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

  1. Specific serum protein biomarkers of rheumatoid arthritis detected by MALDI-TOF-MS combined with magnetic beads.

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    Niu, Qian; Huang, Zhuochun; Shi, Yunying; Wang, Lanlan; Pan, Xiaofu; Hu, Chaojun

    2010-07-01

    To identify novel serum protein biomarkers and establish diagnostic pattern for rheumatoid arthritis (RA) by using proteomic technology. Serum proteomic spectra were generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) combined with weak cationic exchange magnetic beads. A training set of spectra, derived from analyzing sera from 22 patients with RA, 26 patients with other autoimmune diseases and 25 age- and sex-matched healthy volunteers, was used to train and develop a decision tree model with a machine learning algorithm called decision boosting. A blinded testing set, including 21 patients with RA, 24 patients with other autoimmune diseases and 25 healthy people, was used to examine the accuracy of the model. A decision tree model was established, consisting of four potential protein biomarkers whose m/z values were 4966.88, 5065.3, 5636.97 and 7766.87, respectively. In validation test, the decision tree model could differentiate RA from other autoimmune diseases and healthy people with the sensitivity of 85.71% and specificity of 87.76%, respectively. The present data suggested that MALDI-TOF-MS combined with magnetic beads could screen and identify some novel serum protein biomarkers related to RA. The proteomic pattern based on the four candidate biomarkers is of value for laboratory diagnosis of RA.

  2. Proteomic profiling of nephrotic syndrome in serum using magnetic bead based sample fractionation & MALDI-TOF MS

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    Sui, Weiguo; Dai, Yong; Zhang, Yue; Chen, Jiejing; Liu, Huaying; Huang, He

    2012-01-01

    Background & objectives: At present, the diagnosis of nephrotic syndrome (NS) requires a renal biopsy which is an invasive procedure. We undertook this pilot study to develop an alternative method and potential new biomarkers for diagnosis, and validated a set of well-integrated tools called ClinProt to investigate serum petidome in NS patients. Methods: The fasting blood samples from 49 patients diagnosed with NS by renal biopsy, including 17 mesangial proliferative glomerulonephritis (MsPGN), 12 minimal change nephrotic syndrome (MCNS), 10 focal segmental glomerulosclerosis (FSGS) and 10 membranous nephropathy (MN), were collected and screened to describe their variability of the serum peptidome. The results in NS group were compared with those in 10 control healthy individuals. Specimens were purified with magnetic beads-based weak cation exchange chromatography and analyzed in a MALDI-TOF MS. Results: The results showed 43, 61, 45 and 19 differential peptide peaks in MsPGN, MCNS, MN and FSGS groups, respectively. A Genetic Algorithm was used to set up the classification models. Cross validation of healthy controls from MsPGN, MCNS, MN and FSGS was 96.18, 100, 98.53 and 94.12 per cent, respectively. The recognition capabilities were 100 per cent. Interpretation & conclusions: Our results showed that proteomic analysis of serum with MALDI-TOF MS is a fast and reproducible approach, which may give an early idea of the pathology of nephrotic syndrome. PMID:22561615

  3. 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.

  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. MALDI-TOF MS combined with magnetic beads for detecting serum protein biomarkers and establishment of boosting decision tree model for diagnosis of systemic lupus erythematosus.

    Science.gov (United States)

    Huang, Zhuochun; Shi, Yunying; Cai, Bei; Wang, Lanlan; Wu, Yongkang; Ying, Binwu; Qin, Li; Hu, Chaojun; Li, Yongzhe

    2009-06-01

    To discover novel potential biomarkers and establish a diagnostic pattern for SLE by using proteomic technology. Serum proteomic spectra were generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) combined with weak cationic exchange magnetic beads. A training set of spectra, derived from analysing sera from 32 patients with SLE, 43 patients with other autoimmune diseases and 43 age- and sex-matched healthy volunteers, was used to train and develop a decision tree model with a machine learning algorithm called decision boosting. A blinded testing set, including 32 patients with SLE, 42 patients with other autoimmune diseases and 40 healthy people, was used to determine the accuracy of the model. The diagnostic pattern with a panel of four potential protein biomarkers of mass-to-charge (m/z) ratio 4070.09, 7770.45, 28 045.1 and 3376.02 could accurately recognize 25 of 32 patients with SLE, 36 of 42 patients with other autoimmune diseases and 36 of 40 healthy people. The preliminary data suggested a potential application of MALDI-TOF MS combined with magnetic beads as an effective technology to profile serum proteome, and with pattern analysis, a diagnostic model comprising four potential biomarkers was indicated to differentiate individuals with SLE from RA, SS, SSc and healthy controls rapidly and precisely.

  7. Proteomic study of serum using gel chromatography and MALDI-TOF MS reveals diagnostic biomarkers in male patients with liver-cancer

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    Zeng, Xin-Hua; Huang, He-Qing; Chen, Dong-Shi; Jin, Hong-Wei; Huang, Hui-Ying

    2007-03-01

    Human serum has been widely employed clinically for diagnosing various fatal diseases. However, the concentration of most proteins in human serum is too low to be directly measured using normal analytical methods. In order to obtain reliable analytical results from proteomic analysis of human serum, appropriate sample preparation is essential. A combined off-line analytical technique of gel chromatography and matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS) has been successfully established to separate proteins for MS analysis. Using these combined techniques, 176 mass signal peaks of proteins/peptides were found in 6 of 18 fractions from normal male serum (NMS) in the presence of buffer consisting of NH4HCO3 and acetonitrile. A simple gel chromatography column packed with Sephadex G-50 removed most signal-suppressing compounds such as salts and high abundance proteins (HAP). The molecular mass to charge (m/z) ratios of differential peptides revealed in serum of male patient with liver-cancer (LCMPS) compared to NMS were 5365, 5644 and 6462, and these peptides can be used as biomarkers to clinically diagnose liver-cancer. The simple and convenient chromatographic method described here is not only superior to recently described HPLC separation for MS analysis, but also reveals many novel and significant serum biomarkers for the clinical diagnosis of various diseases.

  8. 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

  9. 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,

  10. MALDI-TOF MS identification and tracking of food spoilers and food-borne pathogens

    NARCIS (Netherlands)

    de Koster, C.G.; Brul, S.

    2016-01-01

    Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is an established tool for identification of clinical relevant pathogens. MALDI-TOF MS is increasingly accepted as a molecular characterization tool and method for identification of genera, species and

  11. The application of MALDI-TOF MS in food microrganisms research

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    RAO Mingzhen

    2015-10-01

    Full Text Available Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry(MALDI-TOF MS technology has been widely used in food,medicine,chemical,and other fields.This paper reviews that the detection principles and characteristics of MALDI-TOF MS technology and its application in food microbiological identification,classification,traceability analysis.MALDI-TOF MS technology has advantages of rapid,accurate and efficient in microbiological detection.With the standardization of sample handling,improvemant of databases,and the problems of bioinformatics tool application,being solved,this technology will be important assistive tool in the field of microbiological detection and identification.

  12. MALDI-TOF MS Analysis of Native and Permethylated or Benzimidazole-Derivatized Polysaccharides

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    Chung-Hsuan Chen

    2012-04-01

    Full Text Available MALDI-TOF MS provides rapid and sensitive analyses of larger biomolecules. However, MS analyses of polysaccharide have been reported to have lower sensitivity compared to peptides and proteins. Here, we investigated some polysaccharides chemically derivatized by permethylation and ortho-phenylene diamine (OPD tagging. Methylated glycan is obviously able to improve the sensitivity for mass spectrometry detection. Oxidative condensation by UV-activation tagging to saccharides by OPD and peptide-OPD also improve the sensitivity of MALDI-TOF MS analyses. Polysaccharides including dextran, glucomannan, arabinoxylan, arabinogalactan and beta-1,3-glucan, isolated from nutritional supplements of Ganoderma lucidum and Saccharomyces pastorianus were measured using MALDI-TOF MS with 2,5-dihydroxybenzoic acid (2,5-DHB as the matrix. These glycans were also derivatized to methylated and benzimidazole-tagged glycans by chemical transformation for molecular weight analysis. The derivatized polysaccharides showed excellent MALDI-TOF MS signal enhancement in the molecular weight range from 1 to 5 kDa. Here, we demonstrate an efficient method to give glycan-benzimidazole (glycan-BIM derivatives for polysaccharide determination in MALDI-TOF MS. Therefore, permethylated or benzimidazole-derivatized polysaccharides provide a new option for polysaccharide analysis using MALDI-TOF MS.

  13. Identification of Dermatophyte Species after Implementation of the In-House MALDI-TOF MS Database

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    Calderaro, Adriana; Motta, Federica; Montecchini, Sara; Gorrini, Chiara; Piccolo, Giovanna; Piergianni, Maddalena; Buttrini, Mirko; Medici, Maria Cristina; Arcangeletti, Maria Cristina; Chezzi, Carlo; De Conto, Flora

    2014-01-01

    Despite that matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool in the clinical microbiology setting, few studies have till now focused on MALDI-TOF MS-based identification of dermatophytes. In this study, we analyze dermatophytes strains isolated from clinical samples by MALDI-TOF MS to supplement the reference database available in our laboratory. Twenty four dermatophytes (13 reference strains and 11 field isolated strains), identified by both conventional and molecular standard procedures, were analyzed by MALDI-TOF MS, and the spectra obtained were used to supplement the available database, limited to a few species. To verify the robustness of the implemented database, 64 clinical isolates other than those used for the implementation were identified by MALDI-TOF MS. The implementation allowed the identification of the species not included in the original database, reinforced the identification of the species already present and correctly identified those within the Trichophyton mentagrophytes complex previously classified as Trichophyton. tonsurans by MALDI-TOF MS. The dendrogram obtained by analyzing the proteic profiles of the different species of dermatophytes reflected their taxonomy, showing moreover, in some cases, a different clusterization between the spectra already present in the database and those newly added. In this study, MALDI-TOF MS proved to be a useful tool suitable for the identification of dermatophytes for diagnostic purpose. PMID:25216335

  14. 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.

  15. 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.

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

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    Lima-Neto, Reginaldo; Santos, Cledir; Lima, Nelson; Sampaio, Paula; Pais, Célia; Neves, Rejane P

    2014-01-01

    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.

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

    Science.gov (United States)

    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.

  18. 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...

  19. MALDI-TOF MS in clinical parasitology: applications, constraints and prospects.

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    Singhal, Neelja; Kumar, Manish; Virdi, Jugsharan Singh

    2016-10-01

    Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is currently being used for rapid and reproducible identification of bacteria, viruses and fungi in clinical microbiological laboratories. However, some studies have also reported the use of MALDI-TOF MS for identification of parasites, like Leishmania, Giardia, Cryptosporidium, Entamoeba, ticks and fleas. The present review collates all the information available on the use of this technique for parasites, in an effort to assess its applicability and the constraints for identification/diagnosis of parasites and diseases caused by them. Though MALDI-TOF MS-based identification of parasites is currently done by reference laboratories only, in future, this promising technology might surely replace/augment molecular methods in clinical parasitology laboratories.

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

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    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.

  1. MALDI-TOF MS distinctly differentiates nontypable Haemophilus influenzae from Haemophilus haemolyticus.

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    Zhu, Bingqing; Xiao, Di; Zhang, Huifang; Zhang, Yongchan; Gao, Yuan; Xu, Li; Lv, Jing; Wang, Yingtong; Zhang, Jianzhong; Shao, Zhujun

    2013-01-01

    Nontypable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus exhibit different pathogenicities, but to date, there remains no definitive and reliable strategy for differentiating these strains. In this study, we evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a potential method for differentiating NTHi and H. haemolyticus. The phylogenetic analysis of concatenated 16S rRNA and recombinase A (recA) gene sequences, outer membrane protein P6 gene sequencing and single-gene PCR were used as reference methods. The original reference database (ORD, provided with the Biotyper software) and new reference database (NRD, extended with Chinese strains) were compared for the evaluation of MALDI-TOF MS. Through a search of the ORD, 76.9% of the NTHi (40/52) and none of the H. haemolyticus (0/20) strains were identified at the species level. However, all NTHi and H. haemolyticus strains used for identification were accurately recognized at the species level when searching the NRD. From the dendrogram clustering of the main spectra projections, the Chinese and foreign H. influenzae reference strains were categorized into two distinct groups, and H. influenzae and H. haemolyticus were also separated into two categories. Compared to the existing methods, MALDI-TOF MS has the advantage of integrating high throughput, accuracy and speed. In conclusion, MALDI-TOF MS is an excellent method for differentiating NTHi and H. haemolyticus. This method can be recommended for use in appropriately equipped laboratories.

  2. 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

  3. 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

  4. 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

  5. MALDI-TOF MS identification of Anopheles gambiae Giles blood meal crushed on Whatman filter papers.

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    Niare, Sirama; Almeras, Lionel; Tandina, Fatalmoudou; Yssouf, Amina; Bacar, Affane; Toilibou, Ali; Doumbo, Ogobara; Raoult, Didier; Parola, Philippe

    2017-01-01

    Identification of the source of mosquito blood meals is an important component for disease control and surveillance. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as an effective tool for mosquito blood meal identification, using the abdomens of freshly engorged mosquitoes. In the field, mosquito abdomens are crushed on Whatman filter papers to determine the host feeding patterns by identifying the origin of their blood meals. The aim of this study was to test whether crushing engorged mosquito abdomens on Whatman filter papers was compatible with MALDI-TOF MS for mosquito blood meal identification. Both laboratory reared and field collected mosquitoes were tested. Sixty Anopheles gambiae Giles were experimentally engorged on the blood of six distinct vertebrate hosts (human, sheep, rabbit, dog, chicken and rat). The engorged mosquito abdomens were crushed on Whatman filter papers for MALDI-TOF MS analysis. 150 Whatman filter papers, with mosquitoes engorged on cow and goat blood, were preserved. A total of 77 engorged mosquito abdomens collected in the Comoros Islands and crushed on Whatman filter papers were tested with MALDI-TOF MS. The MS profiles generated from mosquito engorged abdomens crushed on Whatman filter papers exhibited high reproducibility according to the original host blood. The blood meal host was correctly identified from mosquito abdomens crushed on Whatman filter papers by MALDI-TOF MS. The MS spectra obtained after storage were stable regardless of the room temperature and whether or not they were frozen. The MS profiles were reproducible for up to three months. For the Comoros samples, 70/77 quality MS spectra were obtained and matched with human blood spectra. This was confirmed by molecular tools. The results demonstrated that MALDI-TOF MS could identify mosquito blood meals from Whatman filter papers collected in the field during entomological surveys. The

  6. Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS

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    Catalina S. Stingu

    2015-01-01

    Full Text Available Background: Actinomyces are a common part of the residential flora of the human intestinal tract, genitourinary system and skin. Isolation and identification of Actinomyces by conventional methods is often difficult and time consuming. In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS has become a rapid and simple method to identify bacteria. Objective: The present study evaluated a new in-house algorithm using MALDI-TOF-MS for rapid identification of different species of oral Actinomyces cultivated from subgingival biofilm. Design: Eleven reference strains and 674 clinical strains were used in this study. All the strains were preliminarily identified using biochemical methods and then subjected to MALDI-TOF-MS analysis using both similarity-based analysis and classification methods (support vector machine [SVM]. The genotype of the reference strains and of 232 clinical strains was identified by sequence analysis of the 16S ribosomal RNA (rRNA. Results: The sequence analysis of the 16S rRNA gene of all references strains confirmed their previous identification. The MALDI-TOF-MS spectra obtained from the reference strains and the other clinical strains undoubtedly identified as Actinomyces by 16S rRNA sequencing were used to create the mass spectra reference database. Already a visual inspection of the mass spectra of different species reveals both similarities and differences. However, the differences between them are not large enough to allow a reliable differentiation by similarity analysis. Therefore, classification methods were applied as an alternative approach for differentiation and identification of Actinomyces at the species level. A cross-validation of the reference database representing 14 Actinomyces species yielded correct results for all species which were represented by more than two strains in the database. Conclusions: Our results suggest that a combination of MALDI-TOF-MS

  7. 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.

  8. Development of oleic acid-functionalized magnetite nanoparticles as hydrophobic probes for concentrating peptides with MALDI-TOF-MS analysis.

    Science.gov (United States)

    Chen, Hemei; Liu, Shasha; Li, Yan; Deng, Chunhui; Zhang, Xiangmin; Yang, Pengyuan

    2011-03-01

    The oleic acid-functionalized magnetite nanoparticles (OA-Fe(3) O(4) ) with mean diameter of about 15 nm were synthesized through a low-cost, one-pot method and were designed as hydrophobic probes to realize the convenient, efficient and fast concentration of low-concentration peptides followed by MALDI-TOF-MS analysis. The capability of OA-Fe(3) O(4) nanoparticles in concentration of low-abundance peptides from simple and complex solutions were evaluated by comparing them with a sort of C8-modified magnetic microspheres. Samples of standard peptide solution, protein digest solution and human serum were introduced in the evaluating process, and the OA-Fe(3) O(4) nanoparticles exhibited good surface affinity toward low-concentration peptides. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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

    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....../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...... types and clonal complexes. The results of this study clearly show that MALDI-TOF MS can be used for first-line discrimination of MRSA isolates, using a simple and fast method that is easy to implement as part of routine testing....

  10. Identification of Disseminated Cryptococcosis Using MALDI-TOF MS and Clinical Evaluation.

    Science.gov (United States)

    Tarumoto, Norihito; Sakai, Jun; Kodana, Masahiro; Kawamura, Tohru; Ohno, Hideaki; Maesaki, Shigefumi

    2016-01-01

    Disseminated cryptococcosis is rare but can often become severe with a poor outcome. Given recent reports that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analyser is useful for Cryptococcus species identification, it was applied retrospectively to past cases of disseminated cryptococcosis at our hospital over the past 10 years, and their clinical courses were reviewed. For each case, the retained Cryptococcus spp. were used for identification using both MALDI-TOF MS and genetic sequencing, as well as for drug susceptibility testing. A total of eight cases were found. Cryptococcus spp. were found in cerebrospinal fluid in 3 cases and blood in 5 cases; anti-HIV antibody was either negative or untested. MALDI-TOF MS identified Cryptococcus neoformans as the pathogen in all 8 cases, but genetic testing identified one of these as Cryptococcus curvatus. The outcome was death within 30 days in 5 of the total 8 cases and in 2 of the 3 cases in which C. neoformans was detected in the cerebrospinal fluid, despite regimens and dosages that followed IDSA Guidelines in all 3 cases. Drug susceptibility testing showed no drug resistance that would have affected the therapy. In conclusion, the outcomes were very poor in these drug-susceptible cases, despite treatment in full accordance with standard guidelines. This study confirmed the need to develop newer therapies as well as the high capability of MALDI-TOF MS for the identification of C. neoformans. Genetic testing, however, may be necessary if non-neoformans Cryptococcus is suspected.

  11. Potential Pitfalls in MALDI-TOF MS Analysis of Abiotically Synthesized RNA Oligonucleotides

    Science.gov (United States)

    Burcar, Bradley T.; Cassidy, Lauren M.; Moriarty, Elizabeth M.; Joshi, Prakash C.; Coari, Kristin M.; McGown, Linda B.

    2013-06-01

    Demonstration of the abiotic polymerization of ribonucleotides under conditions consistent with conditions that may have existed on the prebiotic Earth is an important goal in "RNA world" research. Recent reports of abiotic RNA polymerization with and without catalysis rely on techniques such as HPLC, gel electrophoresis, and MALDI-TOF MS to analyze the reaction products. It is essential to understand the limitations of these techniques in order to accurately interpret the results of these analyses. In particular, techniques that rely on mass for peak identification may not be able to distinguish between a single, linear RNA oligomer and stable aggregates of smaller linear and/or cyclic RNA molecules. In the case of MALDI-TOF MS, additional complications may arise from formation of salt adducts and MALDI matrix complexes. This is especially true for abiotic RNA polymerization reactions because the concentration of longer RNA chains can be quite low and RNA, as a polyelectrolyte, is highly susceptible to adduct formation and aggregation. Here we focus on MALDI-TOF MS analysis of abiotic polymerization products of imidazole-activated AMP in the presence and absence of montmorillonite clay as a catalyst. A low molecular weight oligonucleotide standard designed for use in MALDI-TOF MS and a 3'-5' polyadenosine monophosphate reference standard were also run for comparison and calibration. Clay-catalyzed reaction products of activated GMP and UMP were also examined. The results illustrate the ambiguities associated with assignment of m/z values in MALDI mass spectra and the need for accurate calibration of mass spectra and careful sample preparation to minimize the formation of adducts and other complications arising from the MALDI process.

  12. 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.

  13. [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.

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

    Science.gov (United States)

    Šalplachta, Jiří; Kubesová, Anna; Horký, Jaroslav; Matoušková, Hana; Tesařová, Marie; Horká, Marie

    2015-10-01

    Dickeya and Pectobacterium species represent an important group of broad-host-range phytopathogens responsible for blackleg and soft rot diseases on numerous plants including many economically important plants. Although these species are commonly detected using cultural, serological, and molecular methods, these methods are sometimes insufficient to classify the bacteria correctly. On that account, this study was undertaken to investigate the feasibility of three individual analytical techniques, capillary zone electrophoresis (CZE), capillary isoelectric focusing (CIEF), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), for reliable classification of Dickeya and Pectobacterium species. Forty-three strains, representing different Dickeya and Pectobacterium species, namely Dickeya dianthicola, Dickeya dadantii, Dickeya dieffenbachiae, Dickeya chrysanthemi, Dickeya zeae, Dickeya paradisiaca, Dickeya solani, Pectobacterium carotovorum, and Pectobacterium atrosepticum, were selected for this purpose. Furthermore, the selected bacteria included one strain which could not be classified using traditional microbiological methods. Characterization of the bacteria was based on different pI values (CIEF), migration velocities (CZE), or specific mass fingerprints (MALDI-TOF MS) of intact cells. All the examined strains, including the undetermined bacterium, were characterized and classified correctly into respective species. MALDI-TOF MS provided the most reliable results in this respect.

  15. 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...... 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...

  16. Evaluation of MALDI-TOF-MS for the Identification of Yeast Isolates Causing Bloodstream Infection.

    Science.gov (United States)

    Turhan, Ozge; Ozhak-Baysan, Betil; Zaragoza, Oscar; Er, Halil; Sarıtas, Zubeyde Eres; Ongut, Gozde; Ogunc, Dilara; Colak, Dilek; Cuenca-Estrella, Manuel

    2017-04-01

    Infections due to Candida species are major causes of morbidity and mortality in humans, causing a diverse spectrum of clinical disease ranging from superficial and mucosal infections to invasive disease. Several authors have demonstrated that mortality is closely linked to both timing of therapy and/or source control. The rapid identification of pathogenic species is helpful to start timely and effective antifungal therapy. The aim of this study was to assess the performance of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system for the correct and rapid identification of yeast isolates causing bloodstream infection. Between January 2014 and January 2015, a total of 117 yeast like organisms isolated from blood culture samples of 117 episodes from 102 patients who had blood stream infections were included in the study. The isolates were identified by MALDI-TOF MS. The results were compared with those obtained by the standard mycological methods and/or sequence analysis. One hundred and seventeen yeast isolates including 115 Candida spp and two non-Candida yeasts were analysed. The Biotyper correctly identified 115 (98.3%) isolates to the genus level and 102 (87.2%) isolates to the species level using the manufacturer's recommended cutoff scores. The Bruker Biotyper is a rapid, easy, inexpensive, and highly reliable system for the identification of yeast isolates. Early identification with MALDI-TOF MS would save time for determination of antifungal susceptibility and proper treatment strategy. The expansion of the database of the library by addition of less common species will improve the performance of the system.

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

    Science.gov (United States)

    Kudirkiene, Egle; Welker, Martin; Knudsen, Nanna R; Bojesen, Anders M

    2015-07-01

    Streptococcus equi includes very important animal and human pathogens. S. equi subsp. equi (SEE) is a highly pathogenic equine specific subspecies, while S. equi subsp. zooepidemicus (SEZ) and S. equi subsp. ruminatorum are opportunistic pathogens of various animal species and humans. Due to great 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 in horses. Superspectra created in this study enabled correct identification of 86 strains belonging to different subspecies of S. equi, isolated from various hosts, infection sites and years. In general, higher average identification accuracy was achieved for SEE (99.0±3.0%) than for SEZ (93.3±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 with spectra analyses using the SARAMIS database. Additionally, first results on subtyping of SEZ indicated that a more refined discrimination, for example for epidemiological surveys, may be possible. Copyright © 2015 Elsevier GmbH. All rights reserved.

  18. MALDI-TOF MS Profiling of Annonaceous Acetogenins in Annona muricata Products for Human Consumption

    Directory of Open Access Journals (Sweden)

    Vincent Guérineau

    2009-12-01

    Full Text Available Annonaceous acetogenins are proposed as environmental neurotoxicants consumed through medicinal and alimentary habits and responsible for atypical parkinsonian syndromes observed in tropical areas. Potential sources of exposure still have to be determined, as, to date, only a few batches of products for human consumption were searched for these compounds. To assess the presence of acetogenins, we propose a fast, sensitive and accurate method of screening, using MALDI-TOF MS, with minimal sample preparation. Development of the technique is discussed. Its application to leaves of herbal tea, pulp and bottled nectar of Annona muricata is presented.

  19. MALDI-TOF MS profiling of annonaceous acetogenins in Annona muricata products for human consumption.

    Science.gov (United States)

    Champy, Pierre; Guérineau, Vincent; Laprévote, Olivier

    2009-12-15

    Annonaceous acetogenins are proposed as environmental neurotoxicants consumed through medicinal and alimentary habits and responsible for atypical parkinsonian syndromes observed in tropical areas. Potential sources of exposure still have to be determined, as, to date, only a few batches of products for human consumption were searched for these compounds. To assess the presence of acetogenins, we propose a fast, sensitive and accurate method of screening, using MALDI-TOF MS, with minimal sample preparation. Development of the technique is discussed. Its application to leaves of herbal tea, pulp and bottled nectar of Annona muricata is presented.

  20. 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.

  1. 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.

  2. Species identification within Acinetobacter calcoaceticus-baumannii complex using MALDI-TOF MS.

    Science.gov (United States)

    Toh, Benjamin E W; Paterson, David L; Kamolvit, Witchuda; Zowawi, Hosam; Kvaskoff, David; Sidjabat, Hanna; Wailan, Alexander; Peleg, Anton Y; Huber, Charlotte A

    2015-11-01

    Acinetobacter baumannii, one of the more clinically relevant species in the Acinetobacter genus is well known to be multi-drug resistant and associated with bacteremia, urinary tract infection, pneumonia, wound infection and meningitis. However, it cannot be differentiated from closely related species such as Acinetobacter calcoaceticus, Acinetobacter pittii and Acinetobacter nosocomialis by most phenotypic tests and can only be differentiated by specific, time consuming genotypic tests with very limited use in clinical microbiological laboratories. As a result, these species are grouped into the A. calcoaceticus-A. baumannii (Acb) complex. Herein we investigated the mass spectra of 73 Acinetobacter spp., representing ten different species, using an AB SCIEX 5800 MALDI-TOF MS to differentiate members of the Acinetobacter genus, including the species of the Acb complex. RpoB gene sequencing, 16S rRNA sequencing, and gyrB multiplex PCR were also evaluated as orthogonal methods to identify the organisms used in this study. We found that whilst 16S rRNA and rpoB gene sequencing could not differentiate A. pittii or A. calcoaceticus, they can be differentiated using gyrB multiplex PCR and MALDI-TOF MS. All ten Acinetobacter species investigated could be differentiated by their MALDI-TOF mass spectra. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Identification of Borrelia species after creation of an in-house MALDI-TOF MS database.

    Science.gov (United States)

    Calderaro, Adriana; Gorrini, Chiara; Piccolo, Giovanna; Montecchini, Sara; Buttrini, Mirko; Rossi, Sabina; Piergianni, Maddalena; Arcangeletti, Maria Cristina; De Conto, Flora; Chezzi, Carlo; Medici, Maria Cristina

    2014-01-01

    Lyme borreliosis (LB) is a multisystemic disease caused by Borrelia burgdorferi sensu lato (sl) complex transmitted to humans by Ixodes ticks. B. burgdorferi sl complex, currently comprising at least 19 genospecies, includes the main pathogenic species responsible for human disease in Europe: B. burgdorferi sensu stricto (ss), B. afzelii, and B. garinii. In this study, for the first time, MALDI-TOF MS was applied to Borrelia spp., supplementing the existing database, limited to the species B. burgdorferi ss, B . spielmanii and B. garinii, with the species B. afzelii, in order to enable the identification of all the species potentially implicated in LB in Europe. Moreover, we supplemented the database also with B. hermsii, which is the primary cause of tick-borne relapsing fever in western North America, B. japonica, circulating in Asia, and another reference strain of B. burgdorferi ss (B31 strain). The dendrogram obtained by analyzing the protein profiles of the different Borrelia species reflected Borrelia taxonomy, showing that all the species included in the Borrelia sl complex clustered in a unique branch, while Borrelia hermsii clustered separately. In conclusion, in this study MALDI-TOF MS proved a useful tool suitable for identification of Borrelia spp. both for diagnostic purpose and epidemiological surveillance.

  4. Identification and typing of free-living Acanthamoeba spp. by MALDI-TOF MS Biotyper.

    Science.gov (United States)

    Del Chierico, Federica; Di Cave, David; Accardi, Cristel; Santoro, Maristella; Masotti, Andrea; D'Alfonso, Rossella; Berrilli, Federica; Urbani, Andrea; Putignani, Lorenza

    2016-11-01

    Over the years, the potential pathogenicity of Acanthamoeba for humans and animals has gained increasing attention from the scientific community. More than 24 species belong to this genus, however only some of them are causative agents of keratitis and encephalitis in humans. Due to technical difficulties in diagnosis, these infections are likely to be under-detected. The introduction of 18S rDNA amplification for the identification of Acanthamoeba has dramatically enhanced diagnosis performances, but the attestation of genotyping requires supplementary sequencing-based procedures. In this study, 15 Acanthamoeba strains were collected and grown on nutrient agar media. Each strain was genotyped by end-point PCR assay for the amplification of the 18S rDNA gene and the genotype was assigned by sequencing analysis through neighbor joining phylogenetic tree. In order to optimize standardization of the MALDI-TOF MS assay, we established the collection time point at the cystic phase. Two strains of each genotype were randomly chosen to customize the biotyper database. For all strains, 24 spectral measurements were acquired and submitted to identification and cluster analysis of spectra. The obtained results highlighted the correct identification of Acanthamoeba strains and the overlapping of spectra dendrogram clusters to the 18S genotype assignations. In conclusion, the MALDI-TOF MS Biotyper revealed the capability to identify and genotype the Acanthamoeba strains, providing a new frontier in the diagnostic identification of amaebae and in taxonomic and phylogenetic studies. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. 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.

  6. Accurate identification of Culicidae at aquatic developmental stages by MALDI-TOF MS profiling.

    Science.gov (United States)

    Dieme, Constentin; Yssouf, Amina; Vega-Rúa, Anubis; Berenger, Jean-Michel; Failloux, Anna-Bella; Raoult, Didier; Parola, Philippe; Almeras, Lionel

    2014-12-02

    The identification of mosquito vectors is generally based on morphological criteria, but for aquatic stages, morphological characteristics may be missing, leading to incomplete or incorrect identification. The high cost of molecular biology techniques requires the development of an alternative strategy. In the last decade, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has proved to be efficient for arthropod identification at the species level. To investigate the usefulness of MALDI-TOF MS for the identification of mosquitoes at aquatic stages, optimizations of sample preparation, diet, body parts and storage conditions were tested. Protein extracts of whole specimens from second larval stage to pupae were selected for the creation of a reference spectra database. The database included a total of 95 laboratory-reared specimens of 6 mosquito species, including Anopheles gambiae (S form), Anopheles coluzzi (M form), Culex pipiens pipiens, Culex pipiens molestus, Aedes aegypti and 2 colonies of Aedes albopictus. The present study revealed that whole specimens at aquatic stages produced reproducible and singular spectra according to the mosquito species. Moreover, MS protein profiles appeared weakly affected by the diet provided. Despite the low diversity of some MS profiles, notably for cryptic species, clustering analyses correctly classified all specimens tested at the species level followed by the clustering of early vs. late aquatic developmental stages. Discriminant mass peaks were recorded for the 6 mosquito species analyzed at larval stage 3 and the pupal stage. Querying against the reference spectra database of 149 new specimens at different aquatic stages from the 6 mosquito species revealed that 147 specimens were correctly identified at the species level and that early and late developmental stages were also distinguished. The present work highlights that MALDI-TOF MS profiling may be useful for the

  7. Assessment of MALDI-TOF MS biotyping for Borrelia burgdorferi sl detection in Ixodes ricinus

    Science.gov (United States)

    Boyer, Pierre H.; Boulanger, Nathalie; Nebbak, Amira; Collin, Elodie; Jaulhac, Benoit; Almeras, Lionel

    2017-01-01

    Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has been demonstrated to be useful for tick identification at the species level. More recently, this tool has been successfully applied for the detection of bacterial pathogens directly in tick vectors. The present work has assessed the detection of Borrelia burgdorferi sensu lato in Ixodes ricinus tick vector by MALDI-TOF MS. To this aim, experimental infection model of I. ricinus ticks by B. afzelii was carried out and specimens collected in the field were also included in the study. Borrelia infectious status of I. ricinus ticks was molecularly controlled using half-idiosome to classify specimens. Among the 39 ticks engorged on infected mice, 14 were confirmed to be infected by B. afzelii. For field collection, 14.8% (n = 12/81) I. ricinus ticks were validated molecularly as infected by B. burgdorferi sl. To determine the body part allowing the detection of MS protein profile changes between non-infected and B. afzelii infected specimens, ticks were dissected in three compartments (i.e. 4 legs, capitulum and half-idiosome) prior to MS analysis. Highly reproducible MS spectra were obtained for I. ricinus ticks according to the compartment tested and their infectious status. However, no MS profile change was found when paired body part comparison between non-infected and B. afzelii infected specimens was made. Statistical analyses did not succeed to discover, per body part, specific MS peaks distinguishing Borrelia-infected from non-infected ticks whatever their origins, laboratory reared or field collected. Despite the unsuccessful of MALDI-TOF MS to classify tick specimens according to their B. afzelii infectious status, this proteomic tool remains a promising method for rapid, economic and accurate identification of tick species. Moreover, the singularity of MS spectra between legs and half-idiosome of I. ricinus could be used to reinforce this proteomic identification

  8. A designed experiments approach to optimizing MALDI-TOF MS spectrum processing parameters enhances detection of antibiotic resistance in Campylobacter jejuni

    Science.gov (United States)

    MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this...

  9. 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.

  10. Analysis of Bacterial Lipooligosaccharides by MALDI-TOF MS with Traveling Wave Ion Mobility

    Science.gov (United States)

    Phillips, Nancy J.; John, Constance M.; Jarvis, Gary A.

    2016-07-01

    Lipooligosaccharides (LOS) are major microbial virulence factors displayed on the outer membrane of rough-type Gram-negative bacteria. These amphipathic glycolipids are comprised of two domains, a core oligosaccharide linked to a lipid A moiety. Isolated LOS samples are generally heterogeneous mixtures of glycoforms, with structural variability in both domains. Traditionally, the oligosaccharide and lipid A components of LOS have been analyzed separately following mild acid hydrolysis, although important acid-labile moieties can be cleaved. Recently, an improved method was introduced for analysis of intact LOS by MALDI-TOF MS using a thin layer matrix composed of 2,4,6-trihydroxyacetophenone (THAP) and nitrocellulose. In addition to molecular ions, the spectra show in-source "prompt" fragments arising from regiospecific cleavage between the lipid A and oligosaccharide domains. Here, we demonstrate the use of traveling wave ion mobility spectrometry (TWIMS) for IMS-MS and IMS-MS/MS analyses of intact LOS from Neisseria spp. ionized by MALDI. Using IMS, the singly charged prompt fragments for the oligosaccharide and lipid A domains of LOS were readily separated into resolved ion plumes, permitting the extraction of specific subspectra, which led to increased confidence in assigning compositions and improved detection of less abundant ions. Moreover, IMS separation of precursor ions prior to collision-induced dissociation (CID) generated time-aligned, clean MS/MS spectra devoid of fragments from interfering species. Incorporating IMS into the profiling of intact LOS by MALDI-TOF MS exploits the unique domain structure of the molecule and offers a new means of extracting more detailed information from the analysis.

  11. 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.

  12. MALDI-TOF MS based carbapenemase detection from culture isolates and from positive blood culture vials.

    Science.gov (United States)

    Ghebremedhin, B; Halstenbach, A; Smiljanic, M; Kaase, M; Ahmad-Nejad, P

    2016-02-02

    Antibiotic resistance in bacteria leads to massive health problems. Incidence of carbapenem and multidrug resistance in Gram-negative bacteria are increasing globally and turn out to be a very urgent challenge in health care. Resistant bacteria play an important clinical role during hospital outbreaks as well as in sepsis. Rapid diagnostic tests are necessary to provide immediate information for antimicrobial treatment and infection control measures. Our mass spectrometry-based assay was validated with 63 carbapenemase-producing Gram-negative bacterial isolates, and 35 carbapenem-resistant Gram-negative species with no carbapenemase production. These were analyzed from solid culture media and positive blood culture vials. After 4 h of incubation the carbapenemase products were analyzed with the MALDI-TOF MS. All the isolates were genotyped for carbapenemase genes by PCR and sequencing. For culture isolates the concordance of hydrolysis assay to genetic results was 98 % for OXA variants, KPC, VIM, IMP, GIM, and NDM. In contrast, only 14 of 29 Acinetobacter baumannii isolates carrying the OXA and NDM genes could be identified from blood culture. However, from blood culture vials our method allowed the detection of carbapenemases in 98 % of Pseudomonas and Enterobacteriaceae isolates harboring different genes. This MALDI-TOF MS-based assay permitted the detection of carbapenemases either from solid culture media (98-100 %) or blood culture vials (96 %) for all non-A. baumannii isolates within 4 h. In case of A. baumannii isolates the assay was highly sensitive for the detection of carbapenemases directly from solid culture media.

  13. 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

  14. 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

  15. High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS.

    Science.gov (United States)

    Miescher Schwenninger, S; Freimüller Leischtfeld, S; Gantenbein-Demarchi, C

    2016-11-01

    Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful biotyping tool increasingly used for high-throughput identification of clinical microbial isolates, however, in food fermentation research this approach is still not well established. This study examines the microbial biodiversity of cocoa bean fermentation based on the isolation of micro-organisms in cocoa-producing regions, followed by MALDI-TOF MS in Switzerland. A preceding 6-week storage test to mimic lengthy transport of microbial samples from cocoa-producing regions to Switzerland was performed with strains of Lactobacillus plantarum, Acetobacter pasteurianus and Saccharomyces cerevisiae. Weekly MALDI-TOF MS analysis was able to successfully identify microbiota to the species level after storing live cultures on slant agar at mild temperatures (7°C) and/or in 75% aqueous ethanol at differing temperatures (-20, 7 and 30°C). The efficacy of this method was confirmed by on-site recording of the microbial biodiversity in cocoa bean fermentation in Bolivia and Brazil, with a total of 1126 randomly selected isolates. MALDI-TOF MS analyses revealed known dominant cocoa bean fermentation species with Lact. plantarum and Lactobacillus fermentum in the lactic acid bacteria taxon, Hanseniaspora opuntiae and S. cerevisiae in the yeast taxon, and Acet. pasteurianus, Acetobacter fabarum, Acetobacter ghanensis and Acetobacter senegalensis in the acetic acid bacteria taxon. Microbial identification with MALDI-TOF MS has increased the number of samples that can be analysed in a given time, a prerequisite for high-throughput methods. This method is already widely used for the identification of clinical microbial isolates, whereas in food fermentation research, including cocoa bean fermentation, microbiota is mostly identified by time-consuming, biochemical-based phenotyping and molecular approaches. This study presents the use of MALDI-TOF MS for characterizing the

  16. Detection and quantification of bacterial spoilage in milk and pork meat using MALDI-TOF-MS and multivariate analysis.

    Science.gov (United States)

    Nicolaou, Nicoletta; Xu, Yun; Goodacre, Royston

    2012-07-17

    Microbiological safety is one of the cornerstones of quality control in the food industry. Identification and quantification of spoilage bacteria in pasteurized milk and meat in the food industry currently relies on accurate and sensitive yet time-consuming techniques which give retrospective values for microbial contamination. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), a proven technique in the field of protein and peptide identification and quantification, may be a valuable alternative approach for the rapid assessment of microbial spoilage. In this work we therefore developed MALDI-TOF-MS as a novel analytical approach for the assessment of food that when combined with chemometrics allows for the detection and quantification of milk and pork meat spoilage bacteria. To develop this approach, natural spoilage of pasteurized milk and raw pork meat samples incubated at 15 °C and at room temperature, respectively, was conducted. Samples were collected for MALDI-TOF-MS analysis (which took 4 min per sample) at regular time intervals throughout the spoilage process, with concurrent calculation and documentation of reference total viable counts using traditional microbiological methods (these took 2 days). Multivariate statistical techniques such as principal component discriminant function analysis, canonical correlation analysis, partial least-squares (PLS) regression, and kernel PLS (KPLS) were used to analyze the data. The results from MALDI-TOF-MS combined with PLS or KPLS gave excellent bacterial quantification results for both milk and meat spoilage, and typical root mean squared errors for prediction in test spectra were between 0.53 and 0.79 log unit. Overall these novel findings strongly indicate that MALDI-TOF-MS when combined with chemometric approaches would be a useful adjunct for routine use in the milk and meat industry as a fast and accurate viable bacterial detection and quantification method.

  17. Identification of blood meal sources in the main African malaria mosquito vector by MALDI-TOF MS.

    Science.gov (United States)

    Niare, Sirama; Berenger, Jean-Michel; Dieme, Constentin; Doumbo, Ogobara; Raoult, Didier; Parola, Philippe; Almeras, Lionel

    2016-02-13

    The identification of blood meal sources in malaria vectors is critical to better understanding host/vector interactions and malaria epidemiology and control. Currently, the identification of mosquito blood meal origins is based on time-consuming and costly techniques such as precipitin tests, ELISA and molecular tools. Although these tools have been validated to identify the blood meal and trophic preferences of female Anopheles mosquitoes, they present several limitations. Recently, matrix-assisted, laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was successfully used as a quick and accurate tool for arthropod identification, including mosquitoes. The aim of the present work was to test whether MALDI-TOF MS could also be applied to identification of blood meal sources from engorged mosquitoes. Abdomen proteins extracted from Anopheles gambiae (stricto sensu, S molecular form) that were either unengorged or artificially engorged on seven distinct types of vertebrate blood (human, horse, sheep, rabbit, mouse, rat, dog) were submitted for MALDI-TOF MS. The comparison of mass spectrometry (MS) spectra from mosquito abdomens collected 1 h post-feeding, were able to discriminate blood meal origins. Moreover, using Aedes albopictus specimens, abdominal protein MS spectra from engorged mosquitoes were found specific to host blood source and independent of the mosquito species. A sequential analysis revealed stability of mosquito abdominal protein spectra up to 24 h post-feeding. These results indicate that MALDI-TOF MS could determine feeding patterns of freshly engorged mosquitoes up to 24 h post-blood meal. The MALDI-TOF MS technique appears to be an efficient tool for large epidemiological surveillance of vector-borne diseases and outbreak source identification.

  18. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists

    Directory of Open Access Journals (Sweden)

    Parveen Rahi

    2016-08-01

    Full Text Available Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.

  19. 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

  20. 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 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. Graphical Abstract ᅟ.

  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 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.

  3. 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

  4. 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.

    2017-11-01

    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. [Figure not available: see fulltext.

  5. 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

    -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......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...... 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...

  6. Immobilized carbon nanotubes as matrix for MALDI-TOF-MS analysis: applications to neutral small carbohydrates.

    Science.gov (United States)

    Ren, Shi-fang; Zhang, Li; Cheng, Zhi-hong; Guo, Yin-long

    2005-03-01

    In this work, we reported on the advantages of immobilized carbon nanotubes as a novel MALDI-matrix. Recently, carbon nanotubes have been reported to be an effective MALDI matrix for small molecules (Anal. Chem.2003, 75, 6191), as it can eliminate the interfering matrix peaks as well as form a web morphology to fully disperse the analyte and allow strong ultraviolet absorption for enhanced pulsed laser desorption and ionization. In our study, to overcome the problem that the carbon nanotube matrix may fly off from the target, a type of polyurethane adhesive, NIPPOLAN-DC-205, is introduced to immobilize carbon nanotubes on the target, which enables widespread application of carbon nanotubes as matrix for MALDI-MS analysis. At the same time, the properties of the carbon nanotubes as an efficient matrix remained after immobilization. The presence of NIPPOLAN-DC-205 increases the time for analysis at a particular desorption spot by minimizing the time-consuming search for "hot spots" and facilitating experiments such as post source decay (PSD) which need longer-lasting signals. Moreover, NIPPOLAN-DC-205 produces no interference peaks and can easily be cleaned with acetone. Fast evaporation technology may be used to enhance signal reproducibility in MALDI analysis using carbon nanotubes as matrix. Consequently, the applicability of the carbon nanotube as matrix for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of low molecular mass analytes is highly improved. The feasibility of the method employing polyurethane is demonstrated by comparison of the results produced from the carbon nanotube matrix with and without immobilization. In addition, neutral small carbohydrates, which are difficult to be ionized normally, can be cationized with high efficiency by MALDI-TOF-MS using the immobilized carbon nanotube matrix. The method was further applied to analyze peptides and detect urine glucose successfully.

  7. MALDI-TOF MS and chemometric based identification of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species.

    Science.gov (United States)

    Sousa, Clara; Botelho, João; Silva, Liliana; Grosso, Filipa; Nemec, Alexandr; Lopes, João; Peixe, Luísa

    2014-07-01

    MALDI-TOF MS is becoming the technique of choice for rapid bacterial identification at species level in routine diagnostics. However, some drawbacks concerning the identification of closely related species such as those belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex lead to high rates of misidentifications. In this work we successfully developed an approach that combines MALDI-TOF MS and chemometric tools to discriminate the six Acb complex species (A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, A. calcoaceticus, genomic species "Close to 13TU" and genomic species "Between 1 and 3"). Mass spectra of 83 taxonomically well characterized clinical strains, reflecting the breadth of currently known phenetic diversity within the Acb complex, were achieved from intact cells and cell extracts and analyzed with hierarchical cluster analysis (HCA) and partial least squares discriminant analysis (PLSDA). This combined approach lead to 100% of correct species identification using mass spectra obtained from intact cells. Moreover, it was possible to discriminate two Acb complex species (genomic species "Close to 13TU" and genomic species "Between 1 and 3") not included in the MALDI Biotyper database. Copyright © 2014 Elsevier GmbH. All rights reserved.

  8. 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.

  9. The Use of MALDI-TOF-MS and In Silico Studies for Determination of Antimicrobial Peptides' Affinity to Bacterial Cells

    Science.gov (United States)

    Mandal, Santi M.; Migliolo, Ludovico; Franco, Octavio L.

    2012-11-01

    Several methods have been proposed for determining the binding affinity of antimicrobial peptides (AMPs) to bacterial cells. Here the utilization of MALDI-TOF-MS was proposed as a reliable and efficient method for high throughput AMP screening. The major advantage of the technique consists of finding AMPs that are selective and specific to a wide range of Gram-negative and -positive bacteria, providing a simple reliable screening tool to determine the potential candidates for broad spectrum antimicrobial drugs. As a prototype, amp-1 and -2 were used, showing highest activity toward Gram-negative and -positive membranes respectively. In addition, in silico molecular docking studies with both peptides were carried out for the membranes. In silico results indicated that both peptides presented affinity for DPPG and DPPE phospholipids, constructed in order to emulate an in vivo membrane bilayer. As a result, amp-1 showed a higher complementary surface for Gram-negative while amp-2 showed higher affinity to Gram-positive membranes, corroborating MS analyses. In summary, results here obtained suggested that in vitro methodology using MALDI-TOF-MS in addition to theoretical studies may be able to improve AMP screening quality.

  10. 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.

  11. 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.

  12. 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.

  13. N-glycosylation profile analysis of Trastuzumab biosimilar candidates by Normal Phase Liquid Chromatography and MALDI-TOF MS approaches.

    Science.gov (United States)

    Sanchez-De Melo, Ivan; Grassi, Paola; Ochoa, Francisco; Bolivar, Jorge; García-Cózar, Francisco J; Durán-Ruiz, Ma Carmen

    2015-09-08

    The pharmaceutical market has entered an era in which the production of new therapeutics is being often replaced by "biosimilars", copies of already commercialized products waiting for the patents to expire in order to be distributed in a more competitive and affordable manners. Due to its relevance, the ErbB2-targeted monoclonal antibody Trastuzumab (Herceptin) used as breast cancer therapy is one of the main targets in the production of biosimilars. A major challenge is to produce antibodies with the same or the closest N-glycosylation pattern seen in the commercialized drug. Several factors, such as growing conditions or cell types employed, can determine the final composition and structure of the glycans, significantly affecting the properties of the generated antibodies. Therefore, an appropriate characterization is essential. In the present study, we describe two different but complementary strategies to characterize the N-glycosylation of two biosimilar candidates of Trastuzumab. In the first case, N-glycans are fluorescently labeled and separated by Normal Phase HPLC. Different sugars will elute at different times and can be identified using specific oligosaccharide standards. In the second approach, released glycans are permethylated and analyzed by MALDI-TOF MS, being able to determine the structure because of the differential sugar masses. The characterization of the N-glycosylation sites of therapeutic recombinant monoclonal antibodies (mAbs) is usually one of the most critical and time consuming steps in the developing process of biosimilars or any other glycosylated drug. Herein we describe two different but complementary approaches to characterize mAbs glycosylation patterns, the use of glycan fluorescence labeling coupled to HPLC and MALDI-TOF MS profile analysis. This article is part of a Special Issue entitled: HUPO 2014. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. 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.

  15. 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

  16. 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.G.M.; Boekhout, T.

    2014-01-01

    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

  17. 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

  18. 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.

  19. 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.

  20. Rapid identification of Enterobacteriaceae in milk and dairy products with the Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS

    Directory of Open Access Journals (Sweden)

    Miroslava Kačániová

    2017-11-01

    Full Text Available Identification of microorganisms by MALDI-TOF MS Biotyper has been demonstrated to be accurate, rapid and lower cost than conventional food investigation methods. Rapid identification of pathogenic and spoilage microorganisms is crucial for dairy industry to ensure the quality and safety of milk and milk products. In this study, the bacterial species representing the Enterobacteriaceae family were identified in raw milk and milk products using the MALDI-TOF MS mass spectrometry. Altogether, 20 samples of Slovak milk and milk products were examined. Samples were cultured on VRBG agar at 37 °C for 24-48 h. Typical bacterial colonies were selected for identification with MALDI-TOF MS Biotyper. Escherichia coli and Enterobacter sp. were the most abundant  Enterobacteriaceae family representatives identified. E. coli was found in nine  and Enterobacter sp. in eight samples. Enterobacter sp. comprised 49 % and Escherichia coli 23 % of all bacterial isolates. The study shows that MALDI-TOF MS Biotyper was reliable identification method of Enterobacteriaceae in milk and dairy products. This method was helpful in evaluation of bacterial contamination of milk.

  1. 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.

  2. 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

  3. 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

  4. 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...

  5. Nosocomial infection due to Enterococcus cecorum identified by MALDI-TOF MS and Vitek 2 from a blood culture of a septic patient

    OpenAIRE

    Warnke, Philipp; K?ller, Thomas; Stoll, Paul; Podbielski, Andreas

    2015-01-01

    We report the case of a nosocomial infection due to Enterococcus cecorum isolated from a blood culture of a 75-year-old septic male patient. Matrix-assisted laser desorption?ionization time-of-flight mass spectrometry (MALDI-TOF MS) and Vitek 2 succeeded in identification of the isolate.

  6. 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…

  7. 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.

  8. 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

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

    Science.gov (United States)

    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

    2014-02-01

    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 neonates, children and adults and can be life-saving for those patients. Ma-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been reported to be a rapid and reliable diagnostic tool to identify clinically important yeasts, but so far no data have been reported on identification of Malassezia isolates with this technique. To create an extensive database of main mass spectra (MSPs) that will allow quick identification of Malassezia species by MALDI-TOF MS. An in-house library of 113 MSPs was created from 48 reference strains from the CBS-KNAW yeast collection. The in-house library was challenged with two test sets of Malassezia strains, namely 165 reference strains from the CBS collection and 338 isolates collected in Greece, Italy, Sweden and Thailand. MALDI-TOF MS allowed correct identification of all 14 Malassezia spp. MALDI-TOF MS results were concordant with those of sequence analyses of the internal transcribed spacers (ITS1/ITS2) and the D1/D2 domains of the large subunit of the ribosomal DNA. Implementation of the MALDI-TOF MS system as a routine identification tool will contribute to correct identification of Malassezia yeasts with minimal effort and in a short turnaround time, which is especially important for the rapid identification of Malassezia in skin diseases and nosocomial outbreaks. © 2013 British Association of Dermatologists.

  10. N-doped graphene: an alternative carbon-based matrix for highly efficient detection of small molecules by negative ion MALDI-TOF MS.

    Science.gov (United States)

    Min, Qianhao; Zhang, Xiaoxia; Chen, Xueqin; Li, Siyuan; Zhu, Jun-Jie

    2014-09-16

    Gas-phase N-doped graphene (gNG) was synthesized by a modified thermal annealing method using gaseous melamine as nitrogen source and then for the first time applied as a matrix in negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for small molecule analysis. Unlike the complicated adducts produced in positive ion mode, MS spectra obtained on gNG matrix in negative ion mode was only featured by deprotonated molecule ion peaks without matrix interference. By the gNG assisted desorption/ionization (D/I) process, some applications were carried out on a wide range of low-molecular weight (MW) analytes including amino acids, fatty acids, peptides, anabolic androgenic steroids as well as anticancer drugs, with an extraordinary laser desorption/ionization (LDI) efficiency over traditional α-cyano-4-hydroxycinnamic acid (CHCA) and other carbon-based materials in the negative ion detection mode. By comparison of a series of graphene-based matrixes, two main factors of matrix gNG were unveiled to play a decisive role in assisting negative ion D/I process: a well-ordered π-conjugated system for laser absorption and energy transfer; pyridinic-doped nitrogen species functioning as deprotonation sites for proton capture on negative ionization. The good salt tolerance and high sensitivity allowed further therapeutic monitoring of anticancer drug nilotinib in the spiked human serum, a real case of biology. Signal response was definitely obtained between 1 mM and 1 μM, meeting the demand of assessing drug level in the patient serum. This work creates a new application branch for nitrogen-doped graphene and provides an alternative solution for small molecule analysis.

  11. Outer Membrane Proteome Analysis of Indian Strain of Pasteurella multocida Serotype B:2 by MALDI-TOF/MS Analysis

    Directory of Open Access Journals (Sweden)

    A. Prasannavadhana

    2014-01-01

    Full Text Available Identification of outer membrane proteins (OMPs is important to understand the bacteria structure and function, host-pathogen interaction, development of novel vaccine candidates, and diagnostic antigens. But till now the key antigens of P. multocida B:2 isolate causing haemorrhagic septicaemia (HS in animals are not clearly defined. In this study, P52 strain of P. multocida serotype B:2 was grown in vitro under iron-rich and iron-limited condition. The OMPs were extracted by sarkosyl method followed by SDS-PAGE and the proteins were identified by MALDI-TOF/MS analysis. In total, 22 proteins were identified, of which 7 were observed exclusively under iron-limited condition. Most of the high molecular weight proteins (TbpA, HgbA, HgbB, HasR, IroA, and HemR identified in this study were involved in iron acquisition. Some hypothetical proteins (HP-KCU-10206, HP and AAUPMB 08244, HP AAUPMB 21592, HP AAUPMB 19766, AAUPMB 11295 were observed for the first time in this study which could be unique to serotype B:2. Further functional in vivo study of the proteins identified are required to explore the utility of these proteins in developing diagnostics and vaccine against HS.

  12. N-(1-naphthyl) ethylenediamine dinitrate: a new matrix for negative ion MALDI-TOF MS analysis of small molecules.

    Science.gov (United States)

    Chen, Rui; Chen, Suming; Xiong, Caiqiao; Ding, Xunlei; Wu, Chih-Che; Chang, Huan-Cheng; Xiong, Shaoxiang; Nie, Zongxiu

    2012-09-01

    An organic salt, N-(1-naphthyl) ethylenediamine dinitrate (NEDN), with rationally designed properties of a strong UV absorbing chromophore, hydrogen binding and nitrate anion donors, has been employed as a matrix to analyze small molecules (m/z negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Compared with conventional matrixes such as α-cyano-4-hydroxycinnamic acid (CCA) and 2,5-dihydroxybenzoic acid (DHB), NEDN provides a significant improvement in detection sensitivity and yields very few matrix-associated fragment and cluster ions interfering with MS analysis. For low-molecular-weight saccharides, the lowest detection limit achieved ranges from 500 amol to 5 pmol, depending on the molecular weight and the structure of the analytes. Additionally, the mass spectra in the lower mass range (m/z matrix particularly useful for structural identification of oligosaccharides by post-source decay (PSD) MALDI-MS. Such a characteristic is illustrated by using maltoheptaose as a model system. This work demonstrates that NEDN is a novel negative ion-mode matrix for MALDI-MS analysis of small molecules with nitrate anion attachment.

  13. Identification and growth dynamics of meat spoilage microorganisms in modified atmosphere packaged poultry meat by MALDI-TOF MS.

    Science.gov (United States)

    Höll, Linda; Behr, Jürgen; Vogel, Rudi F

    2016-12-01

    Modified atmosphere packaging (MAP) is widely used in food industry to extend the microbiological shelf-life of meat. Typically, poultry meat has been packaged in a CO2/N2 atmosphere (with residual low O2). Recently, some producers use high O2 MAP for poultry meat to empirically reach comparable shelf lifes. In this work, we compared spoilage microbiota of skinless chicken breast in high (80% O2, 20% CO2) and low O2 MAP (65% N2 and 35% CO2). Two batches of meat were incubated in each atmosphere for 14 days at 4 °C and 10 °C. Atmospheric composition of each pack and colony forming units (25 °C, 48 h, BHI agar) of poultry samples were determined at seven timepoints. Identification of spoilage organisms was carried out by MALDI-TOF MS. Brochothrix thermosphacta, Carnobacterium sp. and Pseudomonas sp. were the main organisms found after eight days at 4 °C and 10 °C in high O2 MAP. In low O2 MAP, the main spoilage microbiota was represented by species Hafnia alvei at 10 °C, and genera Carnobacterium sp., Serratia sp., and Yersinia sp. at 4 °C. High O2 MAP is suggested as preferential gas because were less detrimental and pathogens like Yersinia were not observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. 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.

  15. Identification and characterization of a new IgE-binding protein in mackerel ( Scomber japonicus) by MALDI-TOF-MS

    Science.gov (United States)

    Wang, Bangping; Li, Zhenxing; Zheng, Lina; Liu, Yixuan; Lin, Hong

    2011-03-01

    As fish is one source of the `big eight' food allergens, the prevalence of fish allergy has increased over the past few years. In order to better understand fish allergy, it is necessary to identify fish allergens. Based on the sera from fish-allergenic patients, a 28 kDa protein from local mackerel ( Scomber japonicus), which has not been reported as a fish allergen, was found to be reactive with most of the patients' sera. The 28 kDa protein was analyzed by MALDI-TOF-MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry). Mascot search in NCBI database (Date: 08/07/2010) showed that the top protein matched, i.e. triosephosphate isomerase (TPI) from Xiphophorus maculatus and Poecilia reticulata, had a mowse (molecular weight search) score of 98. In addition, TPI from Epinephelus coioides also matched this mackerel protein with a mowse score of 96. Because TPI is considered as an allergen in other non-fish organisms, such as lychee, wheat, latex, archaeopotamobius ( Archaeopotamobius sibiriensis) and crangon ( Crangon crangon), we consider that it may also be an allergen in mackerel.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Yi Ming Lin

    2008-12-01

    Full Text Available 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.

  18. Comparison of MALDI-TOF MS, housekeeping gene sequencing, and 16S rRNA gene sequencing for identification of Aeromonas clinical isolates.

    Science.gov (United States)

    Shin, Hee Bong; Yoon, Jihoon; Lee, Yangsoon; Kim, Myung Sook; Lee, Kyungwon

    2015-03-01

    The genus Aeromonas is a pathogen that is well known to cause severe clinical illnesses, ranging from gastroenteritis to sepsis. Accurate identification of A. hydrophila, A. caviae, and A. veronii is important for the care of patients. However, species identification remains difficult using conventional methods. The aim of this study was to compare the accuracy of different methods of identifying Aeromonas at the species level: a biochemical method, matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS), 16S rRNA sequencing, and housekeeping gene sequencing (gyrB, rpoB). We analyzed 65 Aeromonas isolates recovered from patients at a university hospital in Korea between 1996 and 2012. The isolates were recovered from frozen states and tested using the following four methods: a conventional biochemical method, 16S rRNA sequencing, housekeeping gene sequencing with phylogenetic analysis, and MALDI-TOF MS. The conventional biochemical method and 16S rRNA sequencing identified Aeromonas at the genus level very accurately, although species level identification was unsatisfactory. MALDI-TOF MS system correctly identified 60 (92.3%) isolates at the species level and an additional four (6.2%) at the genus level. Overall, housekeeping gene sequencing with phylogenetic analysis was found to be the most accurate in identifying Aeromonas at the species level. The most accurate method of identification of Aeromonas to species level is by housekeeping gene sequencing, although high cost and technical difficulty hinder its usage in clinical settings. An easy-to-use identification method is needed for clinical laboratories, for which MALDI-TOF MS could be a strong candidate.

  19. 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

  20. Rapid detection of the plasmid-mediated quinolone resistance determinant AAC(6')-Ib-cr in Enterobacteriaceae by MALDI-TOF MS analysis.

    Science.gov (United States)

    Oviaño, Marina; Rodríguez-Martínez, Jose Manuel; Pascual, Álvaro; Bou, Germán

    2017-04-01

    Rapid detection of the plasmid-mediated quinolone resistance determinant AAC(6')-Ib-cr in Enterobacteriaceae by measuring acetyltransferase activity against fluoroquinolones by MALDI-TOF MS analysis. The presence of the AAC(6')-Ib-cr enzyme was determined by MS by measuring the acetyltransferase activity of a collection of 81 isogenic Escherichia coli control strains [10 carrying the AAC(6')-Ib-cr enzyme during exposure to ciprofloxacin, norfloxacin and levofloxacin] and further analysis of 36 clinical isolates [25 carrying the AAC(6')-Ib-cr enzyme in addition to different combinations of quinolone resistance mechanisms]. The effect of acetylation yields an increase of 43 Da in the mass of ciprofloxacin and norfloxacin, but not of levofloxacin, that can be observed by visual inspection of the mass peaks in the spectra. Based on the characteristic peak pattern for the acetylated and non-acetylated forms of ciprofloxacin and norfloxacin, a clear differentiation between AAC(6')-Ib-cr-producing isolates and non-AAC(6')-Ib-cr-producing isolates was detected after an incubation time of 30 min, both in the isogenic control strains and in the clinical isolates. Levofloxacin was found intact. A 100% agreement was found between the MALDI-TOF-MS-based assay and the results of the molecular characterization of the tested isolates. MALDI-TOF MS is an outstanding method for detection of the AAC(6')-Ib-cr enzyme in clinical samples. The method is easy to perform and not time consuming, as analytical results can be obtained within minutes. For the first time, MALDI-TOF MS has been used to detect resistance promoted by enzymatic modification of antibiotics aside from β-lactamases, expanding the capacity of analysis into new families of antibiotics. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. 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

  2. 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.

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

    Science.gov (United States)

    Halada, Petr; Hlavackova, Kristyna; Dvorak, Vit; Volf, Petr

    2018-02-01

    The aim of the study was to evaluate the potential of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) for the species identification of sand flies at different developmental stages and map changes in their protein profiles during the course of whole life cycle. Specimens of six different species from laboratory colonies at larval and pupal stages were examined using MALDI-TOF MS. The protein profiles of larvae were stable from the L2 to L4 developmental stages and clearly distinguishable at the species level. In a validation study, 123 larvae of the six species were queried against reference database resulting in 93% correct species identification (log score values higher than 2.0). The spectra generated from sand fly pupae allow species identification as well and surprisingly, in contrast to biting midges and mosquitoes, they did not change during this developmental stage. For adults, thorax was revealed as the optimal body part for sample preparation yielding reproducible spectra regardless age and diet. Only variations were uncovered for freshly engorged females profiles of which were affected by blood signals first two days post bloodmeal. The findings demonstrate that in addition to adult species differentiation MALDI-TOF MS may also serve as a rapid and effective tool for species identification of juvenile stages of phlebotomine sand flies. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. 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.

  5. Identification and Characterization of Lipopeptides from Bacillus subtilis B1 Against Sapstain Fungus of Rubberwood Through MALDI-TOF-MS and RT-PCR.

    Science.gov (United States)

    Sajitha, K L; Dev, Suma Arun; Maria Florence, E J

    2016-07-01

    Bacillus subtilis is a potent biocontrol agent producing a wide array of antifungal lipopeptides for the inhibition of fungal growth. B. subtilis B1 isolated from market-available compost provided an efficient control of rubberwood sapstain fungus, Lasiodiplodia theobromae. The current study is aimed to identify and characterize the lipopeptides responsible for the biocontrol of rubberwood sapstain fungus by Bacillus subtilis B1. The bacterial whole-cell surface extract from the dual culture of B. subtilis B1 and sapstain fungus (L. theobromae) was analysed using MALDI-TOF-MS. The protonated as well as sodium, potassium adducts of homologues of iturin C, surfactin, bacillomycin D and fengycin A and B were identified and expression of the lipopeptide biosynthetic genes could be confirmed through RT-PCR. This is the first report of mycobacillin and trimethylsilyl derivative of bacilysin during antagonism through MALDI-TOF-MS. MALDI-TOF-MS with RT-PCR offered easy platforms to characterize the antifungal lipopeptides. The identification of antifungal lipopeptides can lead to the formulation of prospective biocontrol by-products which have wide-scale utility.

  6. 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.

  7. 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.

  8. Discrepancy in MALDI-TOF MS identification of uncommon Gram-negative bacteria from lower respiratory secretions in patients with cystic fibrosis

    Directory of Open Access Journals (Sweden)

    AbdulWahab A

    2015-04-01

    Full Text Available Atqah AbdulWahab,1,2 Saad J Taj-Aldeen,3 Emad Bashir Ibrahim,3 Eman Talaq,4 Marawan Abu-Madi,4 Rashmi Fotedar5 1Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar; 2Department of Pediatrics, Weill Cornell Medical College, Doha, Qatar; 3Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar; 4Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar; 5Biotechnology Center, Ministry of Environment, Doha, Qatar Introduction: Early identification of microbial organisms from respiratory secretions of patients with cystic fibrosis (CF is important to guide therapeutic decisions. The objective was to compare the accuracy of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS relative to the conventional phenotypic method in identifying common bacterial isolates, including nonfermenting Gram-negative bacteria, in a cohort of patients with CF. Methods: A total of 123 isolates from 50 patients with CF representing 14 bacterial species from respiratory specimens were identified using MALDI-TOF MS in parallel with conventional phenotypic methods. Discrepancies were confirmed by 16S ribosomal RNA (rRNA gene sequencing in five Gram-negative isolates. Results: The MALDI-TOF MS managed to identify 122/123 (99.2% bacterial isolates to the genus level and 118/123 (95.9% were identified to the species level. The MALDI-TOF MS results were 100% consistent to the species level with conventional phenotypic identification for isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenzae, Streptococcus pyogenes, Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and other uncommon organisms such as Chryseobacterium gleum and Enterobacter cloacae. The 5/123 (4.6% isolates misidentified were all Gram-negative bacteria. The isolation of E. cloacae and Haemophilus paraphrohaemolyticus may extend the

  9. Biotyping of Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates from France and Algeria Using MALDI-TOF MS

    Science.gov (United States)

    Berrazeg, Meryem; Diene, Seydina M.; Drissi, Mourad; Kempf, Marie; Richet, Hervé; Landraud, Luce; Rolain, Jean-Marc

    2013-01-01

    Background Klebsiella pneumoniae is one of the most important pathogens responsible for nosocomial outbreaks worldwide. Epidemiological analyses are useful in determining the extent of an outbreak and in elucidating the sources and the spread of infections. The aim of this study was to investigate the epidemiological spread of K. pneumoniae strains using a MALDI-TOF MS approach. Methods Five hundred and thirty-five strains of K. pneumoniae were collected between January 2008 and March 2011 from hospitals in France and Algeria and were identified using MALDI-TOF. Antibiotic resistance patterns were investigated. Clinical and epidemiological data were recorded in an Excel file, including clustering obtained from the MSP dendrogram, and were analyzed using PASW Statistics software. Results Antibiotic susceptibility and phenotypic tests of the 535 isolates showed the presence of six resistance profiles distributed unequally between the two countries. The MSP dendrogram revealed five distinct clusters according to an arbitrary cut-off at the distance level of 500. Data mining analysis of the five clusters showed that K. pneumoniae strains isolated in Algerian hospitals were significantly associated with respiratory infections and the ESBL phenotype, whereas those from French hospitals were significantly associated with urinary tract infections and the wild-type phenotype. Conclusions MALDI-TOF was found to be a promising tool to identify and differentiate between K. pneumoniae strains according to their phenotypic properties and their epidemiological distribution. This is the first time that MALDI-TOF has been used as a rapid tool for typing K. pneumoniae clinical isolates. PMID:23620754

  10. 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.

  11. 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

  12. 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.

  13. Utility of Conventional Culture and MALDI-TOF MS for Identification of Microbial Communities in Bronchoalveolar Lavage Fluid in Comparison with the GS Junior Next Generation Sequencing System.

    Science.gov (United States)

    Sung, Ji Yeon; Hwang, Younjee; Shin, Mi Hwa; Park, Moo Suk; Lee, Sang Hoon; Yong, Dongeun; Lee, Kyungwon

    2018-03-01

    Diverse microbiota exist in the lower respiratory tract. Although next generation sequencing (NGS) is the most widely used microbiome analysis technique, it is difficult to implement NGS in clinical microbiology laboratories. Therefore, we evaluated the performance of conventional culture methods together with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying microbiota in bronchoalveolar lavage (BAL) fluid. BAL fluid samples (n=27) were obtained from patients undergoing diagnostic bronchoscopy for lung mass evaluation. Bacterial and fungal culture was performed with conventional media used in clinical microbiology laboratories. On an average, 20 isolated colonies were picked from each agar plate and identified by MALDI-TOF MS. Microbiome analysis using 16S rRNA NGS was conducted for comparison. Streptococcus spp. and Neisseria spp. were most frequently cultured from the BAL fluid samples. In two samples, Enterobacteriaceae grew predominantly on MacConkey agar. Actinomyces and Veillonella spp. were commonly identified anaerobes; gut bacteria, such as Lactobacillus, Bifidobacterium, and Clostridium, and fungi were also isolated. NGS revealed more diverse bacterial communities than culture, and Prevotella spp. were mainly identified solely by NGS. Some bacteria, such as Staphylococcus spp., Clostridium spp., and Bifidobacterium spp., were identified solely by culture, indicating that culture may be more sensitive for detecting certain bacteria. Culture and NGS of BAL fluid samples revealed common bacteria with some different microbial communities. Despite some limitations, culture combined with MALDI-TOF MS might play a complementary role in microbiome analysis using 16S rRNA NGS. © The Korean Society for Laboratory Medicine

  14. 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

  15. 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.

  16. 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.

    Science.gov (United States)

    Paauw, Armand; Trip, Hein; Niemcewicz, Marcin; Sellek, Ricela; Heng, Jonathan Me; Mars-Groenendijk, Roos H; de Jong, Ad L; Majchrzykiewicz-Koehorst, Joanna A; Olsen, Jaran S; Tsivtsivadze, Evgeni

    2014-06-18

    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 effective response to cholera outbreaks. The use of ferulic acid as a matrix in a new MALDI-TOF MS assay increased the measurable mass range of existing MALDI-TOF MS protocols for bacterial identification. The assay enabled rapid discrimination between epidemic V. cholerae O1/O139 strains and other less pathogenic V. cholerae strains. OmpU, an outer membrane protein whose amino acid sequence is highly conserved among epidemic strains of V. cholerae, appeared as a discriminatory marker in the novel MALDI-TOF MS assay. The extended mass range of MALDI-TOF MS measurements obtained by using ferulic acid improved the screening for biomarkers in complex protein mixtures. Differences in the mass of abundant homologous proteins due to variation in amino acid sequences can rapidly be examined in multiple samples. Here, a rapid MALDI-TOF MS assay was developed that could discriminate between epidemic O1/O139 strains and other less pathogenic V. cholerae strains based on differences in mass of the OmpU protein. It appeared that the amino acid sequence of OmpU from epidemic V. cholerae O1/O139 strains is unique and highly conserved.

  17. 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.

  18. 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.

  19. 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...... 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...... fetuin were site-specifically profiled, and good correlation between peak intensities and relative abundances was found with only a minor loss of sialic acids (r = 0.9664, n = 5). For glycopeptide purification, a range of hydrophilic and graphite materials packed in microcolumn format proved capable...

  20. VibrioBase: A MALDI-TOF MS database for fast identification of Vibrio spp. that are potentially pathogenic in humans.

    Science.gov (United States)

    Erler, René; Wichels, Antje; Heinemeyer, Ernst-August; Hauk, Gerhard; Hippelein, Martin; Reyes, Nadja Torres; Gerdts, Gunnar

    2015-02-01

    Mesophilic marine bacteria of the family Vibrionaceae, specifically V. cholerae, V. parahaemolyticus and V. vulnificus, are considered to cause severe illness in humans. Due to climate-change-driven temperature increases, higher Vibrio abundances and infections are predicted for Northern Europe, which in turn necessitates environmental surveillance programs to evaluate this risk. We propose that whole-cell matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling is a promising tool for the fast and reliable species classification of environmental isolates. Because the reference database does not contain sufficient Vibrio spectra we generated the VibrioBase database in this study. Mass spectrometric data were generated from 997 largely environmental strains and filed in this new database. MALDI-TOF MS clusters were assigned based on the species classification obtained by analysis of partial rpoB (RNA polymerase beta-subunit) sequences. The affiliation of strains to species-specific clusters was consistent in 97% of all cases using both approaches, and the extended VibrioBase generated more specific species identifications with higher matching scores compared to the commercially available database. Therefore, we have made the VibrioBase database freely accessible, which paves the way for detailed risk assessment studies of potentially pathogenic Vibrio spp. from marine environments. Copyright © 2014 Elsevier GmbH. All rights reserved.

  1. Identification of Differential Protein Expression in Hepatocellular Carcinoma Induced Wistar Albino Rats by 2D Electrophoresis and MALDI-TOF-MS Analysis.

    Science.gov (United States)

    Vedarethinam, Vadanasundari; Dhanaraj, Karthik; Soundherrajan, Ilavenil; Sivanesan, Ravikumar

    2016-04-01

    Hepato cellular carcinoma (HCC) is a type of malignant tumor. To investigate the proteins in cancer molecular mechanism and its role in HCC, we have used proteomic tools such as 2DE and MALDI-TOF-MS. Our investigation ravels that, plasma α-fetoprotein and carcinoembryonic antigen levels were elevated in DEN induced rats and gradually decreased after the treatment with 1,3BPMU. 2DE and MALDI-TOF-MS tool offers to identify the up and down regulation of proteins in HCC. Proteomic study reveals that, five differentially expressed proteins were identified in DEN induced rats and 1,3BPMU treated rats i.e. three up regulated protein such as T kininogen, NDPKB, PRMT1 (DEN induced rats), RGS19 and PAF (1,3BPMU treated rats) in 3BPMU treated rats, activation of transcription of a single gene from multiple promoters provides flexibility in the controlled gene expression. The regulations of hepatocyte stimulating factor were slow down the proliferation of hepatic cell and uncontrolled hepatic cell growth and also molecular signals strongly argue for a patho-physiological role in liver metastasis to control the cell aggression. This indicates that, anti cancer property of 1,3BPMU can be used as potent anti cancer agent. The present study also shows the proteomic approach helps to elucidate the tumor maker as well as regulatory marker proteins in HCC.

  2. Whole genome and transcriptome analysis reveal MALDI-TOF MS and SDS-PAGE have limited performance for the detection of the key outer membrane protein in carbapenem-resistantKlebsiella pneumoniaeisolates.

    Science.gov (United States)

    Pinto, Naina Adren; D'Souza, Roshan; Hwang, In Sik; Choi, Jongrak; In, Yong Ha; Park, Hyung Soon; Ryu, Choong-Min; Yong, Dongeun; Lee, Kyungwon

    2017-10-17

    To detect the outer membrane protein (OMP), which plays a key role in carbapenem resistance, whole-genome and transcriptome analysis of the clinical carbapenem-resistant Klebsiella pneumoniae was carried out. The index strain lacked both OmpK35 and OmpK36, whereas the other strains lacked only OmpK35. After SDS-PAGE, the putative OMP bands were excised and identified as OmpA and OmpK36. MALDI-TOF MS showed peaks at ∼36 and ∼38 kDa that corresponded to OmpA and OmpK36, respectively. In all the strains except YMC2014/03/P345, the ∼38 kDa peaks were present. The K . pneumoniae ATCC 13883 isolate showed three bands on SDS-PAGE and three corresponding peaks on MALDI-TOF MS. The additional third peak at ∼37 kDa corresponding to OmpK35 was observed. To verify OmpK35 peak detection in other K. pneumoniae isolates by MALDI-TOF MS, we analyzed six strains from our laboratory's strain bank. Whole genome sequence indicated that only two isolates had intact OmpK35. Both MALDI-TOF MS and SDS-PAGE did not show a ∼37 kDa peak or an OmpK35 band as observed in the K. pneumoniae ATCC 13883 isolate. Separation using SDS-PAGE showed a single peak representing OmpA. Therefore, both SDS-PAGE and MALDI-TOF MS were not completely reliable for OMP detection because they fail to detect OmpK35. To the best of our knowledge, this is the first report on the performance of SDS-PAGE and MALDI-TOF MS for the detection of OMP's using whole-genome and RNA sequencing analyses.

  3. Teaching Microbial Identification with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS and Bioinformatics Tools

    Directory of Open Access Journals (Sweden)

    Wenfa Ng

    2013-01-01

    Full Text Available Ever since the first observation of “animalcules” under a microscope, and the subsequent discovery of microorganisms of myriad size, shape, pigmentation and motility modes, classification in aid of microbial identification is key to understanding inter-relationships between diverse microbes. Combining universal applicability with robustness, 16S rRNA sequencing is the gold standard for microbial typing; however, recent developments in clinical diagnostics have called attention to a shift towards PCR-independent instrumentation and methods given PCR’s requirement for expensive and complex sample preparation. Using ribosomal proteins as biomarkers for evolutionary relatedness, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS - originally developed for the soft ionization of proteins and peptides in proteomics studies - has been successfully applied to identifying bacteria, archaea, fungi and viruses to the species, and, on occasions, sub-species level. Though experimentally proven and increasingly adopted in the clinic, the relatively low-cost (on a per sample basis and rapid MALDI-TOF MS microbial identification technique, along with its theoretical principles and methodology, is a conspicuous absentee in contemporary microbiology curricula. Motivated by a desire to close the curriculum gap, this article describes a discovery-based activity for teaching microbial identification - using MALDI-TOF MS in combination with open-source genomics and proteomics search tools – while providing tips on mass spectra interpretation and activity implementation for lowering the barrier for classroom adoption. Infused with inquiry-based learning concepts guiding students in identifying microbes from environmental water samples with unknown species diversity, the activity spurs students’ learning by igniting their spirit of inquiry, which leads to better mastery of concepts; a significant departure from

  4. A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni

    Directory of Open Access Journals (Sweden)

    Christian ePenny

    2016-05-01

    Full Text Available MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this study was to enhance strain level resolution for Campylobacter jejuni through the optimization of spectrum processing parameters using a series of designed experiments. A collection of 172 strains of C. jejuni were collected from Luxembourg, New Zealand, North America, and South Africa, consisting of four groups of antibiotic resistant isolates. The groups included: 1 65 strains resistant to cefoperazone 2 26 resistant to cefoperazone and beta-lactams 3 5 strains resistant to cefoperazone, beta-lactams, and tetracycline, and 4 76 strains resistant to cefoperazone, teicoplanin, amphotericin B and cephalothin. Initially, a model set of 16 strains (three biological replicates and three technical replicates per isolate, yielding a total of 144 spectra of C. jejuni was subjected to each designed experiment to enhance detection of antibiotic resistance. The most optimal parameters were applied to the larger collection of 172 isolates (two biological replicates and three technical replicates per isolate, yielding a total of 1,031 spectra. We observed an increase in antibiotic resistance detection whenever either a curve based similarity coefficient (Pearson or ranked Pearson was applied rather than a peak based (Dice and/or the optimized preprocessing parameters were applied. Increases in antimicrobial resistance detection were scored using the jackknife maximum similarity technique following cluster analysis. From the first four groups of antibiotic resistant isolates, the optimized preprocessing parameters increased detection respective to the aforementioned groups by: 1 five percent 2 nine percent 3 ten percent, and 4 two percent. An additional second

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

    DEFF Research Database (Denmark)

    Hansen, HG; Overgaard, Julie; Lajer, M

    2010-01-01

    PURPOSE AND EXPERIMENTAL DESIGN: 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...... with a MALDI-TOF-MS readout were successfully established. Using these protocols and a combined univariate (Kruskal-Wallis) and multivariate (independent component analysis) statistical analysis approach, ten single peptides and three multi-peptide candidate biomarkers were found. Employment of RPC18 and weak...... cation exchange magnetic beads proved to be complementary. CONCLUSIONS AND CLINICAL RELEVANCE: The proteins found in this study, including C3f and apolipoprotein C-I, represent new candidate biomarkers for DN from the plasma peptidome. The automated procedures and implementation of independent components...

  6. 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.

    Science.gov (United States)

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

    2014-04-01

    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 identification of BSI Candida isolates. The epidemiology, risk factors, demographic features, species distribution, and clinical outcome associated with candidemia in patients admitted to a single tertiary-care hospital in Qatar, were analyzed. A single-center, retrospective analysis covering the period from January 1, 2004 to December 31, 2010 was performed. Molecular identification used sequence analysis of the D1/D2 domains of the large subunit ribosomal DNA (LSU rDNA) and the ITS1/2 regions of the rDNA. MALDI-TOF MS-based identification of all yeast isolates was performed with the ethanol/formic acid extraction protocol according to Bruker Daltonics (Bremen, Germany). The susceptibility profiles of 201 isolates to amphotericin B, itraconazole, fluconazole, voriconazole, anidulafungin, caspofungin, posaconazole, and isavuconazole were tested using CLSI standard broth microdilution method (M27-A3 and M27 S4) guidelines. Statistical analyses were performed with the statistical package SPSS 19.0. A total of 187 patients with 201 episodes of candidemia were identified. Candida albicans was the most common species isolated (33.8 %; n = 68), whereas non-albicans Candida species represented 66.2 % (n = 133) of the episodes. The species distribution and outcome of candidemia showed a difference in the crude mortality between patients infected with C. albicans (n = 30; 45.5 %) and non-albicans Candida species. For example, C. parapsilosis candidemia was associated with the lowest mortality rate (40.6 %), and patients with other non-albicans species had the highest mortality rate (68-71.4 %). High mortality rates were observed among pediatric (60 years of age). All strains showed low minimum

  7. 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.

  8. Rapid identification of Bacillus anthracis spores in suspicious powder samples by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Dybwad, Marius; van der Laaken, Anton L; Blatny, Janet Martha; Paauw, Armand

    2013-09-01

    Rapid and reliable identification of Bacillus anthracis spores in suspicious powders is important to mitigate the safety risks and economic burdens associated with such incidents. The aim of this study was to develop and validate a rapid and reliable laboratory-based matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis method for identifying B. anthracis spores in suspicious powder samples. A reference library containing 22 different Bacillus sp. strains or hoax materials was constructed and coupled with a novel classification algorithm and standardized processing protocol for various powder samples. The method's limit of B. anthracis detection was determined to be 2.5 × 10(6) spores, equivalent to a 55-μg sample size of the crudest B. anthracis-containing powder discovered during the 2001 Amerithrax incidents. The end-to-end analysis method was able to successfully discriminate among samples containing B. anthracis spores, closely related Bacillus sp. spores, and commonly encountered hoax materials. No false-positive or -negative classifications of B. anthracis spores were observed, even when the analysis method was challenged with a wide range of other bacterial agents. The robustness of the method was demonstrated by analyzing samples (i) at an external facility using a different MALDI-TOF MS instrument, (ii) using an untrained operator, and (iii) using mixtures of Bacillus sp. spores and hoax materials. Taken together, the observed performance of the analysis method developed demonstrates its potential applicability as a rapid, specific, sensitive, robust, and cost-effective laboratory-based analysis tool for resolving incidents involving suspicious powders in less than 30 min.

  9. Novel PDD-PDT system based on spectrophotometric real-time fluorescence monitoring and MALDI-TOF-MS analysis of tumors

    Science.gov (United States)

    Yoshida, Takato O.; Kohno, Eiji; Dodeller, Marc; Sakurai, Takashi; Yamamoto, Seiji; Terakawa, Susumu

    2009-06-01

    In the PDT practice for tumor patients, the dose and irradiation time for the treatment are chosen by experience and not by real need. To establish advanced PDD-PDT model system for patients, we developed a method for monitoring the cell-death based on a spectrophotometric real-time change in fluorescence in HeLa-tumors during Photofrin®-PDT and ALA-PDT. Here, we describe the results of application of the new PDD-PDT system to human tumors. The fluorescence spectra obtained from human tumors were analyzed by the differential spectral analysis. The mass-spectral changes of tumor tissues during PDD-PDT were also examined by MALDI-TOF-MS/MS. The first author's seborrheic keratosis was monitored with this system during the PDD-PDT with a topically applied ALA-ointment. The changes in fluorescence spectrum were successfully detected, and the tumor regressed completely within 5 months. The differential spectral analysis of PDD-PDT-fluorescence monitoring spectra of tumors and isolated mitochondria showed a marked decrease of three peaks in the red region indicative of the PDD (600 - 720 nm), and a transient rise followed by a decline of peaks in the green region indicative of the PDT (450 - 580 nm). The MALDI-TOF-MS analysis of PDD-PDT HeLa-tumors showed a consumption of Photofrin-deuteroporphyrin and ALA-PpIX, and decreases in protein mass in the range of 4,000 - 16,000 Da, m/z 4929, 8564, 10089, 15000, and an increase in m/z 7002 in a Photofrin® PDD-PDT monitoring tumor.

  10. Complementary use of MALDI-TOF MS and real-time PCR-melt curve analysis for rapid identification of methicillin-resistant staphylococci and VRE.

    Science.gov (United States)

    Chan, Wai-Sing; Chan, Tsz-Ming; Lai, Tsz-Wan; Chan, Jasper Fuk-Woo; Lai, Raymond Wai-Man; Lai, Christopher Koon-Chi; Tang, Bone Siu-Fai

    2015-02-01

    To develop a rapid method for routine screening of methicillin-resistant staphylococci and VRE for clinical isolates and positive blood cultures. Our method consisted of two parts: MALDI-TOF MS was used for identification of staphylococci and enterococci, followed by antibiotic resistance detection by real-time PCR-melt curve analysis without DNA extraction. The latter part included a triplex reaction for staphylococcal culture isolates (mecA, mecALGA251 and Panton-Valentine leucocidin genes), dual PCR of mecA/mecALGA251 and nuc genes for staphylococcal blood cultures, and a duplex reaction for enterococci (vanA and vanB genes). A total of 124 clinical isolates and 56 positive blood cultures were tested. MALDI-TOF MS was performed using Microflex LT (Bruker Daltonik, Bremen, Germany) and Rotor-Gene Q (Qiagen, Hilden, Germany) was used for real-time PCR-melt curve analysis. The total assay time was <2.5 h. The results revealed 100% concordance with antibiotic susceptibility testing or other reference methods for all culture isolates and enterococcal blood cultures. The percentage of concordance for staphylococcal blood cultures was 97.5%. The method described herein was fast, economical, reliable and capable of detecting mecALGA251, vanB1 and vanB2 genotypes, which are not included in most commercial assays. Large-scale screening is required to further test the performance of this protocol, especially for genotypes that are infrequently encountered. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. Establishment and application of an analytical in-house database (IHDB) for rapid discrimination of Bacillus subtilis group (BSG) using whole-cell MALDI-TOF MS technology.

    Science.gov (United States)

    Huang, Chien-Hsun; Huang, Lina; Chang, Mu-Tzu; Chen, Kuo-Lung

    2016-10-01

    Members of the Bacillus subtilis group (BSG) possess industrial applicability; unfortunately, B. subtilis and its phylogenetically closest species are indistinguishable from one another using 16S rDNA sequencing, physiological and biochemical tests. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a relatively novel technique for the fast and reliable identification of microorganisms. The aim of this study was to construct a unique analytical in-house database (IHDB) for BSG discrimination based on whole-cell protein fingerprinting using MALDI-TOF MS, as well as to discover biomarkers from the MS peaks to generate a classification model for further differentiation using the ClinProTools software. Type strains of 12 species (included five subspecies) of the BSG were used to build a main spectrum profile (MSP) to create an IHDB under the optimized parameters. The BSG isolates obtained from partial recA gene sequencing were used for IHDB validation. A total of 84 (100%) isolates were correctly identified to the species level and had high score values (mean score: 2.52). However, the IHDB had ambiguous identification at the subspecies level of Bacillus amyloliquefaciens. After implementation of the classification models, the strains could be clearly differentiated. We have successfully developed a rapid, accurate and cost-effective platform for the species- and subspecies-level discrimination of BSG based on the implementation of the IHDB and coupled with ClinProTools, which can be employed as an alternative technology to DNA sequencing and applied for efficient quality control of the microbial agent. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    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

  13. 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

  14. 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.

  15. 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.

    Directory of Open Access Journals (Sweden)

    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.

  16. Rapid discrimination of Haemophilus influenzae, H. parainfluenzae, and H. haemolyticus by fluorescence in situ hybridization (FISH) and two matrix-assisted laser-desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS) platforms.

    Science.gov (United States)

    Frickmann, Hagen; Christner, Martin; Donat, Martina; Berger, Anja; Essig, Andreas; Podbielski, Andreas; Hagen, Ralf Matthias; Poppert, Sven

    2013-01-01

    Due to considerable differences in pathogenicity, Haemophilus influenzae, H. parainfluenzae and H. haemolyticus have to be reliably discriminated in routine diagnostics. Retrospective analyses suggest frequent misidentifications of commensal H. haemolyticus as H. influenzae. In a multi-center approach, we assessed the suitability of fluorescence in situ hybridization (FISH) and matrix-assisted laser-desorption-ionization time-of-flight mass-spectrometry (MALDI-TOF-MS) for the identification of H. influenzae, H. parainfluenzae and H. haemolyticus to species level. A strain collection of 84 Haemophilus spp. comprising 50 H. influenzae, 25 H. parainfluenzae, 7 H. haemolyticus, and 2 H. parahaemolyticus including 77 clinical isolates was analyzed by FISH with newly designed DNA probes, and two different MALDI-TOF-MS systems (Bruker, Shimadzu) with and without prior formic acid extraction. Among the 84 Haemophilus strains analyzed, FISH led to 71 correct results (85%), 13 uninterpretable results (15%), and no misidentifications. Shimadzu MALDI-TOF-MS resulted in 59 correct identifications (70%), 19 uninterpretable results (23%), and 6 misidentifications (7%), using colony material applied directly. Bruker MALDI-TOF-MS with prior formic acid extraction led to 74 correct results (88%), 4 uninterpretable results (5%) and 6 misidentifications (7%). The Bruker MALDI-TOF-MS misidentifications could be resolved by the addition of a suitable H. haemolyticus reference spectrum to the system's database. In conclusion, no analyzed diagnostic procedure was free of errors. Diagnostic results have to be interpreted carefully and alternative tests should be applied in case of ambiguous test results on isolates from seriously ill patients.

  17. Rapid discrimination of Haemophilus influenzae, H. parainfluenzae, and H. haemolyticus by fluorescence in situ hybridization (FISH and two matrix-assisted laser-desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS platforms.

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    Hagen Frickmann

    Full Text Available BACKGROUND: Due to considerable differences in pathogenicity, Haemophilus influenzae, H. parainfluenzae and H. haemolyticus have to be reliably discriminated in routine diagnostics. Retrospective analyses suggest frequent misidentifications of commensal H. haemolyticus as H. influenzae. In a multi-center approach, we assessed the suitability of fluorescence in situ hybridization (FISH and matrix-assisted laser-desorption-ionization time-of-flight mass-spectrometry (MALDI-TOF-MS for the identification of H. influenzae, H. parainfluenzae and H. haemolyticus to species level. METHODOLOGY: A strain collection of 84 Haemophilus spp. comprising 50 H. influenzae, 25 H. parainfluenzae, 7 H. haemolyticus, and 2 H. parahaemolyticus including 77 clinical isolates was analyzed by FISH with newly designed DNA probes, and two different MALDI-TOF-MS systems (Bruker, Shimadzu with and without prior formic acid extraction. PRINCIPAL FINDINGS: Among the 84 Haemophilus strains analyzed, FISH led to 71 correct results (85%, 13 uninterpretable results (15%, and no misidentifications. Shimadzu MALDI-TOF-MS resulted in 59 correct identifications (70%, 19 uninterpretable results (23%, and 6 misidentifications (7%, using colony material applied directly. Bruker MALDI-TOF-MS with prior formic acid extraction led to 74 correct results (88%, 4 uninterpretable results (5% and 6 misidentifications (7%. The Bruker MALDI-TOF-MS misidentifications could be resolved by the addition of a suitable H. haemolyticus reference spectrum to the system's database. In conclusion, no analyzed diagnostic procedure was free of errors. Diagnostic results have to be interpreted carefully and alternative tests should be applied in case of ambiguous test results on isolates from seriously ill patients.

  18. 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.

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    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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. McRAPD unlike MALDI-TOF MS is a suitable candidate for routine discrimination of new Haemophilus influenzae strain acquisition in chronic obstructive pulmonary disease (COPD) and cystic fibrosis.

    Science.gov (United States)

    Raclavsky, Vladislav; Stromerova, Nikola; Safarova, Dana; Bardon, Jan; Zatloukal, Jaromir; Zapalka, Martin; Jakubec, Petr; Navratilova, Lucie; Novotny, Radko

    2016-12-01

    Haemophilus influenzae new strain acquisition has been demonstrated to increase the relative risk of acute exacerbation fourfold in contrast to colonisation or chronic infection by the same strain in chronic obstructive pulmonary disease (COPD). Unfortunately, molecular typing techniques are not suitable for routine use due to cost, labour-intensity and need for special expertise. We tested two techniques potentially useful for routine typing, namely the newly available MALDI-TOF MS and the modified McRAPD compared to MLST as the gold standard. In 10 patients (10.8%) suffering from COPD or cystic fibrosis, H. influenzae isolates were recovered repeatedly at different timepoints from the same patient during the study period. This allowed for thirteen pairwise comparisons of typing results in isolates recovered consecutively from the same patient to test the ability of the techniques to uncover new strain acquisition. MLST detected 9 cases of new strain acquisition among the 13 pairwise comparisons. However, MALDI-TOF MS reported all 13 pairs as different and thus new. In contrast, McRAPD was able to differentiate all the new strain acquisitions from pre-existing ones, both by visual inspection of melting profiles and by Relative Significant Difference values. Unlike MALDI-TOF MS, McRAPD appears to be a suitable candidate for routine discrimination of new strain acquisitions because of its accuracy and, rapid, easy and economic performance.

  5. Single-crystalline EuF3 hollow hexagonal microdisks: synthesis and application as a background-free matrix for MALDI-TOF-MS analysis of small molecules and polyethylene glycols.

    Science.gov (United States)

    Chen, Zhiming; Geng, Zhirong; Shao, Dalin; Mei, Yuhua; Wang, Zhilin

    2009-09-15

    Single-crystalline EuF(3) hexagonal microdisks with hollow interior were fabricated to serve as a background-free matrix for analysis of small molecules and polyethylene glycols (PEGs) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The long-lived excited state of europium ions can transfer energy to high-energy vibrations of organic molecules, which provides the potential technological application in MALDI-TOF-MS analysis of small molecules and PEGs. The efficiency of the hollow microdisks as a novel matrix of low molecular weight compounds was verified by analysis of small peptide, amino acid, organic compounds, and hydroxypropyl beta-cyclodextrin (HP-beta-CD). The advantage of this matrix in comparison with alpha-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) was demonstrated by MALDI-TOF-MS analysis of an amino acid mixture and a peptide mixture. This matrix is successfully used for analysis of PEGs (PEG 2000, PEG 4000, PEG 8000, PEG 15000, and PEG 30000), suggesting a potential for monitoring reactions and for synthetic polymer quality control. The upper limit of detectable mass range was approximately 35,000 Da (PEG 30000). It is believed that this work will not only offer a new technique for high-speed analysis of small molecules and PEGs but also open a new field for applications of rare earth fluorides.

  6. Identification and characterization of Clostridium botulinum group III field strains by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Bano, Luca; Drigo, Ilenia; Tonon, Elena; Pascoletti, Simone; Puiatti, Cinzia; Anniballi, Fabrizio; Auricchio, Bruna; Lista, Florigio; Montecucco, Cesare; Agnoletti, Fabrizio

    2017-12-01

    Animal botulism is primarily due to botulinum neurotoxin (BoNT) types C, D or their chimeric variants C/D or D/C, produced by Clostridium botulinum group III, which appears to include the genetically indistinguishable Clostridium haemolyticum and Clostridium novyi. In the present study, we used matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI TOF MS) to identify and characterize 81 BoNT-producing Clostridia isolated in 47 episodes of animal botulism. The instrument's default database, containing no entries for Clostridium botulinum, permitted reliable identification of 26 strains at the genus level. Although supplementation of the database with reference strains enhanced the instrument's ability to identify the neurotoxic strains at the genus level, resolution was not sufficient to recognize field strains at species level. Characterization by MALDI TOF confirmed the well-documented phenotypic and genetic differences between Clostridium botulinum strains of serotypes normally implicated in human botulism (A, B, E, F) and other Clostridium species able to produce BoNTs type C and D. The chimeric and non-chimeric field strains grouped separately. In particular, very low similarity was found between two non-chimeric type C field strains isolated in the same outbreak and the other field strains. This difference was comparable with the differences among the various Clostridia species included in the study. Characterization by MALDI TOF confirmed that BoNT-producing Clostridia isolated from animals are closely related and indistinguishable at the species level from Clostridium haemolyticum and Clostridium novyi reference strains. On the contrary, there seem to be substantial differences among chimeric and some non-chimeric type C strains. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. NMR, HPLC-ESI-MS, and MALDI-TOF MS analysis of condensed tannins from Delonix regia (Bojer ex Hook.) Raf. and their bioactivities.

    Science.gov (United States)

    Chai, Wei-Ming; Shi, Yan; Feng, Hui-Ling; Qiu, Ling; Zhou, Hai-Chao; Deng, Zi-Wei; Yan, Chong-Ling; Chen, Qing-Xi

    2012-05-16

    The structures of the condensed tannins isolated from leaf, fruit, and stem bark of Delonix regia (Bojer ex Hook.) Raf. have been investigated with (13)C nuclear magnetic resonance ((13)C NMR) and high performance liquid chromatography electrospray ionization mass spectrometry (HPLC-ESI-MS) coupled with thiolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analyses. The results showed that these condensed tannins from D. regia possessed structural heterogeneity in monomer units and degree of polymerization. Propelargonidin (PP) and procyanidin (PC) were found in the leaf, fruit, and stem bark of D. regia, while prodelphinidin (PD) was found only in the leaves. The polymer chain lengths of condensed tannins from leaf and fruit organs were detected to be trimers to hexadecamers but from trimers to tridecamers for stem bark. B-type linkages were present in all these compounds. Condensed tannins from different parts of D. regia can be explored as tyrosinase inhibitors and food antioxidants because of their potent antityrosinase and antioxidant activities. The inhibitor concentration leading to 50% enzyme activity (IC(50)) was estimated to be 38 ± 1, 73 ± 2, and 54 ± 1.5 μg/mL for the condensed tannins of leaf, fruit, and stem bark. Condensed tannins extracted from stem bark exhibited the highest antioxidant activity; the DPPH scavenging activity (IC(50)) and the FRAP values were 90 ± 2 μg/mL and 5.42 ± 0.09 mmol AAE/g, respectively.

  8. 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.

  9. 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.

  10. The Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS identification versus biochemical tests: a study with enterobacteria from a dairy cattle environment

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    Naiara Miranda Bento Rodrigues

    Full Text Available Abstract Mastitis adversely affects milk production and in general cows do not regain their full production levels post recovery, leading to considerable economic losses. Moreover the percentage decrease in milk production depends on the specific pathogen that caused the infection and enterobacteria are responsible for this greater reduction. Phenotypic tests are among the currently available methods used worldwide to identify enterobacteria; however they tend to misdiagnose the species despite the multiple tests carried out. On the other hand The Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS technique has been attracting attention for its precise identification of several microorganisms at species level. In the current study, 183 enterobacteria were detected in milk (n = 47 and fecal samples (n = 94 from cows, and samples from water (n = 23 and milk lines (n = 19. All these samples were collected from a farm in Rio de Janeiro with the specific purpose of presenting the MALDI-TOF MS technique as an efficient methodology to identify Enterobacteriaceae from bovine environments. The MALDI-TOF MS technique results matched the biochemical test results in 92.9% (170/183 of the enterobacteria species and the gyrB sequencing confirmed 100% of the proteomic technique results. The amino acid decarboxylation test made the most misidentifications and Enterobacter spp. was the most misidentified genus (76.9%, 10/13. These results aim to clarify the current biochemical errors in enterobacteria identification, considering isolates from a bovine environment, and show the importance for more careful readings of phenotypic tests which are often used in veterinary microbiology laboratories.

  11. 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

  12. Characterization of Klebsiella isolates by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and determination of antimicrobial resistance with VITEK 2 advanced expert system (AES).

    Science.gov (United States)

    Karagöz, Alper; Acar, Sümeyra; Körkoca, Hanifi

    2015-01-01

    The purpose of the study was to evaluate the performance of the VITEK mass spectrometry (MS) (bioMérieux, France) system for the identification of Klebsiella spp. isolated from different sources. Moreover, while assessing the ability of the VITEK 2 automated expert system (AES) to recognize antimicrobial resistance patterns, the researchers have extended the study to compare VITEK 2 with the routine antimicrobial susceptibility testing method. This study tested 51 Klebsiella spp. isolates that were isolated from environmental examples and clinical examples. Results of conventional methods and the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS were compared. Then, any differing results were compared against a reference 16S rRNA gene sequence, and when indicated, a recA sequencing analysis was done. VITEK MS correctly identified 100% of the Klebsiella spp. isolates. There were two K. oxytoca isolates incorrectly identified to the species level with conventional methods according to the 16S rRNA gene sequencing analysis. In addition, a VITEK 2 AST-N261 card was used for the detection of extended spectrum beta-lactamases (ESBL). Using the VITEK 2 AES, ESBL positivity was found at the rate of 16.3% whereas this rate was 4.08% using the disk diffusion method. MALDI-TOF MS is a rapid and accurate method for the identification of Klebsiella spp. Moreover, the bioMérieux AES provides a useful laboratory tool for the interpretation of susceptibility results.

  13. 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.

  14. 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.

  15. 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.

  16. Structural, MALDI-TOF-MS, magnetic and spectroscopic studies of new dinuclear copper(II), cobalt(II) and zinc(II) complexes containing a biomimicking μ-OH bridge.

    Science.gov (United States)

    Núñez, Cristina; Bastida, Rufina; Macías, Alejandro; Valencia, Laura; Neuman, Nicolás I; Rizzi, Alberto C; Brondino, Carlos D; González, Pablo J; Capelo, José Luis; Lodeiro, Carlos

    2010-12-28

    The Py(2)N(4)S(2) octadentate coordinating ligand afforded dinuclear cobalt, copper and zinc complexes and the corresponding mixed metal compounds. The overall geometry and bonding modes have been deduced on the basis of elemental analysis data, MALDI-TOF-MS, IR, UV-vis and EPR spectroscopies, single-crystal X-Ray diffraction, conductivity and magnetic susceptibility measurements. In the copper and zinc complexes, a μ-hydroxo bridge links the two metal ions. In both cases, the coordination geometry is distorted octahedral. Magnetic and EPR data reveal weakly antiferromagnetic high spin Co(II) ions, compatible with a dinuclear structure. The magnetic characterization of the dinuclear Cu(II) compound indicates a ferromagnetically coupled dimer with weak antiferromagnetic intermolecular interactions. The intra-dimer ferromagnetic behaviour was unexpected for a Cu(II) dimer with such μ-hydroxo bridging topology. We discuss the influence on the magnetic properties of non-covalent interactions between the bridging moiety and the lattice free water molecules.

  17. 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.

  18. Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR.

    Science.gov (United States)

    Foschi, Claudio; Laghi, Luca; Parolin, Carola; Giordani, Barbara; Compri, Monica; Cevenini, Roberto; Marangoni, Antonella; Vitali, Beatrice

    2017-01-01

    Lactobacilli represent a wide range of bacterial species with several implications for the human host. They play a crucial role in maintaining the ecological equilibrium of different biological niches and are essential for fermented food production and probiotic formulation. Despite the consensus about the 'health-promoting' significance of Lactobacillus genus, its genotypic and phenotypic characterization still poses several difficulties. The aim of this study was to assess the integration of different approaches, genotypic (16S rRNA gene sequencing), proteomic (MALDI-TOF MS) and metabolomic (1H-NMR), for the taxonomic and metabolic characterization of Lactobacillus species. For this purpose we analyzed 40 strains of various origin (intestinal, vaginal, food, probiotics), belonging to different species. The high discriminatory power of MALDI-TOF for species identification was underlined by the excellent agreement with the genotypic analysis. Indeed, MALDI-TOF allowed to correctly identify 39 out of 40 Lactobacillus strains at the species level, with an overall concordance of 97.5%. In the perspective to simplify the MALDI TOF sample preparation, especially for routine practice, we demonstrated the perfect agreement of the colony-picking from agar plates with the protein extraction protocol. 1H-NMR analysis, applied to both culture supernatants and bacterial lysates, identified a panel of metabolites whose variations in concentration were associated with the taxonomy, but also revealed a high intra-species variability that did not allow a species-level identification. Therefore, despite not suitable for mere taxonomic purposes, metabolomics can be useful to correlate particular biological activities with taxonomy and to understand the mechanisms related to the antimicrobial effect shown by some Lactobacillus species.

  19. Coumarin tags for analysis of peptides by MALDI-TOF MS and MS/MS. 2. Alexa Fluor 350 tag for increased peptide and protein Identification by LC-MALDI-TOF/TOF MS.

    Science.gov (United States)

    Pashkova, Anna; Chen, Hsuan-Shen; Rejtar, Tomas; Zang, Xin; Giese, Roger; Andreev, Victor; Moskovets, Eugene; Karger, Barry L

    2005-04-01

    The goal of this study was the development of N-terminal tags to improve peptide identification using high-throughput MALDI-TOF/TOF MS. Part 1 of the study was focused on the influence of derivatization on the intensities of MALDI-TOF MS signals of peptides. In part 2, various derivatization approaches for the improvement of peptide fragmentation efficiency in MALDI-TOF/TOF MS are explored. We demonstrate that permanent cation tags, while significantly improving signal intensity in the MS mode, lead to severe suppression of MS/MS fragmentation, making these tags unsuitable for high-throughput MALDI-TOF/TOF MS analysis. In the present work, it was found that labeling with Alexa Fluor 350, a coumarin tag containing a sulfo group, along with guanidation of epsilon-amino groups of Lys, could enhance unimolecular fragmentation of peptides with the formation of a high-intensity y-ion series, while the peptide intensities in the MS mode were not severely affected. LC-MALDI-TOF/TOF MS analysis of tryptic peptides from the SCX fractions of an E. coli lysate revealed improved peptide scores, a doubling of the total number of peptides, and a 30% increase in the number of proteins identified, as a result of labeling. Furthermore, by combining the data from native and labeled samples, confidence in correct identification was increased, as many proteins were identified by different peptides in the native and labeled data sets. Additionally, derivatization was found not to impair chromatographic behavior of peptides. All these factors suggest that labeling with Alexa Fluor 350 is a promising approach to the high-throughput LC-MALDI-TOF/TOF MS analysis of proteomic samples.

  20. Evaluation of MALDI-TOF MS in the microbiology laboratory

    OpenAIRE

    Santos,Anderson Fernandes; Cayô,Rodrigo; Schandert,Lygia; Gales,Ana Cristina

    2013-01-01

    Rapid identification of microorganisms by the clinical microbiology laboratory is of crucial importance for optimal patients’ management and treatment. In general, bacterial identification by conventional methods requires 18-24 hours for colony isolation and at least 24 additional hours for species identification. New technologies in microbiology have focused on the rapid diagnosis of bloodstream infections, since they are associated with high morbidity and mortality rates. A rápida identi...

  1. [Proteomic technologies for identification of serum potential biomarkers of autoimmune demyelinating polyneuropathies].

    Science.gov (United States)

    Ziganshin, R Kh; Arapidi, G P; Azarkin, I V; Balmasova, I P; Timchenko, O L; Fed'kina, Iu A; Morozova, E A; Piradov, M A; Suponeva, N A; Iushchuk, N D; Govorun, V M

    2011-01-01

    Time-of-flight MALDI mass spectrometry (MALDI-TOF-MS) profiling of blood serum of patients with Guillain-Barré syndrome (GBS, 36 samples), chronic inflammatory demyelinating polyneuropathy (CIDP, 24 samples) and practically healthy donors (HD) (35 samples) was carried out in order to identify potential biomarkers of autoimmune demyelinating polyneuropathies (ADP). To simplify the peptide-protein mixture of serum prior to MALDI-TOF-MS analysis samples were pre-fractionated on magnetic microparticles with a weak cation-exchange (MB-WCX) surface. Comparative analysis of mass spectrometric data using the classification algorithms (genetic and neural network-controlled) revealed a characteristic set of peaks, agreed change area with a high specificity and sensitivity of the differentiated mass spectrometry profiles of the blood serum of patients with DPNP and healthy donors (for GBS values of these characteristics reached 100 and 100, and for CIDP 94.1 and 100% respectively). Comparative analysis of mass spectrometric profiles of serum samples obtained from patients with GBS and CIDP, allowed to build a classification model to differentiate these diseases from each other, with a specificity of 88.9 and a sensitivity of 80%.

  2. Identification of novel serum biomarkers for gastric cancer by magnetic bead.

    Science.gov (United States)

    Liu, Wentao; Gao, Xiang; Cai, Qu; Li, Jianfang; Zhu, Zhenglun; Li, Chen; Yao, Xuexin; Yang, Qiumeng; Xiang, Ming; Yan, Min; Zhu, Zhenggang

    2010-06-01

    Early diagnosis and early treatment is known to improve prognosis for gastric cancer. Magnetic affinity beads can be used to extract peptides from un-fractionated serum samples. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) can detect the presence and the molecular mass of peptides. MALDI-TOF-MS mass spectra of peptides and proteins were generated after WCX CLINPROT bead fractionation of 62 gastric cancer serum samples. The discovery set consisted of 44 samples while the validation set was 18 serum samples. The spectra were analyzed statistically using flexAnalysisTM and Clin-ProtTM bioinformatic software. The six most significant peaks were selected out by ClinProTool software and utilized to train a Supervised Neural Network to identify gastric cancer sera from control sera. The sensitivity and specificity of the model when tested on the validation set were 100% and 75%, respectively. A set of 6 peptides that can be used to distinguish serum from gastric cancer patients with good sensitivity and specificity were identified, and these peptides may be useful biomarkers to distinguish cancer individuals who may benefit from radiologic or endoscopic examination.

  3. Proteomic analysis of serum in patients with non-alcoholic steatohepatitis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Ulukaya, Engin; Yilmaz, Yusuf; Moshkovskii, Sergei; Karpova, Maria; Pyatnitskiy, Mikhail; Atug, Ozlen; Dolar, Enver

    2009-01-01

    We sought to investigate whether serum proteomic pattern analysis obtained using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS) may help to diagnose non-alcoholic steatohepatitis (NASH) in the setting of non-alcoholic fatty liver disease (NAFLD). We enrolled 80 patients with biopsy-proven NAFLD and 19 healthy comparison subjects. Patients with NAFLD were classified according to their liver histology as having definite NASH (n = 48), borderline NASH (n = 22) or simple steatosis (n = 10). Liver ultrasound scanning was performed to assess the degree of steatosis. Mass spectra of serum samples were obtained using a Ultraflex II mass spectrometer. The highest accuracy for NASH diagnostics was reached using 15 peaks. Corresponding sensitivity and specificity values were 73.95% +/- 3.38% and 88.71% +/- 1.39%, respectively. However, mass spectra did not allow us to distinguish NASH from simple steatosis. We conclude that proteomic analyses of serum samples from NAFLD patients by MALDI TOF-MS do not seem to have a major clinical value for diagnosing NASH. However, the identification of 15 peaks in our study may help to further elucidate the pathophysiology of NASH and merits further investigation.

  4. 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

  5. Acute generalized livedo racemosa caused by Capnocytophaga canimorsus identified by MALDI-TOF MS

    Directory of Open Access Journals (Sweden)

    Adamantia Sotiriou

    2015-04-01

    Full Text Available Independent of the size of the dog and the type of injury, serious infections may follow a dog bite and these may result in the abrupt onset of multiorgan failure. Early recognition of the warning signs with regard to the underlying severity of the infection is of the utmost importance. Reticulate skin eruptions constitute a precursory phenomenon.

  6. 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

  7. 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

  8. 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.

  9. Identification of Bacillus strains by MALDI TOF MS using geometric approach

    Science.gov (United States)

    Starostin, Konstantin V.; Demidov, Evgeny A.; Bryanskaya, Alla V.; Efimov, Vadim M.; Rozanov, Alexey S.; Peltek, Sergey E.

    2015-11-01

    Microorganism identification by MALDI TOF mass-spectrometry is based on the comparison of the mass spectrum of the studied organism with those of reference strains. It is a rapid and reliable method. However, commercial databases and programs are mostly designed for identification of clinically important strains and can be used only for particular mass spectrometer models. The need for open platforms and reference databases is obvious. In this study we describe a geometric approach for microorganism identification by mass spectra and demonstrate its capabilities by analyzing 24 strains belonging to the Bacillus pumilus group. This method is based on representing mass spectra as points on a multidimensional space, which allows us to use geometric distances to compare the spectra. Delimitation of microorganisms performed by geometric approach correlates well with the results of molecular phylogenetic analysis and clustering using Biotyper 3.1. All three methods used allowed us to reliably divide the strains into two groups corresponding to closely related species, Bacillus pumilus and Bacillus altitudinis. The method developed by us will be implemented in a Web interface designed for using open reference databases for microorganism identification. The data is available at http://www.bionet.nsc.ru/mbl/database/database.html.

  10. 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.

  11. 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.

  12. 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

  13. MALDI-TOF MS stability study of model poly(p-phenylene terephthalamide)s.

    Science.gov (United States)

    Gies, Anthony P; Schotman, Anton; Hercules, David M

    2010-02-01

    In the present study, we address the possibility of matrix-assisted laser desorption/ionization (MALDI)-time-of-flight MS analysis-induced chain fragmentation in poly(p-phenylene terephthalamide) (PPD-T) by considering two possible sources: (1) grinding-induced fragmentation resulting from the evaporation-grinding MALDI sample preparation method (E-G method) and (2) in-source/metastable fragmentation induced by the MALDI laser. An analysis of variance (ANOVA) statistical study found, with a high probability, that obtaining MALDI spectra with the effective laser area as large as possible (the "fanned-out" setting) did not cause any chain fragmentation due to the E-G MALDI sample preparation method, even when three additional grinding steps were used. However, the effect of laser fluence was less clear. A significant effect of laser fluence was observed for lower mass oligomers (measurement (approximately 2,300 Da). Plausible explanations are presented to explain these observations. The most likely scenario is that "unexpected" end-group modifications occur during PPD-T synthesis, producing small quantities of low mass species, which are amplified by the MALDI-EG extraction procedure.

  14. Identification of Nocardia, Streptomyces, and Tsukamurella using MALDI-TOF MS with the Bruker Biotyper.

    Science.gov (United States)

    Yarbrough, Melanie L; Lainhart, William; Burnham, Carey-Ann D

    2017-10-01

    Nocardia species are the most commonly isolated aerobic actinomycetes from human clinical specimens. Our objective was to assess the identification of clinically relevant actinomycetes using the Bruker Biotyper MALDI-TOF system, including comparison of extraction methods, Biotyper library versions, score cutoffs, and media. Banked Streptomyces (n=10), Tsukamurella (n=2), and Nocardia isolates (n=60) were cultured and extracted using three methods: mycobacterial extraction, ethanol formic acid extraction, or direct on-target extraction. Following MALDI-TOF analysis, spectra were analyzed using versions 5 and 6 of the BDAL Biotyper library. Optimal species-level identifications for Nocardia were achieved using BDAL v6 at a score cutoff of ≥1.8 after direct extraction (49/60, 82%). Overall, the Biotyper platform with BDAL v6 accurately identified 12/16 species of Nocardia, demonstrating the utility of MALDI-TOF for identification of clinically relevant actinomycetes without the need for supplementation of the database. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. AGING OF CRYPTOSPORIDIUM PARVUUM OOCYSTS STUDIED BY MALDI-TOF MS

    Science.gov (United States)

    Cryptosporidium parvum is a protozoan parasite, and it causes a potentially fatal gastrointestinal illness. This water borne pathogen has been the subject of several high profile disease outbreaks in the US and abroad. C. parvum presents challenges for both compliance monitorin...

  16. AGING OF CRYPTOSPORIDIUM PARVUM OOCYSTS STUDIED BY MALDI-TOF MS

    Science.gov (United States)

    Cryptosporidium parvum is a protozoan parasite, and it causes a potentially fatal gastrointestinal illness. This water borne pathogen has been the subject of several high profile disease outbreaks in the US and abroad. C. parvum presents challenges for both compliance monitoring ...

  17. 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.

  18. Structural changes of ultrasonicated bovine serum albumin revealed by hydrogen-deuterium exchange and mass spectrometry.

    Science.gov (United States)

    Zhang, Qiuting; Tu, Zongcai; Wang, Hui; Huang, Xiaoqin; Sha, Xiaomei; Xiao, Hui

    2014-11-01

    The structural changes of bovine serum albumin (BSA) under high-intensity ultrasonication were investigated by fluorescence spectroscopy and mass spectrometry. Evidence for the ultrasonication-induced conformational changes of BSA was provided by the intensity changes and maximum-wavelength shift in fluorescence spectrometry. Matrix-assisted laser desorption-ionization time-of-flight mass spectroscopy (MALDI-TOF MS) revealed the increased intensity of the peak at the charge state +5 and a newly emerged peak at charge state +6, indicating that the protein became unfolded after ultrasonication. Prevalent unfolding of BSA after ultrasonication was revealed by hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS). Increased intensity and duration of ultrasonication further promoted the unfolding of the protein. The unfolding induced by ultrasonication goes through an intermediate state similar to that induced by a low concentration of denaturant.

  19. 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

  20. 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.

  1. Time-course analysis of serum hepcidin, iron and cytokines in a C282Y homozygous patient with Schnitzler's syndrome treated with IL-1 receptor antagonist.

    NARCIS (Netherlands)

    Deuren, M. van; Kroot, J.J.C.; Swinkels, D.W.

    2009-01-01

    It is currently unknown if the increase of the hepatic iron regulatory hormone hepcidin during inflammation in man depends on an intact HFE-protein. Here we describe the temporal relationship of serum hepcidin, serum iron and cytokines in a patient with HFE-related (C282Y homozygous) hereditary

  2. 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

  3. Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization

    Science.gov (United States)

    Introduction: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS)is increasingly utilized as a rapid technique to identify microorganisms including pathogenic bacteria. However, little attention has been paid to the significant proteomic information encoded in ...

  4. Peptide nucleic acid probes with charged photocleavable mass markers: Towards PNA-based MALDI-TOF MS genetic analysis

    OpenAIRE

    Ball, Rachel J; Green, Philip S; Gale, Nittaya; Langley, G John; Brown, Tom

    2010-01-01

    Halogen-labelled peptide organic acid (HPOA) monomers have been synthesised and incorporated into sequence-specific peptide nucleic acid (PNA) probes. Three different types of probe have been prepared; the unmodified PNA probe, the PNA probe with a mass marker, and the PNA probe with photocleavable mass marker. All three types of probe have been used in model studies to develop a mass spectrometry-based hybridisation assay for detection of point mutations in DNA.

  5. Peptide nucleic acid probes with charged photocleavable mass markers: Towards PNA-based MALDI-TOF MS genetic analysis.

    Science.gov (United States)

    Ball, Rachel J; Green, Philip S; Gale, Nittaya; Langley, G John; Brown, Tom

    2010-07-01

    Halogen-labelled peptide organic acid (HPOA) monomers have been synthesised and incorporated into sequence-specific peptide nucleic acid (PNA) probes. Three different types of probe have been prepared; the unmodified PNA probe, the PNA probe with a mass marker, and the PNA probe with photocleavable mass marker. All three types of probe have been used in model studies to develop a mass spectrometry-based hybridisation assay for detection of point mutations in DNA.

  6. High Molecular Weight Typing with MALDI-TOF MS - A Novel Method for Rapid Typing of Clostridium difficile

    OpenAIRE

    Rizzardi, Kristina; ?kerlund, Thomas

    2015-01-01

    Clostridium difficile strains were typed by a newly developed MALDI-TOF method, high molecular weight typing, and compared to PCR ribotyping. Among 500 isolates representing 59 PCR ribotypes a total of 35 high molecular weight types could be resolved. Although less discriminatory than PCR ribotyping, the method is extremely fast and simple, and supports for cost-effective screening of isolates during outbreak situations.

  7. 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.

  8. 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

  9. 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.

  10. The Impact of Pre-Analytical Conditions on Human Serum Peptidome Profiling.

    Science.gov (United States)

    Padoan, Andrea

    2018-02-24

    The successful use of proteomic technology for the discovery of clinically relevant, new candidate biomarkers, especially in the low molecular weight range (peptidome), calls for a careful consideration of standardized operating procedures (SOP) for pre-analytical variables, including samples handling and storage. The current lack of standardization, widely considered a relevant source of random and systematic errors, underlies the uncertainty of analytical results and poor comparability, especially in multi-centric or inter-laboratory studies. In their recent study, Tsuchida et al. used the MALDI-TOF/MS technique to investigate the effect of long-term storage at -20 °C, -80 °C, and in liquid nitrogen on serum samples obtained for peptidomic analyses. The authors have also evaluated the effects of different sample thawing modalities. By including results from the same series as that reported on in a previous publication, they have effectively defined some important requirements for the peptidomic analysis of serum samples (e.g., maximum time intervals between venepuncture and serum separation [1 h], minimum temperature for long-term sera storage temperature [-80 °C], ideal conditions for sample thawing). © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

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

    2013-07-01

    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.

  12. 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.

  13. Large-Scale Glycomics of Livestock: Discovery of Highly Sensitive Serum Biomarkers Indicating an Environmental Stress Affecting Immune Responses and Productivity of Holstein Dairy Cows.

    Science.gov (United States)

    Rehan, Ibrahim F; Ueda, Koichiro; Mitani, Tomohiro; Amano, Maho; Hinou, Hiroshi; Ohashi, Tetsu; Kondo, Seiji; Nishimura, Shin-Ichiro

    2015-12-09

    Because various stresses strongly influence the food productivity of livestock, biomarkers to indicate unmeasurable environmental stress in domestic animals are of increasing importance. Thermal comfort is one of the basic principles of dairy cow welfare that enhances productivity. To discover sensitive biomarkers that monitor such environmental stresses in dairy cows, we herein performed, for the first time, large-scale glycomics on 336 lactating Holstein cow serum samples over 9 months between February and October. Glycoblotting combined with MALDI-TOF/MS and DMB/HPLC allowed for comprehensive glycomics of whole serum glycoproteins. The results obtained revealed seasonal alterations in serum N-glycan levels and their structural characteristics, such as an increase in high-mannose type N-glycans in spring, the occurrence of di/triantennary complex type N-glycans terminating with two or three Neu5Gc residues in summer and autumn, and N-glycans in winter dominantly displaying Neu5Ac. A multivariate analysis revealed a correlation between the serum expression levels of these season-specific glycoforms and productivity.

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

    Science.gov (United States)

    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

    2013-11-15

    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. © 2013.

  15. 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.

  16. [Screening of Serum Markers in Primary Immune Thrombocytopenia].

    Science.gov (United States)

    Zhang, Yang; Bai, Ju; Zhang, Wang-Gang; He, Ai-Li

    2016-06-01

    To analyze the serum protein fingerprints of immune thrombocytopenia (ITP) patients and healthy controls by using weak cation exchange nanometer magnetic beads and MALDI-TOF-MAS technology, to identify the proteins with different expression, to establish the diagnostic model for ITP and to explore the pathogenesis of ITP. A total of 40 patients with ITP and 40 healthy controls were selected, the serum protein components were captured by using weak cation exchange nanaometer magnetic beads, the protein spectra of all specimens were detected by Autoflex II matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI- TOF-MS) and then the data were analyzed by CliprotoolsTM2.2 software, by which the distinct protein molecules were screened to set up ITP diagnostic model. To identify the established model, the sera of 20 ITP patients and 20 healthy controls were selected to make category and cross validations. The detection of Clinprot system and the analysis of CliprotoolsTM2.2 software showed that about 55 protein peaks were detected with the range of 700 Da to 10 000 Da of molecular weight in the protein spectrum of serum speciments from 40 ITP patients and 40 healthy controls. Compared with healthy controls, 19 protein expression peaks with statistically significant difference were found in ITP patients (P Neural Network Algorithm (SNN) was established through 10 MS peaks with strongest capability in ITP group and control group automatically distinguished by software, and it is expected that the sensitivity of model group reached to 100%, and the specificity to 100%. The category validation showed that this diagnostic model correctly identificed all 20 ITP patients and 20 healthy controls, and in cross validation, the model sensitivity was 100% and the specificity was 100%. The ITP SNN model ertablished by using ChinProt System with high flax and good repetition is composed of 10 protein peaks with significant difference, this model can

  17. Time course of postoperative hypoxaemia

    DEFF Research Database (Denmark)

    Rosenberg, J; Ullstad, T; Rasmussen, J

    1994-01-01

    , but not with episodes of sudden desaturation after operation. Preoperative overnight oximetry correlated significantly with constant hypoxaemia on all five postoperative nights and with episodic hypoxaemia on nights 3 and 4. CONCLUSION: In the light of these results which show the natural history of postoperative...... hypoxaemia without supplementary oxygen, and because postoperative hypoxaemia may be associated with dysfunction of organ systems after major operations, controlled studies of supplementary oxygen in the late postoperative period are warranted.......OBJECTIVE: To study the time course of nocturnal episodic and constant hypoxaemia during the first five nights after a major abdominal operation in patients not given supplementary oxygen. DESIGN: Open study. SUBJECTS: 17 patients undergoing major elective operations and with no recognised risk...

  18. Detection and Identification of Serum Peptides Biomarker in Papillary Thyroid Cancer.

    Science.gov (United States)

    Lu, Zhao-Lian; Chen, Ying-Jian; Jing, Xin-Yan; Wang, Na-Na; Zhang, Ting; Hu, Cheng-Jin

    2018-03-17

    BACKGROUND Papillary thyroid cancer (PTC) is currently the most commonly diagnosed endocrine malignancy. In addition, the sex- and age-adjusted incidence of PTC has exhibited a greater increase over the last 2 decades than in many other malignancies. Thus, discovering noninvasive specific serum biomarker to distinguish PTC from cancer-free controls in its early stages remains an important goal. MATERIAL AND METHODS Serum samples from 88 PTC patients and 80 cancer-free controls were randomly allocated into training or validation sets. Serum peptide profiling was performed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) after using weak cation exchange magnetic beads (WCX-MB), and the results were evaluated by use of ClinProTools™ Software. To distinguish PTC from cancer-free controls, quick classifier (QC), supervised neural network (SNN), and genetic algorithm (GA) models were established. The models were blindly validated to verify their diagnostic capabilities. The most discriminative peaks were subsequently identified with a nano-liquid chromatography-electrospray ionization-tandem mass spectrometry system. RESULTS Six peptide ions were identified as the most discriminative peaks between the PTC and cancer-free control samples. The QC model exhibited satisfactory sensitivity and specificity among the 3 models that were validated. Two peaks, at m/z 2671.17 and m/z 1464.68, were identified as fragments of the alpha chain of fibrinogen, while a peak at m/z 1738.92 was a fragment of complement component 4A/B. CONCLUSIONS MS combined with ClinProTools™ software was able to detect peptide biomarkers in PTC patients. In addition, the constructed classification models provided a serum peptidome pattern for distinguishing PTC from cancer-free controls. Both fibrinogen a and complement C4A/B were identified as potential markers for diagnosis of PTC.

  19. Serum peptidome patterns of hepatocellular carcinoma based on magnetic bead separation and mass spectrometry analysis.

    Science.gov (United States)

    Ying, Xia; Han, Su-xia; Wang, Jun-lan; Zhou, Xia; Jin, Gui-hua; Jin, Long; Wang, Hao; Wu, Lei; Zhang, Jianying; Zhu, Qing

    2013-08-05

    Hepatocellular carcinoma (HCC) is one of the most common cancers in the world,and the identification of biomarkers for the early detection is a relevant target. The purpose of the study is to discover specific low molecular weight (LMW) serum peptidome biomarkers and establish a diagnostic pattern for HCC. We undertook this pilot study using a combined application of magnetic beads with Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique and ClinPro Tools v2.2 to detect 32 patients with HCC, 16 patients with chronic hepatitis (CH), 16 patients with liver cirrhosis (LC) and 16 healthy volunteers. The results showed 49, 33 and 37 differential peptide peaks respectively appeared in HCC, LC and CH groups. A Supervised Neural Network (SNN) algorithm was used to set up the classification model. Eleven of the identified peaks at m/z 5247.62, 7637.05, 1450.87, 4054.21, 1073.37, 3883.64, 5064.37, 4644.96, 5805.51, 1866.47 and 6579.6 were used to construct the peptides patterns. According to the model, we could clearly distinguish between HCC patients and healthy controls as well as between LC or CH patients and healthy controls. The study demonstrated that a combined application of magnetic beads with MALDI-TOF MB technique was suitable for identification of potential serum biomarkers for HCC and it is a promising way to establish a diagnostic pattern. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1503629821958720.

  20. 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

  1. Negative ion MALDI-TOF MS, ISD and PSD of neutral underivatized oligosaccharides without anionic dopant strategies, using 2,5-DHAP as a matrix.

    Science.gov (United States)

    Jovanović, Marko; Peter-Katalinić, Jasna

    2016-02-01

    Oligosaccharides represent complex class of analytes for mass spectrometric analysis due to the high variety of structural isomers concerning glycosidic linkages and possible branching. A systematic study of the negative ion mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of various neutral oligosaccharides under selection of an appropriate matrix, like 2,5-dihydroxyacetophenone (2,5-DHAP) is reported here, without commonly used anion dopant strategies. Nevertheless, we were able to generate relevant in-source decay (ISD) cross-ring fragment ions, typically obtained in the negative ion mode. Data observed indicate that the intrinsic property of the terminal non-reduced aldose is crucial for this behavior. A systematic study of the post source decay (PSD) of molecular, pseudomolecular and ISD cross-ring cleavage precursor ions is reported here. A direct comparison of the positive and negative ion mode MALDI MS1 and PSD behavior of neutral oligosaccharides could also be performed under the use of the same matrix preparation, because 2,5-DHAP is fully compatible with positive ion mode acquisition. We found that PSD spectra of deprotonated neutral oligosaccharides obtained in the negative ion mode are richer, because they contained both glycosidic and cross-ring fragment ions. However, we also found that cross-ring fragment ions are readily produced in the positive ion mode when potassiated precursor ions were selected. In addition, we show evidence that non-anionic dopants and specific instrumental parameters can also significantly influence the ISD fragmentation. Taken together, our results should increase our understanding of oligosaccharide behavior in the negative ion mode as well as increase our knowledge regarding many aspects of in-source MALDI chemistry. Copyright © 2016 John Wiley & Sons, Ltd.

  2. LC MALDI-TOF MS/MS and LC ESI FTMS analyses of HLA-B27 associated peptides isolated from peripheral blood cells

    Czech Academy of Sciences Publication Activity Database

    Stodůlková, Eva; Novák, Petr; Deininger, S.-O.; Man, Petr; Čapková, Jana; Kavan, Daniel; Ivašková, E.; Flieger, Miroslav

    2008-01-01

    Roč. 116, - (2008), s. 79-85 ISSN 0165-2478 R&D Projects: GA MZd 1A8631 Institutional research plan: CEZ:AV0Z50200510; CEZ:AV0Z50520514 Keywords : hla -b27 * healthy blood donors Subject RIV: EE - Microbiology, Virology Impact factor: 2.858, year: 2008

  3. 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.

  4. 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.

  5. 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 SDS lysis instead of 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.

  6. 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.

  7. 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

  8. 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

  9. MALDI-TOF-MS reveals differential N-linked plasma- and IgG-glycosylation profiles between mothers and their newborns

    NARCIS (Netherlands)

    Jansen, Bas C.; Bondt, Albert; Reiding, Karli R.; Scherjon, Sicco A.; Vidarsson, Gestur; Wuhrer, Manfred

    2016-01-01

    During pregnancy, the mother provides multiple nutrients and substances to the foetus, with maternal immunoglobulin G (IgG) being actively transported to the foetus. Newborns depend on maternal IgG for immune-protection in their first months. The glycosylation of IgG has been shown to influence its

  10. 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

  11. Bacillus subtilis subsp. subtilis CBMDC3f with antimicrobial activity against Gram-positive foodborne pathogenic bacteria: UV-MALDI-TOF MS analysis of its bioactive compounds.

    Science.gov (United States)

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

    2015-06-01

    In this work a new Bacillus sp. strain, isolated from honey, was characterized phylogenetically. Its antibacterial activity against three relevant foodborne pathogenic bacteria was studied; the main bioactive metabolites were analyzed using ultraviolet matrix assisted laser desorption-ionization mass spectrometry (UV-MALDI MS). Bacillus CBMDC3f was phylogenetically characterized as Bacillus subtilis subsp. subtilis after rRNA analysis of the 16S subunit and the gyrA gene (access codes Genbank JX120508 and JX120516, respectively). Its antibacterial potential was evaluated against Listeria monocytogenes (9 strains), B. cereus (3 strains) and Staphylococcus aureus ATCC29213. Its cell suspension and cell-free supernatant (CFS) exerted significant anti-Listeria and anti-S. aureus activities, while the lipopeptides fraction (LF) also showed anti-B. cereus effect. The UV-MALDI-MS analysis revealed surfactin, iturin and fengycin in the CFS, whereas surfactin predominated in the LF. The CFS from CBMDC3f contained surfactin, iturin and fengycin with four, two and four homologues per family, respectively, whereas four surfactin, one iturin and one fengycin homologues were identified in the LF. For some surfactin homologues, their UV-MALDI-TOF/TOF (MS/MS; Laser Induced Decomposition method, LID) spectra were also obtained. Mass spectrometry analysis contributed with relevant information about the type of lipopeptides that Bacillus strains can synthesize. From our results, surfactin would be the main metabolite responsible for the antibacterial effect.

  12. 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.

  13. 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

  14. 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.

  15. Ethrel-stimulated prolongation of latex flow in the rubber tree (Hevea brasiliensis Muell. Arg.): an Hev b 7-like protein acts as a universal antagonist of rubber particle aggregating factors from lutoids and C-serum.

    Science.gov (United States)

    Shi, Min-Jing; Cai, Fu-Ge; Tian, Wei-Min

    2016-02-01

    Ethrel is the most effective stimuli in prolonging the latex flow that consequently increases yield per tapping. This effect is largely ascribed to the enhanced lutoid stability, which is associated with the decreased release of initiators of rubber particle (RP) aggregation from lutoid bursting. However, the increase in both the bursting index of lutoids and the duration of latex flow after applying ethrel or ethylene gas in high concentrations suggests that a new mechanism needs to be introduced. In this study, a latex allergen Hev b 7-like protein in C-serum was identified by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI TOF MS). In vitro analysis showed that the protein acted as a universal antagonist of RP aggregating factors from lutoids and C-serum. Ethrel treatment obviously weakened the effect of C-serum on RP aggregation, which was closely associated with the increase in the level of the Hev b 7-like protein and the decrease in the level of the 37 kDa protein, as revealed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), western blotting analysis and antibody neutralization. Thus, the increase of the Hev b 7-like protein level or the ratio of the Hev b 7-like protein to the 37 kDa protein in C-serum should be primarily ascribed to the ethrel-stimulated prolongation of latex flow duration. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  16. Methodology and Applications of Disease Biomarker Identification in Human Serum

    Directory of Open Access Journals (Sweden)

    Ziad J. Sahab

    2007-01-01

    Full Text Available Biomarkers are biomolecules that serve as indicators of biological and pathological processes, or physiological and pharmacological responses to a drug treatment. Because of the high abundance of albumin and heterogeneity of plasma lipoproteins and glycoproteins, biomarkers are difficult to identify in human serum. Due to the clinical significance the identification of disease biomarkers in serum holds great promise for personalized medicine, especially for disease diagnosis and prognosis. This review summarizes some common and emerging proteomics techniques utilized in the separation of serum samples and identification of disease signatures. The practical application of each protein separation or identification technique is analyzed using specific examples. Biomarkers of cancers of prostate, breast, ovary, and lung in human serum have been reviewed, as well as those of heart disease, arthritis, asthma, and cystic fibrosis. Despite the advancement of technology few biomarkers have been approved by the Food and Drug Administration for disease diagnosis and prognosis due to the complexity of structure and function of protein biomarkers and lack of high sensitivity, specificity, and reproducibility for those putative biomarkers. The combination of different types of technologies and statistical analysis may provide more effective methods to identify and validate new disease biomarkers in blood.Abbreviations: 2-DE, two-dimensional gel electrophoresis; 2DLC-MS, two-dimensional liquid chromatography mass spectrometry; CA 15.3, cancer antigen 15.3; CA 19–9, cancer antigen 19–9, a tumor-associated antigen; CA125, cancer antigen 125, a mucin-like protein; CEA, carcinoembryonic antigen; CF, Cystic Fibrosis; CRP, C-reactive protein; ELISA, enzyme-linked immunosorbent assay; ESI-MS/MS, electrospray ionization tandem mass spectrometry; FDA, Food and Drug Administration; IPG, immobilized pH gradient; MALDI-TOF-MS, matrix-assisted laser desorption

  17. 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...

  18. 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

  19. 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.

  20. Microarray time course experiments: finding profiles.

    Science.gov (United States)

    Irigoien, Itziar; Vives, Sergi; Arenas, Concepción

    2011-01-01

    Time course studies with microarray techniques and experimental replicates are very useful in biomedical research. We present, in replicate experiments, an alternative approach to select and cluster genes according to a new measure for association between genes. First, the procedure normalizes and standardizes the expression profile of each gene, and then, identifies scaling parameters that will further minimize the distance between replicates of the same gene. Then, the procedure filters out genes with a flat profile, detects differences between replicates, and separates genes without significant differences from the rest. For this last group of genes, we define a mean profile for each gene and use it to compute the distance between two genes. Next, a hierarchical clustering procedure is proposed, a statistic is computed for each cluster to determine its compactness, and the total number of classes is determined. For the rest of the genes, those with significant differences between replicates, the procedure detects where the differences between replicates lie, and assigns each gene to the best fitting previously identified profile or defines a new profile. We illustrate this new procedure using simulated data and a representative data set arising from a microarray experiment with replication, and report interesting results.

  1. Universal protocol for the rapid automated detection of carbapenem-resistant Gram-negative bacilli directly from blood cultures by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS).

    Science.gov (United States)

    Oviaño, Marina; Sparbier, Katrin; Barba, Maria José; Kostrzewa, Markus; Bou, Germán

    2016-12-01

    Detection of carbapenemase-producing bacteria directly from blood cultures is a major challenge, as patients with bacteraemia are critically ill. Early detection can be helpful for selection of the most appropriate antibiotic therapy as well as adequate control of outbreaks. In the current study, a novel matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF)-based method was developed for the rapid, automated detection of carbapenemase-producing Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii directly from blood cultures. Carbapenemase activity was determined in 30 min by measuring hydrolysis of imipenem (0.31 mg/mL) in blood cultures spiked with a series of 119 previously characterised isolates, 81 of which carried a carbapenemase enzyme (10 bla KPC , 10 bla VIM , 10 bla NDM , 10 bla IMP , 26 bla OXA-48-type , 9 bla OXA-23 , 1 bla OXA-237 , 3 bla OXA-24 and 2 bla OXA-58 ) . Twenty blood cultures obtained from bacteraemic patients carrying bla OXA-48 -producing isolates were also analysed using the same protocol. Analysis was performed using MALDI-TOF Biotyper ® Compass software, which automatically provides a result of sensitivity or resistance, calculated as the logRQ or ratio of hydrolysis of the antibiotic. This assay is simple to perform, inexpensive, time saving, universal for Gram-negative bacilli, and highly reliable (overall sensitivity and specificity of 98% and 100%, respectively). Moreover, the protocol could be established as a standardised method in clinical laboratories as it does not require specialised training in mass spectrometry. Copyright © 2016 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

  2. Analyses of black fungi by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS): species-level identification of clinical isolates of Exophiala dermatitidis

    NARCIS (Netherlands)

    Kondori, Nahid; Erhard, Marcel; Welinder-Olsson, Christina; Groenewald, Marizeth; Verkley, G.J.M.; Moore, Edward R. B.; Jamieson, Derek

    2015-01-01

    Nahid Kondori1,*, Marcel Erhard2, Christina Welinder-Olsson1, Marizeth Groenewald3, Gerard Verkley3 and Edward R. B. Moore1,41Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40234 Gothenburg, Sweden2RIPAC-LABOR GmbH, D-14476 Potsdam, Germany3Centraalbureau

  3. 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

  4. 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.

  5. 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.

  6. Optimization and Evaluation of Magnetic Bead Separation Combined with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectroscopy (MALDI-TOF MS for Proteins Profiling of Peritoneal Dialysis Effluent

    Directory of Open Access Journals (Sweden)

    Na Guo

    2014-01-01

    Full Text Available Peritoneal dialysis effluent (PDE potentially carries an archive of peptides relevant to pathological processes in abdominal and surrounding tissues. Magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is one such approach that offers a unique tool for profiling of peptides, but this approach has not been used in the PDE analysis. In this study, we developed a strategy for screening PDE proteins <15 kDa and applied this technique to identify potential biomarkers for peritonitis. We examined four kinds of magnetic beads, including a carbon series (C3, C8, weak cation exchange (WCX and immobilized metal-affinity chromatography (IMAC-Cu beads. Samples processed with IMAC-Cu magnetic beads consistently showed more MS signals across all beads within the measured mass range. Moreover, there was no difference in the number and morphology of MS signals between concentrated and unconcentrated samples. The PDE peptidome pattern, based on a panel of 15 peaks, accurately recognized peritonitis PD patients from peritonitis-free patients with sensitivity of 90.5% and specificity of 94.7% respectively. Therefore, IMAC-Cu magnetic beads and unconcentrated samples can be used as a fast and cost-effective approach for sample preparation prior to more in-depth discovery of predictive biomarkers of disease in patients on dialysis.

  7. 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.

  8. 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

  9. 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

  10. Time courses of intrapartum asphyxia: neonatal characteristics and outcomes.

    Science.gov (United States)

    Shah, Prakesh S; Perlman, Max

    2009-01-01

    We compared neonatal characteristics and adverse outcome rates of neonates with hypoxic-ischemic encephalopathy following (1) prolonged partial asphyxia, (2) acute near-total intrapartum asphyxia, and (3) the two combined. The time course of the insult was determined individually by two authors from obstetric data and neonatal charts. "Severe adverse outcome" was defined as death or severe disability detectable by age 2 years. The asphyxial time course was prolonged partial asphyxia in 167 (45%), acute near-total asphyxia in 96 (26%), combined in 78 (21%), and indeterminate in 34 (8%) patients. Among patients with known time course and outcomes, 212 (67%) had severe adverse outcome and 103 (33%) were free of severe adverse outcome. Severe adverse outcome rates were 61% for prolonged partial asphyxia, 67% for acute near-total asphyxia, and 79% for combined time course asphyxia ( P = 0.025). Long-term outcomes differ according to the time course of the insult; infants with combined time course had the worst outcome.

  11. The time course of attention: It's better than we thought.

    NARCIS (Netherlands)

    Olivers, C.N.L.

    2007-01-01

    What is the time course of attention? Research using rapid-stimulus streams has suggested that it is rather slow: Attention takes half a second to recover from processing one thing before it can process the next. This period is referred to as the attentional blink, and it is thought to reflect a

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

    African Journals Online (AJOL)

    Arun Kumar Agnihotri

    KEY WORDS: Exercise stress test; ST segment time course patterns. INTRODUCTIONᴪ. The diagnosis of angina is made on the grounds of typical pain and its relationship to effort and rest. Clinical assessment to determine whether chest pain is of ischemic origin (angina) is often ambiguous when a history of angina is ...

  13. The Time Course of Consolidation in Visual Working Memory

    Science.gov (United States)

    Vogel, Edward K.; Woodman, Geoffrey F.; Luck, Steven J.

    2006-01-01

    How long does it take to form a durable representation in visual working memory? Several theorists have proposed that this consolidation process is very slow. Here, we measured the time course of consolidation. Observers performed a change-detection task for colored squares, and shortly after the presentation of the first array, pattern masks were…

  14. 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…

  15. MALDI-TOF mass spectrometry for the detection and differentiation of Entamoeba histolytica and Entamoeba dispar.

    Science.gov (United States)

    Calderaro, Adriana; Piergianni, Maddalena; Buttrini, Mirko; Montecchini, Sara; Piccolo, Giovanna; Gorrini, Chiara; Rossi, Sabina; Chezzi, Carlo; Arcangeletti, Maria Cristina; Medici, Maria Cristina; De Conto, Flora

    2015-01-01

    Detection of Entamoeba histolytica and its differentiation from Entamoeba dispar is an important goal of the clinical parasitology laboratory. The aim of this study was the identification and differentiation of E. histolytica and E. dispar by MALDI-TOF MS, in order to evaluate the application of this technique in routine diagnostic practice. MALDI-TOF MS was applied to 3 amebic reference strains and to 14 strains isolated from feces that had been differentiated by molecular methods in our laboratory. Protein extracts from cultures of these strains (axenic cultures for the 3 reference strains and monoxenic cultures for the 14 field isolates) were analyzed by MALDI-TOF MS and the spectra obtained were analyzed by statistical software. Five peaks discriminating between E. histolytica and E. dispar reference strains were found by protein profile analysis: 2 peaks (8,246 and 8,303 Da) specific for E. histolytica and 3 (4,714; 5,541; 8,207 Da) for E. dispar. All clinical isolates except one showed the discriminating peaks expected for the appropriate species. For 2 fecal samples from which 2 strains (1 E. histolytica and 1 E. dispar) out of the 14 included in this study were isolated, the same discriminating peaks found in the corresponding isolated amebic strains were detected after only 12h (E. histolytica) and 24h (E. dispar) of incubation of the fecal samples in Robinson's medium without serum. Our study shows that MALDI-TOF MS can be used to discriminate between E. histolytica and E. dispar using in vitro xenic cultures and it also could have potential for the detection of these species in clinical samples.

  16. Time course of muscle soreness following different types of exercise

    Science.gov (United States)

    Vickers, Andrew J

    2001-01-01

    Background Post-exercise muscle soreness is a dull, aching sensation that follows unaccustomed muscular exertion. Primarily on the basis of previous laboratory-based research on eccentric exercise, soreness is usually said to follow an inverted U-shaped curve over time, peaking 24 – 48 hours after exercise. As such, it is often described as "delayed-onset" muscle soreness. In a study of long-distance runners, soreness seemed to peak immediately and then reduce gradually over time. The study is a secondary analysis of clinical trial data that aims to determine whether the time course of soreness following a natural exercise, long-distance running, is different from that following a laboratory-based exercise, bench-stepping. Methods This is a reanalysis of data from three previous clinical trials. The trials included 400 runners taking part in long-distance races and 82 untrained volunteers performing a bench-stepping test. Subjects completed a Likert scale of muscle soreness every morning and evening for the five days following their exercise. Results Interaction between trial and time is highly significant, suggesting a different time course of soreness following running and bench-stepping. 45% of subjects in the bench-stepping trial experienced peak soreness at the third or fourth follow-up (approximately 36 – 48 hours after exercise) compared to only 14% of those in the running trial. The difference between groups is robust to multivariate analysis incorporating possible confounding variables. Conclusion Soreness in runners following long-distance running follows a different time course to that in untrained individuals undertaking bench-stepping. Research on exercise taking place in the laboratory context does not necessarily generalize to exercise undertaken by trained athletes when engaged in their chosen sport. PMID:11701094

  17. 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

  18. Characterization and Comparison of Fumonisin B1-Protein Conjugates by Six Methods

    Directory of Open Access Journals (Sweden)

    Hai-Bin Zhang

    2011-12-01

    Full Text Available In order to generate an antibody against a small hapten molecule, the hapten is cross-linked with carrier protein to make it immunogenic. In this study, the hapten (Fumonisin B1, FB1 was coupled to ovalbumin (OVA and bovine serum albumin (BSA, respectively by a short cross-linker reagent (glutaraldehyde, GA. To develop a technique for detecting the conjugation, the hapten-protein conjugates (FB1-OVA and FB1-BSA were characterized thoroughly by ultraviolet (UV spectroscopy, Fourier transform infrared (FT-IR spectroscopy, gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS, respectively. The molecular weights of FB1-BSA and FB1-OVA were 74,355.301 Da and 48,009.212 Da, respectively determined by the method of MALDI-TOF-MS. The molecular coupling ratios were 11 and 5 in FB1-BSA and FB1-OVA, respectively. In this experiment, MALDI-TOF-MS was selected as the most efficient method to evaluate the cross-linking effect and calculate the molecular coupling ratio.

  19. 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.

  20. INTENSITY- AND TIME COURSE-BASED CLASSIFICATIONS OF OXIDATIVE STRESSES

    Directory of Open Access Journals (Sweden)

    Volodymyr Lushchak

    2015-05-01

    Full Text Available In living organisms, production of reactive oxygen species (ROS is counterbalanced by their elimination and/or prevention of formation which in concert can typically maintain a steady-state (stationary ROS level. However, this balance may be disturbed and lead to elevated ROS levels and enhanced damage to biomolecules. Since 1985, when H. Sies first introduced the definition of oxidative stress, this area has become one of the hot topics in biology and, to date, many details related to ROS-induced damage to cellular components, ROS-based signaling, cellular responses and adaptation have been disclosed. However, some basal oxidative damage always occurs under unstressed conditions, and in many experimental studies it is difficult to show definitely that oxidative stress is indeed induced by the stressor. Therefore, usually researchers experience substantial difficulties in the correct interpretation of oxidative stress development. For example, in many cases an increase or decrease in the activity of antioxidant and related enzymes are interpreted as evidences of oxidative stress. Careful selection of specific biomarkers (ROS-modified targets may be very helpful. To avoid these sorts of problems, I propose several classifications of oxidative stress based on its time-course and intensity. The time-course classification includes acute and chronic stresses. In the intensity based classification, I propose to discriminate four zones of function in the relationship between “Dose/concentration of inducer” and the measured “Endpoint”: I – basal oxidative stress zone (BOS; II – low intensity oxidative stress (LOS; III – intermediate intensity oxidative stress (IOS; IV – high intensity oxidative stress (HOS. The proposed classifications may be helpful to describe experimental data where oxidative stress is induced and systematize it based on its time course and intensity. Perspective directions of investigations in the field include

  1. 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.

  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. On the time course of vocal emotion recognition.

    Directory of Open Access Journals (Sweden)

    Marc D Pell

    Full Text Available 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.

  4. 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

  5. Program Predicts Time Courses of Human/Computer Interactions

    Science.gov (United States)

    Vera, Alonso; Howes, Andrew

    2005-01-01

    CPM X is a computer program that predicts sequences of, and amounts of time taken by, routine actions performed by a skilled person performing a task. Unlike programs that simulate the interaction of the person with the task environment, CPM X predicts the time course of events as consequences of encoded constraints on human behavior. The constraints determine which cognitive and environmental processes can occur simultaneously and which have sequential dependencies. The input to CPM X comprises (1) a description of a task and strategy in a hierarchical description language and (2) a description of architectural constraints in the form of rules governing interactions of fundamental cognitive, perceptual, and motor operations. The output of CPM X is a Program Evaluation Review Technique (PERT) chart that presents a schedule of predicted cognitive, motor, and perceptual operators interacting with a task environment. The CPM X program allows direct, a priori prediction of skilled user performance on complex human-machine systems, providing a way to assess critical interfaces before they are deployed in mission contexts.

  6. 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.

  7. Early perceptual interactions shape the time course of cueing.

    Science.gov (United States)

    Wilschut, Anna; Theeuwes, Jan; Olivers, Christian N L

    2013-09-01

    Performance in spatial cueing tasks is characterized by a rapid attentional enhancement with increasing cue-target SOA. We recently found that this enhancement function also applies when the cue and the target are presented invariably at a single central location, suggesting a universal cueing time course [Wilschut et al., 2011, PLoS ONE, 6, e27661]. However, using a very similar cueing task, Nieuwenstein et al. [2009, JoV, 9, 1-14] have found a rather different pattern, namely a U-shaped deficit in performance after a cue-like stimulus. The present study varied the properties of the cue and the target in order to investigate the mechanisms underlying the different time functions. In four experiments, cueing was found to either improve or decrease performance with increasing SOA, depending on the type of target that was used. In addition, the level of performance at the shortest cue-target intervals (33-83ms) was dependent on the relative strength of the cue and the target, akin to what has been found in visual masking studies. The results suggest that cueing shapes performance via two mechanisms, one sensory-related and one attention-related, the combination of which results in either U-shaped or monotonic patterns. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Time course of cisplatin-induced nephrotoxicity and hepatotoxicity.

    Science.gov (United States)

    Pezeshki, Zahra; Khosravi, Atoosa; Nekuei, Mina; Khoshnood, Samaneh; Zandi, Elnaz; Eslamian, Marjan; Talebi, Ardeshir; Emami, Seyyed Nasir-E-Din; Nematbakhsh, Mehdi

    2017-07-01

    One of the main therapeutic limitations of cisplatin (CP) is nephrotoxicity which is time-dependent. The purpose of this study was to determine the optimal timing for initiation of CP toxicity. Sixty male and female Wistar rats were randomly divided into five groups. All the animals in groups 2-5 received single dose of CP (10 mg/kg; i.p.), and were evaluated 25, 50, 75, and 100 hours after CP administration. Group 1 as an untreated group did not receive any agent and was considered as time zero. The data indicated time-dependent progression of kidney and hepatic toxicity due to CP administration. Histological examination showed increase in kidney tissue damage score (KTDS) at hour 25, which peaked 75-100 hours after CP administration. Significant body weight loss and reduction of alkaline phosphatase (ALP) 50 hours after CP injection were observed. Blood urea nitrogen (BUN), creatinine (Cr), and serum nitrite increased significantly 75 hours after CP injection. Also, enhancement of kidney and testis weights, and alkaline aspartate aminotransferase (AST) level; and reduction of alanine aminotransferase (ALT) level and uterus weight occurred significantly 100 hours after the injection, while kidney malondialdehyde level enhanced significantly 75 hours after CP administration. These findings suggest that the CP-induced nephrotoxicity started to develop almost 3 days after administration of the drug in rats. CP surprisingly reduced the serum levels ALP and ALT while AST increased 100 hours after CP injection. CP-induced nephrotoxicity and hepatotoxicity are time-dependent, and the related biomarkers may alter by different trends.

  9. 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

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

    NARCIS (Netherlands)

    de Groot, P.C.E.; van Kuppevelt, D.; Pons, C.; van der Woude, L.H.V.; 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. Time Course of Early Postadmission Hematoma Expansion in Spontaneous Intracerebral Hemorrhage

    DEFF Research Database (Denmark)

    Ovesen, Christian; Christensen, Anders Fogh; Krieger, Derk W

    2014-01-01

    BACKGROUND AND PURPOSE: Early hematoma expansion (EHE) in patients with intracerebral hematoma is a promising treatment target. To date, the time course of EHE has remained poorly described. We prospectively investigated the time course of EHE. METHODS: We included consecutive patients presenting...

  12. The Time Course of Perception and Retrieval in Matching and Recognition

    Science.gov (United States)

    Kent, Christopher; Lamberts, Koen

    2006-01-01

    A four-part experiment was carried out to study the relationship between the time course of object-feature perception and the time course of retrieval of object information from memory. The experiment consisted of 2 perceptual matching tasks, and 2 perceptual recognition tasks. In all 4 tasks, participants provided speeded judgments of the…

  13. Time course study of intestinal epithelial barrier disruption in acute mesenteric venous thrombosis.

    Science.gov (United States)

    Yang, Shuofei; Chen, Jiaquan; Ni, Qihong; Qi, Haozhe; Guo, Xiangjiang; Zhang, Lan; Xue, Guanhua

    2018-04-01

    Acute superior mesenteric venous thrombosis (ASMVT) is an abdominal vascular condition. Early recanalization is essential to successful treatment. The aim of the study was to establish rabbit models of ASMVT and assess the time course of intestinal epithelial barrier disruption. After surgical exposure of superior mesenteric vein (Sham group), large-vessel (L-group) and small-vessel (S-group) models were established by endothelium damage, stenosis creation, and thrombin injection. At baseline, 6, 9, and 12 h, hemodynamic and serum parameters were tested. Serum from ASMVT patients diagnosed at 24, 36, 48, and 60 h from symptom onset was collected. Intestinal barrier disruption was assessed by tight junction (TJ) protein expression, morphology changes, and bacterial translocation. Mesenteric arteriospasm was measured by flow velocity and intestinal wet/dry weight ratio. The serum level of intestinal fatty acid-binding protein and endotoxin in patients was also measured as an indicator for intestinal barrier function. Severe acidosis and lacticemia were observed in both the groups. The L-group experienced greater hemodynamic alteration than the S-group. Intestinal barrier disruption was detected by significantly decreased TJ protein expression, histology and ultrastructure injury of TJ, increased permeability, and bacterial translocation, at 9 h in the S-group and 12 h in the L-group. Secondary mesenteric arteriospasm occurred at the same time of complete intestinal barrier disruption and could be a significant cause of bowel necrosis. Significant increased level of intestinal fatty acid-binding protein and endotoxin was found in patients at 48 h in the S-group type and 60 h in the L-group type. The ASMVT animal models of both the types were first established. The loss of intestinal barrier function occurred at 6 h in the S-group model and 9 h in the L-group model. For clinical patients, the time window extended to 36 h in the S-group type and 48 h in the L

  14. 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

  15. 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...

  16. 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...

  17. Time Course of Attentional Bias in Anxiety: Emotion and Gender Specificity

    OpenAIRE

    Sass, Sarah M.; Heller, Wendy; Stewart, Jennifer L.; Silton, Rebecca Levin; Edgar, J. Christopher; Fisher, Joscelyn E.; Miller, Gregory A.

    2009-01-01

    Anxiety is characterized by cognitive biases, including attentional bias to emotional (especially threatening) stimuli. Accounts differ on the time course of attention to threat, but the literature generally confounds emotional valence and arousal and overlooks gender effects, both addressed in the present study. Nonpatients high in self-reported anxious apprehension, anxious arousal, or neither completed an emotion-word Stroop task during ERP recording. Hypotheses differentiated time course ...

  18. MoS2/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

  19. 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.

  20. 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.

  1. [The time course of changes in cell immunological parameters during administration of live dry plague vaccine].

    Science.gov (United States)

    Bogacheva, N V; Darmov, I V; Borisevich, I V; Kriuchkov, A V; Pechenkin, D V

    2009-08-01

    The study of the time course of changes in cell immunological parameters by a magnetic separation technique in human beings during the administration of plague vaccine in relation to the immunological load revealed the higher blood levels of all T lymphocyte subpopulations on day 14 after vaccination. These changes are most typical of a primary vaccinated cohort. The increased frequency of plague vaccine administration and multiple immunizations with live plague, anthrax, and tularemia vaccines produce the time-course of changes in T lymphocyte populations (subpopulations) in response to the regular administration of plague vaccine. A high immunological load in man also promotes a significant reduction in the level of B lymphocytes.

  2. Time course of sleep inertia after nighttime and daytime sleep episodes.

    Science.gov (United States)

    Achermann, P; Werth, E; Dijk, D J; Borbely, A A

    1995-12-01

    Sleep inertia refers to the period of reduced vigilance following upon awakening from sleep. To investigate the time course of sleep inertia, self-ratings of alertness and reaction time in a memory task were repeatedly assessed after nighttime and daytime sleep episodes in healthy young men. Alertness gradually increased and reaction time gradually decreased within the first hour after awakening. Their time course could be described by exponential functions with time constants of 0.45 h and 0.3 h, respectively. The data demonstrate that sleep inertia is a robust, quantifiable process that can be incorporated in models of sleep and vigilance.

  3. 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…

  4. 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…

  5. BTNET : boosted tree based gene regulatory network inference algorithm using time-course measurement data.

    Science.gov (United States)

    Park, Sungjoon; Kim, Jung Min; Shin, Wonho; Han, Sung Won; Jeon, Minji; Jang, Hyun Jin; Jang, Ik-Soon; Kang, Jaewoo

    2018-03-19

    Identifying gene regulatory networks is an important task for understanding biological systems. Time-course measurement data became a valuable resource for inferring gene regulatory networks. Various methods have been presented for reconstructing the networks from time-course measurement data. However, existing methods have been validated on only a limited number of benchmark datasets, and rarely verified on real biological systems. We first integrated benchmark time-course gene expression datasets from previous studies and reassessed the baseline methods. We observed that GENIE3-time, a tree-based ensemble method, achieved the best performance among the baselines. In this study, we introduce BTNET, a boosted tree based gene regulatory network inference algorithm which improves the state-of-the-art. We quantitatively validated BTNET on the integrated benchmark dataset. The AUROC and AUPR scores of BTNET were higher than those of the baselines. We also qualitatively validated the results of BTNET through an experiment on neuroblastoma cells treated with an antidepressant. The inferred regulatory network from BTNET showed that brachyury, a transcription factor, was regulated by fluoxetine, an antidepressant, which was verified by the expression of its downstream genes. We present BTENT that infers a GRN from time-course measurement data using boosting algorithms. Our model achieved the highest AUROC and AUPR scores on the integrated benchmark dataset. We further validated BTNET qualitatively through a wet-lab experiment and showed that BTNET can produce biologically meaningful results.

  6. 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.

  7. Importance of measuring the time course of flow-mediated dilatation in humans.

    NARCIS (Netherlands)

    Black, M.A.; Cable, N.T.; Thijssen, D.H.J.; Green, D.J.

    2008-01-01

    Flow-mediated dilatation (FMD) is widely used to describe conduit artery endothelial function. The traditional approaches to FMD calculation assess diameter change at arbitrary time points after occluding cuff deflation. The aim of this study was to examine the time course of brachial artery FMD

  8. Time course of change in vasodilator function and capacity in response to exercise training in humans.

    NARCIS (Netherlands)

    Tinken, T.M.; Thijssen, D.H.J.; Black, M.A.; Cable, N.T.; Green, D.J.

    2008-01-01

    Studies of the impact of exercise training on arterial adaptation in healthy subjects have produced disparate results. It is possible that some studies failed to detect changes because functional and structural adaptations follow a different time course and may therefore not be detected at discrete

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

    NARCIS (Netherlands)

    Čomić, Hata; Rinkel, Gabriel J.E.|info:eu-repo/dai/nl/085712000; Vergouwen, Mervyn D.I.|info:eu-repo/dai/nl/320630544

    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

  10. 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.

  11. 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:

  12. 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.

  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. Time-Course of Semantic Composition: The Case of Aspectual Coercion

    Science.gov (United States)

    Pinango, Maria Mercedes; Winnick, Aaron; Ullah, Rashad; Zurif, Edgar

    2006-01-01

    We examine the time-course of semantic structure formation during real-time sentence comprehension. We do this through the lens of aspectual coercion, a semantic combinatorial operation that lacks morpho-syntactic reflections, yet is indispensable for sentence interpretation. We describe two experiments. Experiment 1 replicates the results of a…

  15. Eye Movements Reveal the Time-Course of Anticipating Behaviour Based on Complex, Conflicting Desires

    Science.gov (United States)

    Ferguson, Heather J.; Breheny, Richard

    2011-01-01

    The time-course of representing others' perspectives is inconclusive across the currently available models of ToM processing. We report two visual-world studies investigating how knowledge about a character's basic preferences (e.g. "Tom's favourite colour is pink") and higher-order desires (his wish to keep this preference secret) compete to…

  16. 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…

  17. 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

  18. pGQL: A probabilistic graphical query language for gene expression time courses

    Directory of Open Access Journals (Sweden)

    Schilling Ruben

    2011-04-01

    Full Text Available Abstract Background Timeboxes are graphical user interface widgets that were proposed to specify queries on time course data. As queries can be very easily defined, an exploratory analysis of time course data is greatly facilitated. While timeboxes are effective, they have no provisions for dealing with noisy data or data with fluctuations along the time axis, which is very common in many applications. In particular, this is true for the analysis of gene expression time courses, which are mostly derived from noisy microarray measurements at few unevenly sampled time points. From a data mining point of view the robust handling of data through a sound statistical model is of great importance. Results We propose probabilistic timeboxes, which correspond to a specific class of Hidden Markov Models, that constitutes an established method in data mining. Since HMMs are a particular class of probabilistic graphical models we call our method Probabilistic Graphical Query Language. Its implementation was realized in the free software package pGQL. We evaluate its effectiveness in exploratory analysis on a yeast sporulation data set. Conclusions We introduce a new approach to define dynamic, statistical queries on time course data. It supports an interactive exploration of reasonably large amounts of data and enables users without expert knowledge to specify fairly complex statistical models with ease. The expressivity of our approach is by its statistical nature greater and more robust with respect to amplitude and frequency fluctuation than the prior, deterministic timeboxes.

  19. 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 ...

  20. Time course of EEG oscillations during repeated listening of a well-known aria

    Directory of Open Access Journals (Sweden)

    Lutz eJäncke

    2015-07-01

    Full Text Available While previous studies have analyzed mean neurophysiological responses to musical stimuli, the current study aimed to identify specific time courses of EEG oscillations, which are associated with dynamic changes in the acoustic features of the musical stimulus. In addition, we were interested in whether these time courses change during a repeated presentation of the same musical piece. A total of 16 subjects repeatedly listened to the well-known aria Nessun dorma, sung by Paul Potts, while continuous 128-channel EEG and heart rate (HR, as well as electrodermal (EDA responses, were recorded. The time courses for the EEG oscillations were calculated using a time resolution of 1 second for several frequency bands, on the basis of individual alpha-peak frequencies (theta, low alpha-1, low alpha-2, upper alpha, and beta. For all frequency bands, we identified a more or less continuous increase in power relative to a baseline period, indicating strong event-related synchronization (ERS during music listening. The ERS time courses, however, did not correlate strongly with the time courses of the acoustic features of the aria. In addition, we did not observe changes in EEG oscillations after repeated presentation of the same musical piece. Aside from this distinctive feature, we identified a remarkable variability in EEG oscillations, both within and between the repeated presentations of the aria. We interpret the continuous increase in ERS observed in all frequency bands during music listening as an indicator of a particular neurophysiological and psychological state evoked by music listening. We suggest that this state is characterized by increased internal attention (accompanied by reduced external attention, increased inhibition of brain networks not involved in the generation of this internal state, the maintenance of a particular level of general alertness, and a type of brain state that can be described as mind wandering. The overall state can be

  1. 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.

  2. Time course of the antiproteinuric and antihypertensive effect of losartan in diabetic nephropathy

    DEFF Research Database (Denmark)

    Andersen, Steen; Jacobsen, Peter; Tarnow, Lise

    2003-01-01

    of losartan treatment and stabilized after 7 days (Parterial blood pressure and albuminuria are concordant, which suggests that systemic and renal haemodynamic mechanisms are of primary......BACKGROUND: Blockade of the renin-angiotensin system is the primary target in the treatment of diabetic kidney disease. Angiotensin II subtype 1 (AT1) receptor antagonists reduce albuminuria and lower blood pressure, but the initial time course of these effects after initiation of treatment...... is unknown. We evaluated the time course of the antihypertensive and antialbuminuric effect after initiation of AT1 receptor blockade by losartan in diabetic nephropathy. METHODS: Ten hypertensive type 1 diabetic patients with diabetic nephropathy were included in the study. After a washout period of 4 weeks...

  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. 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.

  5. 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.

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

    OpenAIRE

    Wiwie, Christian; Rauch, Alexander; Haakonsson, Anders; Barrio-Hernandez, Inigo; Blagoev, Blagoy; Mandrup, Susanne; Röttger, Richard; Baumbach, Jan

    2018-01-01

    Advances in OMICS technologies emerged both massive expression data sets and huge networks modelling the molecular interplay of genes, RNAs, proteins and metabolites. Network enrichment methods combine these two data types to extract subnetwork responses from case/control setups. However, 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). I...

  7. Probing the time course of head-motion cues integration during auditory scene analysis

    Science.gov (United States)

    Kondo, Hirohito M.; Toshima, Iwaki; Pressnitzer, Daniel; Kashino, Makio

    2014-01-01

    The perceptual organization of auditory scenes is a hard but important problem to solve for human listeners. It is thus likely that cues from several modalities are pooled for auditory scene analysis, including sensory-motor cues related to the active exploration of the scene. We previously reported a strong effect of head motion on auditory streaming. Streaming refers to an experimental paradigm where listeners hear sequences of pure tones, and rate their perception of one or more subjective sources called streams. To disentangle the effects of head motion (changes in acoustic cues at the ear, subjective location cues, and motor cues), we used a robotic telepresence system, Telehead. We found that head motion induced perceptual reorganization even when the acoustic scene had not changed. Here we reanalyzed the same data to probe the time course of sensory-motor integration. We show that motor cues had a different time course compared to acoustic or subjective location cues: motor cues impacted perceptual organization earlier and for a shorter time than other cues, with successive positive and negative contributions to streaming. An additional experiment controlled for the effects of volitional anticipatory components, and found that arm or leg movements did not have any impact on scene analysis. These data provide a first investigation of the time course of the complex integration of sensory-motor cues in an auditory scene analysis task, and they suggest a loose temporal coupling between the different mechanisms involved. PMID:25009456

  8. Probing the time course of head-motion cues integration during auditory scene analysis

    Directory of Open Access Journals (Sweden)

    Hirohito M. Kondo

    2014-06-01

    Full Text Available The perceptual organization of auditory scenes is a hard but important problem to solve for human listeners. It is thus likely that cues from several modalities are pooled for auditory scene analysis, including sensory-motor cues related to the active exploration of the scene. We previously reported a strong effect of head motion on auditory streaming. Streaming refers to an experimental paradigm where listeners hear sequences of pure tones, and report their perception of one or more subjective sources called streams. To disentangle the effects of head motion (changes in acoustic cues at the ear, subjective location cues, and motor cues, we used a robotic telepresence system, Telehead. We found that head motion induced perceptual reorganization even when the acoustic scene had not changed. Here we reanalyzed the same data to probe the time course of sensory-motor integration. We show that motor cues had a different time course compared to acoustic or subjective location cues: motor cues impacted perceptual organization earlier and for a shorter time than other cues, with successive positive and negative contributions to streaming. An additional experiment controlled for the effects of volitional anticipatory components, and found that arm or leg movements did not have any impact on scene analysis. These data provide a first investigation of the time course of the complex integration of sensory-motor cues in an auditory scene analysis task, and they suggest a loose temporal coupling between the different mechanisms involved.

  9. Time course study of oxidative and nitrosative stress and antioxidant enzymes in K2Cr2O7-induced nephrotoxicity

    Directory of Open Access Journals (Sweden)

    Saldívar Liliana

    2005-04-01

    Full Text Available Abstract Background Potassium dichromate (K2Cr2O7-induced nephrotoxicity is associated with oxidative and nitrosative stress. In this study we investigated the relation between the time course of the oxidative and nitrosative stress with kidney damage and alterations in the following antioxidant enzymes: Cu, Zn superoxide dismutase (Cu, Zn-SOD, Mn-SOD, glutathione peroxidase (GPx, glutathione reductase (GR, and catalase (CAT. Methods Nephrotoxicity was induced in rats by a single injection of K2Cr2O7. Groups of animals were sacrificed on days 1,2,3,4,6,8,10, and 12. Nephrotoxicity was evaluated by histological studies and by measuring creatinine clearance, serum creatinine, blood urea nitrogen (BUN, and urinary excretion of N-acetyl-β-D-glucosaminidase (NAG and total protein. Oxidative and nitrosative stress were measured by immunohistochemical localization of protein carbonyls and 3-nitrotyrosine, respectively. Cu, Zn-SOD, Mn-SOD, and CAT were studied by immunohistochemical localization. The activity of total SOD, CAT, GPx, and GR was also measured as well as serum and kidney content of chromium and urinary excretion of NO2 -/NO3-. Data were compared by two-way analysis of variance followed by a post hoc test. Results Serum and kidney chromium content increased reaching the highest value on day 1. Nephrotoxicity was made evident by the decrease in creatinine clearance (days 1–4 and by the increase in serum creatinine (days 1–4, BUN (days 1–6, urinary excretion of NAG (days 1–4, and total protein (day 1–6 and by the structural damage to the proximal tubules (days 1–6. Oxidative and nitrosative stress were clearly evident on days 1–8. Urinary excretion of NO2-/NO3- decreased on days 2–6. Mn-SOD and Cu, Zn-SOD, estimated by immunohistochemistry, and total SOD activity remained unchanged. Activity of GPx decreased on days 3–12 and those of GR and CAT on days 2–10. Similar findings were observed by immunohistochemistry of CAT

  10. Time course of 25(OHD3 vitamin D3 as well as PTH (parathyroid hormone during fracture healing of patients with normal and low bone mineral density (BMD

    Directory of Open Access Journals (Sweden)

    Wöfl Christoph

    2013-01-01

    Full Text Available Abstract Background Until now the exact biochemical processes during healing of metaphyseal fractures of healthy and osteoporotic bone remain unclear. Especially the physiological time courses of 25(OHD3 (Vitamin D as well as PTH (Parathyroid Hormone the most important modulators of calcium and bone homeostasis are not yet examined sufficiently. The purpose of this study was to focus on the time course of these parameters during fracture healing. Methods In the presented study, we analyse the time course of 25(OHD3 and PTH during fracture healing of low BMD level fractures versus normal BMD level fractures in a matched pair analysis. Between March 2007 and February 2009 30 patients older than 50 years of age who had suffered a metaphyseal fracture of the proximal humerus, the distal radius or the proximal femur were included in our study. Osteoporosis was verified by DEXA measuring. The time courses of 25(OHD3 and PTH were examined over an eight week period. Friedmann test, the Wilcoxon signed rank test and the Mann-Withney U test were used as post-hoc tests. A p-value ≤ 0.05 was considered significant. Results Serum levels of 25(OHD3 showed no differences in both groups. In the first phase of fracture healing PTH levels in the low BMD level group remained below those of the normal BMD group in absolute figures. Over all no significant differences between low BMD level bone and normal BMD level bone could be detected in our study. Conclusions The time course of 25(OHD3 and PTH during fracture healing of patients with normal and low bone mineral density were examined for the first time in humans in this setting and allowing molecular biological insights into fracture healing in metaphyseal bones on a molecural level. There were no significant differences between patients with normal and low BMD levels. Hence further studies will be necessary to obtain more detailed insight into fracture healing in order to provide reliable decision criteria for

  11. Going, going, gone: characterizing the time-course of congruency sequence effects

    Directory of Open Access Journals (Sweden)

    Tobias eEgner

    2010-09-01

    Full Text Available Performance on traditional selective attention tasks, like the Stroop and flanker protocols, is subject to modulation by trial history, whereby the magnitude of congruency (or conflict effects is often found to decrease following an incongruent trial compared to a congruent one. These ‘congruency sequence effects’ (CSEs typically appear to reflect a mesh of memory- and attention-based processes. The current study aimed to shed new light on the nature of the attention-based contribution to CSEs, by characterizing the shape of the CSE time-course while controlling for mnemonic influences. Existing attention-based accounts of CSEs are either ambiguous in their predictions of CSE time-courses, or predict CSEs to persist or grow over the post-stimulus/response interval in anticipation of an upcoming stimulus. We gauged CSE time-courses by systematically varying inter-stimulus (Experiment 1 and response-to-stimulus (Experiment 2 intervals across a wide temporal range, in a face-word Stroop task. In spite of a an exponential increase in the likelihood of stimulus appearance with increasing interval duration (i.e., an exponential hazard function, results from both experiments showed CSEs to be most pronounced at the shortest intervals, to quickly decay in magnitude with increasing interval length, and to be absent at longer intervals. These data refute the idea that attentional contributions to CSEs remain static over post-stimulus/response intervals and are incompatible with the notion that CSEs reflect expectation-guided preparatory biasing in anticipation of a forthcoming stimulus. The data are compatible, however, with the notion that attentional contributions to CSEs reflect a short-lived, phasic enhancement of attentional set in reaction to processing conflict.

  12. TimeXNet: identifying active gene sub-networks using time-course gene expression profiles.

    Science.gov (United States)

    Patil, Ashwini; Nakai, Kenta

    2014-01-01

    Time-course gene expression profiles are frequently used to provide insight into the changes in cellular state over time and to infer the molecular pathways involved. When combined with large-scale molecular interaction networks, such data can provide information about the dynamics of cellular response to stimulus. However, few tools are currently available to predict a single active gene sub-network from time-course gene expression profiles. We introduce a tool, TimeXNet, which identifies active gene sub-networks with temporal paths using time-course gene expression profiles in the context of a weighted gene regulatory and protein-protein interaction network. TimeXNet uses a specialized form of the network flow optimization approach to identify the most probable paths connecting the genes with significant changes in expression at consecutive time intervals. TimeXNet has been extensively evaluated for its ability to predict novel regulators and their associated pathways within active gene sub-networks in the mouse innate immune response and the yeast osmotic stress response. Compared to other similar methods, TimeXNet identified up to 50% more novel regulators from independent experimental datasets. It predicted paths within a greater number of known pathways with longer overlaps (up to 7 consecutive edges) within these pathways. TimeXNet was also shown to be robust in the presence of varying amounts of noise in the molecular interaction network. TimeXNet is a reliable tool that can be used to study cellular response to stimuli through the identification of time-dependent active gene sub-networks in diverse biological systems. It is significantly better than other similar tools. TimeXNet is implemented in Java as a stand-alone application and supported on Linux, MS Windows and Macintosh. The output of TimeXNet can be directly viewed in Cytoscape. TimeXNet is freely available for non-commercial users.

  13. 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

  14. Time-course of sleep inertia upon awakening from nighttime sleep with different sleep homeostasis conditions.

    Science.gov (United States)

    Ferrara, M; De Gennaro, L; Bertini, M

    2000-03-01

    We assessed the time-course of sleep inertia during the first 75 min after morning awakening from regular nocturnal sleep, as well as from nighttime sleep episodes with altered sleep homeostasis conditions. Ten normal males slept for 6 nights in the laboratory: 1 adaptation (AD), 2 baseline (BSL, BSL-A), 2 selective Slow-Wave Sleep (SWS) deprivation (DEP-1, DEP-2), and 1 recovery night (REC). On morning awakening, performance was assessed by means of: a) Descending Subtraction Task (DST); b) Auditory Reaction Time task (ART); and c) Finger Tapping Task (FTT). The test battery, lasting about 13 min, was repeated for 5 times. In regard to DST, the Correct Response ratio (CR/NR) showed a great increase of sleep inertia on the first testing session of REC. Regarding sleep inertia time-course, a significant linear decrease across the testing sessions during the BSL-A and the DEP-2 was present, whereas a significant quadratic trend during the AD, the DEP-1 and the REC was found. On the other hand, ART performance showed a significant quadratic trend across testing sessions, while FTT performance did not show any significant variation. A uniform pattern of variation of time-course of sleep inertia as a function of the different sleep homeostasis conditions was not recognized. Performance accuracy (CR/NR) on the DST showed the hypothesized increasing linear trend across testing sessions only during 2 out of 6 nights, while the unexpected quadratic trend of ART performance is probably due to a fatigue effect. During sleep inertia, cognitive performance reached the baseline level about 30 min after awakening, while motor performance was still below the baseline levels 75 min after awakening. The finding that cognitive performance recovery is greater and more rapid than motor performance recovery could be very important for operational settings and in sustained operations.

  15. Time course of sleep inertia dissipation in human performance and alertness

    Science.gov (United States)

    Jewett, M. E.; Wyatt, J. K.; Ritz-De Cecco, A.; Khalsa, S. B.; Dijk, D. J.; Czeisler, C. A.

    1999-01-01

    Alertness and performance on a wide variety of tasks are impaired immediately upon waking from sleep due to sleep inertia, which has been found to dissipate in an asymptotic manner following waketime. It has been suggested that behavioural or environmental factors, as well as sleep stage at awakening, may affect the severity of sleep inertia. In order to determine the time course of sleep inertia dissipation under normal entrained conditions, subjective alertness and cognitive throughput were measured during the first 4 h after habitual waketime from a full 8-h sleep episode on 3 consecutive days. We investigated whether this time course was affected by either sleep stage at awakening or behavioural/environmental factors. Sleep inertia dissipated in an asymptotic manner and took 2-4 h to near the asymptote. Saturating exponential functions fitted the sleep inertia data well, with time constants of 0.67 h for subjective alertness and 1.17 h for cognitive performance. Most awakenings occurred out of stage rapid eye movement (REM), 2 or 1 sleep, and no effect of sleep stage at awakening on either the severity of sleep inertia or the time course of its dissipation could be detected. Subjective alertness and cognitive throughput were significantly impaired upon awakening regardless of whether subjects got out of bed, ate breakfast, showered and were exposed to ordinary indoor room light (approximately 150 lux) or whether subjects participated in a constant routine (CR) protocol in which they remained in bed, ate small hourly snacks and were exposed to very dim light (10-15 lux). These findings allow for the refinement of models of alertness and performance, and have important implications for the scheduling of work immediately upon awakening in many occupational settings.

  16. Clinical presentation and time-course of postoperative venous thromboembolism: Results from the RIETE Registry.

    Science.gov (United States)

    Arcelus, Juan Ignacio; Monreal, Manuel; Caprini, Joseph A; Guisado, Javier Gutiérrez; Soto, Maria José; Núñez, Manuel Jesús; Alvárez, Juan Carlos

    2008-03-01

    There is little literature about the clinical presentation and time-course of postoperative venous thromboembolism (VTE) in different surgical procedures. RIETE is an ongoing, prospective registry of consecutive patients with objectively confirmed, symptomatic acute VTE. In this analysis, we analysed the baseline characteristics, thromboprophylaxis and therapeutic patterns, time-course, and three-month outcome of all patients with postoperative VTE. As of January 2006, there were 1,602 patients with postoperative VTE in RIETE: 393 (25%) after major orthopaedic surgery (145 elective hip arthroplasty, 126 knee arthroplasty, 122 hip fracture); 207 (13%) after cancer surgery; 1,002 (63%) after other procedures. The percentage of patients presenting with clinically overt pulmonary embolism (PE) (48%, 48%, and 50% respectively), the average time elapsed from surgery to VTE (22 +/- 16, 24 +/- 16, and 21 +/- 15 days, respectively), and the three-month incidence of fatal PE (1.3%, 1.4%, and 0.8%, respectively), fatal bleeding (0.8%, 1.0%, and 0.2%, respectively), or major bleeding (2.3%, 2.9%, and 2.8%, respectively) were similar in the three groups. However, the percentage of patients who had received thromboprophylaxis (96%, 76% and 52%, respectively), the duration of prophylaxis (17 +/- 9.6, 13 +/- 8.9, and 12 +/- 11 days, respectively) and the mean daily doses of low-molecular-weight heparin (4,252 +/- 1,016, 3,260 +/- 1,141, and 3,769 +/- 1,650 IU, respectively), were significantly lower in those undergoing cancer surgery or other procedures. In conclusion, the clinical presentation, time-course, and three-month outcome of VTE was similar among the different subgroups of patients, but the use of prophylaxis in patients undergoing cancer surgery or other procedures was suboptimal.

  17. 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.

  18. Time course of inhibition of return in a spatial cueing paradigm with distractors.

    Science.gov (United States)

    Eng, Vivian; Lim, Alfred; Janssen, Steve M J; Satel, Jason

    2018-02-01

    Studies of endogenous and exogenous attentional orienting in spatial cueing paradigms have been used to investigate inhibition of return, a behavioral phenomenon characterized by delayed reaction time in response to recently attended locations. When eye movements are suppressed, attention is covertly oriented to central or peripheral stimuli. Overt orienting, on the other hand, requires explicit eye movements to the stimuli. The present study examined the time course of slowed reaction times to previously attended locations when distractors are introduced into overt and covert orienting tasks. In a series of experiments, manual responses were required to targets following central and peripheral cues at three different cue-target intervals, with and without activated oculomotor systems. The results demonstrate that, when eye movements are suppressed, behavioral inhibition is reduced or delayed in magnitude by the presence of a distractor relative to conditions without distractors. However, the time course of behavioral inhibition when eye movements are required remains similar with or without distractors. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. 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

  20. Neural correlates of reconfiguration failure reveal the time course of task-set reconfiguration.

    Science.gov (United States)

    Steinhauser, Marco; Maier, Martin E; Ernst, Benjamin

    2017-11-01

    The ability to actively prepare for new tasks is crucial for achieving goal-directed behavior. The task-switching paradigm is frequently used to investigate this task-set reconfiguration. In the present study, we adopted a novel approach to identify a neural signature of reconfiguration in event-related potentials. Our method was to isolate neural correlates of reconfiguration failure and to use these correlates to reveal the time course of reconfiguration in task switches and task repetitions. We employed a task-switching paradigm in which two types of errors could be distinguished: task errors (the incorrect task was applied) and response errors (an incorrect response for the correct task was provided). Because differential activity between both error types distinguishes successful and failed reconfiguration, this activity could be used as a neural signature of the reconfiguration process. We found that, whereas reconfiguration takes place on task repetitions and task switches, it occurred earlier in the former than in the latter. Single-trial analysis revealed that the same activity predicted the amplitude of error-related brain activity, providing further support that this preparatory activity reflects reconfiguration. Our results implicate that reconfiguration is not switch-specific but that task switches and task repetitions differ with respect to the time course of reconfiguration. Furthermore, this study demonstrates that considering neural correlates of failure is a promising approach to link cognitive mechanisms to specific neural processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. 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.

  2. 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.

  3. Time course of the effects of static stretching on cycling economy.

    Science.gov (United States)

    Wolfe, Alyson E; Brown, Lee E; Coburn, Jared W; Kersey, Robert D; Bottaro, Martim

    2011-11-01

    Stretching has been implemented as part of the warm-up before physical events and widely thought to promote increased sport performance and decreased injury risk. However, recent research has concluded that static stretching before many exercises inhibits acute power, strength, and sprinting performance. There is little research examining the time course of these effects on moderate intensity cycling. The purpose of this study was to examine the time course of static stretching on cycling economy. The subjects consisted of 5 men and 5 women highly trained endurance cyclists. The first of 3 visits was baseline testing of their cycling VO2max. The second and third visits were either stretching or no stretching before a 30-minute stationary ride at 65% of their VO2max. The stretching condition consisted of four 30-second repetitions of 5 stretches with an average total stretching time of 16 minutes. VO2 demonstrated a significant condition by time interaction with the 5-minute time point being significantly less in the nonstretching condition (32.66 ± 5.35 ml·kg(-1)·min(-1)) than stretching (34.39 ± 5.39 ml·kg(-1)·min(-1)). No other time points were different. Our results demonstrate that static stretching yielded an acute increase in submaximal VO2; therefore, coaches and highly trained endurance cyclists should exclude static stretching immediately before moderate intensity cycling because it reduces acute cycling economy.

  4. The time course of feature integration in plaid patterns revealed by meta- and paracontrast masking.

    Science.gov (United States)

    Bruchmann, Maximilian; Hintze, Philipp; Vorwerk, Johannes

    2012-12-14

    When a plaid object is presented, the visual system decomposes it into its constituting orientation primitives and integrates them at later processing stages. The present study reveals the time course of this process by applying meta- and paracontrast masking to both simple oriented and plaid gratings. With various stimulus onset asynchronies (SOA) between target gratings and surrounding mask annuli, subjects were asked to identify whether targets were simple gratings collinear to the masks, orthogonal to the masks, plaid, or whether no target was presented. The resulting time courses for each type of stimulus confusion showed that metacontrast peaked when orientation primitives had already begun to be integrated into one object, indicated by a dominance of "no target" responses given to plaid stimuli at SOAs around 70 ms. At SOAs around 10 to 30 ms masking also had a significant impact but acted on separable components, indicated by a dominance of "orthogonal" responses given plaid stimuli. Probability summation of "no target" responses given simple gratings revealed that only at shorter SOAs performance for plaid stimuli could be predicted assuming independent features but not at SOAs of at 50-70 ms. We discuss in how far these results could also be explained by the dynamics of cross-orientation suppression (COS) and how they might relate to the process of feature integration in plaids.

  5. 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.

  6. 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.

  7. Time course of activation of calcium release from sarcoplasmic reticulum in skeletal muscle.

    Science.gov (United States)

    Simon, B J; Schneider, M F

    1988-12-01

    Myoplasmic free calcium transients were measured with antipyrylazo III in voltage clamped segments of frog skeletal muscle fibers and were used to calculate the rate of release (Rrel) of calcium from the sarcoplasmic reticulum. Intramembrane charge movement was measured for the same pulses in the same fibers. During a depolarizing pulse Rrel rose to an early peak and then decayed relatively rapidly but incompletely due to calcium-dependent inactivation (Schneider M.F., and B.J. Simon. 1988. J. Physiol. (Lond.). 405:727-745). Two approaches were used to determine release activation independent of the effects of inactivation: (a) a mathematical correction based on the assumption that inactivation was a process occurring in parallel with and independently of activation; (b) an experimental procedure in which release was maximally inactivated by a large short prepulse and then the remaining noninactivatable component of release was monitored during a subsequent test pulse. Both procedures gave the same time course of activation of release. Release activation paralleled the time course of intramembrane charge movement but was delayed by a few milliseconds.

  8. Synaptic consolidation as a temporally variable process: Uncovering the parameters modulating its time-course.

    Science.gov (United States)

    Casagrande, Mirelle A; Haubrich, Josué; Pedraza, Lizeth K; Popik, Bruno; Quillfeldt, Jorge A; de Oliveira Alvares, Lucas

    2018-03-06

    Memories are not instantly created in the brain, requiring a gradual stabilization process called consolidation to be stored and persist in a long-lasting manner. However, little is known whether this time-dependent process is dynamic or static, and the factors that might modulate it. Here, we hypothesized that the time-course of consolidation could be affected by specific learning parameters, changing the time window where memory is susceptible to retroactive interference. In the rodent contextual fear conditioning paradigm, we compared weak and strong training protocols and found that in the latter memory is susceptible to post-training hippocampal inactivation for a shorter period of time. The accelerated consolidation process triggered by the strong training was mediated by glucocorticoids, since this effect was blocked by pre-training administration of metyrapone. In addition, we found that pre-exposure to the training context also accelerates fear memory consolidation. Hence, our results demonstrate that the time window in which memory is susceptible to post-training interferences varies depending on fear conditioning intensity and contextual familiarity. We propose that the time-course of memory consolidation is dynamic, being directly affected by attributes of the learning experiences. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Twitch potentiation influences the time course of twitch depression in muscle relaxant studies : A pharmacokinetic-pharmacodynamic explanation

    NARCIS (Netherlands)

    Eleveld, Douglas J.; Proost, Johannes H.; Wierda, J. Mark K. H.

    2006-01-01

    The time course of twitch depression following neuromuscular blocking agent (NMBA) administration is influenced by the duration of control neuromuscular monitoring (twitch stabilization). The physiological mechanism for this interaction is not known. During twitch stabilization twitch response often

  10. 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...

  11. 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

  12. The time course of strategy sequential difficulty effects: an ERP study in arithmetic.

    Science.gov (United States)

    Uittenhove, Kim; Poletti, Celine; Dufau, Stephane; Lemaire, Patrick

    2013-05-01

    Uittenhove and Lemaire (Exp Psychol 59(5):295-301, 2012) found that we are slower when executing a strategy following a difficult strategy than when executing the same strategy following an easier strategy (i.e., strategy sequential difficulty effects). Uittenhove and Lemaire suggested that difficult strategies temporarily reduce available executive capacities, interfering with the next strategy execution. In this study, we used ERP to determine the time course of these effects. In a computational estimation task, we found greater cerebral activities during strategy execution following a more difficult compared to an easier strategy. Interestingly, greater cerebral activities were most apparent immediately after the encoding of the problem and not during encoding or in later stages of processing. This suggests that strategy sequential difficulty effects interfere most with the retrieval of procedures in contrast to execution of these procedures. We discuss implications of these findings for further understanding of execution of cognitive strategies.

  13. Time course of subjective pain ratings, and wound and leg tenderness after hysterectomy

    DEFF Research Database (Denmark)

    Møiniche, S; Dahl, J B; Erichsen, C J

    1997-01-01

    BACKGROUND: Little information is available on time course of wound tenderness and relationship to subjective pain ratings following surgery. Furthermore, it is not clarified whether surgical procedures may induce hyperalgesia to mechanical stimulation outside the area of the surgical incision. We...... on the abdominal wall 0.05, 5, 10 and 15 cm perpendicular to the wound, and on the anterior surface of the left thigh and tuberositas tibia. Furthermore, pain was assessed on a visual analogue scale (VAS) at rest and during cough. RESULTS: PPT decreased significantly 0.5, 5, 10 and 15 cm from skin incision up...... to 96 h after surgery (P wound. There was no significant changes in PPT on the thigh or the tuberositas tibia (P = 0.49 and P = 0.12) and no correlation between changes in PPT near the wound and in remote (areas the legs) (Rs = -0...

  14. The time course of processing difficulties with non-WH extraction in Danish

    DEFF Research Database (Denmark)

    Poulsen, Mads

    clause, both presupposing processing of the dependent clause for judgment of the acceptability of the extraction. Thus assuming that detection of unacceptability causes processing difficulties, these theories predict reading time increases for unacceptable extractions at the earliest late within......-verbs), the parser doesn’t expect to have linked all mentioned arguments with the main verb at the clause boundary. For clauses with intransitive verbs, on the other hand, the parser expects to be able to find a role for all constituents within the clause, i.e. the parser should experience difficulties...... if unintegrated constituents are present at a clause boundary. Thus this theory predicts longer reading times at ‘if’ in (2) compared to ‘that’ in (1). Thus with regard to time course, this account is similar in spirit to work on island constraints in English indicating that extraction constraints work...

  15. Development and time-course of bleomycin-induced pulmonary fibrosis in NMRI mice

    Directory of Open Access Journals (Sweden)

    Jafarian-Dehkordi A.

    2007-04-01

    Full Text Available Bleomycin-induced pulmonary fibrosis is a widely used experimental model for human lung fibrosis. The severity of fibrosis varies among different strains of mice and investigation on different strains and finding the mechanisms of variation is important in understanding the pathogenesis of human lung fibrosis. In the present study, NMRI mice were used to investigate the severity and also time-course of bleomycin-induced pulmonary fibrosis in comparison with C57BL/6 mice. After single dose administration of intratracheal bleomycin, the fibrotic response was studied by biochemical measurement of collagen deposition and semiquantitative analysis of pathological lung changes. NMRI mice developed lung fibrosis from 1 to 4 week after bleomycin instillation, with significant increases in lung collagen content and significant morphological changes (P < 0.05. These findings indicate that NMRI mice might be suitable as an experimental model of bleomycin-induced lung fibrosis.

  16. 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.

  17. 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.

  18. Time course of cesium radionuclides body burden in residents of regions with elevated background radiation

    International Nuclear Information System (INIS)

    Vasil'ev, V.N.; Luchkov, A.B.; Trushin, V.I.; Khazins, E.D.

    1990-01-01

    The authors represent summarized data on the time course of 134 Cs and 137 Cs body burden in the population of the Krasnogorsky District of the Bryansk Region (Byelorussian SSR) over the period of June 1986-Jule 1989. A RISh-5M was used as a whole-body counter, its performance and calibration methods were described. A retrospective analysis has shown that the main accumulation of radionuclides occurred before May 15 1986. The highest half-life noted from August 1986 till Februal 1987. The ratio of accumulated Cs in children and adults was 0.3, in men and women - 1.4. The effectiveness of measures aimed at reducing collective doses of internal irradiation was analyzed

  19. Evidence for serial coercion: a time course analysis using the visual-world paradigm.

    Science.gov (United States)

    Scheepers, Christoph; Keller, Frank; Lapata, Mirella

    2008-02-01

    Metonymic verbs like start or enjoy often occur with artifact-denoting complements (e.g., The artist started the picture) although semantically they require event-denoting complements (e.g., The artist started painting the picture). In case of artifact-denoting objects, the complement is assumed to be type shifted (or coerced) into an event to conform to the verb's semantic restrictions. Psycholinguistic research has provided evidence for this kind of enriched composition: readers experience processing difficulty when faced with metonymic constructions compared to non-metonymic controls. However, slower reading times for metonymic constructions could also be due to competition between multiple interpretations that are being entertained in parallel whenever a metonymic verb is encountered. Using the visual-world paradigm, we devised an experiment which enabled us to determine the time course of metonymic interpretation in relation to non-metonymic controls. The experiment provided evidence in favor of a non-competitive, serial coercion process.

  20. Ultrastructural studies of time-course and cellular specificity of interleukin-1 mediated islet cytotoxicity

    DEFF Research Database (Denmark)

    Mandrup-Poulsen, T; Egeberg, J; Nerup, J

    1987-01-01

    Previous electron-microscopic studies of isolated islets of Langerhans exposed to the monokine interleukin-1 for 7 days have indicated that interleukin-1 is cytotoxic to all islet cells. To study the time-course and possible cellular specificity of interleukin-1 cytotoxicity to islets exposed...... to interleukin-1 for short time periods, isolated rat or human islets were incubated with or without 25 U/ml highly purified human interleukin-1 for 24 h. Samples of rat islets were taken after 5 min, 30 min, 1, 2, 4, 6, 8, 10, 12, 16, 20 and 24 h and samples of human islets after 5 min, 30 min and 24 h...... of incubation and examined by electron microscopy in a blinded fashion. Already after 30 min, accumulation of opaque intracytoplasmic bodies without apparent surrounding membranes, and autophagic vacuoles were seen in about 20% of the beta cells examined in rat islets exposed to interleukin-1. After 16 h...

  1. The time course of processing difficulties with non-WH extraction in Danish

    DEFF Research Database (Denmark)

    Poulsen, Mads

    clause, both presupposing processing of the dependent clause for judgment of the acceptability of the extraction. Thus assuming that detection of unacceptability causes processing difficulties, these theories predict reading time increases for unacceptable extractions at the earliest late within...... if unintegrated constituents are present at a clause boundary. Thus this theory predicts longer reading times at ‘if’ in (2) compared to ‘that’ in (1). Thus with regard to time course, this account is similar in spirit to work on island constraints in English indicating that extraction constraints work...... of the experimental manipulations to theories about acceptability of extraction in Danish was confirmed in a separate acceptability judgment experiment with the same stimuli. The intransitive extraction condition was rated significantly lower than the other conditions. Together, the results of the two experiments...

  2. The time-course of EEG Alpha Power Changes in Creative Ideation

    Directory of Open Access Journals (Sweden)

    Daniela eSchwab

    2014-05-01

    Full Text Available Increases in EEG alpha power during creative ideation are among the most consistent findings in the neuroscientific study of creativity, but existing studies did not focus on time-related changes of EEG alpha activity patterns during the process of creative ideation so far. Since several cognitive processes are involved in the generation of creative ideas, different EEG correlates may result as a function of time. In this study we addressed this crucial point. Forty-five participants worked on the Alternative Uses Task while the EEG was recorded and changes in task-related power (relative to rest in the upper-frequency band (10-12 Hz for three isochronous time intervals of the idea generation period were determined. Alpha power changes during idea generation followed a characteristic time course: We found a general increase of alpha power at the beginning of idea generation that was followed by a decrease and finally by a re-increase of alpha prior to responding that was most pronounced at parietal and temporal sites of the right hemisphere. Additionally, the production of more original ideas was accompanied by increasing hemispheric asymmetry (more alpha in the right than left hemisphere with increasing duration of the idea generation period. The observed time course of brain activity may reflect the progression of different but well-known stages in the idea generation process: That is the initial retrieval of common and old ideas followed by the actual generation of novel and more creative ideas by overcoming typical responses through processes of mental simulation and imagination.

  3. Serial analysis of the apparent diffusion coefficient time course in human stroke

    Energy Technology Data Exchange (ETDEWEB)

    Fiebach, J.B.; Jansen, O.; Heiland, S.; Sartor, K. [Department of Neuroradiology, University of Heidelberg (Germany); Schellinger, P.D.; Hacke, W. [Department of Neurology, University of Heidelberg (Germany)

    2002-04-01

    Acute cerebral ischemic injury can be rapidly detected on diffusion-weighted images. The apparent diffusion coefficient (ADC) depends on the stage of cytotoxic edema and water content in the infarcted parenchyma. The purpose of this study is to determine the time course of ADC during the first days of ischemic stroke. These data should make it possible to distinguish between multiple stroke and a single progressive infarction. Eight patients with clinically diagnosed acute cerebral ischemia were examined by diffusion-weighted MRI from 2 to 20 h after onset of symptoms. Daily control scans were performed for up to 10 days. ADC values were analyzed from 55 MRI studies. Furthermore, ADC was measured in the tissue which showed a hyperintense signal at the first examination and in the contralateral tissue. White and gray matter were analyzed separately. Data were expressed as the ratio ADC (rADC) of lesion to control region of interest. All patients showed a uniform reduction in rADC from the first hours of stroke and decreasing to the 3rd day. The rADC increased again from the 4th day up to the point of pseudo-normalization on day 9. The gray matter showed a slightly faster increase than the white matter. rADC shows significant changes in the first days after stroke, following a rather uniform time course. Together with T2-weighted MRI this makes it possible to differentiate between hyperacute, acute, and chronic stroke. Furthermore, the age of an ischemia can be determined and multiple strokes can be distinguished from a single progressive stroke. (orig.)

  4. 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

  5. Time course of EPSCs in ON‐type starburst amacrine cells is independent of dendritic location

    Science.gov (United States)

    Stincic, Todd; Smith, Robert G.

    2016-01-01

    Key points Direction selectivity has been widely studied as an example of a complex neural computation.Directional GABA release from starburst amacrine cells (SBACs) is critical for generating directional signals in direction‐selective ganglion cells. The mechanisms producing the directional release remain unclear.For SBACs, ordered distribution of sustained and transient bipolar cell inputs along the dendrites is proposed to generate directional GABA release. This study tests whether this hypothesis applies to ON‐type SBACs.EPSCs activated at proximal and distal dendritic locations have the same time course. Therefore, the ordered arrangement of inputs from bipolar cells with different kinetic properties cannot be responsible for generating directional GABA release from ON‐type SBACs. Abstract Direction selectivity in the retina relies critically on directionally asymmetric GABA release from the dendritic tips of starburst amacrine cells (SBACs). GABA release from each radially directed dendrite is larger for motion outward from the soma toward the dendritic tips than for motion inwards toward the soma. The biophysical mechanisms generating these directional signals remain controversial. A model based on electron‐microscopic reconstructions of the mouse retina proposed that an ordered arrangement of kinetically distinct bipolar cell inputs to ON‐ and OFF‐type SBACs could produce directional GABA release. We tested this prediction by measuring the time course of EPSCs in ON‐type SBACs in the mouse retina, activated by proximal and distal light stimulation. Contrary to the prediction, the kinetics of the excitatory inputs were independent of dendritic location. Computer simulations based on 3D reconstructions of SBAC dendrites demonstrated that the response kinetics of distal inputs were not significantly altered by dendritic filtering. These direct physiological measurements, do not support the hypothesis that directional signals in SBACs arise from

  6. Time course of EPSCs in ON-type starburst amacrine cells is independent of dendritic location.

    Science.gov (United States)

    Stincic, Todd; Smith, Robert G; Taylor, W Rowland

    2016-10-01

    Direction selectivity has been widely studied as an example of a complex neural computation. Directional GABA release from starburst amacrine cells (SBACs) is critical for generating directional signals in direction-selective ganglion cells. The mechanisms producing the directional release remain unclear. For SBACs, ordered distribution of sustained and transient bipolar cell inputs along the dendrites is proposed to generate directional GABA release. This study tests whether this hypothesis applies to ON-type SBACs. EPSCs activated at proximal and distal dendritic locations have the same time course. Therefore, the ordered arrangement of inputs from bipolar cells with different kinetic properties cannot be responsible for generating directional GABA release from ON-type SBACs. Direction selectivity in the retina relies critically on directionally asymmetric GABA release from the dendritic tips of starburst amacrine cells (SBACs). GABA release from each radially directed dendrite is larger for motion outward from the soma toward the dendritic tips than for motion inwards toward the soma. The biophysical mechanisms generating these directional signals remain controversial. A model based on electron-microscopic reconstructions of the mouse retina proposed that an ordered arrangement of kinetically distinct bipolar cell inputs to ON- and OFF-type SBACs could produce directional GABA release. We tested this prediction by measuring the time course of EPSCs in ON-type SBACs in the mouse retina, activated by proximal and distal light stimulation. Contrary to the prediction, the kinetics of the excitatory inputs were independent of dendritic location. Computer simulations based on 3D reconstructions of SBAC dendrites demonstrated that the response kinetics of distal inputs were not significantly altered by dendritic filtering. These direct physiological measurements, do not support the hypothesis that directional signals in SBACs arise from the ordered arrangement of

  7. 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.

  8. Feeling backwards? How temporal order in speech affects the time course of vocal emotion recognition

    Science.gov (United States)

    Rigoulot, Simon; Wassiliwizky, Eugen; Pell, Marc D.

    2013-01-01

    Recent studies suggest that the time course for recognizing vocal expressions of basic emotion in speech varies significantly by emotion type, implying that listeners uncover acoustic evidence about emotions at different rates in speech (e.g., fear is recognized most quickly whereas happiness and disgust are recognized relatively slowly; Pell and Kotz, 2011). To investigate whether vocal emotion recognition is largely dictated by the amount of time listeners are exposed to speech or the position of critical emotional cues in the utterance, 40 English participants judged the meaning of emotionally-inflected pseudo-utterances presented in a gating paradigm, where utterances were gated as a function of their syllable structure in segments of increasing duration from the end of the utterance (i.e., gated syllable-by-syllable from the offset rather than the onset of the stimulus). Accuracy for detecting six target emotions in each gate condition and the mean identification point for each emotion in milliseconds were analyzed and compared to results from Pell and Kotz (2011). We again found significant emotion-specific differences in the time needed to accurately recognize emotions from speech prosody, and new evidence that utterance-final syllables tended to facilitate listeners' accuracy in many conditions when compared to utterance-initial syllables. The time needed to recognize fear, anger, sadness, and neutral from speech cues was not influenced by how utterances were gated, although happiness and disgust were recognized significantly faster when listeners heard the end of utterances first. Our data provide new clues about the relative time course for recognizing vocally-expressed emotions within the 400–1200 ms time window, while highlighting that emotion recognition from prosody can be shaped by the temporal properties of speech. PMID:23805115

  9. Nosocomial infections after aneurysmal subarachnoid hemorrhage: time course and causative pathogens.

    Science.gov (United States)

    Laban, Kamil G; Rinkel, Gabriel J E; Vergouwen, Mervyn D I

    2015-07-01

    Nosocomial infections after aneurysmal subarachnoid hemorrhage (aSAH) are associated with prolonged length of stay and poor functional outcome. It remains unclear if infections result in prolonged length of stay or, vice versa, if prolonged length of stay results in more infections. Before strategies can be designed to reduce infections after aneurysmal subarachnoid hemorrhage, more data are needed on time course and causative pathogens of infections. To investigate the time course of infection onset and bacterial microorganisms that cause nosocomial infections after aSAH. In consecutive patients with aneurysmal subarachnoid hemorrhage admitted to the University Medical Center Utrecht between 2009 and 2011, we analyzed the proportion of patients with infections, day of infection onset, and culture results. Of the 291 included patients, 107 (37%) patients developed 115 nosocomial infections. Fifty-six patients (19%) developed an infection within the first week. Median day of infection onset was for pneumonia (n = 49; 17%) day 4 (interquartile range 3-9), respiratory tract infection (n = 16; 6%) day 4 (interquartile range 1-7), urinary tract infection (n = 27; 9%) day 11 (interquartile range 7-14), and meningitis/ventriculitis (n = 10; 3%) day 19 (interquartile range 9-33). Cultures of infections mostly yielded Staphylococcus aureus (20%), Haemophilus influenzae (15%), and Escherichia coli (14%), Nosocomial infections after subarachnoid hemorrhage are common and mostly occur in the first week after ictus. Future studies should investigate if general hygienic measures, infection awareness, minimizing the duration of mechanical ventilation and use of catheters/drains, or prophylactic antibiotics reduce infections and improve functional outcome. © 2015 World Stroke Organization.

  10. Multistart algorithms for MEG empirical data analysis reliably characterize locations and time courses of multiple sources.

    Science.gov (United States)

    Aine, C; Huang, M; Stephen, J; Christner, R

    2000-08-01

    We applied our newly developed Multistart algorithm (M. Huang et al., 1998, Electroencephalogr. Clin. Neurophysiol. 108, 32-44) to high signal-to-noise ratio (SNR) somatosensory responses and low SNR visual data to demonstrate the reliability of this analysis tool for determining source locations and time courses of empirical multisource neuromagnetic data. This algorithm performs a downhill simplex search hundreds to thousands of times with multiple, randomly selected initial starting parameters from within the head volume, in order to avoid problems of local minima. Two subjects participated in two studies: (1) somatosensory (left and right median nerves were stimulated using a square wave pulse of 0.2 ms duration) and (2) visual (small black and white bull's-eye patterns were presented to central and peripheral locations in four quadrants of the visual field). One subject participated in both of the studies mentioned above and in a third study (i.e., simultaneous somatosensory/visual stimulation). The best-fitting solutions were tightly clustered in high SNR somatosensory data and all dominant regions of activity could be identified in some instances by using a single model order (e.g., six dipoles) applied to a single interval of time (e.g., 15-250 ms) that captured the entire somatosensory response. In low SNR visual data, solutions were obtained from several different model orders and time intervals in order to capture the dominant activity across the entire visual response (e.g. , 60-300 ms). Our results demonstrate that Multistart MEG analysis procedures can localize multiple regions of activity and characterize their time courses in a reliable fashion. Sources for visual data were determined by comparing results across several different models, each of which was based on hundreds to thousands of different fits to the data.

  11. Feeling backwards? How temporal order in speech affects the time course of vocal emotion recognition

    Directory of Open Access Journals (Sweden)

    Simon eRigoulot

    2013-06-01

    Full Text Available Recent studies suggest that the time course for recognizing vocal expressions of basic emotion in speech varies significantly by emotion type, implying that listeners uncover acoustic evidence about emotions at different rates in speech (e.g., fear is recognized most quickly whereas happiness and disgust are recognized relatively slowly, Pell and Kotz, 2011. To investigate whether vocal emotion recognition is largely dictated by the amount of time listeners are exposed to speech or the position of critical emotional cues in the utterance, 40 English participants judged the meaning of emotionally-inflected pseudo-utterances presented in a gating paradigm, where utterances were gated as a function of their syllable structure in segments of increasing duration from the end of the utterance (i.e., gated ‘backwards’. Accuracy for detecting six target emotions in each gate condition and the mean identification point for each emotion in milliseconds were analyzed and compared to results from Pell & Kotz (2011. We again found significant emotion-specific differences in the time needed to accurately recognize emotions from speech prosody, and new evidence that utterance-final syllables tended to facilitate listeners’ accuracy in many conditions when compared to utterance-initial syllables. The time needed to recognize fear, anger, sadness, and neutral from speech cues was not influenced by how utterances were gated, although happiness and disgust were recognized significantly faster when listeners heard the end of utterances first. Our data provide new clues about the relative time course for recognizing vocally-expressed emotions within the 400-1200 millisecond time window, while highlighting that emotion recognition from prosody can be shaped by the temporal properties of speech.

  12. Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data.

    Science.gov (United States)

    Kirk, Paul D W; Stumpf, Michael P H

    2009-05-15

    Although widely accepted that high-throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. Here, we present a parametric bootstrapping approach for time-course data, in which Gaussian process regression (GPR) is used to fit a probabilistic model from which replicates may then be drawn. This approach implicitly allows the time dependence of the data to be taken into account, and is applicable to a wide range of problems. We apply GPR bootstrapping to two datasets from the literature. In the first example, we show how the approach may be used to investigate the effects of data uncertainty upon the estimation of parameters in an ordinary differential equations (ODE) model of a cell signalling pathway. Although we find that the parameter estimates inferred from the original dataset are relatively robust to data uncertainty, we also identify a distinct second set of estimates. In the second example, we use our method to show that the topology of networks constructed from time-course gene expression data appears to be sensitive to data uncertainty, although there may be individual edges in the network that are robust in light of present data. Matlab code for performing GPR bootstrapping is available from our web site: http://www3.imperial.ac.uk/theoreticalsystemsbiology/data-software/.

  13. 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.

  14. 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.

  15. An exploratory cohort study of sensory extinction in acute stroke: prevalence, risk factors, and time course.

    Science.gov (United States)

    Kamtchum-Tatuene, Joseph; Allali, Gilles; Saj, Arnaud; Bernati, Thérèse; Sztajzel, Roman; Pollak, Pierre; Momjian-Mayor, Isabelle; Kleinschmidt, Andreas

    2017-04-01

    Most studies on sensory extinction have focused on selected patients with subacute and chronic right hemisphere lesions. In studies conducted on acute stroke patients, risk factors and time course were not evaluated. Our aim was to determine the prevalence, risk factors, and time course of sensory extinction in the acute stroke setting. Consecutive patients with acute stroke were tested for tactile, visual, auditory, and auditory-tactile cross-modal extinction, as well as for peripersonal visuospatial neglect (PVN). Tests were repeated at 2, 7, 15, 30, and 90 days after initial examination. A multivariable logistic regression analysis was performed to test the association between sensory extinction and demographic and clinical risk factors. Seventy-three patients (38.4% women) were recruited: 64 with ischemic stroke and nine with haemorrhagic stroke. Mean age was 62.3 years (95% CI 58.8-65.7), mean NIHSS score was 1.6 (95% CI 1.2-2.1), and mean time to first examination was 4.1 days (95% CI 3.5-4.8). The overall prevalence of all subtypes of sensory extinction was 13.7% (95% CI 6.8-23.8). Tactile extinction was the most frequent subtype with a prevalence of 8.2% (95% CI 3.1-17.0). No extinction was found beyond 15 days after the first examination. After adjustment for age, sex, lesion side, type of stroke, time to first examination and stroke severity, a lesion volume ≥2 mL (adjusted OR = 38.88, p = 0.04), and presence of PVN (adjusted OR = 24.27, p = 0.04) were independent predictors of sensory extinction. The insula, the putamen, and the pallidum were the brain regions most frequently involved in patients with sensory extinction. Extinction is a rare and transient phenomenon in patients with minor stroke. The presence of PVN and lesion volume ≥2 mL are independent predictors of sensory extinction in acute stroke.

  16. Time course of change in vasodilator function and capacity in response to exercise training in humans.

    Science.gov (United States)

    Tinken, Toni M; Thijssen, Dick H J; Black, Mark A; Cable, N Timothy; Green, Daniel J

    2008-10-15

    Studies of the impact of exercise training on arterial adaptation in healthy subjects have produced disparate results. It is possible that some studies failed to detect changes because functional and structural adaptations follow a different time course and may therefore not be detected at discrete time points. To gain insight into the time course of training-induced changes in artery function and structure, we examined conduit artery flow mediated dilatation (FMD), an index of nitric oxide (NO)-mediated artery function, and conduit dilator capacity (DC), a surrogate marker for arterial remodelling, in the brachial and popliteal arteries of 13 healthy male subjects (21.6 +/- 0.6 years) and seven non-active controls (22.8 +/- 0.2 years) studied at 2-week intervals across an 8-week cycle and treadmill exercise training programme. Brachial and popliteal artery FMD and DC did not change in control subjects at any time point. FMD increased from baseline (5.9 +/- 0.5%) at weeks 2 and 4 (9.1 +/- 0.6, 8.5 +/- 0.6%, respectively, P < 0.01), but returned towards baseline levels again by week 8 (6.9 +/- 0.7%). In contrast, brachial artery DC progressively increased from baseline (8.1 +/- 0.4%) at weeks 2, 4, 6 and 8 (9.2 +/- 0.6, 9.9 +/- 0.6, 10.0 +/- 0.5, 10.5 +/- 0.8%, P < 0.05). Similarly, popliteal artery FMD increased from baseline (6.2 +/- 0.7%) at weeks 2, 4 and 6 (9.1 +/- 0.6, 9.5 +/- 0.6, 7.8 +/- 0.5%, respectively, P < 0.05), but decreased again by week 8 (6.5 +/- 0.6%), whereas popliteal DC progressively increased from baseline (8.9 +/- 0.4%) at week 4 and 8 (10.5 +/- 0.7, 12.2 +/- 0.6%, respectively, P < 0.05). These data suggest that functional changes in conduit arteries occur rapidly and precede arterial remodelling in vivo. These data suggest that complimentary adaptations occur in arterial function and structure and future studies should adopt multiple time point assessments to comprehensively assess arterial adaptations to interventions such as exercise

  17. 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

  18. Time-course proteomic analysis of taurocholate-induced necrotizing acute pancreatitis.

    Science.gov (United States)

    Fétaud-Lapierre, Vanessa; Pastor, Catherine M; Jorge-Costa, Manuel; Hochstrasser, Denis F; Morel, Denis R; Frossard, Jean-Louis; Lescuyer, Pierre

    2013-06-24

    Acute pancreatitis is an inflammatory disease of the pancreas, which varies greatly in course and severity. Severe forms are associated with serious local and/or systemic complications, and eventually death. The pathobiology of acute pancreatitis is complex. Animal models have been developed to investigate pathobiological processes and identify factors determining disease course. We performed a time-course proteomic analysis using a rat model of severe necrotizing acute pancreatitis induced by taurocholate perfusion in the pancreatic ducts. Results showed that levels of proteins associated to a given biological process changed in a coordinated fashion after disease onset. It was possible to follow the response of a particular pathobiological process to pancreatitis induction and to compare the course of protein pathways. Proteins involved in acinar cell secretion were found to follow a different kinetics than other cellular processes. After an initial decrease, secretory pathway-associated proteins raised again at 18 h post-induction. This phenomenon coincided with a burst in the expression of pancreatitis-associated protein (REG3A), an acute phase protein produced by the exocrine pancreas, and with the decrease of classical markers of pancreatic injury, suggesting that the expression of proteins associated to the secretory pathway may be a modulating factor of pancreas injury. Acute pancreatitis (AP) is a complex inflammatory disease, the pathobiology of which is not yet fully understood. Various animal models, relying on different mechanisms of disease induction, have been developed in order to investigate pathobiological processes of AP. In this study, we performed a time-course proteomic analysis to investigate changes of the pancreas proteome occurring in an experimental model of AP induced by perfusion of taurocholate, a bile acid, into the pancreatic duct. This experimental model is characterized by a severe disease with pancreatic necrosis and systemic

  19. 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

  20. A Growth Curve Model with Fractional Polynomials for Analysing Incomplete Time-Course Data in Microarray Gene Expression Studies

    Science.gov (United States)

    Tan, Qihua; Thomassen, Mads; Hjelmborg, Jacob v. B.; Clemmensen, Anders; Andersen, Klaus Ejner; Petersen, Thomas K.; McGue, Matthew; Christensen, Kaare; Kruse, Torben A.

    2011-01-01

    Identifying the various gene expression response patterns is a challenging issue in expression microarray time-course experiments. Due to heterogeneity in the regulatory reaction among thousands of genes tested, it is impossible to manually characterize a parametric form for each of the time-course pattern in a gene by gene manner. We introduce a growth curve model with fractional polynomials to automatically capture the various time-dependent expression patterns and meanwhile efficiently handle missing values due to incomplete observations. For each gene, our procedure compares the performances among fractional polynomial models with power terms from a set of fixed values that offer a wide range of curve shapes and suggests a best fitting model. After a limited simulation study, the model has been applied to our human in vivo irritated epidermis data with missing observations to investigate time-dependent transcriptional responses to a chemical irritant. Our method was able to identify the various nonlinear time-course expression trajectories. The integration of growth curves with fractional polynomials provides a flexible way to model different time-course patterns together with model selection and significant gene identification strategies that can be applied in microarray-based time-course gene expression experiments with missing observations. PMID:21966290

  1. Classification of wheat varieties: Use of two-dimensional gel electrophoresis for varieties that can not be classified by matrix assisted laser desorption/ionization-time of flight-mass spectrometry and an artificial neural network

    DEFF Research Database (Denmark)

    Jacobsen, Susanne; Nesic, Ljiljana; Petersen, Marianne Kjerstine

    2001-01-01

    Analyzing a gliadin extract by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI- TOF-MS) combined with an artificial neural network (ANN) is a suitable method for identification of wheat varieties. However, the ANN can not distinguish between all different wheat...... not be separated by MALDI-TOF-MS and NN....

  2. 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.

  3. 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...

  4. 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...

  5. 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

  6. 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.

  7. 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.

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

    Science.gov (United States)

    Ten Haaf, Dianne; Hemmen, Bea; van de Meent, Henk; BovendʼEerdt, Thamar J H

    2017-09-01

    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 of muscle cross-section decrease in acute critically ill patients admitted to the intensive care unit. An observational pilot study was performed in intensive care unit patients. Data of bilateral ultrasound muscle cross-section measurements of the knee extensors and the elbow flexors were collected. Thirty-four intensive care unit patients were included in this study; data are presented from 14 patients who were measured at least three times. Repeated measures analysis of variance shows a significant decrease in muscle cross-section over time (F1,13 = 80.40, P ≤ 0.001).The decrease in muscle cross-section of the arms was significantly higher (F1,13 = 5.38, P = 0.037) than the decrease of the legs. Four weeks after intensive care unit admission, the muscle cross-section decrease had not reached an asymptote yet. The muscle cross-section decrease in bedridden intensive care unit patients is significant for a time of 2 to 4 weeks. The decrease in muscle cross-section of the arms is greater than the decrease of the legs.

  9. Time-course of attention to negative stimuli: negative affectivity, anxiety, or dysphoria?

    Science.gov (United States)

    Oehlberg, Katherine A; Revelle, William; Mineka, Susan

    2012-10-01

    Although biased attention to emotional stimuli is considered a vulnerability factor for anxiety and dysphoria, research has infrequently related such attentional biases to dimensional models of vulnerability for anxiety and mood disorders. In two studies (Study 1, n = 64; Study 2, n = 168), we evaluate the differential associations of general negative affectivity, anxiety, and dysphoria with biases in selective attention among nonclinical participants selected to vary in both anxiety and dysphoria. Across both studies, preferential processing of angry faces at a 300-ms exposure duration was associated with a general tendency to experience a range of negative affect, rather than being specific to symptoms of either anxiety or dysphoria. In the second study, we found evidence of a suppressor relationship between anxiety and dysphoria in the prediction of delayed attentional biases (1,000 ms) for sad faces. In particular, dysphoria was specifically associated with biased attention toward sad cues, but only after statistically accounting for anxiety; by contrast, anxiety was specifically associated with attentional avoidance of sad cues, but only after statistically accounting for dysphoria. These results suggest that the specificity of relationships between components of negative affectivity and attention to emotional stimuli varies as a function of the time course at which attentional biases are assessed, highlighting the importance of evaluating both anxiety and dysphoria in research on attentional processing of emotional stimuli.

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

    Science.gov (United States)

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

    2017-08-15

    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 SAH. We included patients admitted between 2012 and 2015 within 48h after spontaneous SAH with a normal level of consciousness and no focal deficits. We retrieved data on headache severity, measured with a Numeric Rating Scale (NRS), ictus. We analyzed the proportion of patients with a first NRS 0 and NRS ictus and minimal headache duration. Patients were censored in case of a decrease in level of consciousness, aneurysm treatment, or early discharge. We included 106 patients (62 aneurysmal SAH, 33 perimesencephalic hemorrhage, 11 other spontaneous SAH). All patients were treated with analgesics. Within 48h after ictus, a first NRS 0 was reported by 9 patients (8%;95%CI:3%-14%) and a first NRS ictus. In a cohort of SAH patients with a normal level of consciousness and no focal deficits who all used analgetics, headache disappeared in around 10% within 48h after ictus. Our data indicate that a diagnostic work-up for SAH is also needed in patients using analgesics in whom headache has disappeared after 10h. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Time course of corticospinal excitability and intracortical inhibition just before muscle relaxation

    Directory of Open Access Journals (Sweden)

    Tomotaka eSuzuki

    2016-01-01

    Full Text Available Using transcranial magnetic stimulation (TMS, we investigated how short-interval intracortical inhibition (SICI was involved with transient motor cortex excitability changes observed just before the transition from muscle contraction to muscle relaxation. Ten healthy participants performed a simultaneous relaxation task of the ipsilateral finger and foot, relaxing from 10% of their maximal voluntary contraction force after the go signal. In the simple reaction time paradigm, single or paired TMS pulses were randomly delivered after the go signal, and motor evoked potentials were recorded from the right first dorsal interosseous muscle. We analyzed the time course prior to the estimated relaxation reaction time, defined here as the onset of voluntary relaxation. SICI decreased in the 80–100 ms before relaxation reaction time, and motor evoked potentials were significantly greater in amplitude in the 60–80 ms period before relaxation reaction time than in the other intervals in single-pulse trials. TMS pulses did not effectively increase relaxation reaction time. These results show that cortical excitability in the early stage, before muscle relaxation, plays an important role in muscle relaxation control. SICI circuits may vary between decreased and increased activation to continuously maintain muscle relaxation during or after a relaxation response. With regard to motor cortex excitability dynamics, we suggest that SICI also dynamically changes throughout the muscle relaxation process.

  12. Sphingoid Base Metabolism in Yeast: Mapping Gene Expression Patterns Into Qualitative Metabolite Time Course Predictions

    Directory of Open Access Journals (Sweden)

    Tomas Radivoyevitch

    2006-04-01

    Full Text Available Can qualitative metabolite time course predictions be inferred from measured mRNA expression patterns? Speaking against this possibility is the large number of ‘decoupling’ control points that lie between these variables, i.e. translation, protein degradation, enzyme inhibition and enzyme activation. Speaking for it is the notion that these control points might be coordinately regulated such that action exerted on the mRNA level is informative of action exerted on the protein and metabolite levels. A simple kinetic model of sphingoid base metabolism in yeast is postulated. When the enzyme activities in this model are modulated proportional to mRNA expression levels measured in heat shocked yeast, the model yields a transient rise and fall in sphingoid bases followed by a permanent rise in ceramide. This finding is in qualitative agreement with experiments and is thus consistent with the aforementioned coordinated control system hypothesis.

  13. 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.

  14. 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.

  15. The time course of activation of object shape and shape+colour representations during memory retrieval.

    Directory of Open Access Journals (Sweden)

    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.

  16. Time course of airway remodelling after an acute chlorine gas exposure in mice

    Science.gov (United States)

    Tuck, Stephanie A; Ramos-Barbón, David; Campbell, Holly; McGovern, Toby; Karmouty-Quintana, Harry; Martin, James G

    2008-01-01

    Accidental chlorine (Cl2) gas inhalation is a common cause of acute airway injury. However, little is known about the kinetics of airway injury and repair after Cl2 exposure. We investigated the time course of airway epithelial damage and repair in mice after a single exposure to a high concentration of Cl2 gas. Mice were exposed to 800 ppm Cl2 gas for 5 minutes and studied from 12 hrs to 10 days post-exposure. The acute injury phase after Cl2 exposure (≤ 24 hrs post-exposure) was characterized by airway epithelial cell apoptosis (increased TUNEL staining) and sloughing, elevated protein in bronchoalveolar lavage fluid, and a modest increase in airway responses to methacholine. The repair phase after Cl2 exposure was characterized by increased airway epithelial cell proliferation, measured by immunoreactive proliferating cell nuclear antigen (PCNA), with maximal proliferation occurring 5 days after Cl2 exposure. At 10 days after Cl2 exposure the airway smooth muscle mass was increased relative to controls, suggestive of airway smooth muscle hyperplasia and there was evidence of airway fibrosis. No increase in goblet cells occurred at any time point. We conclude that a single exposure of mice to Cl2 gas causes acute changes in lung function, including pulmonary responsiveness to methacholine challenge, associated with airway damage, followed by subsequent repair and airway remodelling. PMID:18702818

  17. Time course of airway remodelling after an acute chlorine gas exposure in mice

    Directory of Open Access Journals (Sweden)

    McGovern Toby

    2008-08-01

    Full Text Available Abstract Accidental chlorine (Cl2 gas inhalation is a common cause of acute airway injury. However, little is known about the kinetics of airway injury and repair after Cl2 exposure. We investigated the time course of airway epithelial damage and repair in mice after a single exposure to a high concentration of Cl2 gas. Mice were exposed to 800 ppm Cl2 gas for 5 minutes and studied from 12 hrs to 10 days post-exposure. The acute injury phase after Cl2 exposure (≤ 24 hrs post-exposure was characterized by airway epithelial cell apoptosis (increased TUNEL staining and sloughing, elevated protein in bronchoalveolar lavage fluid, and a modest increase in airway responses to methacholine. The repair phase after Cl2 exposure was characterized by increased airway epithelial cell proliferation, measured by immunoreactive proliferating cell nuclear antigen (PCNA, with maximal proliferation occurring 5 days after Cl2 exposure. At 10 days after Cl2 exposure the airway smooth muscle mass was increased relative to controls, suggestive of airway smooth muscle hyperplasia and there was evidence of airway fibrosis. No increase in goblet cells occurred at any time point. We conclude that a single exposure of mice to Cl2 gas causes acute changes in lung function, including pulmonary responsiveness to methacholine challenge, associated with airway damage, followed by subsequent repair and airway remodelling.

  18. Variability of the Time Course of Stimulus-Specific Adaptation in the Inferior Colliculus

    Directory of Open Access Journals (Sweden)

    David ePérez-González

    2012-12-01

    Full Text Available Stimulus-specific adaptation (SSA is the ability of some neurons to respond better to rare than to frequent, repetitive stimuli. In the auditory system, it has been found at the level of the midbrain, thalamus and cortex. While previous studies have used the whole overall neuronal response to characterize SSA, here we present a detailed analysis on the variations within the time course of the evoked responses. The extracellular activity of well isolated single neurons from the inferior colliculus (IC was recorded during stimulation using an oddball paradigm, which is able to elicit SSA. At the same time, these responses were evaluated before, during and after the microiontophoretic application of gabazine, a specific antagonist of GABA-A receptors, to study the contribution of inhibition to the responses of these neurons. We then analyzed the difference signal (DS, which is the difference in the PSTH in response to rare and frequent stimuli. We found that, even in a sample of neurons showing strong SSA (i.e., showing larger preference for rare stimuli, the DS was variable and one third of the neurons contained portions that responded significantly better to the frequent stimuli than to the rare. This variability is not observed when averaging the responses of multiple cells. Furthermore, the blockade of GABA-A receptors increased the number of neurons showing portions that responded better to the frequent stimuli, indicating that inhibition in the IC refines and sharpens SSA in the neural responses. 

  19. The onset and time course of semantic priming during rapid recognition of visual words.

    Science.gov (United States)

    Hoedemaker, Renske S; Gordon, Peter C

    2017-05-01

    In 2 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 4 words. In Experiment 2, the same words were encoded for an episodic recognition memory task that did not require a metalinguistic judgment. For both tasks, survival analyses showed that the earliest observable effect (divergence point [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. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  20. 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

  1. 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)

  2. 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.

  3. 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.

  4. Adderall produces increased striatal dopamine release and a prolonged time course compared to amphetamine isomers.

    Science.gov (United States)

    Joyce, B Matthew; Glaser, Paul E A; Gerhardt, Greg A

    2007-04-01

    Adderall is currently used for the treatment of Attention-Deficit Hyperactivity Disorder (ADHD) and is composed of a novel mixture of approximately 24% L-amphetamine and 76% D-amphetamine salts. There are, however, no investigations of the pharmacological effects of this combination in vivo. The technique of high-speed chronoamperometry using Nafion-coated single carbon-fiber microelectrodes was used to study amphetamine-evoked dopamine (DA) release produced by Adderall, D-amphetamine, or D,L-amphetamine in the striatum of anesthetized male Fischer 344 (F344) rats. The amphetamine solutions were locally applied from micropipettes by pressure ejection. Local applications of Adderall resulted in significantly greater DA release signal amplitudes with prolonged time course of dopamine release and re-uptake as compared to D-amphetamine and D,L-amphetamine. These data support the hypothesis that the combination of amphetamine enantiomers and salts in Adderall has effects on DA release, which result in increased and prolonged DA release, compared to D- and D,L-amphetamine.

  5. The 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

    2018-02-21

    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 non-inflammatory 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. Since 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.

  6. Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data.

    Science.gov (United States)

    Kiani, Narsis A; Kaderali, Lars

    2014-07-22

    Network inference deals with the reconstruction of molecular networks from experimental data. Given N molecular species, the challenge is to find the underlying network. Due to data limitations, this typically is an ill-posed problem, and requires the integration of prior biological knowledge or strong regularization. We here focus on the situation when time-resolved measurements of a system's response after systematic perturbations are available. We present a novel method to infer signaling networks from time-course perturbation data. We utilize dynamic Bayesian networks with probabilistic Boolean threshold functions to describe protein activation. The model posterior distribution is analyzed using evolutionary MCMC sampling and subsequent clustering, resulting in probability distributions over alternative networks. We evaluate our method on simulated data, and study its performance with respect to data set size and levels of noise. We then use our method to study EGF-mediated signaling in the ERBB pathway. Dynamic Probabilistic Threshold Networks is a new method to infer signaling networks from time-series perturbation data. It exploits the dynamic response of a system after external perturbation for network reconstruction. On simulated data, we show that the approach outperforms current state of the art methods. On the ERBB data, our approach recovers a significant fraction of the known interactions, and predicts novel mechanisms in the ERBB pathway.

  7. Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

    Directory of Open Access Journals (Sweden)

    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.

  8. Time-course of the DSM-5 cannabis withdrawal symptoms in poly-substance abusers.

    Science.gov (United States)

    Hesse, Morten; Thylstrup, Birgitte

    2013-10-12

    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 use. Symptoms of withdrawal were assessed through patient self-reports during detoxification in Danish residential rehabilitation centers. Patients (n = 90) completed booklets three times during their first month at the treatment centre. Self-reported withdrawal symptoms was rated using 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. 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. The findings yield strong support to the notion of a cannabis withdrawal syndrome, and gives further evidence for the inclusion of the criterion of vivid, unpleasant dreams. Further, the findings speak against the significance of demand characteristics in determining the course of the symptoms of cannabis withdrawal.

  9. Time course of regional brain activity accompanying auditory verbal hallucinations in schizophrenia

    Science.gov (United States)

    Hoffman, Ralph E.; Pittman, Brian; Constable, R. Todd; Bhagwagar, Zubin; Hampson, Michelle

    2011-01-01

    Background The pathophysiology of auditory verbal hallucinations remains poorly understood. Aims To characterise the time course of regional brain activity leading to auditory verbal hallucinations. Method During functional magnetic resonance imaging, 11 patients with schizophrenia or schizoaffective disorder signalled auditory verbal hallucination events by pressing a button. To control for effects of motor behaviour, regional activity associated with hallucination events was scaled against corresponding activity arising from random button-presses produced by 10 patients who did not experience hallucinations. Results Immediately prior to the hallucinations, motor-adjusted activity in the left inferior frontal gyrus was significantly greater than corresponding activity in the right inferior frontal gyrus. In contrast, motor-adjusted activity in a right posterior temporal region overshadowed corresponding activity in the left homologous temporal region. Robustly elevated motor-adjusted activity in the left temporal region associated with auditory verbal hallucinations was also detected, but only subsequent to hallucination events. At the earliest time shift studied, the correlation between left inferior frontal gyrus and right temporal activity was significantly higher for the hallucination group compared with non-hallucinating patients. Conclusions Findings suggest that heightened functional coupling between the left inferior frontal gyrus and right temporal regions leads to coactivation in these speech processing regions that is hallucinogenic. Delayed left temporal activation may reflect impaired corollary discharge contributing to source misattribution of resulting verbal images. PMID:21972276

  10. Time course evolution of ventilatory responses to inspiratory unloading in patients.

    Science.gov (United States)

    Viale, J P; Duperret, S; Mahul, P; Delafosse, B; Delpuech, C; Weismann, D; Annat, G

    1998-02-01

    Inspiratory muscle unloading decreases ventilatory drive. In this study, we examined the time course of this effect in patients with chronic obstructive pulmonary disease receiving two modes of ventilatory support: pressure support ventilation (PSV), during which each cycle was assisted, and biphasic positive airway pressure (BIPAP), set up in such a manner that one spontaneous breath took place between two consecutive pressure-assisted breaths. The first breath following the switch from spontaneous breathing to PSV was associated with an increase in tidal volume (VT) and a drop in mean transdiaphragmatic pressure (mean Pdi) and inspiratory work (WI) performed per liter but with unchanged values of esophageal occlusion pressure at 100 ms (Pes 0.1), diaphragmatic electrical activity (EMGdi), and WI performed by breath. The same phenomena were observed for the assisted breath of BIPAP as compared with the preceding spontaneous breath. During the subsequent breaths of PSV, Pes 0.1, EMGdi, and WI performed per breath decreased progressively up to the sixth to eighth breaths, and VT returned to pre-PSV values. We conclude that in patients with chronic obstructive pulmonary disease the decrease in ventilatory drive associated with PSV takes place from the first breath onwards but requires six to eight breaths to be fully achieved. During BIPAP, as a consequence of the kinetics of the PSV-induced downregulation of ventilatory drive, assisted breaths following spontaneous breaths are characterized by an enhanced inspiratory efficiency.

  11. 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

  12. Time Course of Heart Rate Variability Response to PM2.5 Exposure from Secondhand Smoke.

    Directory of Open Access Journals (Sweden)

    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.

  13. Time course of pulmonary burden in mice exposed to residual oil fly ash

    Directory of Open Access Journals (Sweden)

    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.

  14. Time course and vectorial nature of albumin metabolism in isolated perfused rabbit PCT

    International Nuclear Information System (INIS)

    Park, C.H.

    1988-01-01

    The time course and vectorial nature of renal metabolism of albumin (Alb) were studied. The tubular absorption, accumulation, and hydrolysis of Alb and the release of the hydrolysis products were determined in the isolated rabbit proximal convoluted tubule (PCT) perfused with tritiated Alb ([ 3 H3C]Alb) at 36.4 micrograms/ml. The Alb absorption across the apical membrane was constant (99.9 +/- 4.9 x 10(-3) ng.min-1.mm-1). In contrast, the accumulation and hydrolysis of Alb in the cells increased nonlinearly with time. The bulk of the tritium that accumulated in the cells was associated with intact [ 3 H3C]Alb. Only the final hydrolysis products were released from the cells and these first appeared in the peritubular bath 6-7 min after the start of perfusion of the tubule with [ 3 H3C]Alb. The hydrolysis product was not detectable in the tubule lumen. The proteolytic activity correlated linearly with the protein load to the cells, characteristic of first-order kinetics and a high-capacity system. The results suggest that the renal tubular handling of proteins proceeds from the apical to the basolateral aspect of the cell. The transcellular processing of Alb is rapid and can occur in 6-7 min. The accumulation of intact protein in the cell and the first-order kinetics of hydrolysis of the absorbed protein suggest that the rate-limiting step in proximal tubular handling of proteins may include the initial hydrolysis of protein or reside in steps that precede the hydrolysis

  15. Time course of virulence factors produced by group A streptococcus during a food-borne epidemic.

    Science.gov (United States)

    Kanno, Takeshi; Sakaguchi, Kazuko; Suzuki, Jun

    2012-02-01

    We studied the protein amount and activity of the major virulence factors hemolysin, cysteine protease streptococcal pyrogenic exotoxin B (SpeB), and NAD glycohydrolase (NADase), which are produced by Streptococcus pyogenes type T-25, with a food poisoning outbreak. The three virulence factors were analyzed by activity and amount of protein using supernatants at 2-30 h of culture. All these virulence factors were confirmed by their activity. Streptolysin O (SLO), SpeB, and NADase were immunochemically confirmed at protein level by Western blot analysis. Two hemolytic forms (70 and 60 kDa) of SLO were identified. SpeB was detected as a 44-kDa precursor form and a 30-kDa mature form. NADase was 50 kDa. SLO protein peaked at 8 h of culture, which corresponded with the hemolytic activity peak. Conversion from precursor to SpeB protein peaked at 14 h of culture. The conversion peak corresponded to the activity expression time. Also, mature SpeB protein peaked at 24 h of culture and corresponded to SpeB activity peak. Electrophoretic analysis clarified the relationship between SLO protein and SpeB protein, although amounts of SLO and SpeB have been reported to be inversely proportional to activity. NADase protein peaked at 12 h of culture, but protein level did not correspond to the peak. Because the NADase protein peak was closer to SpeB activity than SLO protein, our results suggested NADase protein was degraded at 12 h of culture. The time course production of these virulence factors is discussed.

  16. The time course of reading processes in children with and without dyslexia: An ERP study

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    Sandra eHasko

    2013-10-01

    Full Text Available The main diagnostic criterion for developmental dyslexia (DD in transparent orthographies is a remarkable reading speed deficit, which is often accompanied by spelling difficulties. These deficits have been traced back to both deficits in orthographic and phonological processing. For a better understanding of the reading speed deficit in DD it is necessary to clarify which processing steps are degraded in children with DD during reading. In order to address this question the present study used EEG to investigate three reading related ERPs: the N170, N400 and LPC. Twenty-nine children without DD and 52 children with DD performed a phonological lexical decision (PLD – task, which tapped both orthographic and phonological processing. Children were presented with words, pseudohomophones, pseudowords and false fonts and had to decide whether the presented stimulus sounded like an existing German word or not. Compared to control children, children with DD showed deficits in all the investigated ERPs. Firstly, a diminished mean area under the curve for the word material - false font contrasts in the time window of the N170 was observed, indicating a reduced degree of print sensitivity; secondly, N400 amplitudes, as suggested to reflect the access to the orthographic lexicon and grapheme-phoneme conversion, were attenuated; and lastly, phonological access as indexed by the LPC was degraded in children with DD. Processing differences dependent on the linguistic material in children without DD were observed only in the LPC, suggesting that similar reading processes were adopted independent of orthographic familiarity. The results of this study suggest that effective treatment should include both orthographic and phonological training. Furthermore, more longitudinal studies utilizing the same task and stimuli are needed to clarify how these processing steps and their time course change during reading development.

  17. 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.

  18. 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

  19. Differential mouse pulmonary dose and time course responses to titanium dioxide nanospheres and nanobelts.

    Science.gov (United States)

    Porter, Dale W; Wu, Nianqiang; Hubbs, Ann F; Mercer, Robert R; Funk, Kathleen; Meng, Fanke; Li, Jiangtian; Wolfarth, Michael G; Battelli, Lori; Friend, Sherri; Andrew, Michael; Hamilton, Raymond; Sriram, Krishnan; Yang, Feng; Castranova, Vincent; Holian, Andrij

    2013-01-01

    Three anatase titanium dioxide (TiO(2)) nanoparticles (NPs) were prepared; nanospheres (NSs), short nanobelts (NB1), and long nanobelts (NB2). These NPs were used to investigate the effect of NP shape and length on lung toxicity. Mice were exposed (0-30 µg per mouse) by pharyngeal aspiration and pulmonary toxicity was assessed over a 112-day time course. Whole lung lavage data indicated that NB1- and NB2-exposed mice, but not NS-exposed mice, had significant dose- and time-dependent pulmonary inflammation and damage. Histopathological analyses at 112 days postexposure determined no interstitial fibrosis in any NS-exposed mice, an increased incidence in 30 µg NB1-exposed mice, and significant interstitial fibrosis in 30 µg NB2-exposed mice. At 112 days postexposure, lung burden of NS was decreased by 96.4% and NB2 by 80.5% from initial deposition levels. At 112 days postexposure, enhanced dark field microscopy determined that alveolar macro- phages were the dominant deposition site, but a fraction of NB1 and NB2 was observed in the alveolar interstitial spaces. For the 30 µg exposure groups at 112 days postexposure, confocal micro- scopy and immunofluorescent staining demonstrated that retained NB2 but not NS were present in the interstitium subjacent to the terminal bronchiole near the normal location of the smallest lymphatic capillaries in the lung. These lymphatic capillaries play a critical role in particle clearance, and the accumulation of NB2, but not NS, suggests possible impaired lymphatic clearance by the high aspect ratio particles. In summary, our data indicate that TiO(2) NP shape alters pulmonary responses, with severity of responses being ranked as NS < NB1 < NB2.

  20. Identifying significant temporal variation in time course microarray data without replicates

    Directory of Open Access Journals (Sweden)

    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.

  1. Time-course of CSF histamine in the wake-consolidated squirrel monkey

    Science.gov (United States)

    Zeitzer, Jamie M.; Kodama, Tohru; Buckmaster, Christine L.; Honda, Yoshiko; Lyons, David M.; Nishino, Seiji; Mignot, Emmanuel

    2011-01-01

    SUMMARY Central nervous system (CNS) histamine is low in individuals with narcolepsy, a disease characterized by severe fragmentation of both sleep and wake. We have developed a primate model, the squirrel monkey, with which we can examine the role of the CNS in the wake-consolidation process as these primates are day-active, have consolidated wake and sleep, and have cerebrospinal fluid (CSF) that is readily accessible. Using this model and three distinct protocols, we herein report on the role of CNS histamine in the wake consolidation process. CSF histamine has a robust daily rhythm, with a mean of 24.9 ± 3.29 pg·mL−1, amplitude of 31.7 ± 6.46 pg·mL−1 and a peak at 17:49 ± 70.3 min (lights on 07:00–19:00). These levels are not significantly affected by increases (up to 161±40.4% of baseline) or decreases (up to 17.2±2.50% of baseline) in locomotion. In direct contrast to the effects of sleep deprivation in non-wake consolidating mammals, in whom CSF histamine increases, pharmacologically-induced sleep (γ-hydroxybutyrate) and wake (modafinil) have no direct effects on CSF histamine concentrations. These data indicate that the time-course of histamine in CSF in the wake-consolidated squirrel monkey is robust against variation in activity and sleep and wake promoting pharmacological compounds, and may indicate that histamine physiology plays a role in wake-consolidation such as present in the squirrel monkey and humans. PMID:21910776

  2. Time-course of cerebrospinal fluid histamine in the wake-consolidated squirrel monkey.

    Science.gov (United States)

    Zeitzer, Jamie M; Kodama, Tohru; Buckmaster, Christine L; Honda, Yoshiko; Lyons, David M; Nishino, Seiji; Mignot, Emmanuel

    2012-04-01

    Central nervous system (CNS) histamine is low in individuals with narcolepsy, a disease characterized by severe fragmentation of both sleep and wake. We have developed a primate model, the squirrel monkey, with which we can examine the role of the CNS in the wake-consolidation process, as these primates are day-active, have consolidated wake and sleep and have cerebrospinal fluid (CSF) that is readily accessible. Using this model and three distinct protocols, we report herein on the role of CNS histamine in the wake consolidation process. CSF histamine has a robust daily rhythm, with a mean of 24.9 ± 3.29 pg mL(-1) , amplitude of 31.7 ± 6.46 pg mL(-1) and a peak at 17:49 ± 70.3 min (lights on 07:00-19:00 hours). These levels are not significantly affected by increases (up to 161 ± 40.4% of baseline) or decreases (up to 17.2 ± 2.50% of baseline) in locomotion. In direct contrast to the effects of sleep deprivation in non-wake-consolidating mammals, in whom CSF histamine increases, pharmacologically induced sleep (γ-hydroxybutyrate) and wake (modafinil) have no direct effects on CSF histamine concentrations. These data indicate that the time-course of histamine in CSF in the wake-consolidated squirrel monkey is robust against variation in activity and sleep and wake-promoting pharmacological compounds, and may indicate that histamine physiology plays a role in wake-consolidation such as is present in the squirrel monkey and humans. © 2011 European Sleep Research Society.

  3. 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)

  4. 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.

  5. 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.

  6. Time Course of Atrophic Remodeling: Effects of Exercise on Cardiac Morpology and Function

    Science.gov (United States)

    Scott, J. M.; Martin, D.; Caine, T.; Matz, T.; Ploutz-Snyder, L. L.

    2014-01-01

    Early and consistent evaluation of cardiac morphology and function throughout an atrophic stimulus is critically important for the design and optimization of interventions. Exercise training is one intervention that has been shown to confer favorable improvements in LV mass and function during unloading. However, the format and intensity of exercise required to induce optimal cardiac improvements has not been investigated. PURPOSE: This randomized, controlled trial was designed to 1) comprehensively characterize the time course of unloading-induced morpho-functional remodeling, and 2) examine the effects of high intensity exercise training on cardiac structural and functional parameters during unloading. METHODS: Twenty six subjects completed 70 days of head down tilt bed rest (HDBR): 17 were randomized to exercise training (ExBR) and 9 remained sedentary. Exercise consisted of integrated high intensity, continuous, and resistance exercise. We assessed cardiac morphology (left ventricular mass; LVM) and function (speckle-tracking assessment of longitudinal, radial, and circumferential strain and twist) before (BR-2), during (BR7,21,31,70), and following (BR+0, +3) HDBR. Cardiorespiratory fitness (VO2max) was evaluated before (BR- 3), during (BR4,25,46,68) and following (BR+0) HDBR. RESULTS: Sedentary HDBR resulted in a progressive decline in LVM, longitudinal, radial, and circumferential strain, and an increase in twist. ExBR mitigated decreases in LVM and function. Change in twist was significantly related to change in VO2max (R=0.68, p<0.01). CONCLUSIONS: Alterations in cardiac morphology and function begin early during unloading. High-intensity exercise attenuates atrophic morphological and functional remodeling.

  7. 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.

  8. 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.

  9. 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.)

  10. ISPC effect is not observed when the word comes too late: a time course analysis.

    Science.gov (United States)

    Atalay, Nart B; Misirlisoy, Mine

    2014-01-01

    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 and 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.

  11. The time course of pupil dilation evoked by visual sexual stimuli: Exploring the underlying ANS mechanisms.

    Science.gov (United States)

    Finke, Johannes B; Deuter, Christian E; Hengesch, Xenia; Schächinger, Hartmut

    2017-10-01

    The early processing of visual sexual stimuli shows signs of automaticity. Moreover, there is evidence for sex-specific patterns in cognitive and physiological responding to erotica. However, little is known about the time course of rapid pupillary responses to sexual stimuli and their correspondence with other measures of autonomic activity in women and men. To study pupil dilation as an implicit measure of sexual arousal at various stages of picture processing, we presented 35 heterosexual participants with pictures showing either erotic couples or single (male/female) erotic nudes, contrasted with people involved in everyday situations. Brightness-adjusted grayscale pictures were shown for a duration of 2,500 ms within the central visual field, alternating with perceptually matched patches. Left pupil diameter was recorded at 500 Hz using a video-based eye tracker. Skin conductance and heart rate were coregistered and correlated with latent components of pupil dilation (dissociated by temporal PCA). Whereas stimulus-evoked changes in pupil size indicated virtually no initial constriction, a rapid effect of appetence emerged (dilation to erotica within 500 ms). Responses at early stages of processing were remarkably consistent across both sexes. In contrast, later phases of pupil dilation, subjective ratings, and skin conductance responses showed a sex-specific pattern. Moreover, evidence for an association of early-onset pupil dilation and heart rate acceleration was found, suggestive of parasympathetic inhibition, whereas the late component was mainly related to sympathetically mediated skin conductance. Taken together, our results indicate that different temporal components of pupil responses to erotic stimuli may reflect divergent underlying neural mechanisms. © 2017 Society for Psychophysiological Research.

  12. Time Course Study of Delayed Wound Healing in a Biofilm-Challenged Diabetic Mouse Model

    Science.gov (United States)

    Zhao, Ge; Usui, Marcia L.; Underwood, Robert A.; Singh, Pradeep K.; James, Garth A.; Stewart, Philip S.; Fleckman, Philip; Olerud, John E.

    2012-01-01

    Bacterial biofilm has been shown to play a role in delaying wound healing of chronic wounds, a major medical problem that results in significant healthcare burden. A reproducible animal model could be very valuable for studying the mechanism and management of chronic wounds. Our previous work demonstrated that Pseudomonas aeruginosa (PAO1) biofilmchallenge on wounds in diabetic (db/db) mice significantly delayed wound healing. In this wound time course study, we further characterize the bacterial burden, delayed wound healing and certain aspects of the host inflammatory response in the PAO1 biofilm-challenged db/db mouse model. PAO1 biofilms were transferred onto 2 day old wounds created on the dorsal surface of db/db mice. Control wounds without biofilm-challenge healed by 4 weeks, consistent with previous studies; none of the biofilm-challenged wounds healed by 4 weeks; 64% of the biofilm-challenged wounds healed by 6 weeks; and all of the biofilm-challenged wounds healed by 8 weeks. During the wound healing process, P. aeruginosa were gradually cleared from the wounds while the presence of S. aureus (part of the normal mouse skin flora) increased. Scabs from all unhealed wounds contained 107 P. aeruginosa, which was 100 fold higher than the counts isolated from wound beds (i.e. 99% of the P. aeruginosa was in the scab). Histology and genetic analysis showed proliferative epidermis, deficient vascularization and increased inflammatory cytokines. Hypoxia inducible factor (HIF) expression increased 3 fold in 4 week wounds. In summary, our study demonstrates that biofilm-challenged wounds typically heal in approximately 6 weeks, at least 2 weeks longer than non biofilm-challenged normal wounds. These data suggest that this delayed wound healing model enables the in vivo study of bacterial biofilm responses to host defenses and the effects of biofilms on host wound healing pathways. It may also be used to test anti-biofilm strategies the treatment of chronic wounds

  13. Time course and vectorial nature of albumin metabolism in isolated perfused rabbit PCT.

    Science.gov (United States)

    Park, C H

    1988-09-01

    The time course and vectorial nature of renal metabolism of albumin (Alb) were studied. The tubular absorption, accumulation, and hydrolysis of Alb and the release of the hydrolysis products were determined in the isolated rabbit proximal convoluted tubule (PCT) perfused with tritiated Alb ([3H3C]Alb) at 36.4 micrograms/ml. The Alb absorption across the apical membrane was constant (99.9 +/- 4.9 x 10(-3) ng.min-1.mm-1). In contrast, the accumulation and hydrolysis of Alb in the cells increased nonlinearly with time. The bulk of the tritium that accumulated in the cells was associated with intact [3H3C]Alb. Only the final hydrolysis products were released from the cells and these first appeared in the peritubular bath 6-7 min after the start of perfusion of the tubule with [3H3C]Alb. The hydrolysis product was not detectable in the tubule lumen. The proteolytic activity correlated linearly with the protein load to the cells, characteristic of first-order kinetics and a high-capacity system. The results suggest that the renal tubular handling of proteins proceeds from the apical to the basolateral aspect of the cell. The transcellular processing of Alb is rapid and can occur in 6-7 min. The accumulation of intact protein in the cell and the first-order kinetics of hydrolysis of the absorbed protein suggest that the rate-limiting step in proximal tubular handling of proteins may include the initial hydrolysis of protein or reside in steps that precede the hydrolysis.

  14. Time course of optical quality and intraocular scattering after refractive lenticule extraction.

    Directory of Open Access Journals (Sweden)

    Kazutaka Kamiya

    Full Text Available PURPOSE: To assess the time course of optical quality and intraocular scattering in relation to visual acuity after femtosecond lenticule extraction (FLEx for the correction of myopia. METHODS: This study evaluated 36 eyes of 36 patients with spherical equivalents of -4.38±1.53 D [mean ± standard deviation] who underwent FLEx. Before surgery, and 1 week and 1, 3 and 6 months after surgery, we assessed the modulation transfer function (MTF cutoff frequency, Strehl ratio, objective scattering index (OSI, and OQAS values (OVs, using a double-pass instrument. We also investigated the relationship of the OSI with corrected distance visual acuity (CDVA preoperatively and postoperatively. RESULTS: The mean changes in MTF cutoff frequency, Strehl ratio, OSI, OV100%, OV20%, and OV9% preoperatively and 6 months postoperatively were -5.51 ± 15.01, -0.03 ± 0.07, 0.35 ± 0.83, -0.17 ± 0.48, -0.14 ± 0.38, and -0.09 ± 0.22, respectively. We found no significant preoperative correlation between the OSI and logMAR CDVA (Spearman rank correlation coefficient r = 0.068, p = 0.69, and modest, but significant correlations 1 week and 1, 3, and 6 months postoperatively (r = 0.572, r = 0.562, r = 0.542, r = 0.540, p<0.001, respectively. CONCLUSIONS: FLEx induced a transient decrease in optical quality in association with an increase in intraocular scattering in the early postoperative period, possibly due to mild interface haze formation, but gradually recovered with time. It is suggested that this transient degradation in optical quality related to an increase in the intraocular scattering may result in a slight delay of CDVA recovery in the early postoperative period.

  15. EEG can track the time course of successful reference resolution in small visual worlds

    Directory of Open Access Journals (Sweden)

    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.

  16. Time-course changes of catabolic proteins following muscle atrophy induced by dexamethasone.

    Science.gov (United States)

    Macedo, Anderson G; Krug, André Luis O; Souza, Lidiane M; Martuscelli, Aline M; Constantino, Paula B; Zago, Anderson S; Rush, James W E; Santos, Carlos F; Amaral, Sandra L

    2016-03-01

    This study was designed to describe the time-course changes of catabolic proteins following muscle atrophy induced by 10 days of dexamethasone (DEX). Rats underwent DEX treatment for 1, 3, 5, 7 and 10 days. Body weight (BW) and lean mass were obtained using a dual energy X-ray absorptiometry (DEXA) scan. Muscle ringer finger1 (MuRF-1), atrogin-1 and myostatin protein levels were analyzed in the tibialis anterior (TA), flexor hallucis longus (FHL) and soleus muscles. DEX treatment reduced lean mass since day-3 and reduced BW since day-5. Specific muscle weight reductions were observed after day-10 in TA (-23%) and after day-5 in FHL (-16%, -17% and -29%, for days 5, 7 and 10, respectively). In TA, myostatin protein level was 36% higher on day-5 and its values were normalized in comparison with controls on day-10. MuRF-1 protein level was increased in TA muscle from day-7 and in FHL muscle only on day-10. This study suggests that DEX-induced muscle atrophy is a dynamic process which involves important signaling factors over time. As demonstrated by DEXA scan, lean mass declines earlier than BW and this response may involve other catabolic proteins than myostatin and MuRF-1. Specifically for TA and FHL, it seems that myostatin may trigger the catabolic process, and MuRF-1 may contribute to maintain muscle atrophy. This information may support any intervention in order to attenuate the muscle atrophy during long period of treatment. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Memory impairment following status epilepticus in immature rats: time-course and environmental effects.

    Science.gov (United States)

    Rutten, Annemarieke; van Albada, Mirjam; Silveira, Diosely C; Cha, Byung Ho; Liu, Xianzeng; Hu, Yingchu N; Cilio, Maria Roberta; Holmes, Gregory L

    2002-08-01

    Status epilepticus (SE) has a high mortality and morbidity rate in children. Disturbances in learning and memory are frequently associated with SE although it is not clear when the cognitive deficits occur. If cognitive dysfunction occurs immediately following the seizure, the window of opportunity for therapeutic intervention is limited. The first goal of this study was to determine the timing of cognitive dysfunction following SE in weanling rats. As there is evidence that enriching the environment can improve cognitive and motor deficits following brain injury, our second goal was to determine whether environmental enrichment improves cognitive function following SE. Rats underwent lithium-pilocarpine-induced SE at postnatal (P) day 20 and were then tested for visual-spatial memory in the water maze at P22, P25, P30, or P50. Rats with SE performed significantly worse in the water maze than control rats at all time points. Once the time-courses of visual-spatial memory deficits were determined, a second group of P20 rats were subjected to SE and were then placed in an enriched environment (enriched group) or remained in standard cages in the vivarium (nonenriched group) for 28 days. Following environmental manipulation, the animals were tested in the water maze. Rats housed in an enriched environment following the SE performed substantially better in the water maze than rats housed in standard cages. However, no differences were found between the enriched and nonenriched groups in EEG or histological evaluation. Although SE results in cognitive impairment within days of the seizure, housing in an enriched environment after SE has a beneficial effect on cognitive performance in rats.

  18. Time course of changes in heart rate and blood pressure variability in rats with myocardial infarction

    Directory of Open Access Journals (Sweden)

    R. Aires

    Full Text Available Our aim was to determine the time course of changes in autonomic balance in the acute (1 and 3 days, sub-acute (7 days and chronic (28 days phases of myocardial infarction (MI in rats. Autonomic balance was assessed by temporal and spectral analyses of blood pressure variability (BPV and heart rate variability (HRV. Pulsatile blood pressure (BP recordings (30 min were obtained in awake and unrestrained male Wistar rats (N = 77; 8-10 weeks old with MI (coronary ligature or sham operation (SO. Data are reported as means±SE. The high frequency (HF component (n.u. of HRV was significantly lower in MI-1- (P0.05. This reduction was mainly due to attenuation of the low frequency (LF band of BPV in absolute and normalized units (SO-1=39.3±7%; SO-3=55±4.5%; SO-7=46.8±4.5%; SO-28=45.7±5%; MI-1=13±3.5%; MI-3=35±4.7%; MI-7=25±2.8%; MI-28=21.4±2.8%. The results suggest that the reduction in HRV was associated with decrease of the HF component of HRV suggesting recovery of the vagal control of heartbeats along the post-infarction healing period. The depression of BPV was more dependent on the attenuation of the LF component, which is linked to the baroreflex modulation of the autonomic balance.

  19. Time Course Changes in Selected Biochemical Stress Indices in Broilers Exposed to Short-term Noise

    Directory of Open Access Journals (Sweden)

    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.

  20. ISPC effect is not observed when the word comes too late: A time course analysis

    Directory of Open Access Journals (Sweden)

    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.

  1. Breathing for answering: the time course of response planning in conversation

    Science.gov (United States)

    Torreira, Francisco; Bögels, Sara; Levinson, Stephen C.

    2015-01-01

    We investigate the timing of pre-answer inbreaths in order to shed light on the time course of response planning and execution in conversational turn-taking. Using acoustic and inductive plethysmography recordings of seven dyadic conversations in Dutch, we show that pre-answer inbreaths in conversation typically begin briefly after the end of questions. We also show that the presence of a pre-answer inbreath usually co-occurs with substantially delayed answers, with a modal latency of 576 vs. 100 ms for answers not preceded by an inbreath. Based on previously reported minimal latencies for internal intercostal activation and the production of speech sounds, we propose that vocal responses, either in the form of a pre-utterance inbreath or of speech proper when an inbreath is not produced, are typically launched in reaction to information present in the last portion of the interlocutor's turn. We also show that short responses are usually made on residual breath, while longer responses are more often preceded by an inbreath. This relation of inbreaths to answer length suggests that by the time an inbreath is launched, typically during the last few hundred milliseconds of the question, the length of the answer is often prepared to some extent. Together, our findings are consistent with a two-stage model of response planning in conversational turn-taking: early planning of content often carried out in overlap with the incoming turn, and late launching of articulation based on the identification of turn-final cues. PMID:25814976

  2. 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

  3. 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…

  4. Tracking the Time Course of Word-Frequency Effects in Auditory Word Recognition with Event-Related Potentials

    Science.gov (United States)

    Dufour, Sophie; Brunelliere, Angele; Frauenfelder, Ulrich H.

    2013-01-01

    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…

  5. Time-courses of lung function and respiratory muscle pressure generating capacity after spinal cord injury: A prospective cohort study.

    NARCIS (Netherlands)

    Mueller, G.; de Groot, S.; van der Woude, L.H.V.; Hopman, M.T.

    2008-01-01

    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

  6. 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

  7. Time-courses of lung function and respiratory muscle pressure generating capacity after spinal cord injury: a prospective cohort study.

    NARCIS (Netherlands)

    Muller, G.; Groot, S. de; Woude, L.H.V. van der; Hopman, M.T.E.

    2008-01-01

    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

  8. Predicting the time course of haemoglobin in children treated with erythropoietin for renal anaemia.

    Science.gov (United States)

    Port, R E; Ding, R W; Fies, T; Schärer, K

    1998-11-01

    To establish a pharmacodynamic model that allows one to predict the haemoglobin (Hb) response to EPO in children as a function of dose and time, and to derive recommendations for initial dosing and subsequent dose adjustment. Haemoglobin was monitored in eight children aged 8-15 years with anaemia due to renal failure during treatment with EPO. All patients were free of conditions known to impair the response to EPO. Pretreatment Hb was 4.9-9.0 g dl(-1). The drug was administered once weekly by subcutaneous injection; doses ranged from 1700 to 6800 U week (-1). Hb was monitored for 4-38 months. The Hb-time data were analysed by applying a population pharmacodynamic model proposed for EPO in adult haemodialysis patients. Internal model validation was carried out by using a bootstrap procedure. The increase of Hb during treatment with EPO was linear until steady state was reached after 103+/-33 days (mean +/- interindividual s.d.). The weekly gain in Hb from the onset of therapy to steady state was 0.0805+/-0.026 g dl(-1) (mean +/- interindividual s.d.) for every 1000 U EPO week (-1); it did not exhibit a dependence on body weight. Estimated mean prediction errors are +/-1.53 g dl(-1) for predictions that are based on the mean population parameters and +/-0.83 g dl(-1) for predictions that take into account the complete individual Hb-time data up to and including steady state. The model describes the time course of the Hb response to EPO in children with renal anaemia. The required weekly EPO dose should initially be calculated from the individual pretreatment Hb and the desired Hb at steady state by using the mean population estimates of the weekly gain in Hb per dose unit before steady state (beta) and the time needed to reach steady state (tau). A reduction of the initial dose according to body weight is not justified by the available evidence. beta should be re-estimated individually after 6 weeks of treatment and dose should be adjusted accordingly. A final dose

  9. Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum

    Directory of Open Access Journals (Sweden)

    Beisser Daniela

    2012-06-01

    Full Text Available Abstract Background Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. Results In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites and 4,378 edges (reactions. Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurable metabolism (e.g. glycolysis and amino acid anabolism during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from

  10. 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

  11. A growth curve model with fractional polynomials for analysing incomplete time-course data in microarray gene expression studies

    DEFF Research Database (Denmark)

    Tan, Qihua; Thomassen, Mads; Hjelmborg, Jacob V B

    2011-01-01

    -course pattern in a gene by gene manner. We introduce a growth curve model with fractional polynomials to automatically capture the various time-dependent expression patterns and meanwhile efficiently handle missing values due to incomplete observations. For each gene, our procedure compares the performances...... among fractional polynomial models with power terms from a set of fixed values that offer a wide range of curve shapes and suggests a best fitting model. After a limited simulation study, the model has been applied to our human in vivo irritated epidermis data with missing observations to investigate...... time-dependent transcriptional responses to a chemical irritant. Our method was able to identify the various nonlinear time-course expression trajectories. The integration of growth curves with fractional polynomials provides a flexible way to model different time-course patterns together with model...

  12. Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution.

    Science.gov (United States)

    Takenaka, Yoichi; Seno, Shigeto; Matsuda, Hideo

    2015-10-01

    Comprehensively understanding the dynamics of biological systems is one of the greatest challenges in biology. Vastly improved biological technologies have provided vast amounts of information that must be understood by bioinformatics and systems biology researchers. Gene regulations have been frequently modeled by ordinary differential equations or graphical models based on time-course gene expression profiles. The state-of-the-art computational approaches for analyzing gene regulations assume that their models are same throughout time-course experiments. However, these approaches cannot easily analyze transient changes at a time point, such as diauxic shift. We propose a score that analyzes the gene regulations at each time point. The score is based on the information gains of information criterion values. The method detects the shifts in gene regulatory networks (GRNs) during time-course experiments with single-time-point resolution. The effectiveness of the method is evaluated on the diauxic shift from glucose to lactose in Escherichia coli. Gene regulation shifts were detected at two time points: the first corresponding to the time at which the growth of E. coli ceased and the second corresponding to the end of the experiment, when the nutrient sources (glucose and lactose) had become exhausted. According to these results, the proposed score and method can appropriately detect the time of gene regulation shifts. The method based on the proposed score provides a new tool for analyzing dynamic biological systems. Because the score value indicates the strength of gene regulation at each time point in a gene expression profile, it can potentially infer hidden GRNs from time-course experiments.

  13. The Time Course of Activity within the Dorsal and Rostral-Ventral Anterior Cingulate Cortex in the Emotional Stroop Task.

    Science.gov (United States)

    Feroz, Farah Shahnaz; Leicht, Gregor; Steinmann, Saskia; Andreou, Christina; Mulert, Christoph

    2017-01-01

    Growing evidence from neuroimaging studies suggest that emotional and cognitive processes are interrelated. Anatomical key structures in this context are the dorsal and rostral-ventral anterior cingulate cortex (dACC and rvACC). However, up to now, the time course of activations within these regions during emotion-cognition interactions has not been disentangled. In the present study, we used event-related potentials (ERP) and standardized low-resolution electromagnetic tomography (sLORETA) region of interest (ROI) source localization analyses to explore the time course of neural activations within the dACC and rvACC using a modified emotional Stroop paradigm. ERP components related to Stroop conflict (N200, N450 and late negativity) were analyzed. The time course of brain activations in the dACC and rvACC was strikingly different with more pronounced initial responses in the rvACC followed by increased dACC activity mainly at the late negativity window. Moreover, emotional valence modulated the earlier N450 stage within the rvACC region with higher neural activations in the positive compared to the negative and neutral conditions. Emotional arousal modulated the late negativity stage; firstly in the significant arousal × congruence ERP effect and then the significant higher current density in the low arousal condition within the dACC. Using sLORETA source localization, substantial differences in the activation time courses in the dACC and rvACC could be found during the emotional Stroop task. We suggest that during late negativity, within the dACC, emotional arousal modulated the processing of response conflict, reflected in the correlation between the ex-Gaussian µ and the current density in the dACC.

  14. The Time-Course of Processing of Grammatical Class and Semantic Attributes of Words: Dissociation by Means of ERP

    Science.gov (United States)

    Yudes, Carolina; Domínguez, Alberto; Cuetos, Fernando; de Vega, Manuel

    2016-01-01

    This study explores the time-course of word processing by grammatical class (verbs vs. nouns) and meaning (action vs. non-action) by means of an ERP experiment. The morphology of Spanish words allows for a noun (e.g., "bail"-e [a dance]) or a verb (e.g., "bail"-ar [to dance]) to be formed by simply changing the suffix attached…

  15. 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.

  16. Ligand-specific Deactivation Time Course of GluN1/GluN2D NMDA Receptors

    Energy Technology Data Exchange (ETDEWEB)

    K Vance; N Simorowski; S Traynelis; H Furukawa

    2011-12-31

    N-methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors that mediate a majority of excitatory synaptic transmission. One unique property of GluN1/GluN2D NMDA receptors is an unusually prolonged deactivation time course following the removal of L-glutamate. Here we show, using x-ray crystallography and electrophysiology, that the deactivation time course of GluN1/GluN2D receptors is influenced by the conformational variability of the ligand-binding domain (LBD) as well as the structure of the activating ligand. L-glutamate and L-CCG-IV induce significantly slower deactivation time courses compared with other agonists. Crystal structures of the isolated GluN2D LBD in complex with various ligands reveal that the binding of L-glutamate induces a unique conformation at the backside of the ligand-binding site in proximity to the region at which the transmembrane domain would be located in the intact receptors. These data suggest that the activity of the GluN1/GluN2D NMDA receptor is controlled distinctively by the endogenous neurotransmitter L-glutamate.

  17. Influence of biological assay conditions on stability assessment of radiometal-labelled peptides exemplified using a {sup 177}Lu-DOTA-minigastrin derivative

    Energy Technology Data Exchange (ETDEWEB)

    Ocak, Meltem [Clinical Department of Nuclear Medicine, Medical University Innsbruck, A-6020, Innsbruck (Austria); Department of Pharmaceutical Technology, Pharmacy Faculty, Istanbul University, 34116, Istanbul (Turkey); Helbok, Anna; Guggenberg, Elisabeth von [Clinical Department of Nuclear Medicine, Medical University Innsbruck, A-6020, Innsbruck (Austria); Ozsoy, Y. [Department of Pharmaceutical Technology, Pharmacy Faculty, Istanbul University, 34116, Istanbul (Turkey); Kabasakal, Levent [Department of Nuclear Medicine, Cerrahpasa Medical Faculty, 34098, Istanbul (Turkey); Kremser, Leopold [Division of Clinical Biochemistry, Protein Micro-Analysis Facility, Biocenter, Medical University Innsbruck, A-6020, Innsbruck (Austria); Decristoforo, Clemens, E-mail: clemens.decristoforo@uki.a [Clinical Department of Nuclear Medicine, Medical University Innsbruck, A-6020, Innsbruck (Austria)

    2011-02-15

    Introduction: Lack of correlation between in vitro and in vivo stability is a general problem for the development of radiopeptides especially in the case of minigastrin derivatives for therapeutic applications. In this study, we compared the influence of experimental conditions on radiopeptide stability results in vitro using a model Minigastrin (MG) analogue labelled with Lu-177. Additionally, we attempted to characterize the main serum enzymatic cleavage sites by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) analysis. Methods: In vitro stability of a DOTA-minigastrin derivative ({sup 177}Lu-DOTA-His-His-Glu-Ala-Tyr-Gly-Trp-NIe-Asp-Phe-NH{sub 2}) was tested in serum, rat tissue homogenates and two different standardised enzymatic mixtures. Quantification of the metabolised radiopeptides at different time intervals was performed using reversed-phase high-performance liquid chromatography (RP-HPLC). Metabolites were characterised by MALDI-TOF-MS. Urine was collected after 15 min p.i. into the mice and compared with in vitro metabolites by RP-HPLC. Results: Faster degradation of the radiopeptide was found in blood in comparison with plasma and serum incubation and in components from rats faster than from human origin. Fast degradation was observed in kidney and liver homogenates as well as in standardised enzymatic mixtures, also revealing variations in the metabolic profile. In urine, no intact peptide was detected already 5 min post injection. MALDI-TOF-MS revealed major cleavage sites at the carboxy terminus of the peptide. Conclusion: Very variable results may be found when different kind of incubation media for testing radiopeptide stabilities is used. Serum incubation studies may overestimate stability; therefore, results should be interpreted with care and combined with alternative in vitro and in vivo investigations.

  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 and Association of Functional and Biochemical Markers in Severe Semitendinosus Damage Following Intensive Eccentric Leg Curls: Differences between and within Subjects

    Science.gov (United States)

    Carmona, Gerard; Mendiguchía, Jurdan; Alomar, Xavier; Padullés, Josep M.; Serrano, David; Nescolarde, Lexa; Rodas, Gil; Cussó, Roser; Balius, Ramón; Cadefau, Joan A.

    2018-01-01

    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

  20. Decreased number of acetylcholine receptors is the mechanism that alters the time course of muscle relaxants in myasthenia gravis : a study in a rat model

    NARCIS (Netherlands)

    De Haes, A; Proost, JH; De Baets, MH; Stassen, MHW; Houwertjes, MC; Wierda, JMKH

    Background: In myasthenic patients, the time course of action of non-depolarizing neuromuscular blocking agents is prolonged and the sensitivity is increased. We used our antegrade perfused rat peroneal nerve anterior tibialis muscle model to investigate if this altered time course of effect and

  1. 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.

  2. [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.

  3. 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.

  4. Promising new assays and technologies for the diagnosis and management of infectious diseases.

    Science.gov (United States)

    Mitsuma, S F; Mansour, M K; Dekker, J P; Kim, J; Rahman, M Z; Tweed-Kent, A; Schuetz, P

    2013-04-01

    In the first decade of the 21st century, we have seen the completion of the human genome project and marked progress in the human microbiome project. The vast amount of data generated from these efforts combined with advances in molecular and biomedical technologies have led to the development of a multitude of assays and technologies that may be useful in the diagnosis and management of infectious diseases. Here, we identify several new assays and technologies that have recently come into clinical use or have potential for clinical use in the near future. The scope of this review is broad and includes topics such as the serum marker procalcitonin, gene expression profiling, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and nucleic acid aptamers. Principles that underlie each assay or technology, their clinical applications, and potential strengths and limitations are addressed.

  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. Identification of the macrophage-specific promoter signature in FANTOM5 mouse embryo developmental time course data.

    Science.gov (United States)

    Summers, Kim M; Hume, David A

    2017-10-01

    The FANTOM5 consortium used cap analysis of gene expression (CAGE) to analyze the time course of gene expression over development from 11 days postcoitum (dpc) to adult in 16 developing organs and the whole body of the mouse. Every tissue in the body contains a large number of resident macrophages that initially infiltrate the embryo from the yolk sac. These cells contribute to organogenesis, and their functions diversify during development as they acquire tissue-specific adaptations. In each of the FANTOM5 time courses, the expression of known macrophage-specific genes, including CSF1 receptor ( Csf1r ), epidermal growth factor-like module-containing mucin-like hormone receptor-like 1 ( Emr1 ), and mer receptor tyrosine kinase ( Mertk ), was readily detectable and increased with time. We reasoned that genes expressed by macrophages would be strongly correlated in their expression with these known markers and might vary between tissues. We used the network analysis tool, Miru, to extract the sets of coexpressed genes from the time course and identified a core set of coexpressed genes attributable to embryonic macrophages, including some, such as dehydrogenase/reductase 3 ( Dhrs3 ), that may have unique functions in development. The FANTOM5 data also detected the appearance of tissue-specific macrophage-expressed genes, such as T cell Ig and mucin domain-containing 4 ( Timd4 ) and V-set and Ig domain-containing 4 ( Vsig4 ) in liver and sialic acid-binding Ig-like lectin 5 ( Siglec5 ) in lung, and confirmed that macrophage content increases with time in each organ as the proliferative phases end, and tissue-specific gene-expression increases. The FANTOM5 data are available on a comprehensive browser (http://fantom.gsc.riken.jp/zenbu/), which provides a resource for the study of macrophage transcriptional regulation and roles in mouse development. © Society for Leukocyte Biology.

  7. 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.

  8. 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.

  9. The differential time course for consonant and vowel processing in Arabic: Implications for language learning and rehabilitation

    Directory of Open Access Journals (Sweden)

    Sami eBoudelaa

    2015-01-01

    Full Text Available Educators and therapists in the Arab world have not been able to benefit from the recent integration of basic behavioural science with neuroscience. This is due to the paucity of basic research on Arabic. The present study is a step towards establishing the necessary structure for the emergence of neuro-rehabilitory and educational practices. It focuses on the recent claim that consonants and vowels have distinct representations, carry different kinds of information, and engage different processing mechanisms. This proposal has received support from various research fields, however it suprisingly stops short of making any claims about the time course of consonant and vowel processing in speech. This study specifically asks if consonants and vowels are processed differentially over time, and whether these time courses vary depending on the kind of information they are associated with. It does so in the context of a Semitic language, Arabic, where consonants typically convey semantic meaning in the form of tri-consonantal roots, and vowels carry phonological and morpho-syntactic information in the form of word patterns. Two cross-modal priming experiments evaluated priming by fragments of consonants that belong to the root, and fragments of vowels belonging to the word pattern. Consonant fragments were effective primes while vowel fragments were not. This demonstrates the existence of a differential processing time course for consonants and vowels in the auditory domain, reflecting in part the different linguistic functions they are associated with, and argues for the importance of assigning distinct representational and processing properties to these elements. At broader theoretical and practical levels, the present results provide a significant building block for the emergence of neuro-rehabilitory and neuro-educational traditions for Arabic.

  10. 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.

  11. 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.

  12. 10-Month-Old Infants Are Sensitive to the Time Course of Perceived Actions: Eye-Tracking and EEG Evidence

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    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.

  13. The time course of emotional picture processing: an event-related potential study using a rapid serial visual presentation paradigm.

    Science.gov (United States)

    Zhu, Chuanlin; He, Weiqi; Qi, Zhengyang; Wang, Lili; Song, Dongqing; Zhan, Lei; Yi, Shengnan; Luo, Yuejia; Luo, Wenbo

    2015-01-01

    The present study recorded event-related potentials using rapid serial visual presentation paradigm to explore the time course of emotionally charged pictures. Participants completed a dual-target task as quickly and accurately as possible, in which they were asked to judge the gender of the person depicted (task 1) and the valence (positive, neutral, or negative) of the given picture (task 2). The results showed that the amplitudes of the P2 component were larger for emotional pictures than they were for neutral pictures, and this finding represents brain processes that distinguish emotional stimuli from non-emotional stimuli. Furthermore, positive, neutral, and negative pictures elicited late positive potentials with different amplitudes, implying that the differences between emotions are recognized. Additionally, the time course for emotional picture processing was consistent with the latter two stages of a three-stage model derived from studies on emotional facial expression processing and emotional adjective processing. The results of the present study indicate that in the three-stage model of emotion processing, the middle and late stages are more universal and stable, and thus occur at similar time points when using different stimuli (faces, words, or scenes).

  14. 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.

  15. Short-term time course of liver metabolic response to acute handling stress in rainbow trout, Oncorhynchus mykiss.

    Science.gov (United States)

    López-Patiño, Marcos A; Hernández-Pérez, Juan; Gesto, Manuel; Librán-Pérez, Marta; Míguez, Jesús M; Soengas, José L

    2014-02-01

    To elucidate the short-term time-course of liver metabolic response in rainbow trout to acute handling stress we subjected rainbow trout to 5min chasing and obtained samples 0 to 480min post-stress. Levels of cortisol, glucose and lactate were measured in plasma, whereas metabolite levels, enzyme activities, mRNA abundance of parameters related to energy metabolism, and glucocorticoid receptors were assessed in liver. Acute stress affected many parameters related to energy metabolism, with most of them turning back to normal levels after 480min. In general, the present results support the existence of two stages in the short-term time-course of metabolic response to handling stress. A first stage occurring few minutes post-stress (15-45min), was characterized by increased mobilization of liver glycogen resulting in increased production of endogenous glucose, reduced use of exogenous glucose and reduced lipogenic potential. A second stage, occurring 60-120min post-stress onwards was characterized by the recovery of liver glycogen levels, the increased capacity of liver for releasing glucose, and the recovery of lipogenic capacity whereas no changes were noted in gluconeogenic potential, which probably needs longer time periods to become enhanced. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Time Course of the Soleus M Response and H Reflex after Lidocaine Tibial Nerve Block in the Rat

    Directory of Open Access Journals (Sweden)

    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.

  17. The gene expression and immunohistochemical time-course of diphenylcyclopropenone-induced contact allergy in healthy humans following repeated epicutaneous challenges

    DEFF Research Database (Denmark)

    Mose, Kristian F.; Burton, Mark; Thomassen, Mads

    2017-01-01

    The gene expression time-course of repeated challenge of contact allergy (CA) remains largely unknown. Therefore, using diphenylcyclopropenone (DPCP) as model allergen in healthy humans we set out to examine: (i) the monotonous and complex gene expression time-course trajectories following repeated...... DPCP challenges 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...

  18. Fusobacterium nucleatum subspecies identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

    Science.gov (United States)

    Nie, Shuping; Tian, Baoyu; Wang, Xiaowei; Pincus, David H; Welker, Martin; Gilhuley, Kathleen; Lu, Xuedong; Han, Yiping W; Tang, Yi-Wei

    2015-04-01

    We explored the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for identification of Fusobacterium nucleatum subspecies. MALDI-TOF MS spectra of five F. nucleatum subspecies (animalis, fusiforme, nucleatum, polymorphum, and vincentii) were analyzed and divided into four distinct clusters, including subsp. animalis, nucleatum, polymorphum, and fusiforme/vincentii. MALDI-TOF MS with the modified SARAMIS database further correctly identified 28 of 34 F. nucleatum clinical isolates to the subspecies level. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  19. Effect of supraphysiological dose of Nandrolone Decanoate on the testis and testosterone concentration in mature and immature male rats: A time course study

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    Rahil Jannatifar

    2015-12-01

    Full Text Available Background: Most studies on anabolic-androgenic steroids abuse have been done in adult rats, but few data are available to immature. Objective: This study was conducted to assay the effect of Nandrolone Decanoate (ND on the testis and testosterone concentration in male immature rats compare with mature ones in short and long time. Materials and Methods: 40 mature rats were divided into 4 groups: group A (short term and group B (long-term received 10 mg/kg/day ND interaperitoneally for 35 and 70 days, respectively. Group C (control without any treatment, and group D (vehicle received dimethyl sulfoxide (DMSO solution in two periods 35 and 70 days. 40 immature rats were divided into 4 groups same as mature ones. After surgery body weight, testis size, histomorphometry of testis, and serum testosterone level were evaluated. Results: Our results showed that ND decreased the number of Leydig cells in group B (39.9 ±. 919, group A (43.4 ±. 120, and long term (40.6 ±. 299 immature rats, which could result in a reduction of testosterone concentration significantly in all experimental groups except short term mature group. Number of sertoli cells, testis size, and diameter of seminiferous tubules decreased in the long-term immature group. Eventually, the number of sperm was decreased in mature and immature groups, but a severe depletion of sperm was occurred in both mature and immature in long time in comparison to the control group (p< 0.05. Conclusion: This time course study showed that supraphysiological dose of ND may negatively affect the number of Leydig cells, sperm cell, and testosterone concentration of immature rats in the same matter of mature rats. However, the number of sertoli cell, testis size, and seminferous diameter were decreased only in the long immature rats.

  20. Glucose and insulin variations in patients during the time course of a FDG-PET study and implications for the 'glucose-corrected' SUV

    International Nuclear Information System (INIS)

    Hadi, Mohiuddin; Bacharach, Stephen L.; Whatley, Millie; Libutti, Steven K.; Straus, Stephen E.; Rao, V. Koneti; Wesley, Robert; Carrasquillo, Jorge A.

    2008-01-01

    Introduction: 2-Deoxy-2[ 18 F]fluoro-D-glucose (FDG) positron emission tomography (PET) has an established role in the evaluation of cancer. Generally, tumor uptake and response to treatment are evaluated using the standardized uptake value (SUV). Some authors have proposed correcting SUV for glucose levels. Insulin is also thought to influence tumor uptake by changing uptake in other tissues. However, little attention has been paid to understanding the variability of glucose or insulin during a single PET study. Method: We studied the biological and instrumental variability of glucose and insulin measurements in 71 nondiabetic patients undergoing FDG-PET studies. Multiple glucose measurements were obtained in all 71 subjects, and in 69 of these 71 subjects, multiple serum insulin measurements were made. We determined the coefficient of observed variation (CV ow ) and the coefficient of variation attributable to biological variability (CV bv ) for both glucose and insulin. Results: The mean glucose concentration was 78.9±13.5 mg/dl. The mean insulin value was 6.49±5.92 μU/ml. The weighted mean CV ow and CV bv was 5.0% and 3.6%, respectively, for glucose and 14.2% and 8.3%, respectively, for insulin. Conclusions: Variations in the range of 3.6% are observed in glucose measurements during the time course of an FDG scan even after accounting for analytical error; larger variations of 8.3% are observed in insulin levels. Therefore, corrections of SUV for blood glucose, especially if obtained from single measurements, can introduce additional errors of at least this much

  1. The time course of metabolites in human plasma after 6-[{sup 18}F]fluoro-l-m-tyrosine administration

    Energy Technology Data Exchange (ETDEWEB)

    Wahl, L.M. [Institute for Advanced Study, Princeton, NJ (United States). Theoretical Biology; Chen, J.J.; Thompson, M.; Chirakal, R.; Nahmias, C. [McMaster University Medical Centre, Hamilton, ON (Canada). Nuclear Medicine

    1999-11-01

    For the investigation of intracerebral dopamine metabolism, 6-[{sup 18}F]fluoro-l-m-tyrosine (FmT) has been proposed as an alternative tracer that, unlike 6-[{sup 18}F]fluoro-l-dopa, is not subjected to O-methylation. We have studied the time course of FmT and its labelled metabolites in plasma after intravenous injection into humans, employing a method that we have developed and validated to analyze labelled metabolites of FmT in plasma. The study population comprised 38 subjects, 14 of whom were taking an aromatic amino acid decarboxylase inhibitor (carbidopa), and obtained arterialized venous blood samples at various times after an intravenous injection of between 185 and 370 MBq of FmT. The major metabolite of FmT present in plasma was 6-[{sup 18}F]fluoro-3-hydroxyphenylacetic acid. The time course of the fraction of radioactivity in plasma attributable to FmT was fitted well by the decay of two exponential functions. The fast component of the decay accounted for 40%-50% of the radioactivity and had a half-life of about 5 min. The slow component of the decay had a half-life of about 6 h in the subjects not taking carbidopa and 20 h in the patients taking carbidopa. When the total available FmT was calculated for each individual subject and expressed as a proportion of total radioactivity, this quantity did not differ significantly from that determined from the corresponding population mean. There was significantly more (15% on average) FmT available over the course of the 2-h experiment in the group pretreated with carbidopa. Our results demonstrate that the major metabolite in plasma after an intravenous injection of FmT is 6-[{sup 18}F]fluoro-3-hydroxyphenylacetic acid. The clearance of FmT from plasma compares well with the clearance of intravenously administered levodopa. Carbidopa increases significantly the availability of FmT in plasma. These results verify, in a large number of human subjects, earlier analyses of FmT metabolism in other species. We

  2. 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

  3. Disseminated Candidiasis in a Young, Previously Healthy, Dog and Review of Literature.

    Science.gov (United States)

    Willems, Nicole; Houwers, Dirk J; Schlotter, Yvette M; Theelen, Bart; Boekhout, Teun

    2017-06-01

    The reports on disseminated candidiasis in dogs so far describe at least one predisposing factor. This case report, however, highlights candidiasis in a dog without any known predisposition. A 1.5-year-old intact female Hovawart dog was presented with subcutaneous nodules and polyuria/polydipsia. An excisional biopsy revealed a chronic pyogranulomatous and necrotizing inflammation with mycotic structures. The patient became febrile and lethargic, and developed lameness. A physical examination, blood tests, urinalysis, thoracic radiographs, abdominal ultrasonography of the abdomen, fine-needle aspiration biopsies, and a culture of a subcutaneous nodule aspirate were obtained. Selected sections of multiple organs were collected for routine histology postmortem. The isolate and a subcutaneous mass were subjected to molecular identification and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis. Clinical, laboratory, and radiological findings were consistent with a granulomatous chronic systemic inflammation. Cytology and histology showed a pyogranulomatous and necrotizing inflammation with myriads of intra- and extra-cellular yeasts and extracellular hyphae. Culture yielded numerous yeast colonies, which appeared Candida albicans-like, but showed a negative serum test and a low identification in API 20 C AUX. Nucleic acid sequences showed homology with the C. albicans-type strain CBS 562. Multilocus sequence typing (MLST) resulted in a new type with designation DST121. The identification of the isolates was confirmed by MALDI-TOF-MS analysis. Future MLST typing and investigation of virulence can provide further evidence whether this MLST-type is associated with clinical cases of disseminated candidiasis without an apparent predisposing condition.

  4. MoS2/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.

    Science.gov (United States)

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

    2016-09-21

    This paper reports a facile synthesis of molybdenum disulfide nanosheets/silver nanoparticles (MoS2/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 MoS2. Moreover, both Ag nanoparticles and the edge of the MoS2 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 MoS2/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 MoS2/Ag hybrid, and provides a new platform for use in the rapid and high throughput analysis of small molecules by mass spectrometry. Copyright © 2016. Published by Elsevier B.V.

  5. 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.

  6. TIME-COURSE OF HEMODYNAMIC-CHANGES AND IMPROVEMENT OF EXERCISE TOLERANCE AFTER CARDIOVERSION OF CHRONIC ATRIAL-FIBRILLATION UNASSOCIATED WITH CARDIAC-VALVE DISEASE

    NARCIS (Netherlands)

    VANGELDER, IC; CRIJNS, HJGM; BLANKSMA, PK; LANDSMAN, MLJ; POSMA, JL; VANDENBERG, MP; MEIJLER, FL; LIE, KI

    1993-01-01

    This study prospectively assessed the time course, magnitude and mechanism of the hemodynamic changes after restoration of sinus rhythm in patients with chronic atrial fibrillation (AF) unassociated with valvular disease. Severe cardiac dysfunction may occur after chronic supraventricular

  7. Time course of hemodynamic changes and improvement of exercise tolerance after cardioversion of chronic atrial fibrillation unassociated with cardiac valve disease

    NARCIS (Netherlands)

    Gelder, I.C. van; Crijns, H.J.G.M.; Blanksma, P.K.; Landsman, M.L.J.; Posma, J.L.; Berg, M.P. van den; Meijler, F.L.; Lie, K.I.

    1993-01-01

    This study prospectively assessed the time course, magnitude and mechanism of the hemodynamic changes after restoration of sinus rhythm in patients with chronic atrial fibrillation (AF) unassociated with valvular disease. Severe cardiac dysfunction may occur after chronic

  8. 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

    Directory of Open Access Journals (Sweden)

    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.

  9. Time-course investigation of the gene expression profile during Fasciola hepatica infection: A microarray-based study.

    Science.gov (United States)

    Rojas-Caraballo, Jose; López-Abán, Julio; Fernández-Soto, Pedro; Vicente, Belén; Collía, Francisco; Muro, Antonio

    2015-12-01

    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].

  10. 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.)

  11. Time-course investigation of the gene expression profile during Fasciola hepatica infection: A microarray-based study

    Directory of Open Access Journals (Sweden)

    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].

  12. Time course of ultraviolet B-induced erythema in people with red hair harbouring homozygous melanocortin 1 receptor mutations.

    Science.gov (United States)

    Ha, Thomas K K; Waterston, Karen; Bisset, Yvonne; Ray, Amanda; Rees, Jonathan L

    2003-08-01

    It has previously been reported that the time course of erythema may be delayed in those with sun-sensitive skin types and those with skin cancer. One molecular explanation for this putative phenotype would be that it is caused by mutations of the melanocortin 1 receptor (MC1R). In the present study of 20 persons, 10 of whom were MC1R homozygous, we measured erythema over a 21-day period in response to a range of ultraviolet B doses using methods that improved on previous studies. We could detect no consistent differences in ultraviolet radiation-induced erythema between the groups studied. The pharmacological mechanisms underpinning such prolonged inflammatory responses merit further investigation.

  13. 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.

  14. 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.

  15. Time course of arterial remodelling in diameter and wall thickness above and below the lesion after a spinal cord injury.

    Science.gov (United States)

    Thijssen, Dick H J; De Groot, Patricia C E; van den Bogerd, Arne; Veltmeijer, Matthijs; Cable, N Timothy; Green, Daniel J; Hopman, Maria T E

    2012-12-01

    Physical inactivity in response to a spinal cord injury (SCI) represents a potent stimulus for conduit artery remodelling. Changes in conduit artery characteristics may be induced by the local effects of denervation (and consequent extreme inactivity below the level of the lesion), and also by systemic adaptations due to whole body inactivity. Therefore, we assessed the time course of carotid (i.e. above lesion) and common femoral artery (i.e. below lesion) lumen diameter and wall thickness across the first 24 weeks after an SCI. Eight male subjects (mean age 35 ± 14 years) with a traumatic motor complete spinal cord lesion between T5 and L1 (i.e. paraplegia) were included. Four subjects were measured across the first 6 weeks after SCI, whilst another four subjects were measured from 8 until 24 weeks after SCI. Ultrasound was used to examine the diameter and wall thickness from the carotid and common femoral arteries. Carotid artery diameter did not change across 24 weeks, whilst femoral artery diameter stabilised after the rapid initial decrease during the first 3 weeks after the SCI. Carotid and femoral artery wall thickness showed no change during the first few weeks, but increased both between 6 and 24 weeks (P < 0.05). In conclusion, SCI leads to a rapid and localised decrease in conduit artery diameter which is isolated to the denervated and paralyzed region, whilst wall thickness gradually increases both above and below the lesion. This distinct time course of change in conduit arterial diameter and wall thickness suggests that distinct mechanisms may contribute to these adaptations.

  16. 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.

  17. 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.

  18. 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.

  19. Individual differences in cognitive reappraisal usage modulate the time course of brain activation during symptom provocation in specific phobia

    Science.gov (United States)

    2013-01-01

    Background Extinction learning is proposed to be one key mechanism of action underlying exposure-based cognitive-behavioral therapy (CBT) in specific phobia. Beyond that, cognitive reappraisal, one important strategy to regulate negative emotions, is a crucial component of CBT interventions, but has been disregarded in previous studies investigating neural change processes in specific phobia. The aim of this study was to investigate the association of individual differences in habitual/dispositional cognitive reappraisal usage and the time course of brain activation during phobic stimulation in specific phobia. Methods Dental phobic patients and healthy control subjects participated in a functional magnetic resonance imaging (fMRI) study whilst being confronted with phobic, disgust, fear and neutral pictures. Individual differences in cognitive reappraisal usage were assessed via a self-report questionnaire and correlated with activation decreases over the course of time. Results Phobic individuals with higher dispositional cognitive reappraisal scores showed a more pronounced activation decline in the right dorsomedial prefrontal cortex (dmPFC) which might be associated with a diminution of explicit cognitive emotion regulation over the course of time. Less decrease of activation in the right ventromedial prefrontal cortex (vmPFC) and the lateral orbitofrontal cortex (lOFC) over time in subjects with higher cognitive reappraisal scores might be related to a stronger automatic regulation of emotions or even emotional relearning. Additionally, phobic subjects compared with healthy controls showed a stronger habituation of the left dmPFC over the course of symptom provocation. Conclusions The results of this study show for the first time that individual differences in cognitive reappraisal usage are associated with the time course of brain activation during symptom provocation in specific phobia. Additionally, the present study gives first indications for the

  20. 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.)

  1. 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.)

  2. Eye-tracking the time-course of novel word learning and lexical competition in adults and children.

    Science.gov (United States)

    Weighall, A R; Henderson, L M; Barr, D J; Cairney, S A; Gaskell, M G

    2017-04-01

    Lexical competition is a hallmark of proficient, automatic word recognition. Previous research suggests that there is a delay before a new spoken word becomes engaged in this process, with sleep playing an important role. However, data from one method - the visual world paradigm - consistently show competition without a delay. We trained 42 adults and 40 children (aged 7-8) on novel word-object pairings, and employed this paradigm to measure the time-course of lexical competition. Fixations to novel objects upon hearing existing words (e.g., looks to the novel object biscal upon hearing "click on the biscuit") were compared to fixations on untrained objects. Novel word-object pairings learned immediately before testing and those learned the previous day exhibited significant competition effects, with stronger competition for the previous day pairings for children but not adults. Crucially, this competition effect was significantly smaller for novel than existing competitors (e.g., looks to candy upon hearing "click on the candle"), suggesting that novel items may not compete for recognition like fully-fledged lexical items, even after 24h. Explicit memory (cued recall) was superior for words learned the day before testing, particularly for children; this effect (but not the lexical competition effects) correlated with sleep-spindle density. Together, the results suggest that different aspects of new word learning follow different time courses: visual world competition effects can emerge swiftly, but are qualitatively different from those observed with established words, and are less reliant upon sleep. Furthermore, the findings fit with the view that word learning earlier in development is boosted by sleep to a greater degree. Copyright © 2016. Published by Elsevier Inc.

  3. 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.

  4. Time course of programmed cell death, which included autophagic features, in hybrid tobacco cells expressing hybrid lethality.

    Science.gov (United States)

    Ueno, Naoya; Nihei, Saori; Miyakawa, Naoto; Hirasawa, Tadashi; Kanekatsu, Motoki; Marubashi, Wataru; van Doorn, Wouter G; Yamada, Tetsuya

    2016-12-01

    PCD with features of vacuolar cell death including autophagy-related features were detected in hybrid tobacco cells, and detailed time course of features of vacuolar cell death were established. A type of interspecific Nicotiana hybrid, Nicotiana suaveolens × N. tabacum exhibits temperature-sensitive lethality. This lethality results from programmed cell death (PCD) in hybrid seedlings, but this PCD occurs only in seedlings and suspension-cultured cells grown at 28 °C, not those grown at 36 °C. Plant PCD can be classified as vacuolar cell death or necrotic cell death. Induction of autophagy, vacuolar membrane collapse and actin disorganization are each known features of vacuolar cell death, but observed cases of PCD showing all these features simultaneously are rare. In this study, these features of vacuolar cell death were evident in hybrid tobacco cells expressing hybrid lethality. Ion leakage, plasma membrane disruption, increased activity of vacuolar processing enzyme, vacuolar membrane collapse, and formation of punctate F-actin foci were each evident in these cells. Transmission electron microscopy revealed that macroautophagic structures formed and tonoplasts ruptured in these cells. The number of cells that contained monodansylcadaverine (MDC)-stained structures and the abundance of nine autophagy-related gene transcripts increased just before cell death at 28 °C; these features were not evident at 36 °C. We assessed whether an autophagic inhibitor, wortmannin (WM), influenced lethality in hybrid cells. After the hybrid cell began to die, WM suppressed increases in ion leakage and cell deaths, and it decreased the number of cells containing MDC-stained structures. These results showed that several features indicative of autophagy and vacuolar cell death were evident in the hybrid tobacco cells subject to lethality. In addition, we documented a detailed time course of these vacuolar cell death features.

  5. Differences in time course activation of dorsolateral prefrontal cortex associated with low or high risk choicesin a gambling task

    Directory of Open Access Journals (Sweden)

    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

  6. 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 ...

  7. Time course of osteoporotic vertebral fractures by magnetic resonance imaging using a simple classification: a multicenter prospective cohort study.

    Science.gov (United States)

    Takahashi, S; Hoshino, M; Takayama, K; Iseki, K; Sasaoka, R; Tsujio, T; Yasuda, H; Sasaki, T; Kanematsu, F; Kono, H; Toyoda, H; Nakamura, H

    2017-02-01

    This study revealed the time course of osteoporotic vertebral fracture by magnetic resonance imaging using a simple classification. Signal changes were associated with the compression degree and mobility of the fractured vertebral body. This classification showed sufficient reliability in categorizing magnetic resonance imaging findings of osteoporotic vertebral fractures. Magnetic resonance imaging (MRI) is useful in diagnosing osteoporotic vertebral fractures (OVFs). This study investigated the time course of OVFs by MRI using a simple classification. This multicenter cohort study was performed from 2012 to 2015. Consecutive patients with ≤2-week-old OVFs were enrolled in 11 institutions. MRI was performed at enrollment and at 1-, 3-, 6-, and 12-month follow-up. Signal changes on T1-weighted imaging (T1WI), T2WI, and short τ inversion recovery (STIR) were classified according to signal intensity. Height and angular motion of vertebral bodies were also measured. The 6-month follow-up was completed by 153 patients. At enrollment, fractured vertebrae signal changes were 43 % diffuse and 57 % confined low on T1WI; on T2WI, 56, 24, and 5 % were confined low, high, and diffuse low, respectively; on STIR, 100 % were high. On T1WI, diffuse low remained most common (90 % at 1 month and 60 % at 3 months) until 6 and 12 months, when most were confined low (54 and 52 %, respectively). On T2WI, confined low remained most common (decreasing to 41 % at 12 months). On STIR, high signal change was shown in 98, 87, and 64 % at 3, 6, and 12 months, respectively. At 3, 6, and 12 months, diffuse low signal change was associated with significantly lower vertebral height, and high signal change was associated with significantly greater angular motion. MRI signal changes were associated with the compression degree and angular motion of fractured vertebrae. This classification showed sufficient reliability in categorizing MRI findings of OVFs.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Time course analysis of influence of food hardness on head posture and pitching of head during masticatory movement.

    Science.gov (United States)

    Shinya, Akimasa; Sato, Toru; Hisanaga, Ryuichi; Miho, Otoaki; Nomoto, Syuntaro

    2013-01-01

    The purpose of the present study was to investigate the relationship between mastication and head posture using foods with different degrees of hardness. A total of 12 healthy, dentulous volunteers participated in the study. Each participant was required to chew two types of gummy candy with two levels of hardness while sitting upright. Measurements were conducted using an optoelectric jaw-tracking system with 6 degrees of freedom (Gnatho-Hexagraph II JM-2000®). The horizontal plane perpendicular to the direction of gravitational force served as the reference plane. Analysis of the gradient of the Frankfurt plane (head posture) and pitching of the head during masticatory movement was conducted. The influence of the type of test food on these parameters was evaluated during mastication. During stable mastication, the gradient of the Frankfurt plane was 4.66 degrees on average, close to the horizontal plane. The time course of the Frankfurt plane gradient revealed a tendency toward dorsal flexion during the first to middle phases of mastication, and a tendency toward ventral flexion during the middle to last phases, regardless of the hardness of the test food. The participants were divided into two groups based on change in head posture during chewing. The results showed while there was no change in head posture in the group with marked pitching of the head, head posture did change in the group with little pitching.

  13. Seeing the same words differently: the time course of automaticity and top-down intention in reading.

    Science.gov (United States)

    Strijkers, Kristof; Bertrand, Daisy; Grainger, Jonathan

    2015-08-01

    We investigated how linguistic intention affects the time course of visual word recognition by comparing the brain's electrophysiological response to a word's lexical frequency, a well-established psycholinguistic marker of lexical access, when participants actively retrieve the meaning of the written input (semantic categorization) versus a situation where no language processing is necessary (ink color categorization). In the semantic task, the ERPs elicited by high-frequency words started to diverge from those elicited by low-frequency words as early as 120 msec after stimulus onset. On the other hand, when categorizing the colored font of the very same words in the color task, word frequency did not modulate ERPs until some 100 msec later (220 msec poststimulus onset) and did so for a shorter period and with a smaller scalp distribution. The results demonstrate that, although written words indeed elicit automatic recognition processes in the brain, the speed and quality of lexical processing critically depends on the top-down intention to engage in a linguistic task.

  14. Empirical assessment of the time course of innovation in biomedical engineering: first results of a comparative approach

    Directory of Open Access Journals (Sweden)

    Farkas Robert

    2016-09-01

    Full Text Available The pathway from the flash of a technological invention until its use as a medical device in every day care is tedious and burdensome. But the often postulated acceleration has to balance the speed of innovation and the indispensable product safety by an improved understanding of the innovation cycle. While several studies investigated the time course of pharmaceutical innovation, a comparable empirical analysis of medical devices is lacking. Thus we evaluated the time between the patent priority date and the corresponding receipt of the CE mark as a function of a medical device risk class in 61 cases. The statistical analysis yielded a time increment (trend from medical devices in risk category I (median = 5.8 years compared to risk category III (median = 10.4 years, which is close to literature reported values for drug development (9–12 years. The difference between products in risk classes I and II did not reach significance. To investigate the underlying facts, a text-mining approach especially to resolve the ambiguity of, e.g. patents, CE Marks etc. is suggested for increasing the sample size.