science.gov (United States)

    Mogaki, Rina

    2015-01-01

    Water-soluble bioadhesive polymers bearing multiple guanidinium ion (Gu+) pendants at their side-chain termini (Gluen–BA, n = 10 and 29) that were conjugated with benzamidine (BA) as a trypsin inhibitor were developed. The Gluen–BA molecules are supposed to adhere to oxyanionic regions of the trypsin surface, even in buffer, via a multivalent Gu+/oxyanion salt-bridge interaction, such that their BA group properly blocks the substrate-binding site. In fact, Glue10–BA and Glue29–BA exhibited 35- and 200-fold higher affinities for trypsin, respectively, than a BA derivative without the glue moiety (TEG–BA). Most importantly, Glue10–BA inhibited the protease activity of trypsin 13-fold more than TEG–BA. In sharp contrast, mGlue27–BA, which bears 27 Gu+ units along the main chain and has a 5-fold higher affinity than TEG–BA for trypsin, was inferior even to TEG–BA for trypsin inhibition. PMID:28706668

  16. Degradation and Stabilization of Peptide Hormones in Human Blood Specimens.

    Directory of Open Access Journals (Sweden)

    Jizu Yi

    Full Text Available Plasma hormone peptides, including GLP-1, GIP, Glucagon, and OXM, possess multiple physiological roles and potential therapeutic and diagnostic utility as biomarkers in the research of metabolic disorders. These peptides are subject to proteolytic degradation causing preanalytical variations. Stabilization for accurate quantitation of these active peptides in ex vivo blood specimens is essential for drug and biomarker development. We investigated the protease-driven instability of these peptides in conventional serum, plasma, anticoagulated whole blood, as well as whole blood and plasma stabilized with protease inhibitors. The peptide was monitored by both time-course Matrix-Assisted Laser Desorption Ionization Time-to-Flight Mass Spectrometry (MALDI -TOF MS and Ab-based assay (ELISA or RIA. MS enabled the identification of proteolytic fragments. In non-stabilized blood samples, the results clearly indicated that dipeptidyl peptidase-IV (DPP-IV removed the N-terminal two amino acid residues from GLP-1, GIP and OXM(1-37 and not-yet identified peptidase(s cleave(s the full-length OXM(1-37 and its fragments. DPP-IV also continued to remove two additional N-terminal residues of processed OXM(3-37 to yield OXM(5-37. Importantly, both DPP-IV and other peptidase(s activities were inhibited efficiently by the protease inhibitors included in the BD P800* tube. There was preservation of GLP-1, GIP, OXM and glucagon in the P800 plasma samples with half-lives > 96, 96, 72, and 45 hours at room temperature (RT, respectively. In the BD P700* plasma samples, the stabilization of GLP-1 was also achieved with half-life > 96 hours at RT. The stabilization of these variable peptides increased their utility in drug and/or biomarker development. While stability results of GLP-1 obtained with Ab-based assay were consistent with those obtained by MS analysis, the Ab-based results of GIP, Glucagon, and OXM did not reflect the time-dependent degradations revealed by MS

  17. The neural time course of art perception: an ERP study on the processing of style versus content in art.

    Science.gov (United States)

    Augustin, M Dorothee; Defranceschi, Birgit; Fuchs, Helene K; Carbon, Claus-Christian; Hutzler, Florian

    2011-06-01

    A central prerequisite to understand the phenomenon of art in psychological terms is to investigate the nature of the underlying perceptual and cognitive processes. Building on a study by Augustin, Leder, Hutzler, and Carbon (2008) the current ERP study examined the neural time course of two central aspects of representational art, one of which is closely related to object- and scene perception, the other of which is art-specific: content and style. We adapted a paradigm that has repeatedly been employed in psycholinguistics and that allows one to examine the neural time course of two processes in terms of when sufficient information is available to allow successful classification. Twenty-two participants viewed pictures that systematically varied in style and content and conducted a combined go/nogo dual choice task. The dependent variables of interest were the Lateralised Readiness Potential (LRP) and the N200 effect. Analyses of both measures support the notion that in the processing of art style follows content, with style-related information being available at around 224 ms or between 40 and 94 ms later than content-related information. The paradigm used here offers a promising approach to further explore the time course of art perception, thus helping to unravel the perceptual and cognitive processes that underlie the phenomenon of art and the fascination it exerts. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Time Course and Association of Functional and Biochemical Markers in Severe Semitendinosus Damage Following Intensive Eccentric Leg Curls: Differences between and within Subjects

    Directory of Open Access Journals (Sweden)

    Gerard Carmona

    2018-02-01

    Full Text Available Purpose: To investigate the extent and evolution of hamstring muscle damage caused by an intensive bout of eccentric leg curls (ELCs by (1 assessing the time course and association of different indirect markers of muscle damage such as changes in the force-generating capacity (FGC, functional magnetic resonance (fMRI, and serum muscle enzyme levels and (2 analyzing differences in the degree of hamstring muscle damage between and within subjects (limb-to-limb comparison.Methods: Thirteen male participants performed six sets of 10 repetitions of an ELC with each leg. Before and at regular intervals over 7 days after the exercise, FGC was measured with maximal isometric voluntary contraction (MVC. Serum enzyme levels, fMRI transverse relaxation time (T2 and perceived muscle soreness were also assessed and compared against the FGC.Results: Two groups of subjects were identified according to the extent of hamstring muscle damage based on decreased FGC and increased serum enzyme levels: high responders (n = 10, severe muscle damage and moderate responders (n = 3, moderate muscle damage. In the high responders, fMRI T2 analysis revealed that the semitendinosus (ST muscle suffered severe damage in the three regions measured (proximal, middle, and distal. The biceps femoris short head (BFsh muscle was also damaged and there were significant differences in the FGC within subjects in the high responders.Conclusion: FGC and serum enzyme levels measured in 10 of the subjects from the sample were consistent with severe muscle damage. However, the results showed a wide range of peak MVC reductions, reflecting different degrees of damage between subjects (high and moderate responders. fMRI analysis confirmed that the ST was the hamstring muscle most damaged by ELCs, with uniform T2 changes across all the measured sections of this muscle. During intensive ELCs, the ST muscle could suffer an anomalous recruitment pattern due to fatigue and damage, placing an

  19. Time course of collagen peak in bile duct-ligated rats.

    Science.gov (United States)

    Tarcin, Orhan; Basaranoglu, Metin; Tahan, Veysel; Tahan, Gülgün; Sücüllü, Ilker; Yilmaz, Nevin; Sood, Gagan; Snyder, Ned; Hilman, Gilbert; Celikel, Cigdem; Tözün, Nurdan

    2011-04-28

    One of the most useful experimental fibrogenesis models is the "bile duct-ligated rats". Our aim was to investigate the quantitative hepatic collagen content by two different methods during the different stages of hepatic fibrosis in bile duct-ligated rats on a weekly basis. We questioned whether the 1-wk or 4-wk bile duct-ligated model is suitable in animal fibrogenesis trials. Of the 53 male Wistar rats, 8 (Group 0) were used as a healthy control group. Bile duct ligation (BDL) had been performed in the rest. Bile duct-ligated rates were sacrificed 7 days later in group 1 (10 rats), 14 days later in group 2 (9 rats), 21 days later in group 3(9 rats) and 28 days later in group 4 (9 rats). Eight rats underwent sham-operation (Sham). Hepatic collagen measurements as well as serum levels of liver enzymes and function tests were all analysed. The peak level of collagen was observed biochemically and histomorphometricly at the end of third week (P fibrosis in bile duct-ligated rats is transient, i.e. reverses spontaneously after 3 weeks. This contrasts any situation in patients where hepatic fibrosis is progressive and irreversible as countless studies performed by many investigators in the same animal model.

  20. Time course of collagen peak in bile duct-ligated rats

    Directory of Open Access Journals (Sweden)

    Snyder Ned

    2011-04-01

    Full Text Available Abstract Background One of the most useful experimental fibrogenesis models is the "bile duct-ligated rats". Our aim was to investigate the quantitative hepatic collagen content by two different methods during the different stages of hepatic fibrosis in bile duct-ligated rats on a weekly basis. We questioned whether the 1-wk or 4-wk bile duct-ligated model is suitable in animal fibrogenesis trials. Methods Of the 53 male Wistar rats, 8 (Group 0 were used as a healthy control group. Bile duct ligation (BDL had been performed in the rest. Bile duct-ligated rates were sacrificed 7 days later in group 1 (10 rats, 14 days later in group 2 (9 rats, 21 days later in group 3(9 rats and 28 days later in group 4 (9 rats. Eight rats underwent sham-operation (Sham. Hepatic collagen measurements as well as serum levels of liver enzymes and function tests were all analysed. Results The peak level of collagen was observed biochemically and histomorphometricly at the end of third week (P Conclusion We have shown that fibrosis in bile duct-ligated rats is transient, i.e. reverses spontaneously after 3 weeks. This contrasts any situation in patients where hepatic fibrosis is progressive and irreversible as countless studies performed by many investigators in the same animal model.

  1. [Search for potential gastric cancer biomarkers using low molecular weight blood plasma proteome profiling by mass spectrometry].

    Science.gov (United States)

    Shevchenko, V E; Arnotskaia, N E; Ogorodnikova, E V; Davydov, M M; Ibraev, M A; Turkin, I N; Davydov, M I

    2014-01-01

    Gastric cancer, one of the most widespread malignant tumors, still lacks reliable serum/plasma biomarkers of its early detection. In this study we have developed, unified, and tested a new methodology for search of gastric cancer biomarkers based on profiling of low molecular weight proteome (LMWP) (1-17 kDa). This approach included three main components: sample pre-fractionation, matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS), data analysis by a bioinformatics software package. Applicability and perspectives of the developed approach for detection of potential gastric cancer markers during LMWP analysis have been demonstrated using 69 plasma samples from patients with gastric cancer (stages I-IV) and 238 control samples. The study revealed peptides/polypeptides, which may be potentially used for detection of this pathology.

  2. Trueperella pyogenes and Brucella abortus Coinfection in a Dog and a Cat on a Dairy Farm in Egypt with Recurrent Cases of Mastitis and Abortion

    Directory of Open Access Journals (Sweden)

    Gamal Wareth

    2018-01-01

    Full Text Available Trueperella pyogenes was isolated from a dog and a cat with a mixed infection with Brucella abortus. Both lived on a dairy cattle farm with a history of regular cases of abortion and mastitis. Identification of the bacteria was done by means of MALDI-TOF MS, loop-mediated isothermal amplification (LAMP based on cpn60, partial 16S rRNA sequencing, and growth on Loeffler Serum Medium. Isolation of Trueperella pyogenes on the dairy farm highlights its neglected role in reproduction failure and draws attention to its effects in the dairy industry in Egypt. Diagnosis and control of abortion in Egypt should include Trueperella pyogenes as one of possible causes of abortion.

  3. TLC-Blot (Far-Eastern Blot) and Its Application to Functional Lipidomics.

    Science.gov (United States)

    Taki, Takao

    2015-01-01

    A simple method for transfer of lipids-including phospholipids, glycolipids, and neutral lipids-from a high performance thin layer chromatography (HPTLC) plate to a polyvinylidene difluoride (PVDF) membrane, TLC-Blot (Far-Eastern Blot), and its biochemical applications are presented. This chapter presents the conventional procedures for separating lipid from tissue samples, cultured cells, and serum and the subsequent development of TLC. Individual lipids separated on an HPTLC plate can be transferred to the PVDF membrane quantitatively and also isolated from the lipid-blotted membrane by a one-step purification procedure. Immunodetection with monoclonal antibodies and treatment with lipid-metabolizing enzymes on the lipid-blotted membrane are possible. The method for identification of individual lipids transferred on the PVDF membrane using matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (TLC-Blot/MALDI-TOF MS) is shown as a functional lipidomics application.

  4. Simultaneous pre-concentration and separation on simple paper-based analytical device for protein analysis.

    Science.gov (United States)

    Niu, Ji-Cheng; Zhou, Ting; Niu, Li-Li; Xie, Zhen-Sheng; Fang, Fang; Yang, Fu-Quan; Wu, Zhi-Yong

    2018-02-01

    In this work, fast isoelectric focusing (IEF) was successfully implemented on an open paper fluidic channel for simultaneous concentration and separation of proteins from complex matrix. With this simple device, IEF can be finished in 10 min with a resolution of 0.03 pH units and concentration factor of 10, as estimated by color model proteins by smartphone-based colorimetric detection. Fast detection of albumin from human serum and glycated hemoglobin (HBA1c) from blood cell was demonstrated. In addition, off-line identification of the model proteins from the IEF fractions with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was also shown. This PAD IEF is potentially useful either for point of care test (POCT) or biomarker analysis as a cost-effective sample pretreatment method.

  5. Bacterial flora analysis of coliforms in sewage, river water, and ground water using MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Suzuki, Yoshihiro; Niina, Kouki; Matsuwaki, Tomonori; Nukazawa, Kei; Iguchi, Atsushi

    2018-01-28

    The aim of this study was to rapidly and effectively analyze coliforms, which are the most fundamental indicators of water quality for fecal pollution, using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Coliform bacteria were isolated from municipal sewage, river water, and groundwater. For each sample, 100 isolates were determined by MALDI-TOF MS. In addition, these same 100 isolates were also identified via 16S rRNA gene sequence analysis. Obtained MALDI-TOF MS data were compared with the 16S rRNA sequencing analysis, and the validity of MALDI-TOF MS for classification of coliform bacteria was examined. The concordance rate of bacterial identification for the 100 isolates obtained by MALDI-TOF MS analysis and 16S rRNA gene sequence analysis for sewage, river water, and ground water were 96%, 74%, and 62% at the genus level, respectively. Among the sewage, river water, and ground water samples, the coliform bacterial flora were distinct. The dominant genus of coliforms in sewage, river water, and groundwater were Klebsiella spp., Enterobacter spp., and Serratia spp., respectively. We determined that MALDI-TOF MS is a rapid and accurate tool that can be used to identify coliforms. Therefore, without using conventional 16S rRNA sequencing, it is possible to rapidly and effectively classify coliforms in water using MALDI-TOF MS.

  6. THE INFLUENCE OF HYPOTHERMIA (SURFACE COOLING) ON THE TIME-COURSE OF ACTION AND ON THE PHARMACOKINETICS OF ROCURONIUM IN HUMANS

    NARCIS (Netherlands)

    BEAUFORT, AM; WIERDA, JMKH; BELOPAVLOVIC, M; NEDERVEEN, PJ; KLEEF, UW; AGOSTON, S

    Hypothermia prolongs the time-course of action of non-depolarizing neuromuscular blocking agents. The mechanism, however, is unknown. We studied the influence of hypothermia (by surface cooling, nasopharyngeal temperature less than or equal to 31 degrees C) on the time-course of action and on the

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

    Science.gov (United States)

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

    2010-03-01

    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.

  8. Differential uptake of salicylate in serum, cerebrospinal fluid, and perilymph.

    Science.gov (United States)

    Jastreboff, P J; Hansen, R; Sasaki, P G; Sasaki, C T

    1986-10-01

    After intraperitoneal administration of salicylate in anesthetized rats and guinea pigs, we found that salicylate levels in perilymph (PL) are closely related to both drug levels in cerebrospinal fluid (CSF) and in serum, with higher levels systematically observed in PL than in CSF. Further analysis suggests that salicylate is not passively transported into PL across CSF but, rather, is transported from blood directly to PL. The time course of salicylate uptake in rats reveals maximum levels at 1 1/2 hours (serum) and two to four hours (CSF and PL). On the other hand, salicylate uptake into serum and CSF of guinea pigs exhibits a longer time course, with maximum levels reached at four hours (serum) and five hours (CSF). These data, not previously available, are basic to our understanding of salicylate-related auditory effects.

  9. Time course of recovery of erectile function after radical retropubic prostatectomy: does anyone recover after 2 years?

    Science.gov (United States)

    Rabbani, Farhang; Schiff, Jeffrey; Piecuch, Michael; Yunis, Luis Herran; Eastham, James A; Scardino, Peter T; Mulhall, John P

    2010-12-01

    Given the paucity of literature on the time course of recovery of erectile function (EF) after radical prostatectomy (RP), many publications have led patients and clinicians to believe that erections are unlikely to recover beyond 2 years after RP. We sought to determine the time course of recovery of EF beyond 2 years after bilateral nerve sparing (BNS) RP and to determine factors predictive of continued improved recovery beyond 2 years. EF was assessed prospectively on a 5-point scale: (i) full erections; (ii) diminished erections routinely sufficient for intercourse; (iii) partial erections occasionally satisfactory for intercourse; (iv) partial erections unsatisfactory for intercourse; and (v) no erections. From 01/1999 to 01/2007, 136 preoperatively potent (levels 1-2) men who underwent BNS RP without prior treatment and who had not recovered consistently functional erections (levels 1-2) at 24 months had further follow-up regarding EF. Median follow-up after the 2-year visit was 36.0 months. Recovery of improved erections at a later date: recovery of EF level 1-2 in those with level 3 EF at 2 years and recovery of EF level 1-3 in those with level 4-5 EF at 2 years. The actuarial rates of further improved recovery of EF to level 1-2 in those with level 3 EF at 2 years and to level 1-3 in those with level 4-5 EF at 2 years were 8%, 20%, and 23% at 3, 4, and 5 years postoperatively, and 5%, 17%, and 21% at 3, 4, and 5 years postoperatively, respectively. Younger age was predictive of greater likelihood of recovery beyond 2 years. There is continued improvement in EF beyond 2 years after BNS RP. Discussion of this prolonged time course of recovery may allow patients to have a more realistic expectation. © 2010 International Society for Sexual Medicine.

  10. Riding the lexical speedway: a critical review on the time course of lexical selection in speech production.

    Science.gov (United States)

    Strijkers, Kristof; Costa, Albert

    2011-01-01

    Speech requires time. How much time often depends on the amount of labor the brain has to perform in order to retrieve the linguistic information related to the ideas we want to express. Although most psycholinguistic research in the field of language production has focused on the net result of time required to utter words in various experimental conditions, over the last years more and more researchers pursued the objective to flesh out the time course of particular stages implicated in language production. Here we critically review these studies, with particular interest for the time course of lexical selection. First, we evaluate the data underlying the estimates of an influential temporal meta-analysis on language production (Indefrey and Levelt, 2004). We conclude that those data alone are not sufficient to provide a reliable time frame of lexical selection. Next, we discuss recent neurophysiological evidence which we argue to offer more explicit insights into the time course of lexical selection. Based on this evidence we suggest that, despite the absence of a clear time frame of how long lexical selection takes, there is sufficient direct evidence to conclude that the brain initiates lexical access within 200 ms after stimulus presentation, hereby confirming Indefrey and Levelt's estimate. In a final section, we briefly review the proposed mechanisms which could lead to this rapid onset of lexical access, namely automatic spreading activation versus specific concept selection, and discuss novel data which support the notion of spreading activation, but indicate that the speed with which this principle takes effect is driven by a top-down signal in function of the intention to engage in a speech act.

  11. Riding the Lexical Speedway: A Critical Review on the Time Course of Lexical Selection in Speech Production

    Science.gov (United States)

    Strijkers, Kristof; Costa, Albert

    2011-01-01

    Speech requires time. How much time often depends on the amount of labor the brain has to perform in order to retrieve the linguistic information related to the ideas we want to express. Although most psycholinguistic research in the field of language production has focused on the net result of time required to utter words in various experimental conditions, over the last years more and more researchers pursued the objective to flesh out the time course of particular stages implicated in language production. Here we critically review these studies, with particular interest for the time course of lexical selection. First, we evaluate the data underlying the estimates of an influential temporal meta-analysis on language production (Indefrey and Levelt, 2004). We conclude that those data alone are not sufficient to provide a reliable time frame of lexical selection. Next, we discuss recent neurophysiological evidence which we argue to offer more explicit insights into the time course of lexical selection. Based on this evidence we suggest that, despite the absence of a clear time frame of how long lexical selection takes, there is sufficient direct evidence to conclude that the brain initiates lexical access within 200 ms after stimulus presentation, hereby confirming Indefrey and Levelt’s estimate. In a final section, we briefly review the proposed mechanisms which could lead to this rapid onset of lexical access, namely automatic spreading activation versus specific concept selection, and discuss novel data which support the notion of spreading activation, but indicate that the speed with which this principle takes effect is driven by a top-down signal in function of the intention to engage in a speech act. PMID:22144973

  12. Training haptic stiffness discrimination: time course of learning with or without visual information and knowledge of results.

    Science.gov (United States)

    Teodorescu, Kinneret; Bouchigny, Sylvain; Korman, Maria

    2013-08-01

    In this study, we explored the time course of haptic stiffness discrimination learning and how it was affected by two experimental factors, the addition of visual information and/or knowledge of results (KR) during training. Stiffness perception may integrate both haptic and visual modalities. However, in many tasks, the visual field is typically occluded, forcing stiffness perception to be dependent exclusively on haptic information. No studies to date addressed the time course of haptic stiffness perceptual learning. Using a virtual environment (VE) haptic interface and a two-alternative forced-choice discrimination task, the haptic stiffness discrimination ability of 48 participants was tested across 2 days. Each day included two haptic test blocks separated by a training block Additional visual information and/or KR were manipulated between participants during training blocks. Practice repetitions alone induced significant improvement in haptic stiffness discrimination. Between days, accuracy was slightly improved, but decision time performance was deteriorated. The addition of visual information and/or KR had only temporary effects on decision time, without affecting the time course of haptic discrimination learning. Learning in haptic stiffness discrimination appears to evolve through at least two distinctive phases: A single training session resulted in both immediate and latent learning. This learning was not affected by the training manipulations inspected. Training skills in VE in spaced sessions can be beneficial for tasks in which haptic perception is critical, such as surgery procedures, when the visual field is occluded. However, training protocols for such tasks should account for low impact of multisensory information and KR.

  13. Current status of matrix-assisted laser desorption ionisation-time of flight mass spectrometry in the clinical microbiology laboratory.

    Science.gov (United States)

    Kok, Jen; Chen, Sharon C A; Dwyer, Dominic E; Iredell, Jonathan R

    2013-01-01

    The integration of matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) into many clinical microbiology laboratories has revolutionised routine pathogen identification. MALDI-TOF MS complements and has good potential to replace existing phenotypic identification methods. Results are available in a more clinically relevant timeframe, particularly in bacteraemic septic shock. Novel applications include strain typing and the detection of antimicrobial resistance, but these are not widely used. This review discusses the technical aspects, current applications, and limitations of MALDI-TOF MS.

  14. Differential Levels of Alpha-2-Macroglobulin, Haptoglobin and Sero-Transferrin as Adjunct Markers for TB Diagnosis and Disease Progression in the Malnourished Tribal Population of Melghat, India.

    Science.gov (United States)

    Bapat, Prachi R; Satav, Ashish R; Husain, Aliabbas A; Shekhawat, Seema D; Kawle, Anuja P; Chu, Justin J; Purohit, Hemant J; Daginawala, Hatim F; Taori, Girdhar M; Kashyap, Rajpal S

    2015-01-01

    Lack of diagnostic capacity has been a crucial barrier preventing an effective response to the challenges of malnutrition and tuberculosis (TB). Point-of-care diagnostic tests for TB in immuno-incompetent, malnourished population are thus needed to ensure rapid and accurate detection. The aim of the study was to identify potential biomarkers specific for TB infection and progression to overt disease in the malnourished population of Melghat. A prospective cohort study was conducted in the year 2009 through 2011 in six villages of the Melghat region. 275 participants consisting of malnourished cases with a) active TB (n = 32), b) latent TB infection (n = 90), c) with no clinical or bacteriological signs of active or latent TB (n = 130) and healthy control subjects (n = 23) were recruited for the study. The proteome changes of the host serum in response to Mycobacterium tuberculosis (M.tb) infection were investigated using one dimensional electrophoresis in combination with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Three most differentially expressed proteins; alpha-2-macroglobulin (A-2-M), sero-transferrin and haptoglobin were identified by MALDI-TOF MS analysis, which were up-regulated in the malnourished patients with active TB and down-regulated in the malnourished patients compared with the healthy controls. Additionally, follow-up studies indicated that the expression of these proteins increased to nearly two folds in patients who developed active disease from latent state. Our preliminary results suggest that A-2-M, sero-transferrin and haptoglobin may be clinically relevant host biomarkers for TB diagnosis and disease progression in the malnourished population. This study provides preliminary framework for an in-depth analysis of the biomarkers in larger well-characterized cohorts. Evaluation of these biomarkers in follow-up cases may further aid in improving TB diagnosis.

  15. Tobacco Control Measures to Reduce Socioeconomic Inequality in Smoking: The Necessity, Time-Course Perspective, and Future Implications.

    Science.gov (United States)

    Tabuchi, Takahiro; Iso, Hiroyasu; Brunner, Eric

    2018-04-05

    Previous systematic reviews of population-level tobacco control interventions and their effects on smoking inequality by socioeconomic factors concluded that tobacco taxation reduce smoking inequality by income (although this is not consistent for other socioeconomic factors, such as education). Inconsistent results have been reported for socioeconomic differences, especially for other tobacco control measures, such as smoke-free policies and anti-tobacco media campaigns. To understand smoking inequality itself and to develop strategies to reduce smoking inequality, knowledge of the underlying principles or mechanisms of the inequality over a long time-course may be important. For example, the inverse equity hypothesis recognizes that inequality may evolve in stages. New population-based interventions are initially primarily accessed by the affluent and well-educated, so there is an initial increase in socioeconomic inequality (early stage). These inequalities narrow when the deprived population can access the intervention after the affluent have gained maximum benefit (late stage). Following this hypothesis, all tobacco control measures may have the potential to reduce smoking inequality, if they continue for a long term, covering and reaching all socioeconomic subgroups. Re-evaluation of the impact of the interventions on smoking inequality using a long time-course perspective may lead to a favorable next step in equity effectiveness. Tackling socioeconomic inequality in smoking may be a key public health target for the reduction of inequality in health.

  16. Time course of affective bias in visual attention: convergent evidence from steady-state visual evoked potentials and behavioral data.

    Science.gov (United States)

    Hindi Attar, Catherine; Andersen, Søren K; Müller, Matthias M

    2010-12-01

    Selective attention to a primary task can be biased by the occurrence of emotional distractors that involuntary attract attention due to their intrinsic stimulus significance. What is largely unknown is the time course and magnitude of competitive interactions between a to-be-attended foreground task and emotional distractors. We used pleasant, unpleasant and neutral pictures from the International Affective Picture System (IAPS) that were either presented in intact or phase-scrambled form. Pictures were superimposed by a flickering display of moving random dots, which constituted the primary task and enabled us to record steady-state visual evoked potentials (SSVEPs) as a continuous measure of attentional resource allocation directed to the task. Subjects were required to attend to the dots and to detect short intervals of coherent motion while ignoring the background pictures. We found that pleasant and unpleasant relative to neutral pictures more strongly influenced task-related processing as reflected in a significant decrease in SSVEP amplitudes and target detection rates, both covering a time window of several hundred milliseconds. Strikingly, the effect of semantic relative to phase-scrambled pictures on task-related activity was much larger, emerged earlier and lasted longer in time compared to the specific effect of emotion. The observed differences in size and duration of time courses of semantic and emotional picture processing strengthen the assumption of separate functional mechanisms for both processes rather than a general boosting of neural activity in favor of emotional stimulus processing. Copyright © 2010 Elsevier Inc. All rights reserved.

  17. Time Course of the Soleus M Response and H Reflex after Lidocaine Tibial Nerve Block in the Rat

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    Kévin Buffenoir

    2013-01-01

    Full Text Available Aims. In spastic subjects, lidocaine is often used to induce a block predictive of the result provided by subsequent surgery. Lidocaine has been demonstrated to inhibit the Hoffmann (H reflex to a greater extent than the direct motor (M response induced by electrical stimulation, but the timecourse of these responses has not been investigated. Methods. An animal (rat model of the effects of lidocaine on M and H responses was therefore developed to assess this time course. M and H responses were recorded in 18 adult rats before and after application of lidocaine to the sciatic nerve. Results. Two to five minutes after lidocaine injection, M responses were markedly reduced (mean reduction of 44% and H reflexes were completely abolished. Changes were observed more rapidly for the H reflex. The effects of lidocaine then persisted for 100 minutes. The effect of lidocaine was therefore more prolonged on the H reflex than on the M response. Conclusion. This study confirms that lidocaine blocks not only alpha motoneurons but also Ia afferent fibres responsible for the H reflex. The authors describe, for the first time, the detailed time course of the effect of lidocaine on direct or reflex activation of motoneurons in the rat.

  18. Spectral Analysis on Time-Course Expression Data: Detecting Periodic Genes Using a Real-Valued Iterative Adaptive Approach

    Directory of Open Access Journals (Sweden)

    Kwadwo S. Agyepong

    2013-01-01

    Full Text Available Time-course expression profiles and methods for spectrum analysis have been applied for detecting transcriptional periodicities, which are valuable patterns to unravel genes associated with cell cycle and circadian rhythm regulation. However, most of the proposed methods suffer from restrictions and large false positives to a certain extent. Additionally, in some experiments, arbitrarily irregular sampling times as well as the presence of high noise and small sample sizes make accurate detection a challenging task. A novel scheme for detecting periodicities in time-course expression data is proposed, in which a real-valued iterative adaptive approach (RIAA, originally proposed for signal processing, is applied for periodogram estimation. The inferred spectrum is then analyzed using Fisher’s hypothesis test. With a proper -value threshold, periodic genes can be detected. A periodic signal, two nonperiodic signals, and four sampling strategies were considered in the simulations, including both bursts and drops. In addition, two yeast real datasets were applied for validation. The simulations and real data analysis reveal that RIAA can perform competitively with the existing algorithms. The advantage of RIAA is manifested when the expression data are highly irregularly sampled, and when the number of cycles covered by the sampling time points is very reduced.

  19. Contextual Change After Fear Acquisition Affects Conditioned Responding and the Time Course of Extinction Learning-Implications for Renewal Research.

    Science.gov (United States)

    Sjouwerman, Rachel; Niehaus, Johanna; Lonsdorf, Tina B

    2015-01-01

    Context plays a central role in retrieving (fear) memories. Accordingly, context manipulations are inherent to most return of fear (ROF) paradigms (in particular renewal), involving contextual changes after fear extinction. Context changes are, however, also often embedded during earlier stages of ROF experiments such as context changes between fear acquisition and extinction (e.g., in ABC and ABA renewal). Previous studies using these paradigms have however focused exclusively on the context switch after extinction (i.e., renewal). Thus, the possibility of a general effect of context switch on conditioned responding that may not be conditional to preceding extinction learning remains unstudied. Hence, the current study investigated the impact of a context switch between fear acquisition and extinction on immediate conditioned responding and on the time-course of extinction learning by using a multimodal approach. A group that underwent contextual change after fear conditioning (AB; n = 36) was compared with a group without a contextual change from acquisition to extinction (AA; n = 149), while measuring physiological (skin conductance and fear potentiated startle) measures and subjective fear ratings. Contextual change between fear acquisition and extinction had a pronounced effect on both immediate conditioned responding and on the time course of extinction learning in skin conductance responses and subjective fear ratings. This may have important implications for the mechanisms underlying and the interpretation of the renewal effect (i.e., contextual switch after extinction). Consequently, future studies should incorporate designs and statistical tests that disentangle general effects of contextual change from genuine ROF effects.

  20. 10-Month-Old Infants Are Sensitive to the Time Course of Perceived Actions: Eye-Tracking and EEG Evidence

    Directory of Open Access Journals (Sweden)

    Cathleen Bache

    2017-07-01

    Full Text Available Research has shown that infants are able to track a moving target efficiently – even if it is transiently occluded from sight. This basic ability allows prediction of when and where events happen in everyday life. Yet, it is unclear whether, and how, infants internally represent the time course of ongoing movements to derive predictions. In this study, 10-month-old crawlers observed the video of a same-aged crawling baby that was transiently occluded and reappeared in either a temporally continuous or non-continuous manner (i.e., delayed by 500 ms vs. forwarded by 500 ms relative to the real-time movement. Eye movement and rhythmic neural brain activity (EEG were measured simultaneously. Eye movement analyses showed that infants were sensitive to slight temporal shifts in movement continuation after occlusion. Furthermore, brain activity associated with sensorimotor processing differed between observation of continuous and non-continuous movements. Early sensitivity to an action’s timing may hence be explained within the internal real-time simulation account of action observation. Overall, the results support the hypothesis that 10-month-old infants are well prepared for internal representation of the time course of observed movements that are within the infants’ current motor repertoire.

  1. THE TIME COURSE OF ABNORMALITIES IN THE BRAIN SUBCORTICAL VISUAL CENTRE FOLLOWING EARLY IMPAIRMENT OF BINOCULAR EXPERIENCE

    Directory of Open Access Journals (Sweden)

    S. V. Alekseenko

    2016-01-01

    Full Text Available Background: Amblyopia related to congenital strabismus belongs to neurological disorders since it is caused by structural and functional remodeling of the visual parts of the brain without any baseline retinal pathology. Although a large number of animal studies on experimentally induced strabismus, as well as clinical cases have been published, the mechanisms and time course of the processes within the brain structures are not fully understood. Aim: To study the time course of abnormalities in the dorsal lateral geniculate nucleus (LGNd in animals with surgically induced convergent strabismus. LGNd is the structure through which the information from the retina goes to the visual cortex separately for each eye. Materials and methods: 14 strabismic and 17 intact kittens of four age groups were studied. Histochemical method was used to identify cytochrome oxidase which is a  mitochondrial respiratory chain enzyme whose activity correlates with neuronal functional activity. Optical density in eye-specific layers  A  and A1 was measured on the images of stained LGNd sections, with calculation of the contrast difference between them. Results: In strabismic kittens, there were changes in activity of A and A1 layers in the projection of the central part of visual field in LGNd of both hemispheres. At early stages of their formation, a relative decrease in activity was found in both hemispheres in the LGNd layers innervated through non-crossed pathways from both retinae. Thereafter, the time course of abnormalities in LGNd of both hemispheres was different. In the hemisphere ipsilateral to the squinting eye, the difference in layer activity was highest at the age from 3 to 5 months. However, in the opposite hemisphere the same difference indicating a decreased activity in the layer of the squinting eye were observed only at the age of 5 months. Conclusion: The process of amblyopia development during congenital convergent strabismus is

  2. Relationship between fetal heart rate patterns and a time course for evaluation of fetal well-being: “the 30 minutes rule” for decision of mechanical delivery

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    Shintaro Makino

    2017-12-01

    Conclusions: We confirmed the time indices for predicting and preventing acidosis in fetuses showing decelerations. To prevent fetal acidosis, the decision related to proper timing for performing assisted delivery by considering the time course is important.

  3. Normal time course of auditory recognition in schizophrenia, despite impaired precision of the auditory sensory ("echoic") memory code.

    Science.gov (United States)

    March, L; Cienfuegos, A; Goldbloom, L; Ritter, W; Cowan, N; Javitt, D C

    1999-02-01

    Prior studies have demonstrated impaired precision of processing within the auditory sensory memory (ASM) system in schizophrenia. This study used auditory backward masking to evaluate the degree to which such deficits resulted from impaired overall precision versus premature decay of information within the short-term auditory store. ASM performance was evaluated in 14 schizophrenic participants and 16 controls. Schizophrenic participants were severely impaired in their ability to match tones following delay. However, when no-mask performance was equated across participants, schizophrenic participants were no more susceptible to the effects of backward maskers than were controls. Thus, despite impaired precision of ASM performance, schizophrenic participants showed no deficits in the time course over which short-term representations could be used within the ASM system.

  4. Time-course investigation of the gene expression profile during Fasciola hepatica infection: A microarray-based study

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    Jose Rojas-Caraballo

    2015-12-01

    Full Text Available Fasciolosis is listed as one of the most important neglected tropical diseases according with the World Health Organization and is also considered as a reemerging disease in the human beings. Despite there are several studies describing the immune response induced by Fasciola hepatica in the mammalian host, investigations aimed at identifying the expression profile of genes involved in inducing hepatic injury are currently scarce. Data presented here belong to a time-course investigation of the gene expression profile in the liver of BALB/c mice infected with F. hepatica metacercariae at 7 and 21 days after experimental infection. The data published here have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE69588, previously published by Rojas-Caraballo et al. (2015 in PLoS One [1].

  5. The Time Course of Knee Swelling Post Total Knee Arthroplasty and Its Associations with Quadriceps Strength and Gait Speed.

    Science.gov (United States)

    Pua, Yong-Hao

    2015-07-01

    This study examines the time course of knee swelling post total knee arthroplasty (TKA) and its associations with quadriceps strength and gait speed. Eighty-five patients with unilateral TKA participated. Preoperatively and on post-operative days (PODs) 1, 4, 14, and 90, knee swelling was measured using bioimpedance spectrometry. Preoperatively and on PODs 14 and 90, quadriceps strength was measured using isokinetic dynamometry while fast gait speed was measured using the timed 10-meter walk. On POD1, knee swelling increased ~35% from preoperative levels after which, knee swelling reduced but remained at ~11% above preoperative levels on POD90. In longitudinal, multivariable analyses, knee swelling was associated with quadriceps weakness (P<0.01) and slower gait speed (P=0.03). Interventions to reduce post-TKA knee swelling may be indicated to improve quadriceps strength and gait speed. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. The time course of repair of ultraviolet-induced DNA damage; implications for the structural organization of repair

    International Nuclear Information System (INIS)

    Collins, A.; Squires, S.

    1986-01-01

    Alternative molecular mechanisms can be envisaged for the cellular repair of UV-damaged DNA. In the 'random collision' model, DNA damage distributed throughout the genome is recognised and repaired by a process of random collision between DNA damage and repair enzymes. The other model assumes a 'processive' mechanism, whereby DNA is scanned for damage by a repair complex moving steadily along its length. Random collision should result in a declining rate of repair with time as the concentration of lesions in the DNA falls; but the processive model predicts a constant rate until scanning is complete. The authors have examined the time course of DNA repair in human fibroblasts given low doses of UV light. Using 3 distinct assays, the authors find no sign of a constant repair rate after 4 J/m 2 or less, even when the first few hours after irradiation are examined. Thus DNA repair is likely to depend on random collision. (Auth.)

  7. Interoceptive Processes in Anorexia Nervosa in the Time Course of Cognitive-Behavioral Therapy: A Pilot Study.

    Science.gov (United States)

    Fischer, Dana; Berberich, Götz; Zaudig, Michael; Krauseneck, Till; Weiss, Sarah; Pollatos, Olga

    2016-01-01

    Previous studies report reduced interoceptive abilities in anorexia nervosa (AN) using various methods. Recent research suggests that different levels of interoceptive processes aiming at different subdomains of interoceptive abilities must be further distinguished as these levels can be differentially affected. Two important levels refer to interoceptive accuracy (IA) derived from objective performance tasks such as the heartbeat detection task and interoceptive sensibility (IS) as assessed by self-report. There is a lack of studies investigating both IA and IS in AN and examining them in the time course of therapy. The aim of this pilot study was to evaluate the different interoceptive processes - especially IA and IS - in the time course of therapy. Fifteen patients with AN (restricting type) from the Psychosomatic Clinic in Windach were investigated three times (T1, T2, T3) during a standardized cognitive-behavioral therapy and compared with 15 matched healthy controls assessed at Ulm University in a comparable design. All participants performed the heartbeat detection task examining IA and completed standard psychological assessments including an assessment of IS. Patients with AN showed a significantly decreased weight, higher levels of depression, and both reduced IA and IS compared to healthy controls at T1. Following therapy, patients recovered in terms of weight and depression symptomatology. A descriptive trend for recovering from IA and IS was observed. Our findings suggest that interoceptive deficits are present in recovered patients. Therefore, further investigations are needed with more patients, differentiating between relapsed and recovered patients, and more specific training methods to improve interoceptive processes.

  8. Differences in time course activation of dorsolateral prefrontal cortex associated with low or high risk choicesin a gambling task

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    Stefano eBembich

    2014-06-01

    Full Text Available Prefrontal cortex plays an important role in decision making (DM, supporting choices in the ordinary uncertainty of everyday life. To assess DM in an unpredictable situation, a playing card task, such as the Iowa Gambling Task (IGT, has been proposed. This task is supposed to specifically test emotion-based learning, linked to the integrity of the ventromedial prefrontal cortex (VMPFC. However, the dorsolateral prefrontal cortex (DLPFC has demonstrated a role in IGT performance too. Our aim was to study, by multichannel near-infrared spectroscopy, the contribution of DLPFC to the IGT execution over time. We tested the hypothesis that low and high risk choices would differentially activate DLPFC, as IGT execution progressed. We enrolled 11 healthy adults. To identify DLPFC activation associated with IGT choices, we compared regional differences in oxy-haemoglobin variation, from baseline to the event. The time course of task execution was divided in four periods, each one consisting of 25 choices, and DLPFC activation was distinctly analyzed for low and high risk choices in each period. We found different time courses in DLPFC activation, associated with low or high risk choices. During the first period, a significant DLPFC activation emerged with low risk choices, whereas, during the second period, we found a cortical activation with high risk choices. Then, DLPFC activation decreased to non-significant levels during the third and fourth period. This study shows that DLPFC involvement in IGT execution is differentiated over time and according to choice risk level. DLPFC is activated only in the first half of the task, earlier by low risk and later by high risk choices. We speculate that DLPFC may sustain initial and more cognitive functions, such as attention shifting and response inhibition. The lack of DLPFC activation, as the task progresses, may be due to VMPFC activation, not detectable by fNIRS, which takes over the IGT execution in its

  9. Interoceptive processes in anorexia nervosa in the time course of cognitive-behavioral therapy: A pilot study

    Directory of Open Access Journals (Sweden)

    Dana Fischer

    2016-12-01

    Full Text Available Objective: Previous studies report reduced interoceptive abilities in anorexia nervosa (AN using various methods. Recent research suggests that different levels of interoceptive processes aiming at different subdomains of interoceptive abilities must be further distinguished as these levels can be differentially affected. Two important levels refer to interoceptive accuracy (IA derived from objective performance tasks such as the heartbeat detection task, and interoceptive sensibility (IS as assessed by self-report. There is a lack of studies investigating both IA and IS in AN, and examining them in the time course of therapy. Aim of the pilot study was to evaluate the different interoceptive processes – especially IA and IS – in the time course of therapy.Methods: Fifteen patients with AN (restricting type from the Psychosomatic Clinic in Windach were investigated three times (T1, T2, T3 during a standardized cognitive-behavioral therapy and compared to fifteen matched healthy controls assessed at Ulm University in a comparable design. All participants performed the heartbeat detection task examining IA and completed standard psychological assessments including an assessment of IS. Results: Patients with AN showed a significantly decreased weight, higher levels of depression and both reduced IA and IS compared to healthy controls at T1. Following therapy, patients recovered in terms of weight and depression symptomatology. A descriptive trend for recovering from IA and IS was observed. Discussion: Our findings suggest that interoceptive deficits are present in recovered patients. Therefore, further investigations are needed with more patients, differentiating between relapsed and recovered patients, and more specific training methods to improve interoceptive processes.

  10. Acute and Time-Course Effects of Traditional and Dynamic Warm-Up Routines in Young Elite Junior Tennis Players.

    Directory of Open Access Journals (Sweden)

    Francisco Ayala

    Full Text Available Despite the large number of studies that have examined the acute effects of different warm up modalities (WU on physical performance, none of them have documented the time course of potential performance recovery in tennis players. The aim of this study was twofold: (a to analyze and compare the acute effects of two different WU modalities (traditional WU [TWU] and dynamic WU [DWU] on physical performance (i.e., CMJ, sprint, serve speed and accuracy in elite junior players, as well as (b to monitor the time course of any WU-induced changes after 30 and 60 min of simulated match-play. Twelve junior elite players completed both WUs modalities (TWU and DWU in a counterbalanced order on separate days. In each experimental session, counter movement jump (CMJ, 20-m sprint, tennis serve speed and accuracy tests were performed before (immediately after TWU or DWU during (30 min and after 60 min of a simulated match play. Measures were compared via four factorial (WU intervention and time repeated measures ANOVAs. There were main effects of WU (TWU and DWU throughout the time for all the variables analysed. The results indicate that DWU routine led to significantly faster 20 m sprint times and higher CMJs as well as faster and more accurate tennis serves at both post warm-up and 30 min match-play testing moments in comparison with the scores reported by the TWU routine (p 75-99%. No significant intergroup differences were found at 60-min match-play testing moment in any variable (except for the 20 m sprint. Therefore, the findings of this study recommend for optimal performance in these elite tennis players, DWU routines should be performed prior to formal training and competition rather than TWU routines.

  11. Contextual change after fear acquisition affects conditioned responding and the time course of extinction learning – Implications for renewal research

    Directory of Open Access Journals (Sweden)

    Rachel eSjouwerman

    2015-12-01

    Full Text Available Context plays a central role in retrieving (fear memories. Accordingly, context manipulations are inherent to most return of fear (ROF paradigms (in particular renewal, involving contextual changes after fear extinction. Context changes are, however, also often embedded during earlier stages of ROF experiments such as context changes between fear acquisition and extinction (e.g. in ABC and ABA renewal. Previous studies using these paradigms have however focused exclusively on the context switch after extinction (i.e. renewal. Thus, the possibility of a general effect of a context switch on conditioned responding that may not be conditional to preceding extinction learning remains unstudied.Hence, the current study investigated the impact of a context switch between fear acquisition and extinction on immediate conditioned responding and on the time-course of extinction learning by using a multimodal approach. A group that underwent contextual change after fear conditioning (AB; n = 36 was compared with a group without a contextual change from acquisition to extinction (AA; n = 149, while measuring autonomic (skin conductance and fear potentiated startle measures and subjective fear ratings. Contextual change between fear acquisition and extinction had a pronounced effect on both immediate conditioned responding and on the time course of extinction learning in skin conductance responses and subjective fear ratings. This may have important implications for the mechanisms underlying and the interpretation of the renewal effect (i.e. contextual switch after extinction. Consequently, future studies should incorporate designs and statistical tests that disentangle general effects of contextual change from genuine ROF effects.

  12. Time course of late rectal- and urinary bladder side effects after MRI-guided adaptive brachytherapy for cervical cancer

    Energy Technology Data Exchange (ETDEWEB)

    Georg, P.; Georg, D.; Poetter, R.; Doerr, W. [Medical University Vienna/ AKH Wien (Austria). Dept. of Radiooncology; Medical University Vienna (Austria). Christian Doppler Laboratory for Medical Radiation Research for Radiation Oncology; Medical University Vienna/ AKH Wien (Austria). Comprehensive Cancer Centre; Boni, A.; Ghabuous, A. [Medical University Vienna/ AKH Wien (Austria). Dept. of Radiooncology; Goldner, G.; Schmid, M.P. [Medical University Vienna/ AKH Wien (Austria). Dept. of Radiooncology; Medical University Vienna/ AKH Wien (Austria). Comprehensive Cancer Centre

    2013-07-15

    Background and purpose: To analyze the time course of late rectal- and urinary bladder complications after brachytherapy for cervical cancer and to compare the incidence- and prevalence rates thereof. Patients and methods: A total of 225 patients were treated with external-beam radiotherapy (EBRT) and magnetic resonance imaging (MRI)-guided brachytherapy with or without chemotherapy. Late side effects were assessed prospectively using the Late Effects in Normal Tissue - Subjective, Objective, Management and Analytic (LENT/SOMA) scale. The parameters analyzed were time to onset, duration, actuarial incidence- (occurrence of new side effects during a defined time period) and prevalence rates (side effects existing at a defined time point). Results: Median follow-up was 44 months. Side effects (grade 1-4) in rectum and bladder were present in 31 and 49 patients, 14 and 27 months (mean time to onset) after treatment, respectively. All rectal and 76 % of bladder side effects occurred within 3 years after radiotherapy. Mean duration of rectal events was 19 months; 81 % resolved within 3 years of their initial diagnosis. Mean duration of bladder side effects was 20 months; 61 % resolved within 3 years. The 3- and 5-year actuarial complication rates were 16 and 19 % in rectum and 18 and 28 % in bladder, respectively. The corresponding prevalence rates were 9 and 2 % (rectum) and 18 and 21 % (bladder), respectively. Conclusion: Late side effects after cervical cancer radiotherapy are partially reversible, but their time course is organ-dependent. The combined presentation of incidence- and prevalence rates provides the most comprehensive information. (orig.)

  13. Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Liang; Chowdhury, Saiful M.; Smallwood, Heather S.; Yoon, Hyunjin; Mottaz-Brewer, Heather M.; Norbeck, Angela D.; McDermott, Jason E.; Clauss, Therese RW; Heffron, Fred; Smith, Richard D.; Adkins, Joshua N.

    2009-08-01

    Macrophages plan important roles in controlling Salmonella-mediated systemic infection. To investigate the responses of macrophages to Salmonella infection, we infected RAW 264.7 macrophages with Salmonella enterica serovar Typhimurium (STM) and then performed a comparative liquid chromatography-tandem mass spectrometry [LC-MS(/MS)]-based proteomics analysis of the infected macrophages. A total of 1006 macrophage and 115 STM proteins were indentified from this study. Most of STM proteins were found at late stage of the time course of infection, consistent with the fact that STM proliferates inside RAW 264.7 macrophages. Majority of the identified macrophage proteins were house keeping-related, including cytoplasmic superoxide dismutase 1 (SOD1), whose peptide abundances were relatively constant during the time course of infection. Compared to those in no infection control, the peptide abundances of 244 macrophage proteins (or 24% of total indentified macrophage proteins) changed considerably after STM infection. The functions of these STM infection-affected macrophage proteins were diverse and ranged from production of antibacterial nitric oxide (i.e., inducible nitric oxide synthase or iNOS) or production of prostaglandin H2 (i.e., prostaglandin-endoperoxide synthase 2, also know as cyclooxygenase-2 or COX-2) to regulation of intracellular traffic (e.g., sorting nexin or SNX 5, 6 and 9), demonstrating a global impact of STM infection on macrophage proteome. Western-blot analysis not only confirmed the LC-MS(/MS) results of SOD1, COX-2 and iNOS, but also revealed that the protein abundances of mitochondrial SOD2 increased after STM infection, indicating an infection-induced oxidative stress in mitochondria.

  14. Documenting the kinetic time course of lambda-cyhalothrin metabolites in orally exposed volunteers for the interpretation of biomonitoring data.

    Science.gov (United States)

    Khemiri, Rania; Côté, Jonathan; Fetoui, Hamadi; Bouchard, Michèle

    2017-07-05

    Lambda-cyhalothrin is a pyrethroid pesticide largely used in agriculture. Exposure assessment can be performed by measuring key urinary metabolites. For a proper use of biomonitoring data, it is however important to gain information on the toxicokinetics of these key biomarkers of exposure. A human volunteer study was performed to document the plasma and urinary time courses of major lambda-cyhalothrin metabolites. Seven volunteers ingested 0.025mgkg -1 body weight of lambda-cyhalothrin. Blood samples were withdrawn prior to dosing and at fixed time periods over the 72 h-period following ingestion and complete urine voids were collected pre-exposure and at pre-established intervals over 84h post-dosing. The cis-3-(2-chloro-3,3,3-trifluoroprop-1-en-1-yl)-2,2-dimethylcyclopropanecarboxylic acid (CFMP) and 3-phenoxybenzoic acid (3-PBA) metabolites were quantified in these samples. Plasma concentrations of CFMP and 3-PBA increased rapidly after ingestion, with average peak values at 3.1 and 4.0h post-dosing, respectively; subsequent elimination phase showed a rapid decay with a mean half-life (t ½ ) of ≈5.3 and 6.4h for CFMP and 3-PBA, respectively. Urinary rate time courses displayed a profile similar to the plasma concentration-time curves with corresponding mean t ½ of ≈4.2 and 5.9h. In the 84-h period post-treatment, on average 21% of lambda-cyhalothrin dose were excreted in urine as CFMP as compared to 30% as 3-PBA. Overall, CFMP and 3-PBA metabolites were confirmed to be major metabolites of lambda-cyhalothrin and exhibited similar kinetics with short half-lives; they thus both appear as useful biomarkers of exposure to lambda-cyhalothrin in humans. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Time course of late rectal- and urinary bladder side effects after MRI-guided adaptive brachytherapy for cervical cancer

    International Nuclear Information System (INIS)

    Georg, P.; Georg, D.; Poetter, R.; Doerr, W.; Medical University Vienna; Medical University Vienna/ AKH Wien; Boni, A.; Ghabuous, A.; Goldner, G.; Schmid, M.P.; Medical University Vienna/ AKH Wien

    2013-01-01

    Background and purpose: To analyze the time course of late rectal- and urinary bladder complications after brachytherapy for cervical cancer and to compare the incidence- and prevalence rates thereof. Patients and methods: A total of 225 patients were treated with external-beam radiotherapy (EBRT) and magnetic resonance imaging (MRI)-guided brachytherapy with or without chemotherapy. Late side effects were assessed prospectively using the Late Effects in Normal Tissue - Subjective, Objective, Management and Analytic (LENT/SOMA) scale. The parameters analyzed were time to onset, duration, actuarial incidence- (occurrence of new side effects during a defined time period) and prevalence rates (side effects existing at a defined time point). Results: Median follow-up was 44 months. Side effects (grade 1-4) in rectum and bladder were present in 31 and 49 patients, 14 and 27 months (mean time to onset) after treatment, respectively. All rectal and 76 % of bladder side effects occurred within 3 years after radiotherapy. Mean duration of rectal events was 19 months; 81 % resolved within 3 years of their initial diagnosis. Mean duration of bladder side effects was 20 months; 61 % resolved within 3 years. The 3- and 5-year actuarial complication rates were 16 and 19 % in rectum and 18 and 28 % in bladder, respectively. The corresponding prevalence rates were 9 and 2 % (rectum) and 18 and 21 % (bladder), respectively. Conclusion: Late side effects after cervical cancer radiotherapy are partially reversible, but their time course is organ-dependent. The combined presentation of incidence- and prevalence rates provides the most comprehensive information. (orig.)

  16. Kanpur epidemic: Time course

    Indian Academy of Sciences (India)

    The first peak was related to water contamination which began in December 1990. The second peak was related to failure of municipal authorities to chlorinate water during the 2nd week of February 1991. The epidemic came under control quickly after water contamination was controlled, providing confirmation for role of ...

  17. Reproducibility in protein profiling by MALDI-TOF mass spectrometry

    DEFF Research Database (Denmark)

    Albrethsen, Jakob

    2007-01-01

    , immunocapture, prestructured target surfaces, standardized matrix (co)crystallization, improved MALDI-TOF MS instrument components, internal standard peptides, quality-control samples, replicate measurements, and algorithms for normalization and peak detection. CONCLUSIONS: Further evaluation and optimization...

  18. Characterization of Bacteria in Ballast Water Using MALDI-TOF Mass Spectrometry

    Digital Repository Service at National Institute of Oceanography (India)

    Emami, K.; Askari, V.; Ullrich, M.; Mohinudeen, K.; Anil, A.C.; Khandeparker, L.; Burgess, J.G.; Mesbahi, E.

    To evaluate a rapid and cost-effective method for monitoring bacteria in ballast water, several marine bacterial isolates were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Since...

  19. Prevalence of antimicrobial resistance and the cfiA resistance gene in Danish Bacteroides fragilis group isolates since 1973

    DEFF Research Database (Denmark)

    Ferløv-Schwensen, Simon Andreas; Sydenham, Thomas Vognbjerg; Hansen, Kia Cirkeline Møller

    2017-01-01

    Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) on the Biotyper platform. Antimicrobial resistance was determined using a disk diffusion screening method and commercial antibiotic gradient strips. Division I (cfiA-negative) and division II (cfiA-positive) B. fragilis strains were...... differentiated using MALDI-TOF MS and real-time polymerase chain reaction (PCR). RESULTS: From 1973-1980 to 2010-2015 the prevalence of antimicrobial resistance rose from 0% to 21.2%, 2.5%, and 1% for clindamycin, meropenem, and metronidazole, respectively. MALDI-TOF MS and real-time PCR identified 16 of 266 (6...... established in the recent decades in Europe. Resistance to meropenem, facilitated by expression of the cfiA resistance gene, seems to be increasing; therefore, it is imperative to monitor the occurrence of this gene, e.g. using MALDI-TOF MS....

  20. CASE REPORT

    African Journals Online (AJOL)

    Blood results showed C-Reactive. Protein 395 mg/L ... Blood cultures were repeatedly negative as were tests for ... extension from infected tissues nearby or direct inoculation into the ... (MALDI-TOF MS) is another helpful method for identifying.

  1. White Spot Syndrome Virus infection in Penaeus monodon is ...

    Indian Academy of Sciences (India)

    2013-11-06

    assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to identify the host ..... and early feature of cell death in different cell types triggered to die with different suicidal stimuli (Ucker et al. 2012).

  2. The microbial epidemiology of breast implant infections in a regional referral centre for plastic and reconstructive surgery in the south of France

    Directory of Open Access Journals (Sweden)

    Piseth Seng

    2015-06-01

    Conclusions: The microbiological epidemiology was noted by an increasing the proportion of Gram-negative bacteria and anaerobic bacteria detected with the advent of MALDI-TOF MS and molecular identification for diagnosis.

  3. The ATP hydrolysis and phosphate release steps control the time course of force development in rabbit skeletal muscle.

    Science.gov (United States)

    Sleep, John; Irving, Malcolm; Burton, Kevin

    2005-03-15

    The time course of isometric force development following photolytic release of ATP in the presence of Ca(2+) was characterized in single skinned fibres from rabbit psoas muscle. Pre-photolysis force was minimized using apyrase to remove contaminating ATP and ADP. After the initial force rise induced by ATP release, a rapid shortening ramp terminated by a step stretch to the original length was imposed, and the time course of the subsequent force redevelopment was again characterized. Force development after ATP release was accurately described by a lag phase followed by one or two exponential components. At 20 degrees C, the lag was 5.6 +/- 0.4 ms (s.e.m., n = 11), and the force rise was well fitted by a single exponential with rate constant 71 +/- 4 s(-1). Force redevelopment after shortening-restretch began from about half the plateau force level, and its single-exponential rate constant was 68 +/- 3 s(-1), very similar to that following ATP release. When fibres were activated by the addition of Ca(2+) in ATP-containing solution, force developed more slowly, and the rate constant for force redevelopment following shortening-restretch reached a maximum value of 38 +/- 4 s(-1) (n = 6) after about 6 s of activation. This lower value may be associated with progressive sarcomere disorder at elevated temperature. Force development following ATP release was much slower at 5 degrees C than at 20 degrees C. The rate constant of a single-exponential fit to the force rise was 4.3 +/- 0.4 s(-1) (n = 22), and this was again similar to that after shortening-restretch in the same activation at this temperature, 3.8 +/- 0.2 s(-1). We conclude that force development after ATP release and shortening-restretch are controlled by the same steps in the actin-myosin ATPase cycle. The present results and much previous work on mechanical-chemical coupling in muscle can be explained by a kinetic scheme in which force is generated by a rapid conformational change bracketed by two

  4. Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry for caspofungin susceptibility testing of Candida and Aspergillus species.

    Science.gov (United States)

    De Carolis, Elena; Vella, Antonietta; Florio, Ada R; Posteraro, Patrizia; Perlin, David S; Sanguinetti, Maurizio; Posteraro, Brunella

    2012-07-01

    Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was evaluated for testing susceptibility to caspofungin of wild-type and fks mutant isolates of Candida and Aspergillus. Complete essential agreement was observed with the CLSI reference method, with categorical agreement for 94.1% of the Candida isolates tested. Thus, MALDI-TOF MS is a reliable and accurate method to detect fungal isolates with reduced caspofungin susceptibility.

  5. Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Caspofungin Susceptibility Testing of Candida and Aspergillus Species

    Science.gov (United States)

    De Carolis, Elena; Vella, Antonietta; Florio, Ada R.; Posteraro, Patrizia; Perlin, David S.; Posteraro, Brunella

    2012-01-01

    Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) was evaluated for testing susceptibility to caspofungin of wild-type and fks mutant isolates of Candida and Aspergillus. Complete essential agreement was observed with the CLSI reference method, with categorical agreement for 94.1% of the Candida isolates tested. Thus, MALDI-TOF MS is a reliable and accurate method to detect fungal isolates with reduced caspofungin susceptibility. PMID:22535984

  6. Detection of Bacteriocins by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

    OpenAIRE

    Rose, Natisha L.; Sporns, Peter; McMullen, Lynn M.

    1999-01-01

    The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the detection of bacteriocins was investigated. A 30-s water wash of the sample on the MALDI-TOF MS probe was effective in removing contaminants of the analyte. This method was used for rapid detection of nisin, pediocin, brochocin A and B, and enterocin A and B from culture supernatants and for detection of enterocin B throughout its purification.

  7. Time course of changes in sperm morphometry and semen variables during testosterone-induced suppression of human spermatogenesis.

    Science.gov (United States)

    Garrett, C; Liu, D Y; McLachlan, R I; Baker, H W G

    2005-11-01

    Quantification of changes in semen may give insight into the testosterone (T)-induced disruption of spermatogenesis in man. A model analogous to flushing of sperm from the genital tract after vasectomy was used to quantify the time course of semen changes in subjects participating in male contraceptive trials using 800 mg T-implant (n = 25) or 200 mg weekly intramuscular injection (IM-T; n = 33). A modified exponential decay model allowed for delayed onset and incomplete disruption to spermatogenesis. Semen variables measured weekly during a 91-day period after initial treatment were fitted to the model. Sperm concentration, total count, motility and morphometry exhibited similar average decay rates (5 day half-life). The mean delay to onset of decline in concentration was 15 (IM-T) and 18 (T-implant) days. The significantly longer (P sperm viability (43 and 55 days), and the change of morphometry to smaller more compact sperm heads are consistent with sperm being progressively cleared from the genital tract rather than continued shedding of immature or abnormal sperm by the seminiferous epithelium. A significant negative relationship was found between lag time and baseline sperm concentration, consistent with longer sperm-epididymal transit times associated with lower daily production rates.

  8. Time-Course Analysis of the Neuroanatomical Correlates of Sexual Arousal Evoked by Erotic Video Stimuli in Healthy Males

    Energy Technology Data Exchange (ETDEWEB)

    Sundaram, Thirunavukkarasu; Jeong, Gwang Woo; Kim, Tae Hoon; Kim, Gwang Won; Baek, Han Su; Kang, Heoung Keun [Chonnam National University Hospital, Chonnam National University Medical School, Gwangju (Korea, Republic of)

    2010-06-15

    To assess the dynamic activations of the key brain areas associated with the time-course of the sexual arousal evoked by visual sexual stimuli in healthy male subjects. Fourteen right-handed heterosexual male volunteers participated in this study. Alternatively combined rest period and erotic video visual stimulation were used according to the standard block design. In order to illustrate and quantify the spatiotemporal activation patterns of the key brain regions, the activation period was divided into three different stages as the EARLY, MID and LATE stages. For the group result (p < 0.05), when comparing the MID stage with the EARLY stage, a significant increase of the brain activation was observed in the areas that included the inferior frontal gyrus, the supplementary motor area, the hippocampus, the head of the caudate nucleus, the midbrain, the superior occipital gyrus and the fusiform gyrus. At the same time, when comparing the EARLY stage with the MID stage, the putamen, the globus pallidus, the pons, the thalamus, the hypothalamus, the lingual gyrus and the cuneus yielded significantly increased activations. When comparing the LATE stage with the MID stage, all the above mentioned brain regions showed elevated activations except the hippocampus. Our results illustrate the spatiotemporal activation patterns of the key brain regions across the three stages of visual sexual arousal.

  9. Time-course analysis of the neuroanatomical correlates of sexual arousal evoked by erotic video stimuli in healthy males.

    Science.gov (United States)

    Sundaram, Thirunavukkarasu; Jeong, Gwang-Woo; Kim, Tae-Hoon; Kim, Gwang-Won; Baek, Han-Su; Kang, Heoung-Keun

    2010-01-01

    To assess the dynamic activations of the key brain areas associated with the time-course of the sexual arousal evoked by visual sexual stimuli in healthy male subjects. Fourteen right-handed heterosexual male volunteers participated in this study. Alternatively combined rest period and erotic video visual stimulation were used according to the standard block design. In order to illustrate and quantify the spatiotemporal activation patterns of the key brain regions, the activation period was divided into three different stages as the EARLY, MID and LATE stages. For the group result (p < 0.05), when comparing the MID stage with the EARLY stage, a significant increase of the brain activation was observed in the areas that included the inferior frontal gyrus, the supplementary motor area, the hippocampus, the head of the caudate nucleus, the midbrain, the superior occipital gyrus and the fusiform gyrus. At the same time, when comparing the EARLY stage with the MID stage, the putamen, the globus pallidus, the pons, the thalamus, the hypothalamus, the lingual gyrus and the cuneus yielded significantly increased activations. When comparing the LATE stage with the MID stage, all the above mentioned brain regions showed elevated activations except the hippocampus. Our results illustrate the spatiotemporal activation patterns of the key brain regions across the three stages of visual sexual arousal.

  10. Time Course of Symptomatic Recovery After Endoscopic Transsphenoidal Surgery for Pituitary Adenoma Apoplexy in the Modern Era.

    Science.gov (United States)

    Zaidi, Hasan A; Cote, David J; Burke, William T; Castlen, Joseph P; Bi, Wenya Linda; Laws, Edward R; Dunn, Ian F

    2016-12-01

    Pituitary tumor apoplexy can result from either hemorrhagic or infarctive expansion of pituitary adenomas, and the related mass effect can result in compression of critical neurovascular structures. The time course of recovery of visual field deficits, headaches, ophthalmoparesis, and pituitary dysfunction after endoscopic transsphenoidal surgery has not been well established. Medical records were retrospectively reviewed for all patients who underwent endoscopic transsphenoidal surgery for pituitary tumor apoplexy from April 2008 to November 2014. Of 578 patients who underwent transsphenoidal surgery, pituitary tumor apoplexy was identified in 44 patients (7.6%). Two patients had prior surgery, leaving 42 patients for final analysis. These included infarction-related apoplexy in 7 (14.4%) patients, and hemorrhagic apoplexy in 35 (85.6%) patients. Hemorrhagic adenomas had a larger axial tumor diameter than patients with infarctive adenomas (4.4 ± 4.1 cm vs. 1.8 ± 0.8 cm; P surgery. Endoscopic transsphenoidal surgery can provide durable resolution of symptoms for patients presenting with pituitary tumor apoplexy. Recovery from headaches, visual, and pituitary dysfunction may be more rapid compared with ophthalmoparesis. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Health anxiety and attentional bias: the time course of vigilance and avoidance in light of pictorial illness information.

    Science.gov (United States)

    Jasper, Fabian; Witthöft, Michael

    2011-12-01

    Cognitive-behavioral models of health anxiety stress the importance of selective attention not only towards internal but also towards external health threat related stimuli. Yet, little is known about the time course of this attentional bias. The current study investigates threat related attentional bias in participants with varying degrees of health anxiety. Attentional bias was assessed using a visual dot-probe task with health-threat and neutral pictures at two exposure durations, 175ms and 500ms. A baseline condition was added to the dot-probe task to dissociate indices of vigilance towards threat and difficulties to disengage from threat. Substantial positive correlations of health anxiety, anxiety sensitivity, and absorption with difficulties to disengage from threat were detected at 500ms exposure time. At an early stage (i.e., at 175ms exposure time), we found significant positive correlations of health anxiety and absorption with orientation towards threat. Results suggest a vigilance avoidance pattern of selective attention associated with pictorial illness related stimuli in health anxiety. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Eye-movement evidence of the time-course of attentional bias for threatening pictures in test-anxious students.

    Science.gov (United States)

    Dong, Yunying; De Beuckelaer, Alain; Yu, Liang; Zhou, Renlai

    2017-06-01

    Protocols for measuring attentional bias to threat in test-anxiety, a special form of trait-anxiety, are rarely found in the literature. In our eye-tracking study, we introduced a new protocol, and studied the time-course of attention to test-related pictures with varying threat levels in 22 high test-anxious (HTA) and 22 low test-anxious (LTA) subjects. To determine whether attentional bias to test-related pictures is due to test-anxiety and not to state-anxiety, we also included a third group of 22 subjects with high state-anxiety but low test-anxiety (HSA). The subjects completed a free viewing task (FVT) in which high threat-neutral (HT-N) and low threat-neutral (LT-N) picture pairs were presented for 3 s. The results demonstrated that: (1) HTA subjects showed initial orienting to LT pictures, early attentional engagement with HT pictures later on and avoidance of HT pictures at the very end; (2) LTA subjects showed initial orienting to HT pictures and maintenance of attention on them later on; while (3) HSA subjects showed an initial orientation towards LT pictures and maintenance of attention on LT and HT pictures later on. These results suggest that, (high) test-anxiety is also prone to attentional bias towards test-related threat stimuli. Implications for future research are discussed.

  13. Chronic levothyroxine and acute T3 treatments enhance the amplitude and time course of uterine contractions in human.

    Science.gov (United States)

    Corriveau, Stéphanie; Pasquier, Jean-Charles; Blouin, Simon; Bellabarba, Diego; Rousseau, Éric

    2013-03-01

    This study compares the functional consequences of levothyroxine (T4) treatment during pregnancy as well as the acute affects of triiodothyronine (T3) on spontaneous uterine contractile activities observed in vitro. Uterine biopsies were obtained from consenting women undergoing elective caesarean at term (n = 28). Spontaneous contractile activities from T4-treated pregnant women (n = 8) were compared with control patients (n = 20) by isometric tension measurements. Effects of acute T3 and T4 on control tissues were also monitored. Area under the curve, amplitude, time to peak, duration, and frequency were quantified. In uterine strips from women treated for hypothyroidism, phasic uterine contractions of larger amplitude (+77%) were observed, with a prolonged duration at 90% relaxation (+138%) and reduced frequency (-55%) compared with values of the control group. The addition of exogenous T3 in vitro on control strips induced a significant increase in the duration of the contractions and a significant decrease in frequency (P women. Significant modifications of contractile properties were observed in strips from pregnant women treated with levothyroxine, consistent with those observed with the addition of exogenous T3. Clinical practices of modern obstetrics should take into account the effect of thyroid hormones on uterine contractions' time course to ensure a tighter followup at the end of pregnancy to achieve safer delivery.

  14. Time course of hydrogen peroxide-thioredoxin balance and its influence on the intracellular signalling in myocardial infarction.

    Science.gov (United States)

    Schenkel, Paulo Cavalheiro; Tavares, Angela Maria Vicente; Fernandes, Rafael Oliveira; Diniz, Gabriela Placoná; Ludke, Ana Raquel Lehenbauer; Ribeiro, Maria Flavia Marques; Araujo, Alex Sander da Rosa; Barreto-Chaves, Maria Luiza; Belló-Klein, Adriane

    2012-06-01

    We investigated the myocardial thioredoxin-1 and hydrogen peroxide concentrations and their association with some prosurvival and pro-apoptotic proteins, during the transition from myocardial infarction (MI) to heart failure in rats. Male Wistar rats were divided into the following six groups: three sham-operated groups and three MI groups, each at at 2, 7 and 28 days postsurgery. Cardiac function was analysed by echocardiography; the concentration of H(2)O(2) and the ratio of reduced to oxidized glutathione were measured spectrophotometrically, while the myocardial immunocontent of thioredoxin-1, angiotensin II, angiotensin II type 1 and type 2 receptors, p-JNK/JNK, p-ERK/ERK, p-Akt/Akt, p-mTOR/mTOR and p-GSK3β/GSK3β was evaluated by Western blot. Our results show that thioredoxin-1 appears to make an important contribution to the reduced H(2)O(2) concentration. It was associated with lower JNK expression in the early period post-MI (2 days). However, thioredoxin-1 decreased, while renin-angiotensin system markers and levels of H(2)O(2) increased, over 28 days post-MI, in parallel with some signalling proteins involved in maladaptative cardiac remodelling and ventricular dysfunction. These findings provide insight into the time course profile of endogenous antioxidant adaptation to ischaemic injury, which may be useful for the design of therapeutical strategies targeting oxidative stress post-MI.

  15. Time-course of attentional bias for positive social words in individuals with high and low social anxiety.

    Science.gov (United States)

    Yu, Hongyu; Li, Songwei; Qian, Mingyi; Yang, Peng; Wang, Xiaoling; Lin, Muyu; Yao, Nisha

    2014-07-01

    Although accumulating research demonstrates the association between attentional bias and social anxiety, the bias for positive stimuli has so far not been adequately studied. The aim is to investigate the time-course of attentional bias for positive social words in participants with high and low social anxiety. In a modified dot-probe task, word-pairs of neutral and positive social words were randomly presented for 100, 500, and 1250 milliseconds in a nonclinical sample of students to test their attentional bias. Non-significant interaction of Group × Exposure Duration was found. However, there was a significant main effect of group, with significantly different response latencies between the high social anxiety (HSA) and low social anxiety (LSA) groups in the 100 ms condition, without for 500 or 1250 ms. With respect to attentional bias, the LSA group showed enhanced preferential attention for positive social words to which the HSA group showed avoidance in the 100 ms condition. In the 500 ms condition, preferential attention to positive social words was at trend in the LSA group, relative to the HSA group. Neither group showed attentional bias in the 1250 ms condition. These findings extend recent research about the attention training program and add to the empirical literature suggesting that the initial avoidance of positive stimuli may contribute to maintaining social anxiety.

  16. I scan, therefore I decline: The time course of difficulty monitoring in humans (homo sapiens) and macaques (macaca mulatta).

    Science.gov (United States)

    Smith, J David; Boomer, Joseph; Church, Barbara A; Zakrzewski, Alexandria C; Beran, Michael J; Baum, Michael L

    2018-05-01

    The study of nonhumans' metacognitive judgments about trial difficulty has grown into an important comparative literature. However, the potential for associative-learning confounds in this area has left room for behaviorist interpretations that are strongly asserted and hotly debated. This article considers how researchers may be able to observe animals' strategic cognitive processes more clearly by creating temporally extended problems within which associative cues are not always immediately available. We asked humans and rhesus macaques to commit to completing spatially extended mazes or to decline completing them through a trial-decline response. The mazes could sometimes be completed successfully, but other times had a constriction that blocked completion. A deliberate, systematic scanning process could preevaluate a maze and determine the appropriate response. Latency analyses charted the time course of the evaluative process. Both humans and macaques appeared, from the pattern of their latencies, to scan the mazes through before committing to completing them. Thus monkeys, too, can base trial-decline responses on temporally extended evaluation processes, confirming that those responses have strategic cognitive-processing bases in addition to behavioral-reactive bases. The results also show the value of temporally and spatially extended problems to let researchers study the trajectory of animals' online cognitive processes. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  17. The time course of episodic associative retrieval: electrophysiological correlates of cued recall of unimodal and crossmodal pair-associate learning.

    Science.gov (United States)

    Tibon, Roni; Levy, Daniel A

    2014-03-01

    Little is known about the time course of processes supporting episodic cued recall. To examine these processes, we recorded event-related scalp electrical potentials during episodic cued recall following pair-associate learning of unimodal object-picture pairs and crossmodal object-picture and sound pairs. Successful cued recall of unimodal associates was characterized by markedly early scalp potential differences over frontal areas, while cued recall of both unimodal and crossmodal associates were reflected by subsequent differences recorded over frontal and parietal areas. Notably, unimodal cued recall success divergences over frontal areas were apparent in a time window generally assumed to reflect the operation of familiarity but not recollection processes, raising the possibility that retrieval success effects in that temporal window may reflect additional mnemonic processes beyond familiarity. Furthermore, parietal scalp potential recall success differences, which did not distinguish between crossmodal and unimodal tasks, seemingly support attentional or buffer accounts of posterior parietal mnemonic function but appear to constrain signal accumulation, expectation, or representational accounts.

  18. Tracking the time course of word-frequency effects in auditory word recognition with event-related potentials.

    Science.gov (United States)

    Dufour, Sophie; Brunellière, Angèle; Frauenfelder, Ulrich H

    2013-04-01

    Although the word-frequency effect is one of the most established findings in spoken-word recognition, the precise processing locus of this effect is still a topic of debate. In this study, we used event-related potentials (ERPs) to track the time course of the word-frequency effect. In addition, the neighborhood density effect, which is known to reflect mechanisms involved in word identification, was also examined. The ERP data showed a clear frequency effect as early as 350 ms from word onset on the P350, followed by a later effect at word offset on the late N400. A neighborhood density effect was also found at an early stage of spoken-word processing on the PMN, and at word offset on the late N400. Overall, our ERP differences for word frequency suggest that frequency affects the core processes of word identification starting from the initial phase of lexical activation and including target word selection. They thus rule out any interpretation of the word frequency effect that is limited to a purely decisional locus after word identification has been completed. Copyright © 2012 Cognitive Science Society, Inc.

  19. The time course of lexical competition during spoken word recognition in Mandarin Chinese: an event-related potential study.

    Science.gov (United States)

    Huang, Xianjun; Yang, Jin-Chen

    2016-01-20

    The present study investigated the effect of lexical competition on the time course of spoken word recognition in Mandarin Chinese using a unimodal auditory priming paradigm. Two kinds of competitive environments were designed. In one session (session 1), only the unrelated and the identical primes were presented before the target words. In the other session (session 2), besides the two conditions in session 1, the target words were also preceded by the cohort primes that have the same initial syllables as the targets. Behavioral results showed an inhibitory effect of the cohort competitors (primes) on target word recognition. The event-related potential results showed that the spoken word recognition processing in the middle and late latency windows is modulated by whether the phonologically related competitors are presented or not. Specifically, preceding activation of the competitors can induce direct competitions between multiple candidate words and lead to increased processing difficulties, primarily at the word disambiguation and selection stage during Mandarin Chinese spoken word recognition. The current study provided both behavioral and electrophysiological evidences for the lexical competition effect among the candidate words during spoken word recognition.

  20. Get rich quick: the signal to respond procedure reveals the time course of semantic richness effects during visual word recognition.

    Science.gov (United States)

    Hargreaves, Ian S; Pexman, Penny M

    2014-05-01

    According to several current frameworks, semantic processing involves an early influence of language-based information followed by later influences of object-based information (e.g., situated simulations; Santos, Chaigneau, Simmons, & Barsalou, 2011). In the present study we examined whether these predictions extend to the influence of semantic variables in visual word recognition. We investigated the time course of semantic richness effects in visual word recognition using a signal-to-respond (STR) paradigm fitted to a lexical decision (LDT) and a semantic categorization (SCT) task. We used linear mixed effects to examine the relative contributions of language-based (number of senses, ARC) and object-based (imageability, number of features, body-object interaction ratings) descriptions of semantic richness at four STR durations (75, 100, 200, and 400ms). Results showed an early influence of number of senses and ARC in the SCT. In both LDT and SCT, object-based effects were the last to influence participants' decision latencies. We interpret our results within a framework in which semantic processes are available to influence word recognition as a function of their availability over time, and of their relevance to task-specific demands. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Quantitation of intracellular metabolites of [35S]-6-mercaptopurine in L5178Y cells grown in time-course incubates.

    Science.gov (United States)

    Breter, H J; Zahn, R K

    1979-09-01

    6-Mercaptopurine (6MP) metabolism was quantitatively determined in L5178Y murine lymphoma. Cells grown in time-course incubates with [35S]-6MP were extracted with cold perchloric acid, and the buffered extracts were subjected to high-performance liquid cation-exchange chromatography prior to and after hydrolysis with alkaline phosphatase. Free sulfate, 6-thiouric acid, 6-thioxanthosine, 6-thioguanosine, 6-thioinosine, free 6MP, and 6-methylthioinosine were separated from each other; identified in the radiochromatograms by elution volume, UV spectroscopic data, and enzymatic peak-shifting analyses with purine nucleoside phosphorylase; and quantitatively determined by means of 35S radioactivity. Gross intracellular 35S concentrations remained constant at 5 x 10(-5) M after 1 hr of incubation. 6MP metabolism in L5178Y cells was distinguished into an early phase (to 1 hr of incubation) in which 6MP was predominantly catabolized to 6-thiouric acid and free sulfate, into an intermediate phase (to 8 hr) in which substantial amounts of free 6MP and of ribonucleotides of 6-thioxanthosine and 6-thioguanosine were present while the concentrations of nonnucleotide oxidation products sharply decreased, and into a late phase (to 24 hr) in which the ribonucleotides of 6MP, of 6-thioguanosine and, in particular, of 6-methylthioinosine were the most abundant metabolites.

  2. Time-Course Analysis of the Neuroanatomical Correlates of Sexual Arousal Evoked by Erotic Video Stimuli in Healthy Males

    International Nuclear Information System (INIS)

    Sundaram, Thirunavukkarasu; Jeong, Gwang Woo; Kim, Tae Hoon; Kim, Gwang Won; Baek, Han Su; Kang, Heoung Keun

    2010-01-01

    To assess the dynamic activations of the key brain areas associated with the time-course of the sexual arousal evoked by visual sexual stimuli in healthy male subjects. Fourteen right-handed heterosexual male volunteers participated in this study. Alternatively combined rest period and erotic video visual stimulation were used according to the standard block design. In order to illustrate and quantify the spatiotemporal activation patterns of the key brain regions, the activation period was divided into three different stages as the EARLY, MID and LATE stages. For the group result (p < 0.05), when comparing the MID stage with the EARLY stage, a significant increase of the brain activation was observed in the areas that included the inferior frontal gyrus, the supplementary motor area, the hippocampus, the head of the caudate nucleus, the midbrain, the superior occipital gyrus and the fusiform gyrus. At the same time, when comparing the EARLY stage with the MID stage, the putamen, the globus pallidus, the pons, the thalamus, the hypothalamus, the lingual gyrus and the cuneus yielded significantly increased activations. When comparing the LATE stage with the MID stage, all the above mentioned brain regions showed elevated activations except the hippocampus. Our results illustrate the spatiotemporal activation patterns of the key brain regions across the three stages of visual sexual arousal

  3. Time course of physiological and psychological responses in humans during a 20-day severe-cold-acclimation programme.

    Directory of Open Access Journals (Sweden)

    Marius Brazaitis

    Full Text Available The time course of physiological and psychological markers during cold acclimation (CA was explored. The experiment included 17 controlled (i.e., until the rectal temperature reached 35.5°C or 170 min had elapsed; for the CA-17 session, the subjects (n = 14 were immersed in water for the same amount of time as that used in the CA-1 session head-out water immersions at a temperature of 14°C over 20 days. The data obtained in this study suggest that the subjects exhibited a thermoregulatory shift from peripheral-to-central to solely central input thermoregulation, as well as from shivering to non-shivering thermogenesis throughout the CA. In the first six CA sessions, a hypothermic type of acclimation was found; further CA (CA-7 to CA-16 led to a transitional shift to a hypothermic-insulative type of acclimation. Interestingly, when the subjects were immersed in water for the same time as that used in the CA-1 session (CA-17, the CA led to a hypothermic type of acclimation. The presence of a metabolic type of thermogenesis was evident only under thermoneutral conditions. Cold-water immersion decreased the concentration of cold-stress markers, reduced the activity of t